From Stefan.Melber at DLR.de  Thu Sep  1 06:00:32 2016
From: Stefan.Melber at DLR.de (Stefan Melber)
Date: Thu, 1 Sep 2016 12:00:32 +0200
Subject: [Paraview] Data handling in ParaView
Message-ID: <3d4fb626-b36e-e9aa-d3d7-baec3b1c0245@DLR.de>

Hi,


i have (maybe) a simple problem: For the visualization of the so called 
dual-cells of an unstructured grid i use currently the block-structured 
vtu-format. The data thereby consists of many complex cells which are 
itself consists of a number of triangles - see the picture d1 attached. 
Therefore i have to write out EVERY cell in another vtu-file and group 
them with am vtm-file together. This way works well with a small number 
of cells (~1000 - as for the picture) however the aim is to go up to 
100e6 cells. Depending on the numbers i got from 1000 cells this process 
will take ~70 days!

The bottleneck is clearly the huge number of files i have to write (and 
read in ParaView). So are there ideas to have another representation in 
only one file for such kind of data?

I did some experiments writing all cells in one vtk(vtu)-file and give 
them scalar values depending on the cell number. But then, the n-th cell 
(its last point) is connected to the n+1 (its first point) and so on. 
Looks ugly if the n-th cell is not a direct neighbor to the n+1 cell - 
and that can be the case in my data. And - cutting then the resulting 
stuff in ParaView i did not get the cutting pictures (like d4) i like to 
have ...

Best regards and hoping for some nice ideas,


         Stefan






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From kmorel at sandia.gov  Thu Sep  1 09:54:49 2016
From: kmorel at sandia.gov (Moreland, Kenneth)
Date: Thu, 1 Sep 2016 13:54:49 +0000
Subject: [Paraview] Data handling in ParaView
Message-ID: <5157d847a846460db7edb4cc22a276b1@ES08AMSNLNT.srn.sandia.gov>

Stefan,

The idea of identifying each "cell" by a scalar value should work just fine and be scalable.

However, I do not understand what the issue is that the n-th cell's last point is connected to the n+1-th cell's first point. If there is no connection. I honestly do not see anything wrong with the pictures you posted except that in d4.png it looks like the lines of some "cells" are drawn on top of other lines. But that is exactly what I would expect if the cells are adjacent to each other, which I would also expect.

The only advice I can think of is to define the scalar values on the triangles (what ParaView calls cells) instead of the points. This will generally be more robust.

-Ken

-----Original Message-----
From: ParaView [mailto:paraview-bounces at paraview.org] On Behalf Of Stefan Melber
Sent: Thursday, September 1, 2016 4:01 AM
To: paraview <paraview at paraview.org>
Subject: [EXTERNAL] [Paraview] Data handling in ParaView

Hi,


i have (maybe) a simple problem: For the visualization of the so called dual-cells of an unstructured grid i use currently the block-structured vtu-format. The data thereby consists of many complex cells which are itself consists of a number of triangles - see the picture d1 attached. 
Therefore i have to write out EVERY cell in another vtu-file and group them with am vtm-file together. This way works well with a small number of cells (~1000 - as for the picture) however the aim is to go up to
100e6 cells. Depending on the numbers i got from 1000 cells this process will take ~70 days!

The bottleneck is clearly the huge number of files i have to write (and read in ParaView). So are there ideas to have another representation in only one file for such kind of data?

I did some experiments writing all cells in one vtk(vtu)-file and give them scalar values depending on the cell number. But then, the n-th cell (its last point) is connected to the n+1 (its first point) and so on. 
Looks ugly if the n-th cell is not a direct neighbor to the n+1 cell - and that can be the case in my data. And - cutting then the resulting stuff in ParaView i did not get the cutting pictures (like d4) i like to have ...

Best regards and hoping for some nice ideas,


         Stefan







From sebastien.jourdain at kitware.com  Thu Sep  1 10:45:39 2016
From: sebastien.jourdain at kitware.com (Sebastien Jourdain)
Date: Thu, 1 Sep 2016 08:45:39 -0600
Subject: [Paraview] pv_web_visualizer.py segmentation fault when loading
 a pvsm file
In-Reply-To: <CAN4UQ49SAsxoK-pLxYQLAGUa0niPC24QNjLiETJTQB5Lj2C4Ow@mail.gmail.com>
References: <CAN4UQ49SAsxoK-pLxYQLAGUa0niPC24QNjLiETJTQB5Lj2C4Ow@mail.gmail.com>
Message-ID: <CABObKxcBXCc7nObCYfeCe1X7P_C8QAEPPHCifNdmTzaZyYqPcA@mail.gmail.com>

Hi Pepe,

I am not aware of the issue do you mind sharing your state file with me so
I can see what you were doing in your state file?

Did you generate your state file from the Visualizer or ParaView?

Thanks,

Seb



On Wed, Aug 31, 2016 at 4:49 AM, Jose Luis Cerc?s <jlcercos at gmail.com>
wrote:

> Hi community!
>
> In Paraview 4.4.0, 5.1.0, and 5.1.2, I'm having a weird error (I don't
> know if other versions are affected as well)... After launching the
> ParaViewWeb visualizer script:
>
> ./bin/pvpython ./lib/paraview-5.1/site-packages/paraview/web/pv_web_visualizer.py
> --content ./share/paraview-5.1/www --data-dir /PATH_TO_THE_FILES/ --port
> 8080
>
> Connecting with it (http://localhost:8080/apps/Visualizer/), loading a
> pvsm file, and reloading the web page (to close the connection and the
> ParaViewWeb visualizer instance), I'm receiving a segmentation fault:
>
> (...)
> 2016-08-31 12:39:23+0200 [twisted.web.server.Site] (TCP Port 8080 Closed)
> 2016-08-31 12:39:23+0200 [twisted.web.server.Site] Stopping factory
> <twisted.web.server.Site instance at 0x7ff8117d1908>
> 2016-08-31 12:39:23+0200 [HTTPChannel,6,127.0.0.1] connection_lost:
> connection count = 0
> 2016-08-31 12:39:23+0200 [HTTPChannel,6,127.0.0.1] Starting timer, process
> will terminate in: 300sec
> 2016-08-31 12:39:23+0200 [-] Main loop terminated.
> *Segmentation fault (core dumped)*
>
> However, it is not happening if I manually load the data and reproduce all
> the process (In such case it is just logging "Main loop terminated" and
> conveniently closing the app)
>
> The half good news are that, in Paraview >= 5.1.0 at least it is ever
> terminating (with the segfault), while in Paraview 4.4 it may become hanged
> (instead of crashing).
>
> Someone else with the same problem? Any idea to fix that?
>
> Thanks!
> Pepe
>
> _______________________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at http://www.kitware.com/
> opensource/opensource.html
>
> Please keep messages on-topic and check the ParaView Wiki at:
> http://paraview.org/Wiki/ParaView
>
> Search the list archives at: http://markmail.org/search/?q=ParaView
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/paraview
>
>
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From samuelkey at bresnan.net  Thu Sep  1 10:59:40 2016
From: samuelkey at bresnan.net (Samuel Key)
Date: Thu, 1 Sep 2016 08:59:40 -0600
Subject: [Paraview] Data handling in ParaView
In-Reply-To: <3d4fb626-b36e-e9aa-d3d7-baec3b1c0245@DLR.de>
References: <3d4fb626-b36e-e9aa-d3d7-baec3b1c0245@DLR.de>
Message-ID: <30f2c27e-eecd-77a6-3ae1-51a1d532be4e@bresnan.net>

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FORMAT
type: ensight gold
GEOMETRY
model:                   1  1  fmaego.data.geom    change_coords_only
VARIABLE
vector per node:         1  1  Displacement          fmaego.data.ndis
vector per node:         1  1  Velocity              fmaego.data.nvel
vector per node:         1  1  Acceleration          fmaego.data.nacc
scalar per element:      1  1  Material              fmaego.data.emat
scalar per element:      1  1  Material-State        fmaego.data.esta
scalar per element:      1  1  Pressure              fmaego.data.eprs
scalar per element:      1  1  Bulk-Strain           fmaego.data.elnv
scalar per element:      1  1  Strain-Energy-Density fmaego.data.esed
scalar per element:      1  1  Effective-Stress      fmaego.data.edev
vector per element:      1  1  Stress*Vel            fmaego.data.estv
tensor symm per element: 1  1  Stress                fmaego.data.estr
TIME
time set:                1
number of steps:       201
time values:                  1.135706545708E-05      7.510083486017E-04
      1.506686838611E-03      2.252834993299E-03      3.009862207507E-03
      3.754289853559E-03      4.501681358858E-03      5.259721808682E-03
      6.001133812252E-03      6.755695891865E-03      7.507178882983E-03
      8.251019758060E-03      9.008508227774E-03      9.755119012261E-03
      1.050816477068E-02      1.125051397494E-02      1.200334927870E-02
      1.275177946391E-02      1.350386299058E-02      1.425686628738E-02
      1.500013197714E-02      1.575065627625E-02      1.650647022703E-02
      1.726034549558E-02      1.800499393936E-02      1.875747916251E-02
      1.950057447621E-02      2.025325459683E-02      2.100486800422E-02
      2.175111827764E-02      2.250476104062E-02      2.325334450393E-02
      2.400571217228E-02      2.475515174863E-02      2.550312431023E-02
      2.625685079589E-02      2.700739609549E-02      2.775310871535E-02
      2.850219439561E-02      2.925939435768E-02      3.000741665484E-02
      3.075951207667E-02      3.150940310880E-02      3.225031394943E-02
      3.300877978516E-02      3.375139946392E-02      3.450730431057E-02
      3.525090830169E-02      3.600478912645E-02      3.675119932702E-02
      3.750973996393E-02      3.825657795276E-02      3.900912975865E-02
      3.975412654055E-02      4.050156929690E-02      4.125827953748E-02
      4.200019271649E-02      4.275130619413E-02      4.350078524153E-02
      4.425636266059E-02      4.500665872550E-02      4.575548609583E-02
      4.650711546674E-02      4.725766027267E-02      4.800920720254E-02
      4.875679833620E-02      4.950759568895E-02      5.025500083664E-02
      5.100711750997E-02      5.175357419166E-02      5.250191098929E-02
      5.326004631345E-02      5.400112530737E-02      5.475522095984E-02
      5.550201876243E-02      5.625050059031E-02      5.701038217536E-02
      5.775304522555E-02      5.850009065977E-02      5.925724966350E-02
      6.000461530232E-02      6.075970880254E-02      6.150406051512E-02
      6.225916534067E-02      6.300546379456E-02      6.376062094249E-02
      6.450218236205E-02      6.525713116602E-02      6.600205209382E-02
      6.675574335050E-02      6.750686905764E-02      6.825136633059E-02
      6.900448593906E-02      6.975634458693E-02      7.050838472404E-02
      7.125175605114E-02      7.200263796358E-02      7.275471166755E-02
      7.350548687386E-02      7.425687397517E-02      7.500728103869E-02
      7.575949151659E-02      7.650735617717E-02      7.725805161875E-02
      7.800851026764E-02      7.875841205930E-02      7.950553856777E-02
      8.025583529525E-02      8.100467200241E-02      8.175275603602E-02
      8.250038037505E-02      8.325927055252E-02      8.400553441522E-02
      8.475368893755E-02      8.550027551741E-02      8.625732313315E-02
      8.700382547197E-02      8.775086240815E-02      8.850584762662E-02
      8.925091532937E-02      9.000831877609E-02      9.075319044399E-02
      9.150719809598E-02      9.225207443253E-02      9.300768276546E-02
      9.375070925662E-02      9.450518259445E-02      9.525905018085E-02
      9.600180978851E-02      9.675502650138E-02      9.750893345388E-02
      9.825994787074E-02      9.900234189646E-02      9.975533738660E-02
      1.005064100176E-01      1.012576811165E-01      1.020096158790E-01
      1.027606866877E-01      1.035005980593E-01      1.042509031319E-01
      1.050017403088E-01      1.057508505901E-01      1.065014632260E-01
      1.072502251936E-01      1.080094729555E-01      1.087590996409E-01
      1.095076109100E-01      1.102552011489E-01      1.110032534791E-01
      1.117519536253E-01      1.125094244926E-01      1.132559647594E-01
      1.140037704465E-01      1.147607503568E-01      1.155064647159E-01
      1.162532661739E-01      1.170095008975E-01      1.177542775018E-01
      1.185003094921E-01      1.192557569101E-01      1.200104553728E-01
      1.207548489023E-01      1.215097327001E-01      1.222532195120E-01
      1.230074869874E-01      1.237508126779E-01      1.245040227974E-01
      1.252571777206E-01      1.260003058517E-01      1.267526673305E-01
      1.275049568734E-01      1.282576671556E-01      1.290091374302E-01
      1.297602125838E-01      1.305013099117E-01      1.312524808261E-01
      1.320025906316E-01      1.327531368027E-01      1.335038548286E-01
      1.342533775067E-01      1.350029935987E-01      1.357525392008E-01
      1.365014468823E-01      1.372504277974E-01      1.380097881989E-01
      1.387576446184E-01      1.395057258528E-01      1.402540790427E-01
      1.410010990781E-01      1.417577206470E-01      1.425053407827E-01
      1.432522709387E-01      1.440085672177E-01      1.447547013651E-01
      1.455010712959E-01      1.462565390059E-01      1.470015751222E-01
      1.477573559956E-01      1.485021620599E-01      1.492569650178E-01
      1.500011989818E-01
FILE
file set:                   1
number of steps:          201

From Stefan.Melber at dlr.de  Thu Sep  1 11:43:57 2016
From: Stefan.Melber at dlr.de (Stefan.Melber at dlr.de)
Date: Thu, 1 Sep 2016 15:43:57 +0000
Subject: [Paraview] Data handling in ParaView
In-Reply-To: <30f2c27e-eecd-77a6-3ae1-51a1d532be4e@bresnan.net>
References: <3d4fb626-b36e-e9aa-d3d7-baec3b1c0245@DLR.de>,
 <30f2c27e-eecd-77a6-3ae1-51a1d532be4e@bresnan.net>
Message-ID: <BEEFDF249A3F6947B5BDFA4AE5492A1430606F27@dlrexmbx02.intra.dlr.de>

Hi Samuel,

ok - interresting idea. I will check out what finally performs better. However - as my tests with the multible block format in vtk (using one binary file for each cell) show, that the handling of more then about 10k files is really a mess. For my final case i will have around 100M cells - means theoretically 100M files - and this can be a real problem for the filesystem and for paraview ...

Best regards,

     Stefan


________________________________
Von: ParaView [paraview-bounces at paraview.org]" im Auftrag von "Samuel Key [samuelkey at bresnan.net]
Gesendet: Donnerstag, 1. September 2016 16:59
An: paraview at paraview.org
Betreff: Re: [Paraview] Data handling in ParaView


Stefan,

The solution I use for this problem is the PART-construct that is provided by the EnSight gold binary format. My 'PARTS' are defined by material ID's. Each Point datum-item has its own file with all time-steps. Each Cell datum-item has its own file with all time-steps. I have attached a typical EnSight case-file. (The PART-construct is contained in the individual files.)

ParaView reads this format. EnSight reads this format. If you are interested in pursuing this simulation results format, I can provide the format documentation and an example Fortran95 writer.

Samuel W Key
FMA Development, LLC
1005 39th Ave NE
Great Falls, Montana 59404




On 9/1/2016 4:00 AM, Stefan Melber wrote:
Hi,


i have (maybe) a simple problem: For the visualization of the so called dual-cells of an unstructured grid i use currently the block-structured vtu-format. The data thereby consists of many complex cells which are itself consists of a number of triangles - see the picture d1 attached. Therefore i have to write out EVERY cell in another vtu-file and group them with am vtm-file together. This way works well with a small number of cells (~1000 - as for the picture) however the aim is to go up to 100e6 cells. Depending on the numbers i got from 1000 cells this process will take ~70 days!

The bottleneck is clearly the huge number of files i have to write (and read in ParaView). So are there ideas to have another representation in only one file for such kind of data?

I did some experiments writing all cells in one vtk(vtu)-file and give them scalar values depending on the cell number. But then, the n-th cell (its last point) is connected to the n+1 (its first point) and so on. Looks ugly if the n-th cell is not a direct neighbor to the n+1 cell - and that can be the case in my data. And - cutting then the resulting stuff in ParaView i did not get the cutting pictures (like d4) i like to have ...

Best regards and hoping for some nice ideas,


        Stefan









_______________________________________________
Powered by www.kitware.com<http://www.kitware.com>

Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html

Please keep messages on-topic and check the ParaView Wiki at: http://paraview.org/Wiki/ParaView

Search the list archives at: http://markmail.org/search/?q=ParaView

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From Stefan.Melber at dlr.de  Thu Sep  1 11:44:57 2016
From: Stefan.Melber at dlr.de (Stefan.Melber at dlr.de)
Date: Thu, 1 Sep 2016 15:44:57 +0000
Subject: [Paraview] WG:  Data handling in ParaView
In-Reply-To: <BEEFDF249A3F6947B5BDFA4AE5492A1430605E99@dlrexmbx02.intra.dlr.de>
References: <5157d847a846460db7edb4cc22a276b1@ES08AMSNLNT.srn.sandia.gov>,
 <BEEFDF249A3F6947B5BDFA4AE5492A1430605E99@dlrexmbx02.intra.dlr.de>
Message-ID: <BEEFDF249A3F6947B5BDFA4AE5492A1430606F33@dlrexmbx02.intra.dlr.de>


________________________________________
Von: Melber-Wilkending, Stefan
Gesendet: Donnerstag, 1. September 2016 16:52
An: Moreland, Kenneth
Betreff: AW: [Paraview] Data handling in ParaView

Hi Kenneth,

after some search i found a bug in the code: one variable which holds the offset from cell to cell was one to small - so this leads to the effect the cells are "connected". Fixing this and going from "unstructured grid" to "polygon data" i can now write in one file and read that in paraview.

By the way the pics i had attached are the version "each cell has its own file" - which looks good because the offset error did not work there. The pics with the offset error and one file are so ugly you cant find any cell there.

Regarding the colors i found it is not a good idea to take the cell number itself as color - it gives to much colors. Instead i use the modulo-function to limit the color to e.g. 100 instead 1e5.

For polygon data how to i "color" the triangle instead of the points? Do you have an example file?

Best regards,

     Stefan
________________________________________
Von: Moreland, Kenneth [kmorel at sandia.gov]
Gesendet: Donnerstag, 1. September 2016 15:54
An: Melber-Wilkending, Stefan; paraview
Betreff: RE: [Paraview] Data handling in ParaView

Stefan,

The idea of identifying each "cell" by a scalar value should work just fine and be scalable.

However, I do not understand what the issue is that the n-th cell's last point is connected to the n+1-th cell's first point. If there is no connection. I honestly do not see anything wrong with the pictures you posted except that in d4.png it looks like the lines of some "cells" are drawn on top of other lines. But that is exactly what I would expect if the cells are adjacent to each other, which I would also expect.

The only advice I can think of is to define the scalar values on the triangles (what ParaView calls cells) instead of the points. This will generally be more robust.

-Ken

-----Original Message-----
From: ParaView [mailto:paraview-bounces at paraview.org] On Behalf Of Stefan Melber
Sent: Thursday, September 1, 2016 4:01 AM
To: paraview <paraview at paraview.org>
Subject: [EXTERNAL] [Paraview] Data handling in ParaView

Hi,


i have (maybe) a simple problem: For the visualization of the so called dual-cells of an unstructured grid i use currently the block-structured vtu-format. The data thereby consists of many complex cells which are itself consists of a number of triangles - see the picture d1 attached.
Therefore i have to write out EVERY cell in another vtu-file and group them with am vtm-file together. This way works well with a small number of cells (~1000 - as for the picture) however the aim is to go up to
100e6 cells. Depending on the numbers i got from 1000 cells this process will take ~70 days!

The bottleneck is clearly the huge number of files i have to write (and read in ParaView). So are there ideas to have another representation in only one file for such kind of data?

I did some experiments writing all cells in one vtk(vtu)-file and give them scalar values depending on the cell number. But then, the n-th cell (its last point) is connected to the n+1 (its first point) and so on.
Looks ugly if the n-th cell is not a direct neighbor to the n+1 cell - and that can be the case in my data. And - cutting then the resulting stuff in ParaView i did not get the cutting pictures (like d4) i like to have ...

Best regards and hoping for some nice ideas,


         Stefan







From charles.boivin at mayahtt.com  Fri Sep  2 10:43:17 2016
From: charles.boivin at mayahtt.com (Charles Boivin)
Date: Fri, 2 Sep 2016 14:43:17 +0000
Subject: [Paraview] Building Paraview 5.2.1 on Windows (Visual Studio)
Message-ID: <C1142B0660A0384C9B52008C63E3685A0169289E1F@exchange2.pc.mayahtt.ca>

Trying to build PV 5.2.1 on Windows 7. I have tried with both VS2015 and VS2013 and facing the same issue.

Using Qt 4.8.6 (compiled in 'Release' mode - no debugging info)

I point CMake to the Qt folder and easily get VS projects and solutions. I can compile without any issue (had missing libs with one project, but turned off VTK_BUILD_QT_DESIGNER_PLUGIN to avoid that issue for now).

It builds and links fine. However, Paraview crashes when I try to run it, without any kind of message whatsoever. Debugging in VS, I can see that it gets to pqApplicationCore::createOutputWindow(), and it crashes when it tries to execute the following line:

  this->OutputWindow = new pqOutputWindow(0);

(it doesn't even reach the interior of pqOutputWindow::pqOutputWindow() - looks like it crashes in the SuperClass maybe? Hard to say).

Has someone ever encountered something similar? If not, is there any way to get more info as to what might be going on here in order to fix this in some way (maybe some log file)? As mentioned before, I tried with both VS2013 and VS2015 (and corresponding builds of Qt 4.8.6), and I get the same problem.

Thank you,


Charles Boivin
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From dennis_conklin at goodyear.com  Fri Sep  2 10:09:04 2016
From: dennis_conklin at goodyear.com (Dennis Conklin)
Date: Fri, 2 Sep 2016 14:09:04 +0000
Subject: [Paraview] EXODUS: How to find nodes that are common to more than 1
	sideset
Message-ID: <CY1PR07MB250688F4283C26F2004A9E539FE50@CY1PR07MB2506.namprd07.prod.outlook.com>

All,

I want to search or query for nodes that are in more than 1 sideset, as common nodes drive Multi-Point Constraints crazy.  I don't have any great ideas.   Do any of you?

Thanks for any hints you may have.

Dennis


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From mathieu.westphal at kitware.com  Mon Sep  5 04:10:14 2016
From: mathieu.westphal at kitware.com (Mathieu Westphal)
Date: Mon, 5 Sep 2016 10:10:14 +0200
Subject: [Paraview] VTK/Paraview Courses in October
In-Reply-To: <CAC2t4USH9Vp85YCWtu+Uw9kvbPrOUVQwFk7q2T0JOJXfGoZKdA@mail.gmail.com>
References: <CAC2t4USH9Vp85YCWtu+Uw9kvbPrOUVQwFk7q2T0JOJXfGoZKdA@mail.gmail.com>
Message-ID: <CAC2t4UQGrpbH1Ef+bZZKZVqoRiMKosytv_4H6peER9hUVFSwgQ@mail.gmail.com>

Hello
Kitware will be holding a 2-day VTK and ParaView course on October 11th and
12th 2016 in Lyon, France.

Please visit our web site for more information and registration details at
VTK (English) : http://training.kitware.fr/browse/130
VTK (French) : http://formations.kitware.fr/browse/130
ParaView (English) : http://training.kitware.fr/browse/131
ParaView (French) : http://formations.kitware.fr/browse/131


Note that the course will be taught in English. If you have any question,
please contact us at formations at http://www.kitware.fr

Thank you,

Mathieu Westphal

Mathieu Westphal

On Wed, Jul 6, 2016 at 4:49 PM, Mathieu Westphal <
mathieu.westphal at kitware.com> wrote:

> Hello
> Kitware will be holding a 2-day VTK and ParaView course on October 11th
> and 12th 2016 in Lyon, France.
>
> Please visit our web site for more information and registration details at
> VTK (English) : http://training.kitware.fr/browse/130
> VTK (French) : http://formations.kitware.fr/browse/130
> ParaView (English) : http://training.kitware.fr/browse/131
> ParaView (French) : http://formations.kitware.fr/browse/131
>
>
> Note that the course will be taught in English. If you have any question,
> please contact us at formations at http://www.kitware.fr
>
> Thank you,
>
> Mathieu Westphal
>
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From matthias at familie-sitte.org  Mon Sep  5 04:22:04 2016
From: matthias at familie-sitte.org (Matthias Sitte)
Date: Mon, 5 Sep 2016 10:22:04 +0200
Subject: [Paraview] in-plane vector field from 3D vector field
Message-ID: <2ed76ada-bdbb-b9a7-66e3-a9cd5130bfe8@familie-sitte.org>

Hi list,

first steps in Paraview...

I have a 3D vector field over a regular grid of Nx*Ny*1 cells. I would 
like to plot the z component as surface and the in-plane xy components 
as an in-plane vector field. The Glyph filter only plots the full 3D 
vector field -- I haven't been able to figure out how to project the 
data into the plane.

Any ideas?

Best,

Matthias


From giuseppe.bilotta at gmail.com  Mon Sep  5 04:49:57 2016
From: giuseppe.bilotta at gmail.com (Giuseppe Bilotta)
Date: Mon, 5 Sep 2016 10:49:57 +0200
Subject: [Paraview] in-plane vector field from 3D vector field
In-Reply-To: <2ed76ada-bdbb-b9a7-66e3-a9cd5130bfe8@familie-sitte.org>
References: <2ed76ada-bdbb-b9a7-66e3-a9cd5130bfe8@familie-sitte.org>
Message-ID: <CAOxFTcxyWiKYbPOhgzoM1mGpuofsr9p7Ba3ay85TADKE9N1Euw@mail.gmail.com>

On Mon, Sep 5, 2016 at 10:22 AM, Matthias Sitte
<matthias at familie-sitte.org> wrote:
> Hi list,
>
> first steps in Paraview...
>
> I have a 3D vector field over a regular grid of Nx*Ny*1 cells. I would like
> to plot the z component as surface and the in-plane xy components as an
> in-plane vector field. The Glyph filter only plots the full 3D vector field
> -- I haven't been able to figure out how to project the data into the plane.
>
> Any ideas?

What about using the Calculator to create new vector fields with only
the components you care about?

-- 
Giuseppe "Oblomov" Bilotta

From felipebordeu at gmail.com  Mon Sep  5 05:02:25 2016
From: felipebordeu at gmail.com (Felipe Bordeu)
Date: Mon, 05 Sep 2016 09:02:25 +0000
Subject: [Paraview] Embedding Python source as Modules And Python
	Programmable Filter
Message-ID: <CAJbHkX874b-iFrG5wmrx4xunLL6pHi+PY9RNeioAXVtZ+RmOjw@mail.gmail.com>

Hi,

I have a home made plugin and I have some python code to do post
processing. Now I want to embed this pythons routines in my plugin (using
the Embedding Python Source As Modules of
http://www.paraview.org/Wiki/ParaView/Plugin_HowTo). this work great, if I
open a python console (using the GUI) and then typing the "import mymodule"
I can access my routines.

Now I want to use this routines in a programmable filter. The problem is
that my module is no available directly in the python environnement of the
python programmable sources.

For the moment I have to do this (reload my plugin inside the programmable
filter):
Script of the programmable filter:

from paraview.simple import servermanager
servermanager.LoadPlugin('libZ7ToolsNative.so')
import zsetpythonpostpro
zsetpythonpostpro.CalcPostQuantitiesFromSigma(self)

for the  moment this work but, the "LoadPlugin('...) line takes about 3
seconds every time (and my routine less than 1 s).

Working in linux with paraview 5.0.0 (gcc, 64-bits) from sources.

Any ideas of how to solve this issue.
Thanks
Felipe
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From antech777 at gmail.com  Mon Sep  5 09:03:11 2016
From: antech777 at gmail.com (Andrew)
Date: Mon, 5 Sep 2016 16:03:11 +0300
Subject: [Paraview] in-plane vector field from 3D vector field
In-Reply-To: <CAOxFTcxyWiKYbPOhgzoM1mGpuofsr9p7Ba3ay85TADKE9N1Euw@mail.gmail.com>
References: <2ed76ada-bdbb-b9a7-66e3-a9cd5130bfe8@familie-sitte.org>
 <CAOxFTcxyWiKYbPOhgzoM1mGpuofsr9p7Ba3ay85TADKE9N1Euw@mail.gmail.com>
Message-ID: <CANMVBVzNMdBEUjvc8pWS11pvr9HOW=9GXQtfPo-qBEN4tG-EMQ@mail.gmail.com>

AFAIK, ParaView has no capability of projecting vector on surfaces. That's
why you need to work around with Calculator every time you need to get a
vector projection. If your plane is not just a coordinate plane, you can
use Generate Surface Normals filter, but it doesn't work on all datasets
(in my case it doesn't work on Fluent data exported as EnSight Gold Binary,
it generates normals but then the Calculator only shows that Normals in
vector list, Applying leads to error message that the Normals vector
doesn't exits, so one in the listbox is, probably, a ghost or something
:)). I used this method (Generate normals + Calculator + Normals.Velocity)
extensively with EnSight Gold files exported from CFX and it worked good in
ParaView 4.3 (it was the actual version).
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From jlcercos at gmail.com  Tue Sep  6 03:27:09 2016
From: jlcercos at gmail.com (=?UTF-8?Q?Jose_Luis_Cerc=C3=B3s?=)
Date: Tue, 6 Sep 2016 09:27:09 +0200
Subject: [Paraview] pv_web_visualizer.py segmentation fault when loading
 a pvsm file
In-Reply-To: <CABObKxcBXCc7nObCYfeCe1X7P_C8QAEPPHCifNdmTzaZyYqPcA@mail.gmail.com>
References: <CAN4UQ49SAsxoK-pLxYQLAGUa0niPC24QNjLiETJTQB5Lj2C4Ow@mail.gmail.com>
 <CABObKxcBXCc7nObCYfeCe1X7P_C8QAEPPHCifNdmTzaZyYqPcA@mail.gmail.com>
Message-ID: <CAN4UQ49pukejYOggVyb2-Apn_mWEHQORdO4t8=XT1+ihB9B02g@mail.gmail.com>

Hey Sebastien!

In order to demonstrate the problem, I created a simplified version of the
state file. I just simply loaded a VTK file and moved the camera... As I
said, everything is working fine if I do the same stuff manually, without
loading the pvstate. Following the resulting pvstate file:

<ParaView>
  <ServerManagerState version="5.0.1">
    <Proxy group="animation" type="AnimationScene" id="263" servers="16">
      <Property name="AnimationTime" id="263.AnimationTime"
number_of_elements="1">
        <Element index="0" value="0"/>
      </Property>
      <Property name="Cues" id="263.Cues" number_of_elements="1">
        <Proxy value="265"/>
        <Domain name="groups" id="263.Cues.groups"/>
      </Property>
      <Property name="Duration" id="263.Duration" number_of_elements="1">
        <Element index="0" value="10"/>
      </Property>
      <Property name="EndTime" id="263.EndTime" number_of_elements="1">
        <Element index="0" value="1"/>
      </Property>
      <Property name="FramesPerTimestep" id="263.FramesPerTimestep"
number_of_elements="1">
        <Element index="0" value="1"/>
        <Domain name="range" id="263.FramesPerTimestep.range"/>
      </Property>
      <Property name="GoToFirst" id="263.GoToFirst"/>
      <Property name="GoToLast" id="263.GoToLast"/>
      <Property name="GoToNext" id="263.GoToNext"/>
      <Property name="GoToPrevious" id="263.GoToPrevious"/>
      <Property name="LockEndTime" id="263.LockEndTime"
number_of_elements="1">
        <Element index="0" value="0"/>
        <Domain name="bool" id="263.LockEndTime.bool"/>
      </Property>
      <Property name="LockStartTime" id="263.LockStartTime"
number_of_elements="1">
        <Element index="0" value="0"/>
        <Domain name="bool" id="263.LockStartTime.bool"/>
      </Property>
      <Property name="Loop" id="263.Loop" number_of_elements="1">
        <Element index="0" value="0"/>
        <Domain name="bool" id="263.Loop.bool"/>
      </Property>
      <Property name="NumberOfFrames" id="263.NumberOfFrames"
number_of_elements="1">
        <Element index="0" value="10"/>
        <Domain name="range" id="263.NumberOfFrames.range"/>
      </Property>
      <Property name="Play" id="263.Play"/>
      <Property name="PlayMode" id="263.PlayMode" number_of_elements="1">
        <Element index="0" value="0"/>
        <Domain name="enum" id="263.PlayMode.enum">
          <Entry value="0" text="Sequence"/>
          <Entry value="1" text="Real Time"/>
          <Entry value="2" text="Snap To TimeSteps"/>
        </Domain>
      </Property>
      <Property name="StartTime" id="263.StartTime" number_of_elements="1">
        <Element index="0" value="0"/>
      </Property>
      <Property name="Stop" id="263.Stop"/>
      <Property name="TimeKeeper" id="263.TimeKeeper"
number_of_elements="1">
        <Proxy value="259"/>
      </Property>
      <Property name="ViewModules" id="263.ViewModules"
number_of_elements="2">
        <Proxy value="1945"/>
        <Proxy value="1945"/>
        <Domain name="groups" id="263.ViewModules.groups"/>
      </Property>
    </Proxy>
    <Proxy group="animation" type="TimeAnimationCue" id="265" servers="16">
      <Property name="AnimatedDomainName" id="265.AnimatedDomainName"
number_of_elements="1">
        <Element index="0" value=""/>
      </Property>
      <Property name="AnimatedElement" id="265.AnimatedElement"
number_of_elements="1">
        <Element index="0" value="0"/>
      </Property>
      <Property name="AnimatedPropertyName" id="265.AnimatedPropertyName"
number_of_elements="1">
        <Element index="0" value="Time"/>
      </Property>
      <Property name="AnimatedProxy" id="265.AnimatedProxy"
number_of_elements="1">
        <Proxy value="259"/>
        <Domain name="groups" id="265.AnimatedProxy.groups"/>
      </Property>
      <Property name="Enabled" id="265.Enabled" number_of_elements="1">
        <Element index="0" value="1"/>
        <Domain name="bool" id="265.Enabled.bool"/>
      </Property>
      <Property name="EndTime" id="265.EndTime" number_of_elements="1">
        <Element index="0" value="1"/>
      </Property>
      <Property name="KeyFrames" id="265.KeyFrames">
        <Domain name="groups" id="265.KeyFrames.groups"/>
      </Property>
      <Property name="LastAddedKeyFrameIndex"
id="265.LastAddedKeyFrameIndex"/>
      <Property name="StartTime" id="265.StartTime" number_of_elements="1">
        <Element index="0" value="0"/>
      </Property>
      <Property name="TimeMode" id="265.TimeMode" number_of_elements="1">
        <Element index="0" value="0"/>
        <Domain name="enum" id="265.TimeMode.enum">
          <Entry value="0" text="Normalized"/>
          <Entry value="1" text="Relative"/>
        </Domain>
      </Property>
      <Property name="UseAnimationTime" id="265.UseAnimationTime"
number_of_elements="1">
        <Element index="0" value="1"/>
        <Domain name="bool" id="265.UseAnimationTime.bool"/>
      </Property>
    </Proxy>
    <Proxy group="misc" type="ViewLayout" id="1917" servers="16">
      <Layout number_of_elements="1">
        <Item direction="0" fraction="0.5" view="1945"/>
      </Layout>
    </Proxy>
    <Proxy group="annotations" type="GridAxes3DActor" id="1943"
servers="21">
      <Property name="AxesToLabel" id="1943.AxesToLabel"
number_of_elements="1">
        <Element index="0" value="63"/>
        <Domain name="range" id="1943.AxesToLabel.range"/>
      </Property>
      <Property name="DataPosition" id="1943.DataPosition"
number_of_elements="3">
        <Element index="0" value="0"/>
        <Element index="1" value="0"/>
        <Element index="2" value="0"/>
        <Domain name="range" id="1943.DataPosition.range"/>
      </Property>
      <Property name="DataScale" id="1943.DataScale" number_of_elements="3">
        <Element index="0" value="1"/>
        <Element index="1" value="1"/>
        <Element index="2" value="1"/>
        <Domain name="range" id="1943.DataScale.range"/>
      </Property>
      <Property name="FacesToRender" id="1943.FacesToRender"
number_of_elements="1">
        <Element index="0" value="63"/>
        <Domain name="range" id="1943.FacesToRender.range"/>
      </Property>
      <Property name="LabelUniqueEdgesOnly" id="1943.LabelUniqueEdgesOnly"
number_of_elements="1">
        <Element index="0" value="1"/>
        <Domain name="bool" id="1943.LabelUniqueEdgesOnly.bool"/>
      </Property>
      <Property name="ModelBounds" id="1943.ModelBounds"
number_of_elements="6">
        <Element index="0" value="0"/>
        <Element index="1" value="1"/>
        <Element index="2" value="0"/>
        <Element index="3" value="1"/>
        <Element index="4" value="0"/>
        <Element index="5" value="1"/>
      </Property>
      <Property name="ModelTransformMatrix" id="1943.ModelTransformMatrix"
number_of_elements="16">
        <Element index="0" value="1"/>
        <Element index="1" value="0"/>
        <Element index="2" value="0"/>
        <Element index="3" value="0"/>
        <Element index="4" value="0"/>
        <Element index="5" value="1"/>
        <Element index="6" value="0"/>
        <Element index="7" value="0"/>
        <Element index="8" value="0"/>
        <Element index="9" value="0"/>
        <Element index="10" value="1"/>
        <Element index="11" value="0"/>
        <Element index="12" value="0"/>
        <Element index="13" value="0"/>
        <Element index="14" value="0"/>
        <Element index="15" value="1"/>
      </Property>
      <Property name="ShowEdges" id="1943.ShowEdges" number_of_elements="1">
        <Element index="0" value="1"/>
        <Domain name="bool" id="1943.ShowEdges.bool"/>
      </Property>
      <Property name="ShowGrid" id="1943.ShowGrid" number_of_elements="1">
        <Element index="0" value="0"/>
        <Domain name="bool" id="1943.ShowGrid.bool"/>
      </Property>
      <Property name="ShowTicks" id="1943.ShowTicks" number_of_elements="1">
        <Element index="0" value="1"/>
        <Domain name="bool" id="1943.ShowTicks.bool"/>
      </Property>
      <Property name="UseModelTransform" id="1943.UseModelTransform"
number_of_elements="1">
        <Element index="0" value="0"/>
        <Domain name="range" id="1943.UseModelTransform.range"/>
      </Property>
      <Property name="Visibility" id="1943.Visibility"
number_of_elements="1">
        <Element index="0" value="0"/>
        <Domain name="bool" id="1943.Visibility.bool"/>
      </Property>
      <Property name="XAxisLabels" id="1943.XAxisLabels">
        <Domain name="scalar_range" id="1943.XAxisLabels.scalar_range"/>
      </Property>
      <Property name="XAxisNotation" id="1943.XAxisNotation"
number_of_elements="1">
        <Element index="0" value="0"/>
        <Domain name="enum" id="1943.XAxisNotation.enum">
          <Entry value="0" text="Mixed"/>
          <Entry value="1" text="Scientific"/>
          <Entry value="2" text="Fixed"/>
        </Domain>
      </Property>
      <Property name="XAxisPrecision" id="1943.XAxisPrecision"
number_of_elements="1">
        <Element index="0" value="2"/>
        <Domain name="range" id="1943.XAxisPrecision.range"/>
      </Property>
      <Property name="XAxisUseCustomLabels" id="1943.XAxisUseCustomLabels"
number_of_elements="1">
        <Element index="0" value="0"/>
        <Domain name="bool" id="1943.XAxisUseCustomLabels.bool"/>
      </Property>
      <Property name="XTitle" id="1943.XTitle" number_of_elements="1">
        <Element index="0" value="X Axis"/>
      </Property>
      <Property name="YAxisLabels" id="1943.YAxisLabels">
        <Domain name="scalar_range" id="1943.YAxisLabels.scalar_range"/>
      </Property>
      <Property name="YAxisNotation" id="1943.YAxisNotation"
number_of_elements="1">
        <Element index="0" value="0"/>
        <Domain name="enum" id="1943.YAxisNotation.enum">
          <Entry value="0" text="Mixed"/>
          <Entry value="1" text="Scientific"/>
          <Entry value="2" text="Fixed"/>
        </Domain>
      </Property>
      <Property name="YAxisPrecision" id="1943.YAxisPrecision"
number_of_elements="1">
        <Element index="0" value="2"/>
        <Domain name="range" id="1943.YAxisPrecision.range"/>
      </Property>
      <Property name="YAxisUseCustomLabels" id="1943.YAxisUseCustomLabels"
number_of_elements="1">
        <Element index="0" value="0"/>
        <Domain name="bool" id="1943.YAxisUseCustomLabels.bool"/>
      </Property>
      <Property name="YTitle" id="1943.YTitle" number_of_elements="1">
        <Element index="0" value="Y Axis"/>
      </Property>
      <Property name="ZAxisLabels" id="1943.ZAxisLabels">
        <Domain name="scalar_range" id="1943.ZAxisLabels.scalar_range"/>
      </Property>
      <Property name="ZAxisNotation" id="1943.ZAxisNotation"
number_of_elements="1">
        <Element index="0" value="0"/>
        <Domain name="enum" id="1943.ZAxisNotation.enum">
          <Entry value="0" text="Mixed"/>
          <Entry value="1" text="Scientific"/>
          <Entry value="2" text="Fixed"/>
        </Domain>
      </Property>
      <Property name="ZAxisPrecision" id="1943.ZAxisPrecision"
number_of_elements="1">
        <Element index="0" value="2"/>
        <Domain name="range" id="1943.ZAxisPrecision.range"/>
      </Property>
      <Property name="ZAxisUseCustomLabels" id="1943.ZAxisUseCustomLabels"
number_of_elements="1">
        <Element index="0" value="0"/>
        <Domain name="bool" id="1943.ZAxisUseCustomLabels.bool"/>
      </Property>
      <Property name="ZTitle" id="1943.ZTitle" number_of_elements="1">
        <Element index="0" value="Z Axis"/>
      </Property>
      <Property name="CullBackface" id="1943.CullBackface"
number_of_elements="1">
        <Element index="0" value="0"/>
        <Domain name="bool" id="1943.CullBackface.bool"/>
      </Property>
      <Property name="CullFrontface" id="1943.CullFrontface"
number_of_elements="1">
        <Element index="0" value="1"/>
        <Domain name="bool" id="1943.CullFrontface.bool"/>
      </Property>
      <Property name="GridColor" id="1943.GridColor" number_of_elements="3">
        <Element index="0" value="1"/>
        <Element index="1" value="1"/>
        <Element index="2" value="1"/>
        <Domain name="range" id="1943.GridColor.range"/>
      </Property>
      <Property name="XLabelBold" id="1943.XLabelBold"
number_of_elements="1">
        <Element index="0" value="0"/>
        <Domain name="bool" id="1943.XLabelBold.bool"/>
      </Property>
      <Property name="XLabelColor" id="1943.XLabelColor"
number_of_elements="3">
        <Element index="0" value="1"/>
        <Element index="1" value="1"/>
        <Element index="2" value="1"/>
        <Domain name="range" id="1943.XLabelColor.range"/>
      </Property>
      <Property name="XLabelFontFamily" id="1943.XLabelFontFamily"
number_of_elements="1">
        <Element index="0" value="0"/>
        <Domain name="enum" id="1943.XLabelFontFamily.enum">
          <Entry value="0" text="Arial"/>
          <Entry value="1" text="Courier"/>
          <Entry value="2" text="Times"/>
        </Domain>
      </Property>
      <Property name="XLabelFontSize" id="1943.XLabelFontSize"
number_of_elements="1">
        <Element index="0" value="12"/>
        <Domain name="range" id="1943.XLabelFontSize.range"/>
      </Property>
      <Property name="XLabelItalic" id="1943.XLabelItalic"
number_of_elements="1">
        <Element index="0" value="0"/>
        <Domain name="bool" id="1943.XLabelItalic.bool"/>
      </Property>
      <Property name="XLabelOpacity" id="1943.XLabelOpacity"
number_of_elements="1">
        <Element index="0" value="1"/>
        <Domain name="range" id="1943.XLabelOpacity.range"/>
      </Property>
      <Property name="XLabelShadow" id="1943.XLabelShadow"
number_of_elements="1">
        <Element index="0" value="0"/>
        <Domain name="bool" id="1943.XLabelShadow.bool"/>
      </Property>
      <Property name="XTitleBold" id="1943.XTitleBold"
number_of_elements="1">
        <Element index="0" value="0"/>
        <Domain name="bool" id="1943.XTitleBold.bool"/>
      </Property>
      <Property name="XTitleColor" id="1943.XTitleColor"
number_of_elements="3">
        <Element index="0" value="1"/>
        <Element index="1" value="1"/>
        <Element index="2" value="1"/>
        <Domain name="range" id="1943.XTitleColor.range"/>
      </Property>
      <Property name="XTitleFontFamily" id="1943.XTitleFontFamily"
number_of_elements="1">
        <Element index="0" value="0"/>
        <Domain name="enum" id="1943.XTitleFontFamily.enum">
          <Entry value="0" text="Arial"/>
          <Entry value="1" text="Courier"/>
          <Entry value="2" text="Times"/>
        </Domain>
      </Property>
      <Property name="XTitleFontSize" id="1943.XTitleFontSize"
number_of_elements="1">
        <Element index="0" value="12"/>
        <Domain name="range" id="1943.XTitleFontSize.range"/>
      </Property>
      <Property name="XTitleItalic" id="1943.XTitleItalic"
number_of_elements="1">
        <Element index="0" value="0"/>
        <Domain name="bool" id="1943.XTitleItalic.bool"/>
      </Property>
      <Property name="XTitleOpacity" id="1943.XTitleOpacity"
number_of_elements="1">
        <Element index="0" value="1"/>
        <Domain name="range" id="1943.XTitleOpacity.range"/>
      </Property>
      <Property name="XTitleShadow" id="1943.XTitleShadow"
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</ParaView>

2016-09-01 16:45 GMT+02:00 Sebastien Jourdain <
sebastien.jourdain at kitware.com>:

> Hi Pepe,
>
> I am not aware of the issue do you mind sharing your state file with me so
> I can see what you were doing in your state file?
>
> Did you generate your state file from the Visualizer or ParaView?
>
> Thanks,
>
> Seb
>
>
>
> On Wed, Aug 31, 2016 at 4:49 AM, Jose Luis Cerc?s <jlcercos at gmail.com>
> wrote:
>
>> Hi community!
>>
>> In Paraview 4.4.0, 5.1.0, and 5.1.2, I'm having a weird error (I don't
>> know if other versions are affected as well)... After launching the
>> ParaViewWeb visualizer script:
>>
>> ./bin/pvpython ./lib/paraview-5.1/site-packag
>> es/paraview/web/pv_web_visualizer.py --content ./share/paraview-5.1/www
>> --data-dir /PATH_TO_THE_FILES/ --port 8080
>>
>> Connecting with it (http://localhost:8080/apps/Visualizer/), loading a
>> pvsm file, and reloading the web page (to close the connection and the
>> ParaViewWeb visualizer instance), I'm receiving a segmentation fault:
>>
>> (...)
>> 2016-08-31 12:39:23+0200 [twisted.web.server.Site] (TCP Port 8080 Closed)
>> 2016-08-31 12:39:23+0200 [twisted.web.server.Site] Stopping factory
>> <twisted.web.server.Site instance at 0x7ff8117d1908>
>> 2016-08-31 12:39:23+0200 [HTTPChannel,6,127.0.0.1] connection_lost:
>> connection count = 0
>> 2016-08-31 12:39:23+0200 [HTTPChannel,6,127.0.0.1] Starting timer,
>> process will terminate in: 300sec
>> 2016-08-31 12:39:23+0200 [-] Main loop terminated.
>> *Segmentation fault (core dumped)*
>>
>> However, it is not happening if I manually load the data and reproduce
>> all the process (In such case it is just logging "Main loop terminated"
>> and conveniently closing the app)
>>
>> The half good news are that, in Paraview >= 5.1.0 at least it is ever
>> terminating (with the segfault), while in Paraview 4.4 it may become hanged
>> (instead of crashing).
>>
>> Someone else with the same problem? Any idea to fix that?
>>
>> Thanks!
>> Pepe
>>
>> _______________________________________________
>> Powered by www.kitware.com
>>
>> Visit other Kitware open-source projects at
>> http://www.kitware.com/opensource/opensource.html
>>
>> Please keep messages on-topic and check the ParaView Wiki at:
>> http://paraview.org/Wiki/ParaView
>>
>> Search the list archives at: http://markmail.org/search/?q=ParaView
>>
>> Follow this link to subscribe/unsubscribe:
>> http://public.kitware.com/mailman/listinfo/paraview
>>
>>
>
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From jlcercos at gmail.com  Tue Sep  6 03:35:14 2016
From: jlcercos at gmail.com (=?UTF-8?Q?Jose_Luis_Cerc=C3=B3s?=)
Date: Tue, 6 Sep 2016 09:35:14 +0200
Subject: [Paraview] pv_web_visualizer.py segmentation fault when loading
 a pvsm file
In-Reply-To: <CAN4UQ49pukejYOggVyb2-Apn_mWEHQORdO4t8=XT1+ihB9B02g@mail.gmail.com>
References: <CAN4UQ49SAsxoK-pLxYQLAGUa0niPC24QNjLiETJTQB5Lj2C4Ow@mail.gmail.com>
 <CABObKxcBXCc7nObCYfeCe1X7P_C8QAEPPHCifNdmTzaZyYqPcA@mail.gmail.com>
 <CAN4UQ49pukejYOggVyb2-Apn_mWEHQORdO4t8=XT1+ihB9B02g@mail.gmail.com>
Message-ID: <CAN4UQ4-YhvLkXyMqd-6V3+jikzFfSZOgzxBRa8vM-oXba1ncGA@mail.gmail.com>

Moreover, I created a cube (Sources/Box), saved the state, launched the
pv_web_visualizer.py server, connected, reloaded the page (i.e. disconnect)
and... the same problem. Again, doing it manually everything works fine.

Thanks!
Pepe


2016-09-06 9:27 GMT+02:00 Jose Luis Cerc?s <jlcercos at gmail.com>:

> Hey Sebastien!
>
> In order to demonstrate the problem, I created a simplified version of the
> state file. I just simply loaded a VTK file and moved the camera... As I
> said, everything is working fine if I do the same stuff manually, without
> loading the pvstate. Following the resulting pvstate file:
>
> <ParaView>
>   <ServerManagerState version="5.0.1">
>     <Proxy group="animation" type="AnimationScene" id="263" servers="16">
>       <Property name="AnimationTime" id="263.AnimationTime"
> number_of_elements="1">
>         <Element index="0" value="0"/>
>       </Property>
>       <Property name="Cues" id="263.Cues" number_of_elements="1">
>         <Proxy value="265"/>
>         <Domain name="groups" id="263.Cues.groups"/>
>       </Property>
>       <Property name="Duration" id="263.Duration" number_of_elements="1">
>         <Element index="0" value="10"/>
>       </Property>
>       <Property name="EndTime" id="263.EndTime" number_of_elements="1">
>         <Element index="0" value="1"/>
>       </Property>
>       <Property name="FramesPerTimestep" id="263.FramesPerTimestep"
> number_of_elements="1">
>         <Element index="0" value="1"/>
>         <Domain name="range" id="263.FramesPerTimestep.range"/>
>       </Property>
>       <Property name="GoToFirst" id="263.GoToFirst"/>
>       <Property name="GoToLast" id="263.GoToLast"/>
>       <Property name="GoToNext" id="263.GoToNext"/>
>       <Property name="GoToPrevious" id="263.GoToPrevious"/>
>       <Property name="LockEndTime" id="263.LockEndTime"
> number_of_elements="1">
>         <Element index="0" value="0"/>
>         <Domain name="bool" id="263.LockEndTime.bool"/>
>       </Property>
>       <Property name="LockStartTime" id="263.LockStartTime"
> number_of_elements="1">
>         <Element index="0" value="0"/>
>         <Domain name="bool" id="263.LockStartTime.bool"/>
>       </Property>
>       <Property name="Loop" id="263.Loop" number_of_elements="1">
>         <Element index="0" value="0"/>
>         <Domain name="bool" id="263.Loop.bool"/>
>       </Property>
>       <Property name="NumberOfFrames" id="263.NumberOfFrames"
> number_of_elements="1">
>         <Element index="0" value="10"/>
>         <Domain name="range" id="263.NumberOfFrames.range"/>
>       </Property>
>       <Property name="Play" id="263.Play"/>
>       <Property name="PlayMode" id="263.PlayMode" number_of_elements="1">
>         <Element index="0" value="0"/>
>         <Domain name="enum" id="263.PlayMode.enum">
>           <Entry value="0" text="Sequence"/>
>           <Entry value="1" text="Real Time"/>
>           <Entry value="2" text="Snap To TimeSteps"/>
>         </Domain>
>       </Property>
>       <Property name="StartTime" id="263.StartTime" number_of_elements="1">
>         <Element index="0" value="0"/>
>       </Property>
>       <Property name="Stop" id="263.Stop"/>
>       <Property name="TimeKeeper" id="263.TimeKeeper"
> number_of_elements="1">
>         <Proxy value="259"/>
>       </Property>
>       <Property name="ViewModules" id="263.ViewModules"
> number_of_elements="2">
>         <Proxy value="1945"/>
>         <Proxy value="1945"/>
>         <Domain name="groups" id="263.ViewModules.groups"/>
>       </Property>
>     </Proxy>
>     <Proxy group="animation" type="TimeAnimationCue" id="265" servers="16">
>       <Property name="AnimatedDomainName" id="265.AnimatedDomainName"
> number_of_elements="1">
>         <Element index="0" value=""/>
>       </Property>
>       <Property name="AnimatedElement" id="265.AnimatedElement"
> number_of_elements="1">
>         <Element index="0" value="0"/>
>       </Property>
>       <Property name="AnimatedPropertyName" id="265.AnimatedPropertyName"
> number_of_elements="1">
>         <Element index="0" value="Time"/>
>       </Property>
>       <Property name="AnimatedProxy" id="265.AnimatedProxy"
> number_of_elements="1">
>         <Proxy value="259"/>
>         <Domain name="groups" id="265.AnimatedProxy.groups"/>
>       </Property>
>       <Property name="Enabled" id="265.Enabled" number_of_elements="1">
>         <Element index="0" value="1"/>
>         <Domain name="bool" id="265.Enabled.bool"/>
>       </Property>
>       <Property name="EndTime" id="265.EndTime" number_of_elements="1">
>         <Element index="0" value="1"/>
>       </Property>
>       <Property name="KeyFrames" id="265.KeyFrames">
>         <Domain name="groups" id="265.KeyFrames.groups"/>
>       </Property>
>       <Property name="LastAddedKeyFrameIndex" id="265.
> LastAddedKeyFrameIndex"/>
>       <Property name="StartTime" id="265.StartTime" number_of_elements="1">
>         <Element index="0" value="0"/>
>       </Property>
>       <Property name="TimeMode" id="265.TimeMode" number_of_elements="1">
>         <Element index="0" value="0"/>
>         <Domain name="enum" id="265.TimeMode.enum">
>           <Entry value="0" text="Normalized"/>
>           <Entry value="1" text="Relative"/>
>         </Domain>
>       </Property>
>       <Property name="UseAnimationTime" id="265.UseAnimationTime"
> number_of_elements="1">
>         <Element index="0" value="1"/>
>         <Domain name="bool" id="265.UseAnimationTime.bool"/>
>       </Property>
>     </Proxy>
>     <Proxy group="misc" type="ViewLayout" id="1917" servers="16">
>       <Layout number_of_elements="1">
>         <Item direction="0" fraction="0.5" view="1945"/>
>       </Layout>
>     </Proxy>
>     <Proxy group="annotations" type="GridAxes3DActor" id="1943"
> servers="21">
>       <Property name="AxesToLabel" id="1943.AxesToLabel"
> number_of_elements="1">
>         <Element index="0" value="63"/>
>         <Domain name="range" id="1943.AxesToLabel.range"/>
>       </Property>
>       <Property name="DataPosition" id="1943.DataPosition"
> number_of_elements="3">
>         <Element index="0" value="0"/>
>         <Element index="1" value="0"/>
>         <Element index="2" value="0"/>
>         <Domain name="range" id="1943.DataPosition.range"/>
>       </Property>
>       <Property name="DataScale" id="1943.DataScale"
> number_of_elements="3">
>         <Element index="0" value="1"/>
>         <Element index="1" value="1"/>
>         <Element index="2" value="1"/>
>         <Domain name="range" id="1943.DataScale.range"/>
>       </Property>
>       <Property name="FacesToRender" id="1943.FacesToRender"
> number_of_elements="1">
>         <Element index="0" value="63"/>
>         <Domain name="range" id="1943.FacesToRender.range"/>
>       </Property>
>       <Property name="LabelUniqueEdgesOnly" id="1943.LabelUniqueEdgesOnly"
> number_of_elements="1">
>         <Element index="0" value="1"/>
>         <Domain name="bool" id="1943.LabelUniqueEdgesOnly.bool"/>
>       </Property>
>       <Property name="ModelBounds" id="1943.ModelBounds"
> number_of_elements="6">
>         <Element index="0" value="0"/>
>         <Element index="1" value="1"/>
>         <Element index="2" value="0"/>
>         <Element index="3" value="1"/>
>         <Element index="4" value="0"/>
>         <Element index="5" value="1"/>
>       </Property>
>       <Property name="ModelTransformMatrix" id="1943.ModelTransformMatrix"
> number_of_elements="16">
>         <Element index="0" value="1"/>
>         <Element index="1" value="0"/>
>         <Element index="2" value="0"/>
>         <Element index="3" value="0"/>
>         <Element index="4" value="0"/>
>         <Element index="5" value="1"/>
>         <Element index="6" value="0"/>
>         <Element index="7" value="0"/>
>         <Element index="8" value="0"/>
>         <Element index="9" value="0"/>
>         <Element index="10" value="1"/>
>         <Element index="11" value="0"/>
>         <Element index="12" value="0"/>
>         <Element index="13" value="0"/>
>         <Element index="14" value="0"/>
>         <Element index="15" value="1"/>
>       </Property>
>       <Property name="ShowEdges" id="1943.ShowEdges"
> number_of_elements="1">
>         <Element index="0" value="1"/>
>         <Domain name="bool" id="1943.ShowEdges.bool"/>
>       </Property>
>       <Property name="ShowGrid" id="1943.ShowGrid" number_of_elements="1">
>         <Element index="0" value="0"/>
>         <Domain name="bool" id="1943.ShowGrid.bool"/>
>       </Property>
>       <Property name="ShowTicks" id="1943.ShowTicks"
> number_of_elements="1">
>         <Element index="0" value="1"/>
>         <Domain name="bool" id="1943.ShowTicks.bool"/>
>       </Property>
>       <Property name="UseModelTransform" id="1943.UseModelTransform"
> number_of_elements="1">
>         <Element index="0" value="0"/>
>         <Domain name="range" id="1943.UseModelTransform.range"/>
>       </Property>
>       <Property name="Visibility" id="1943.Visibility"
> number_of_elements="1">
>         <Element index="0" value="0"/>
>         <Domain name="bool" id="1943.Visibility.bool"/>
>       </Property>
>       <Property name="XAxisLabels" id="1943.XAxisLabels">
>         <Domain name="scalar_range" id="1943.XAxisLabels.scalar_range"/>
>       </Property>
>       <Property name="XAxisNotation" id="1943.XAxisNotation"
> number_of_elements="1">
>         <Element index="0" value="0"/>
>         <Domain name="enum" id="1943.XAxisNotation.enum">
>           <Entry value="0" text="Mixed"/>
>           <Entry value="1" text="Scientific"/>
>           <Entry value="2" text="Fixed"/>
>         </Domain>
>       </Property>
>       <Property name="XAxisPrecision" id="1943.XAxisPrecision"
> number_of_elements="1">
>         <Element index="0" value="2"/>
>         <Domain name="range" id="1943.XAxisPrecision.range"/>
>       </Property>
>       <Property name="XAxisUseCustomLabels" id="1943.XAxisUseCustomLabels"
> number_of_elements="1">
>         <Element index="0" value="0"/>
>         <Domain name="bool" id="1943.XAxisUseCustomLabels.bool"/>
>       </Property>
>       <Property name="XTitle" id="1943.XTitle" number_of_elements="1">
>         <Element index="0" value="X Axis"/>
>       </Property>
>       <Property name="YAxisLabels" id="1943.YAxisLabels">
>         <Domain name="scalar_range" id="1943.YAxisLabels.scalar_range"/>
>       </Property>
>       <Property name="YAxisNotation" id="1943.YAxisNotation"
> number_of_elements="1">
>         <Element index="0" value="0"/>
>         <Domain name="enum" id="1943.YAxisNotation.enum">
>           <Entry value="0" text="Mixed"/>
>           <Entry value="1" text="Scientific"/>
>           <Entry value="2" text="Fixed"/>
>         </Domain>
>       </Property>
>       <Property name="YAxisPrecision" id="1943.YAxisPrecision"
> number_of_elements="1">
>         <Element index="0" value="2"/>
>         <Domain name="range" id="1943.YAxisPrecision.range"/>
>       </Property>
>       <Property name="YAxisUseCustomLabels" id="1943.YAxisUseCustomLabels"
> number_of_elements="1">
>         <Element index="0" value="0"/>
>         <Domain name="bool" id="1943.YAxisUseCustomLabels.bool"/>
>       </Property>
>       <Property name="YTitle" id="1943.YTitle" number_of_elements="1">
>         <Element index="0" value="Y Axis"/>
>       </Property>
>       <Property name="ZAxisLabels" id="1943.ZAxisLabels">
>         <Domain name="scalar_range" id="1943.ZAxisLabels.scalar_range"/>
>       </Property>
>       <Property name="ZAxisNotation" id="1943.ZAxisNotation"
> number_of_elements="1">
>         <Element index="0" value="0"/>
>         <Domain name="enum" id="1943.ZAxisNotation.enum">
>           <Entry value="0" text="Mixed"/>
>           <Entry value="1" text="Scientific"/>
>           <Entry value="2" text="Fixed"/>
>         </Domain>
>       </Property>
>       <Property name="ZAxisPrecision" id="1943.ZAxisPrecision"
> number_of_elements="1">
>         <Element index="0" value="2"/>
>         <Domain name="range" id="1943.ZAxisPrecision.range"/>
>       </Property>
>       <Property name="ZAxisUseCustomLabels" id="1943.ZAxisUseCustomLabels"
> number_of_elements="1">
>         <Element index="0" value="0"/>
>         <Domain name="bool" id="1943.ZAxisUseCustomLabels.bool"/>
>       </Property>
>       <Property name="ZTitle" id="1943.ZTitle" number_of_elements="1">
>         <Element index="0" value="Z Axis"/>
>       </Property>
>       <Property name="CullBackface" id="1943.CullBackface"
> number_of_elements="1">
>         <Element index="0" value="0"/>
>         <Domain name="bool" id="1943.CullBackface.bool"/>
>       </Property>
>       <Property name="CullFrontface" id="1943.CullFrontface"
> number_of_elements="1">
>         <Element index="0" value="1"/>
>         <Domain name="bool" id="1943.CullFrontface.bool"/>
>       </Property>
>       <Property name="GridColor" id="1943.GridColor"
> number_of_elements="3">
>         <Element index="0" value="1"/>
>         <Element index="1" value="1"/>
>         <Element index="2" value="1"/>
>         <Domain name="range" id="1943.GridColor.range"/>
>       </Property>
>       <Property name="XLabelBold" id="1943.XLabelBold"
> number_of_elements="1">
>         <Element index="0" value="0"/>
>         <Domain name="bool" id="1943.XLabelBold.bool"/>
>       </Property>
>       <Property name="XLabelColor" id="1943.XLabelColor"
> number_of_elements="3">
>         <Element index="0" value="1"/>
>         <Element index="1" value="1"/>
>         <Element index="2" value="1"/>
>         <Domain name="range" id="1943.XLabelColor.range"/>
>       </Property>
>       <Property name="XLabelFontFamily" id="1943.XLabelFontFamily"
> number_of_elements="1">
>         <Element index="0" value="0"/>
>         <Domain name="enum" id="1943.XLabelFontFamily.enum">
>           <Entry value="0" text="Arial"/>
>           <Entry value="1" text="Courier"/>
>           <Entry value="2" text="Times"/>
>         </Domain>
>       </Property>
>       <Property name="XLabelFontSize" id="1943.XLabelFontSize"
> number_of_elements="1">
>         <Element index="0" value="12"/>
>         <Domain name="range" id="1943.XLabelFontSize.range"/>
>       </Property>
>       <Property name="XLabelItalic" id="1943.XLabelItalic"
> number_of_elements="1">
>         <Element index="0" value="0"/>
>         <Domain name="bool" id="1943.XLabelItalic.bool"/>
>       </Property>
>       <Property name="XLabelOpacity" id="1943.XLabelOpacity"
> number_of_elements="1">
>         <Element index="0" value="1"/>
>         <Domain name="range" id="1943.XLabelOpacity.range"/>
>       </Property>
>       <Property name="XLabelShadow" id="1943.XLabelShadow"
> number_of_elements="1">
>         <Element index="0" value="0"/>
>         <Domain name="bool" id="1943.XLabelShadow.bool"/>
>       </Property>
>       <Property name="XTitleBold" id="1943.XTitleBold"
> number_of_elements="1">
>         <Element index="0" value="0"/>
>         <Domain name="bool" id="1943.XTitleBold.bool"/>
>       </Property>
>       <Property name="XTitleColor" id="1943.XTitleColor"
> number_of_elements="3">
>         <Element index="0" value="1"/>
>         <Element index="1" value="1"/>
>         <Element index="2" value="1"/>
>         <Domain name="range" id="1943.XTitleColor.range"/>
>       </Property>
>       <Property name="XTitleFontFamily" id="1943.XTitleFontFamily"
> number_of_elements="1">
>         <Element index="0" value="0"/>
>         <Domain name="enum" id="1943.XTitleFontFamily.enum">
>           <Entry value="0" text="Arial"/>
>           <Entry value="1" text="Courier"/>
>           <Entry value="2" text="Times"/>
>         </Domain>
>       </Property>
>       <Property name="XTitleFontSize" id="1943.XTitleFontSize"
> number_of_elements="1">
>         <Element index="0" value="12"/>
>         <Domain name="range" id="1943.XTitleFontSize.range"/>
>       </Property>
>       <Property name="XTitleItalic" id="1943.XTitleItalic"
> number_of_elements="1">
>         <Element index="0" value="0"/>
>         <Domain name="bool" id="1943.XTitleItalic.bool"/>
>       </Property>
>       <Property name="XTitleOpacity" id="1943.XTitleOpacity"
> number_of_elements="1">
>         <Element index="0" value="1"/>
>         <Domain name="range" id="1943.XTitleOpacity.range"/>
>       </Property>
>       <Property name="XTitleShadow" id="1943.XTitleShadow"
> number_of_elements="1">
>         <Element index="0" value="0"/>
>         <Domain name="bool" id="1943.XTitleShadow.bool"/>
>       </Property>
>       <Property name="YLabelBold" id="1943.YLabelBold"
> number_of_elements="1">
>         <Element index="0" value="0"/>
>         <Domain name="bool" id="1943.YLabelBold.bool"/>
>       </Property>
>       <Property name="YLabelColor" id="1943.YLabelColor"
> number_of_elements="3">
>         <Element index="0" value="1"/>
>         <Element index="1" value="1"/>
>         <Element index="2" value="1"/>
>         <Domain name="range" id="1943.YLabelColor.range"/>
>       </Property>
>       <Property name="YLabelFontFamily" id="1943.YLabelFontFamily"
> number_of_elements="1">
>         <Element index="0" value="0"/>
>         <Domain name="enum" id="1943.YLabelFontFamily.enum">
>           <Entry value="0" text="Arial"/>
>           <Entry value="1" text="Courier"/>
>           <Entry value="2" text="Times"/>
>         </Domain>
>       </Property>
>       <Property name="YLabelFontSize" id="1943.YLabelFontSize"
> number_of_elements="1">
>         <Element index="0" value="12"/>
>         <Domain name="range" id="1943.YLabelFontSize.range"/>
>       </Property>
>       <Property name="YLabelItalic" id="1943.YLabelItalic"
> number_of_elements="1">
>         <Element index="0" value="0"/>
>         <Domain name="bool" id="1943.YLabelItalic.bool"/>
>       </Property>
>       <Property name="YLabelOpacity" id="1943.YLabelOpacity"
> number_of_elements="1">
>         <Element index="0" value="1"/>
>         <Domain name="range" id="1943.YLabelOpacity.range"/>
>       </Property>
>       <Property name="YLabelShadow" id="1943.YLabelShadow"
> number_of_elements="1">
>         <Element index="0" value="0"/>
>         <Domain name="bool" id="1943.YLabelShadow.bool"/>
>       </Property>
>       <Property name="YTitleBold" id="1943.YTitleBold"
> number_of_elements="1">
>         <Element index="0" value="0"/>
>         <Domain name="bool" id="1943.YTitleBold.bool"/>
>       </Property>
>       <Property name="YTitleColor" id="1943.YTitleColor"
> number_of_elements="3">
>         <Element index="0" value="1"/>
>         <Element index="1" value="1"/>
>         <Element index="2" value="1"/>
>         <Domain name="range" id="1943.YTitleColor.range"/>
>       </Property>
>       <Property name="YTitleFontFamily" id="1943.YTitleFontFamily"
> number_of_elements="1">
>         <Element index="0" value="0"/>
>         <Domain name="enum" id="1943.YTitleFontFamily.enum">
>           <Entry value="0" text="Arial"/>
>           <Entry value="1" text="Courier"/>
>           <Entry value="2" text="Times"/>
>         </Domain>
>       </Property>
>       <Property name="YTitleFontSize" id="1943.YTitleFontSize"
> number_of_elements="1">
>         <Element index="0" value="12"/>
>         <Domain name="range" id="1943.YTitleFontSize.range"/>
>       </Property>
>       <Property name="YTitleItalic" id="1943.YTitleItalic"
> number_of_elements="1">
>         <Element index="0" value="0"/>
>         <Domain name="bool" id="1943.YTitleItalic.bool"/>
>       </Property>
>       <Property name="YTitleOpacity" id="1943.YTitleOpacity"
> number_of_elements="1">
>         <Element index="0" value="1"/>
>         <Domain name="range" id="1943.YTitleOpacity.range"/>
>       </Property>
>       <Property name="YTitleShadow" id="1943.YTitleShadow"
> number_of_elements="1">
>         <Element index="0" value="0"/>
>         <Domain name="bool" id="1943.YTitleShadow.bool"/>
>       </Property>
>       <Property name="ZLabelBold" id="1943.ZLabelBold"
> number_of_elements="1">
>         <Element index="0" value="0"/>
>         <Domain name="bool" id="1943.ZLabelBold.bool"/>
>       </Property>
>       <Property name="ZLabelColor" id="1943.ZLabelColor"
> number_of_elements="3">
>         <Element index="0" value="1"/>
>         <Element index="1" value="1"/>
>         <Element index="2" value="1"/>
>         <Domain name="range" id="1943.ZLabelColor.range"/>
>       </Property>
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>       <GlobalPropertyLink global_name="TextAnnotationColor" proxy="1943"
> property="YTitleColor"/>
>       <GlobalPropertyLink global_name="TextAnnotationColor" proxy="1943"
> property="ZLabelColor"/>
>       <GlobalPropertyLink global_name="TextAnnotationColor" proxy="1943"
> property="ZTitleColor"/>
>       <GlobalPropertyLink global_name="TextAnnotationColor" proxy="1945"
> property="OrientationAxesLabelColor"/>
>       <GlobalPropertyLink global_name="UseGradientBackground"
> proxy="1945" property="UseGradientBackground"/>
>     </Links>
>   </ServerManagerState>
> </ParaView>
>
> 2016-09-01 16:45 GMT+02:00 Sebastien Jourdain <sebastien.jourdain at kitware.
> com>:
>
>> Hi Pepe,
>>
>> I am not aware of the issue do you mind sharing your state file with me
>> so I can see what you were doing in your state file?
>>
>> Did you generate your state file from the Visualizer or ParaView?
>>
>> Thanks,
>>
>> Seb
>>
>>
>>
>> On Wed, Aug 31, 2016 at 4:49 AM, Jose Luis Cerc?s <jlcercos at gmail.com>
>> wrote:
>>
>>> Hi community!
>>>
>>> In Paraview 4.4.0, 5.1.0, and 5.1.2, I'm having a weird error (I don't
>>> know if other versions are affected as well)... After launching the
>>> ParaViewWeb visualizer script:
>>>
>>> ./bin/pvpython ./lib/paraview-5.1/site-packag
>>> es/paraview/web/pv_web_visualizer.py --content ./share/paraview-5.1/www
>>> --data-dir /PATH_TO_THE_FILES/ --port 8080
>>>
>>> Connecting with it (http://localhost:8080/apps/Visualizer/), loading a
>>> pvsm file, and reloading the web page (to close the connection and the
>>> ParaViewWeb visualizer instance), I'm receiving a segmentation fault:
>>>
>>> (...)
>>> 2016-08-31 12:39:23+0200 [twisted.web.server.Site] (TCP Port 8080 Closed)
>>> 2016-08-31 12:39:23+0200 [twisted.web.server.Site] Stopping factory
>>> <twisted.web.server.Site instance at 0x7ff8117d1908>
>>> 2016-08-31 12:39:23+0200 [HTTPChannel,6,127.0.0.1] connection_lost:
>>> connection count = 0
>>> 2016-08-31 12:39:23+0200 [HTTPChannel,6,127.0.0.1] Starting timer,
>>> process will terminate in: 300sec
>>> 2016-08-31 12:39:23+0200 [-] Main loop terminated.
>>> *Segmentation fault (core dumped)*
>>>
>>> However, it is not happening if I manually load the data and reproduce
>>> all the process (In such case it is just logging "Main loop terminated"
>>> and conveniently closing the app)
>>>
>>> The half good news are that, in Paraview >= 5.1.0 at least it is ever
>>> terminating (with the segfault), while in Paraview 4.4 it may become hanged
>>> (instead of crashing).
>>>
>>> Someone else with the same problem? Any idea to fix that?
>>>
>>> Thanks!
>>> Pepe
>>>
>>> _______________________________________________
>>> Powered by www.kitware.com
>>>
>>> Visit other Kitware open-source projects at
>>> http://www.kitware.com/opensource/opensource.html
>>>
>>> Please keep messages on-topic and check the ParaView Wiki at:
>>> http://paraview.org/Wiki/ParaView
>>>
>>> Search the list archives at: http://markmail.org/search/?q=ParaView
>>>
>>> Follow this link to subscribe/unsubscribe:
>>> http://public.kitware.com/mailman/listinfo/paraview
>>>
>>>
>>
>
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From claire.guilbaud at cea.fr  Tue Sep  6 03:53:48 2016
From: claire.guilbaud at cea.fr (GUILBAUD Claire)
Date: Tue, 6 Sep 2016 09:53:48 +0200
Subject: [Paraview] a lot of Generic Warning for vtkBuffer in PV5.1
In-Reply-To: <CA+=e1ouj0Wet4ac8NAGhQeyTxEKf5Tv4CXwZGRrEq5kQSNTYNQ@mail.gmail.com>
References: <7f6b211b39e643d2b09a21fcea5ff1fa@U-MYKONOS2.dif.dam.intra.cea.fr>
 <CA+=e1osskDj+6QByPpjQJ6qQrXvqU+36E4KR+hfK2bbBqrBPfw@mail.gmail.com>
 <CA+=e1ouj0Wet4ac8NAGhQeyTxEKf5Tv4CXwZGRrEq5kQSNTYNQ@mail.gmail.com>
Message-ID: <fde85eb5-3599-c933-4a92-8b7078976b01@cea.fr>

Hi David,

The trouble happens when ParaView is compiled with 
VTK_ALL_NEW_OBJECT_FACTORY=ON.
It seems there is a naming problem when using factories: the name used 
in the New method is not the same as the one used in the destructor.
One of my colleague fixed it: in VTK/Common/Core, he modified 
vtkObjectFactory.h and .cxx, vtkPoints.cxx (New method), vtkPoints2D.cxx 
(New method).
If you are interested, I can send you those 3 files.

Have a good day.

Claire

On 08/12/16 15:21, David Lonie wrote:
> Oops, I sent that too quickly -- the vtkBuffer.h line should actually be:
>
>     vtkTemplateTypeMacro(vtkBuffer<ScalarTypeT>, vtkObject)
>
> with the template argument.
>
> Dave


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From felipebordeu at gmail.com  Tue Sep  6 04:27:49 2016
From: felipebordeu at gmail.com (Felipe Bordeu)
Date: Tue, 6 Sep 2016 10:27:49 +0200
Subject: [Paraview] Embedding Python source as Modules And Python
	Programmable Filter
In-Reply-To: <CAJbHkX874b-iFrG5wmrx4xunLL6pHi+PY9RNeioAXVtZ+RmOjw@mail.gmail.com>
References: <CAJbHkX874b-iFrG5wmrx4xunLL6pHi+PY9RNeioAXVtZ+RmOjw@mail.gmail.com>
Message-ID: <CAJbHkX9hagaS2ip4JdrtuzU18CmcKsRMCbJLjTAyCQads2toZg@mail.gmail.com>

Hi,

I have a home made plugin and I have some python code to do post
processing. Now I want to embed this pythons routines in my plugin (using
the Embedding Python Source As Modules of
http://www.paraview.org/Wiki/ParaView/Plugin_HowTo). this work great, if I
open a python console (using the GUI) and then typing the "import mymodule"
I can access my routines.

Now I want to use this routines in a programmable filter. The problem is
that my module is no available directly in the python environnement of the
python programmable sources.

For the moment I have to do this (reload my plugin inside the programmable
filter):
Script of the programmable filter:

from paraview.simple import servermanager
servermanager.LoadPlugin('libZ7ToolsNative.so')
import zsetpythonpostpro
zsetpythonpostpro.CalcPostQuantitiesFromSigma(self)

for the  moment this work but, the "LoadPlugin('...) line takes about 3
seconds every time (and my routine less than 1 s).

Working in linux with paraview 5.0.0 (gcc, 64-bits) from sources.

Any ideas of how to solve this issue.
Thanks
Felipe
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From rahulsoni at immt.res.in  Tue Sep  6 06:30:15 2016
From: rahulsoni at immt.res.in (Rahul Kumar Soni)
Date: Tue, 6 Sep 2016 16:00:15 +0530
Subject: [Paraview] Reload button in paraviw
Message-ID: <CA+PKs7dwggpGxwSWD47PUfkaoPTHW2xzHcKE+wgn65piLaAOZQ@mail.gmail.com>

The particular feature discussed in following link is not available in the
latest paraview. When can I expect this much awaited feature in the
standard paraview. Is there a way to get it early.

https://gitlab.kitware.com/paraview/paraview/merge_requests/1000
--
Regards

[image: photo]
*Rahul K Soni*
Scientist, Council of Scientific & Industrial Research
+91 674 237 9370 | +91 94790 58522 | +91 674 2567160 | rahulsoni at immt.res.in
| https://sites.google.com/site/rahuliitdhn | Skype: rksoni209 <#> | # 204,
CSIR - Institute of Minerals & Materials Technology, Bhubaneswar
<http://sites.google.com/site/rahuliitdhn>
<http://www.facebook.com/RahulSoni.ISM>
<http://in.linkedin.com/in/rahuliitdhn>  <http://twitter.com/rahul_ism>
<http://instagram.com/rahulksoni>  <http://plus.google.com/+RahulKumarSoni>
<http://www.youtube.com/channel/UC6gl0SYsQBQ5we3QcsJEHFw>
<http://github.com/rahulksoni>
Get a signature like this: Click here!
<http://ws-promos.appspot.com/r?rdata=eyJydXJsIjogImh0dHA6Ly93d3cud2lzZXN0YW1wLmNvbS9lbWFpbC1pbnN0YWxsP3dzX25jaWQ9NjcyMjk0MDA4JnV0bV9zb3VyY2U9ZXh0ZW5zaW9uJnV0bV9tZWRpdW09ZW1haWwmdXRtX2NhbXBhaWduPXByb21vXzU3MzI1Njg1NDg3Njk3OTIiLCAiZSI6ICI1NzMyNTY4NTQ4NzY5NzkyIn0=&u=773292617407621>
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From andy.bauer at kitware.com  Tue Sep  6 08:25:02 2016
From: andy.bauer at kitware.com (Andy Bauer)
Date: Tue, 6 Sep 2016 08:25:02 -0400
Subject: [Paraview] Compiling Catalyst Examples
In-Reply-To: <DM5PR20MB13387BF9CED44911675BF31781E70@DM5PR20MB1338.namprd20.prod.outlook.com>
References: <DM5PR20MB1338F5BB01F03C298700D19181E00@DM5PR20MB1338.namprd20.prod.outlook.com>
 <CAMaOp+Fy-+tifFRmB0GhBb7S-bY9Ui=YmqLD4dqwkn+CaE4MqA@mail.gmail.com>
 <DM5PR20MB13387BF9CED44911675BF31781E70@DM5PR20MB1338.namprd20.prod.outlook.com>
Message-ID: <CAMaOp+Gmxf7aKKgb0A1-27fTbEwyiz_y=s8W5Rr03SO0ga4M=w@mail.gmail.com>

Please keep the conversations on the mailing list so that everyone that
wants to can participate.

Do you have Python and MPI enabled for your ParaView build? Sharing your
CMakeCache.txt from your build directory may help diagnose the problem.


On Sun, Sep 4, 2016 at 11:18 AM, Hermano ... <hermano_lustosa at hotmail.com>
wrote:

>
> I've followed the wiki for building paraview:
> http://www.paraview.org/Wiki/ParaView:Build_And_Install#On_
> Unix-like_operating_systems
>
> Cloned git repositories, used ccmake to configure (I enabled the build
> examples flag and all) and this is what my build/bin directory looks like:
>
> CMakeCache.txt                          vtkH5make_libsettings
> CMakeFiles                              vtkHashSource-pv5.1
> DemoApp0                                vtkImagingMorphologicalCxxTests
> DemoApp1                                vtkIOAMRCxxTests
> multiserverclient                       vtkIOCoreCxxTests
> paraview                                vtkIOExodusCxxTests
> paraview-config                         vtkIOExportCxxTests
> paraview_revised                        vtkIOExportOpenGLCxxTests
> paraview_revised_2                      vtkIOGeometryCxxTests
> particles_viewer                        vtkIOImportCxxTests
> pqCoreBasicApp                          vtkIOLegacyCxxTests
> pqPipelineApp                           vtkIOMovieCxxTests
> pqWidgetsTest                           vtkIOParallelExodusCxxTests
> protoc                                  vtkIOPLYCxxTests
> pvdataserver                            vtkIOTecplotTableCxxTests
> pvrenderserver                          vtkIOXdmf2CxxTests
> pvserver                                vtkIOXMLCxxTests
> QtTestingCppTests                       vtkkwProcessXML-pv5.1
> smTestDriver                            vtkLegacyColorMapXMLToJSON
> spreadsheet                             vtkParallelCoreCxxTests
> TestingDemo                             vtkParallelCore-
> TestSocketCommunicator
> TestXMLCInterface                       vtkParseJava-pv5.1
> vtkChartsCoreCxxTests                   vtkParseOGLExt-pv5.1
> vtkClientServerCxxTests                 vtkPVAnimationCxxTests
> vtkCommonColorCxxTests                  vtkPVCatalystCxxTests
> vtkCommonComputationalGeometryCxxTests  vtkPVClientServerCoreDefaultCx
> xTests
> vtkCommonCoreCxxTests                   vtkPVCommonCxxTests
> vtkCommonDataModelCxxTests              vtkPVServerManagerCoreCxxTests
> vtkCommonExecutionModelCxxTests         vtkPVServerManagerDefaultCxxTests
> vtkCommonMathCxxTests                   vtkPVServerManagerRenderingCxx
> Tests
> vtkCommonMiscCxxTests                   vtkPVVTKExtensionsRenderingCxx
> Tests
> vtkCommonSystemCxxTests                 vtkRenderingAnnotationCxxTests
> vtkCommonTransformsCxxTests             vtkRenderingContext2DCxxTests
> vtkDomainsChemistryCxxTests             vtkRenderingCoreCxxTests
> vtkEncodeString-pv5.1                   vtkRenderingFreeTypeCxxTests
> vtkFiltersAMRCxxTests                   vtkRenderingGL2PSCxxTests
> vtkFiltersCoreCxxTests                  vtkRenderingLabelCxxTests
> vtkFiltersExtractionCxxTests            vtkRenderingLICCxxTests
> vtkFiltersGenericCxxTests               vtkRenderingLODCxxTests
> vtkFiltersGeometryCxxTests              vtkRenderingVolumeCxxTests
> vtkFiltersHyperTreeCxxTests             vtkSciberQuestCxxTests
> vtkFiltersModelingCxxTests              vtkWrapClientServer-pv5.1
> vtkFiltersPointsCxxTests                vtkWrapHierarchy-pv5.1
> vtkFiltersProgrammableCxxTests          vtkWrapJava-pv5.1
> vtkFiltersSourcesCxxTests               vtkWrapPythonInit-pv5.1
> vtkFiltersStatisticsCxxTests            vtkWrapPython-pv5.1
> vtkFiltersVerdictCxxTests               vtkWrapTclInit-pv5.1
> vtkGUISupportQtCxxTests                 vtkWrapTcl-pv5.1
> vtkH5detect
>
> When I try to find CxxFullExample in the build/ directory:
>
> find -name CxxFullExample
>
> Nothing is found. The sources for the examples are in the source as you
> mentioned, but nothing appears on the build directory. I am must be doing
> something wrong!
>
>
> ------------------------------
> *De:* Andy Bauer <andy.bauer at kitware.com>
> *Enviado:* ter?a-feira, 30 de agosto de 2016 11:42
> *Para:* Hermano ...
> *Cc:* paraview at paraview.org
> *Assunto:* Re: [Paraview] Compiling Catalyst Examples
>
> Hi,
>
> The examples have been moved into the ParaView source tree at
> <source>/Examples/Catalyst. This makes it easier to test the examples and
> keep them in sync with the PV source. You can still compile them separately
> and individually if you want to.
>
> On my Linux machine, when I build ParaView master (a bit beyond 5.1.2) the
> example executables get put in the bin subdirectory of the build directory.
> They may not get installed to the install bin directory though if that's
> where you're looking for them. If you're looking for them in the build
> directory, what gets returned when you search for CxxFullExample? That's
> where all of the Catalyst examples should get put.
>
> Best,
> Andy
>
> On Tue, Aug 30, 2016 at 9:16 AM, Hermano ... <hermano_lustosa at hotmail.com>
> wrote:
>
>> Hello Everyone
>>
>> I am looking for some help in order to run the catalyst examples found in:
>> https://github.com/Kitware/ParaViewCatalystExampleCode-MOVED-
>>
>>
>> I've downloaded and compile paraview with Examples flag set to on in
>> ccmake during configuration. But I can't find any binaries in the build
>> directory for the examples in the page above. Is there another flag
>> specifically for catalyst examples? And where will the corresponding
>> binaries by placed in the build directory?
>>
>> If you could point me to some reference I'll be very glad. Thanks in
>> advance
>>
>> _______________________________________________
>> Powered by www.kitware.com
>>
>> Visit other Kitware open-source projects at
>> http://www.kitware.com/opensource/opensource.html
>>
>> Please keep messages on-topic and check the ParaView Wiki at:
>> http://paraview.org/Wiki/ParaView
>>
>> Search the list archives at: http://markmail.org/search/?q=ParaView
>>
>> Follow this link to subscribe/unsubscribe:
>> http://public.kitware.com/mailman/listinfo/paraview
>>
>>
>
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From utkarsh.ayachit at kitware.com  Tue Sep  6 08:43:06 2016
From: utkarsh.ayachit at kitware.com (Utkarsh Ayachit)
Date: Tue, 6 Sep 2016 08:43:06 -0400
Subject: [Paraview] Reload button in paraviw
In-Reply-To: <CA+PKs7dwggpGxwSWD47PUfkaoPTHW2xzHcKE+wgn65piLaAOZQ@mail.gmail.com>
References: <CA+PKs7dwggpGxwSWD47PUfkaoPTHW2xzHcKE+wgn65piLaAOZQ@mail.gmail.com>
Message-ID: <CADHSJjDoFvJpZNuWtFqzLMY=q0C+QogthnXcAru-5Sy-JPXUDQ@mail.gmail.com>

Rahul,

It's under development. You can build from source, if you're keen. Or
wait till the changes get merged in `master` and try the nightly
binaries. The feature is targeted for 5.2 release slated for Oct/Nov
timeframe.

From david.lonie at kitware.com  Tue Sep  6 08:55:10 2016
From: david.lonie at kitware.com (David Lonie)
Date: Tue, 6 Sep 2016 08:55:10 -0400
Subject: [Paraview] a lot of Generic Warning for vtkBuffer in PV5.1
In-Reply-To: <fde85eb5-3599-c933-4a92-8b7078976b01@cea.fr>
References: <7f6b211b39e643d2b09a21fcea5ff1fa@U-MYKONOS2.dif.dam.intra.cea.fr>
 <CA+=e1osskDj+6QByPpjQJ6qQrXvqU+36E4KR+hfK2bbBqrBPfw@mail.gmail.com>
 <CA+=e1ouj0Wet4ac8NAGhQeyTxEKf5Tv4CXwZGRrEq5kQSNTYNQ@mail.gmail.com>
 <fde85eb5-3599-c933-4a92-8b7078976b01@cea.fr>
Message-ID: <CA+=e1os2nxa=wUqjwuMW2Ke8ayJHaXBE_=Km+0Cf40-EGoY1bQ@mail.gmail.com>

Hi Claire,

Sure, if you can send me the files I'll push them for review/merging.

Thanks,
Dave

On Tue, Sep 6, 2016 at 3:53 AM, GUILBAUD Claire <claire.guilbaud at cea.fr> wrote:
> Hi David,
>
> The trouble happens when ParaView is compiled with
> VTK_ALL_NEW_OBJECT_FACTORY=ON.
> It seems there is a naming problem when using factories: the name used in
> the New method is not the same as the one used in the destructor.
> One of my colleague fixed it: in VTK/Common/Core, he modified
> vtkObjectFactory.h and .cxx, vtkPoints.cxx (New method), vtkPoints2D.cxx
> (New method).
> If you are interested, I can send you those 3 files.
>
> Have a good day.
>
> Claire
>
> On 08/12/16 15:21, David Lonie wrote:
>
> Oops, I sent that too quickly -- the vtkBuffer.h line should actually be:
>
>    vtkTemplateTypeMacro(vtkBuffer<ScalarTypeT>, vtkObject)
>
> with the template argument.
>
> Dave
>
>

From utkarsh.ayachit at kitware.com  Tue Sep  6 09:04:27 2016
From: utkarsh.ayachit at kitware.com (Utkarsh Ayachit)
Date: Tue, 6 Sep 2016 09:04:27 -0400
Subject: [Paraview] Building Paraview 5.2.1 on Windows (Visual Studio)
In-Reply-To: <C1142B0660A0384C9B52008C63E3685A0169289E1F@exchange2.pc.mayahtt.ca>
References: <C1142B0660A0384C9B52008C63E3685A0169289E1F@exchange2.pc.mayahtt.ca>
Message-ID: <CADHSJjCmLXiYamU7P_Vz4uXn=1hJzyr=o8fA3bh-eSyEJGF6Uw@mail.gmail.com>

Are you building Debug ParaView with Release Qt? That won't work. If
not, make sure your PATH is clean and is not bringing in other
versions of Qt, ParaView. We build/test with VS2013 with no issues. I
personally have built with VS2015 with no issues to report either --
although in both cases we use Ninja as the generator rather than the
VS project files.

On Fri, Sep 2, 2016 at 10:43 AM, Charles Boivin
<charles.boivin at mayahtt.com> wrote:
> Trying to build PV 5.2.1 on Windows 7. I have tried with both VS2015 and
> VS2013 and facing the same issue.
>
>
>
> Using Qt 4.8.6 (compiled in ?Release? mode ? no debugging info)
>
>
>
> I point CMake to the Qt folder and easily get VS projects and solutions. I
> can compile without any issue (had missing libs with one project, but turned
> off VTK_BUILD_QT_DESIGNER_PLUGIN to avoid that issue for now).
>
>
>
> It builds and links fine. However, Paraview crashes when I try to run it,
> without any kind of message whatsoever. Debugging in VS, I can see that it
> gets to pqApplicationCore::createOutputWindow(), and it crashes when it
> tries to execute the following line:
>
>
>
>   this->OutputWindow = new pqOutputWindow(0);
>
>
>
> (it doesn?t even reach the interior of pqOutputWindow::pqOutputWindow() ?
> looks like it crashes in the SuperClass maybe? Hard to say).
>
>
>
> Has someone ever encountered something similar? If not, is there any way to
> get more info as to what might be going on here in order to fix this in some
> way (maybe some log file)? As mentioned before, I tried with both VS2013 and
> VS2015 (and corresponding builds of Qt 4.8.6), and I get the same problem.
>
>
>
> Thank you,
>
>
>
>
>
> Charles Boivin
>
>
> _______________________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Please keep messages on-topic and check the ParaView Wiki at:
> http://paraview.org/Wiki/ParaView
>
> Search the list archives at: http://markmail.org/search/?q=ParaView
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/paraview
>

From utkarsh.ayachit at kitware.com  Tue Sep  6 13:42:11 2016
From: utkarsh.ayachit at kitware.com (Utkarsh Ayachit)
Date: Tue, 6 Sep 2016 13:42:11 -0400
Subject: [Paraview] Building Paraview 5.2.1 on Windows (Visual Studio)
In-Reply-To: <C1142B0660A0384C9B52008C63E3685A016928C3DE@exchange2.pc.mayahtt.ca>
References: <C1142B0660A0384C9B52008C63E3685A0169289E1F@exchange2.pc.mayahtt.ca>
 <CADHSJjCmLXiYamU7P_Vz4uXn=1hJzyr=o8fA3bh-eSyEJGF6Uw@mail.gmail.com>
 <C1142B0660A0384C9B52008C63E3685A016928C3DE@exchange2.pc.mayahtt.ca>
Message-ID: <CADHSJjBjLJcWCtJYKMAdmmO62F9Tv7ckZqGPdd68N4Jv2G6cdA@mail.gmail.com>

> Is there any reason why switching to shared libs would break things (aside from the obvious -- i.e. wrong DLL being picked up)?

None that I can think of.

> Does Qt have to be built with shared libs as well for this to work (Qt is built statically -- which I wouldn't think would be a problem)?

I don't think we've ever tried Qt-static + ParaView-shared. I can
believe that may cause some issues. Qt-shared + ParaView-static should
be okay, on the other hand.

From charles.boivin at mayahtt.com  Tue Sep  6 13:36:41 2016
From: charles.boivin at mayahtt.com (Charles Boivin)
Date: Tue, 6 Sep 2016 17:36:41 +0000
Subject: [Paraview] Building Paraview 5.2.1 on Windows (Visual Studio)
In-Reply-To: <CADHSJjCmLXiYamU7P_Vz4uXn=1hJzyr=o8fA3bh-eSyEJGF6Uw@mail.gmail.com>
References: <C1142B0660A0384C9B52008C63E3685A0169289E1F@exchange2.pc.mayahtt.ca>
 <CADHSJjCmLXiYamU7P_Vz4uXn=1hJzyr=o8fA3bh-eSyEJGF6Uw@mail.gmail.com>
Message-ID: <C1142B0660A0384C9B52008C63E3685A016928C3DE@exchange2.pc.mayahtt.ca>

Utkarsh,

Thanks for your reply. 

I eventually managed to get something working, but I had to turn off shared libraries. Is there any reason why switching to shared libs would break things (aside from the obvious -- i.e. wrong DLL being picked up)? Does Qt have to be built with shared libs as well for this to work (Qt is built statically -- which I wouldn't think would be a problem)?

Thanks again,

Charles

-----Original Message-----
From: Utkarsh Ayachit [mailto:utkarsh.ayachit at kitware.com] 
Sent: Tuesday, September 06, 2016 9:04 AM
To: Charles Boivin
Cc: paraview at paraview.org
Subject: Re: [Paraview] Building Paraview 5.2.1 on Windows (Visual Studio)

Are you building Debug ParaView with Release Qt? That won't work. If not, make sure your PATH is clean and is not bringing in other versions of Qt, ParaView. We build/test with VS2013 with no issues. I personally have built with VS2015 with no issues to report either -- although in both cases we use Ninja as the generator rather than the VS project files.

On Fri, Sep 2, 2016 at 10:43 AM, Charles Boivin <charles.boivin at mayahtt.com> wrote:
> Trying to build PV 5.2.1 on Windows 7. I have tried with both VS2015 
> and
> VS2013 and facing the same issue.
>
>
>
> Using Qt 4.8.6 (compiled in ?Release? mode ? no debugging info)
>
>
>
> I point CMake to the Qt folder and easily get VS projects and 
> solutions. I can compile without any issue (had missing libs with one 
> project, but turned off VTK_BUILD_QT_DESIGNER_PLUGIN to avoid that issue for now).
>
>
>
> It builds and links fine. However, Paraview crashes when I try to run 
> it, without any kind of message whatsoever. Debugging in VS, I can see 
> that it gets to pqApplicationCore::createOutputWindow(), and it 
> crashes when it tries to execute the following line:
>
>
>
>   this->OutputWindow = new pqOutputWindow(0);
>
>
>
> (it doesn?t even reach the interior of 
> pqOutputWindow::pqOutputWindow() ? looks like it crashes in the SuperClass maybe? Hard to say).
>
>
>
> Has someone ever encountered something similar? If not, is there any 
> way to get more info as to what might be going on here in order to fix 
> this in some way (maybe some log file)? As mentioned before, I tried 
> with both VS2013 and
> VS2015 (and corresponding builds of Qt 4.8.6), and I get the same problem.
>
>
>
> Thank you,
>
>
>
>
>
> Charles Boivin
>
>
> _______________________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at 
> http://www.kitware.com/opensource/opensource.html
>
> Please keep messages on-topic and check the ParaView Wiki at:
> http://paraview.org/Wiki/ParaView
>
> Search the list archives at: http://markmail.org/search/?q=ParaView
>
> Follow this link to subscribe/unsubscribe:
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>

From hermano_lustosa at hotmail.com  Tue Sep  6 15:58:23 2016
From: hermano_lustosa at hotmail.com (Hermano ...)
Date: Tue, 6 Sep 2016 19:58:23 +0000
Subject: [Paraview] Compiling Catalyst Examples
In-Reply-To: <CAMaOp+Gmxf7aKKgb0A1-27fTbEwyiz_y=s8W5Rr03SO0ga4M=w@mail.gmail.com>
References: <DM5PR20MB1338F5BB01F03C298700D19181E00@DM5PR20MB1338.namprd20.prod.outlook.com>
 <CAMaOp+Fy-+tifFRmB0GhBb7S-bY9Ui=YmqLD4dqwkn+CaE4MqA@mail.gmail.com>
 <DM5PR20MB13387BF9CED44911675BF31781E70@DM5PR20MB1338.namprd20.prod.outlook.com>,
 <CAMaOp+Gmxf7aKKgb0A1-27fTbEwyiz_y=s8W5Rr03SO0ga4M=w@mail.gmail.com>
Message-ID: <DM5PR20MB13380CB87BCD48DB2AB862AC81F90@DM5PR20MB1338.namprd20.prod.outlook.com>

Sorry. My mistake!

I've cleaned up my build directory and enabled the python flag during configuration. I assumed it was enabled but I guess there was something wrong with my python installation. I've compiled and the examples are know in the /bin dir of the build tree.

Thank you very much!

________________________________
De: Andy Bauer <andy.bauer at kitware.com>
Enviado: ter?a-feira, 6 de setembro de 2016 10:25
Para: Hermano ...; paraview at paraview.org
Assunto: Re: [Paraview] Compiling Catalyst Examples

Please keep the conversations on the mailing list so that everyone that wants to can participate.

Do you have Python and MPI enabled for your ParaView build? Sharing your CMakeCache.txt from your build directory may help diagnose the problem.


On Sun, Sep 4, 2016 at 11:18 AM, Hermano ... <hermano_lustosa at hotmail.com<mailto:hermano_lustosa at hotmail.com>> wrote:


I've followed the wiki for building paraview:
http://www.paraview.org/Wiki/ParaView:Build_And_Install#On_Unix-like_operating_systems

Cloned git repositories, used ccmake to configure (I enabled the build examples flag and all) and this is what my build/bin directory looks like:

CMakeCache.txt                          vtkH5make_libsettings
CMakeFiles                              vtkHashSource-pv5.1
DemoApp0                                vtkImagingMorphologicalCxxTests
DemoApp1                                vtkIOAMRCxxTests
multiserverclient                       vtkIOCoreCxxTests
paraview                                vtkIOExodusCxxTests
paraview-config                         vtkIOExportCxxTests
paraview_revised                        vtkIOExportOpenGLCxxTests
paraview_revised_2                      vtkIOGeometryCxxTests
particles_viewer                        vtkIOImportCxxTests
pqCoreBasicApp                          vtkIOLegacyCxxTests
pqPipelineApp                           vtkIOMovieCxxTests
pqWidgetsTest                           vtkIOParallelExodusCxxTests
protoc                                  vtkIOPLYCxxTests
pvdataserver                            vtkIOTecplotTableCxxTests
pvrenderserver                          vtkIOXdmf2CxxTests
pvserver                                vtkIOXMLCxxTests
QtTestingCppTests                       vtkkwProcessXML-pv5.1
smTestDriver                            vtkLegacyColorMapXMLToJSON
spreadsheet                             vtkParallelCoreCxxTests
TestingDemo                             vtkParallelCore-TestSocketCommunicator
TestXMLCInterface                       vtkParseJava-pv5.1
vtkChartsCoreCxxTests                   vtkParseOGLExt-pv5.1
vtkClientServerCxxTests                 vtkPVAnimationCxxTests
vtkCommonColorCxxTests                  vtkPVCatalystCxxTests
vtkCommonComputationalGeometryCxxTests  vtkPVClientServerCoreDefaultCxxTests
vtkCommonCoreCxxTests                   vtkPVCommonCxxTests
vtkCommonDataModelCxxTests              vtkPVServerManagerCoreCxxTests
vtkCommonExecutionModelCxxTests         vtkPVServerManagerDefaultCxxTests
vtkCommonMathCxxTests                   vtkPVServerManagerRenderingCxxTests
vtkCommonMiscCxxTests                   vtkPVVTKExtensionsRenderingCxxTests
vtkCommonSystemCxxTests                 vtkRenderingAnnotationCxxTests
vtkCommonTransformsCxxTests             vtkRenderingContext2DCxxTests
vtkDomainsChemistryCxxTests             vtkRenderingCoreCxxTests
vtkEncodeString-pv5.1                   vtkRenderingFreeTypeCxxTests
vtkFiltersAMRCxxTests                   vtkRenderingGL2PSCxxTests
vtkFiltersCoreCxxTests                  vtkRenderingLabelCxxTests
vtkFiltersExtractionCxxTests            vtkRenderingLICCxxTests
vtkFiltersGenericCxxTests               vtkRenderingLODCxxTests
vtkFiltersGeometryCxxTests              vtkRenderingVolumeCxxTests
vtkFiltersHyperTreeCxxTests             vtkSciberQuestCxxTests
vtkFiltersModelingCxxTests              vtkWrapClientServer-pv5.1
vtkFiltersPointsCxxTests                vtkWrapHierarchy-pv5.1
vtkFiltersProgrammableCxxTests          vtkWrapJava-pv5.1
vtkFiltersSourcesCxxTests               vtkWrapPythonInit-pv5.1
vtkFiltersStatisticsCxxTests            vtkWrapPython-pv5.1
vtkFiltersVerdictCxxTests               vtkWrapTclInit-pv5.1
vtkGUISupportQtCxxTests                 vtkWrapTcl-pv5.1
vtkH5detect

When I try to find CxxFullExample in the build/ directory:

find -name CxxFullExample

Nothing is found. The sources for the examples are in the source as you mentioned, but nothing appears on the build directory. I am must be doing something wrong!


________________________________
De: Andy Bauer <andy.bauer at kitware.com<mailto:andy.bauer at kitware.com>>
Enviado: ter?a-feira, 30 de agosto de 2016 11:42
Para: Hermano ...
Cc: paraview at paraview.org<mailto:paraview at paraview.org>
Assunto: Re: [Paraview] Compiling Catalyst Examples

Hi,

The examples have been moved into the ParaView source tree at <source>/Examples/Catalyst. This makes it easier to test the examples and keep them in sync with the PV source. You can still compile them separately and individually if you want to.

On my Linux machine, when I build ParaView master (a bit beyond 5.1.2) the example executables get put in the bin subdirectory of the build directory. They may not get installed to the install bin directory though if that's where you're looking for them. If you're looking for them in the build directory, what gets returned when you search for CxxFullExample? That's where all of the Catalyst examples should get put.

Best,
Andy

On Tue, Aug 30, 2016 at 9:16 AM, Hermano ... <hermano_lustosa at hotmail.com<mailto:hermano_lustosa at hotmail.com>> wrote:

Hello Everyone

I am looking for some help in order to run the catalyst examples found in:
https://github.com/Kitware/ParaViewCatalystExampleCode-MOVED-


I've downloaded and compile paraview with Examples flag set to on in ccmake during configuration. But I can't find any binaries in the build directory for the examples in the page above. Is there another flag specifically for catalyst examples? And where will the corresponding binaries by placed in the build directory?

If you could point me to some reference I'll be very glad. Thanks in advance

_______________________________________________
Powered by www.kitware.com<http://www.kitware.com>

Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html

Please keep messages on-topic and check the ParaView Wiki at: http://paraview.org/Wiki/ParaView

Search the list archives at: http://markmail.org/search/?q=ParaView

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From tim.gallagher at gatech.edu  Tue Sep  6 14:52:44 2016
From: tim.gallagher at gatech.edu (Gallagher, Timothy P)
Date: Tue, 6 Sep 2016 18:52:44 +0000
Subject: [Paraview] Status of BoxLib AMR reader
In-Reply-To: <CADHSJjCtJ3GNQz_8YQuUYdmePFRqs43y4Qnyt0RavPPp57ksnQ@mail.gmail.com>
References: <CY1PR0701MB2058DA767925F078D7697F619DED0@CY1PR0701MB2058.namprd07.prod.outlook.com>
 <CADHSJjBZ2+dkxt-zCaMm1i-2YRCEfEA2x9njh=kRvEDsbWRwog@mail.gmail.com>
 <CY1PR0701MB205876961A89DA1389157B3B9DEC0@CY1PR0701MB2058.namprd07.prod.outlook.com>
 <CY1PR0701MB2058C1F7A05DE29385DFE5AF9DEC0@CY1PR0701MB2058.namprd07.prod.outlook.com>
 <CADHSJjDiKQruLPGw3cOBcjP9LSTyBkyPWtGJETWKmfnU0i4LWg@mail.gmail.com>
 <CY1PR0701MB2058273B5F97EC7DA780DCFE9DE10@CY1PR0701MB2058.namprd07.prod.outlook.com>
 <CADHSJjD=bOtc2SH7WMET+HxycP+TPF-eZ8YDev8_hmuKubDumw@mail.gmail.com>
 <CY1PR0701MB2058055C46034B39CFC609059DE10@CY1PR0701MB2058.namprd07.prod.outlook.com>
 <CY1PR0701MB205870806EF0B4D8EA415DD19DE10@CY1PR0701MB2058.namprd07.prod.outlook.com>,
 <CADHSJjCtJ3GNQz_8YQuUYdmePFRqs43y4Qnyt0RavPPp57ksnQ@mail.gmail.com>
Message-ID: <CY1PR0701MB2058FD60B33B1C6BCCA733719DF90@CY1PR0701MB2058.namprd07.prod.outlook.com>

Hi Utkarsh,


Have you had a chance to take a look at this yet? I will have some time later this week to pick it back up -- just wanted to check if there was anything new about it before I dove back in.


Thanks,


Tim


________________________________
From: Utkarsh Ayachit <utkarsh.ayachit at kitware.com>
Sent: Tuesday, August 30, 2016 7:51 AM
To: Gallagher, Timothy P
Cc: paraview at paraview.org
Subject: Re: [Paraview] Status of BoxLib AMR reader

Thanks, Tim. I'll take a look in next few days.

Utkarsh

On Mon, Aug 29, 2016 at 4:12 PM, Gallagher, Timothy P <tim.gallagher at gatech.edu<mailto:tim.gallagher at gatech.edu>> wrote:

I have to throw in the towel on this one for now and get back to some other deadlines... but, I put what I have so far online and created a merge request with information about the error and an example dataset attached.


Hopefully somebody better with VTK than I am can take a look and figure out what I'm missing. I tried comparing the files for Chombo against the original Visit source files to see if any special modifications were required and none are (the only changes are HDF5 related). It looks like the Chombo reader is from Visit 2.7.0 -- the Boxlib files I added are from 2.10.3, but I tried it with the Boxlib reader from Visit 2.7.0 also and it's the same issue.


If anybody has a chance to take a look, I'd appreciate it. Hopefully it's something simple. If not, I'll try to pick it back up in a few days. I apologize for the hacked CMakeLists to link against the library, I will fix it to do it properly once everything else works!


Tim


________________________________
From: ParaView <paraview-bounces at paraview.org<mailto:paraview-bounces at paraview.org>> on behalf of Gallagher, Timothy P <tim.gallagher at gatech.edu<mailto:tim.gallagher at gatech.edu>>
Sent: Monday, August 29, 2016 12:41 PM

To: Utkarsh Ayachit
Cc: paraview at paraview.org<mailto:paraview at paraview.org>
Subject: Re: [Paraview] Status of BoxLib AMR reader


Thanks for the quick response, the case didn't match between the two files and that was the issue. I'm able to use the reader to select the file and it sees the names of the variables in it properly, but when I hit Apply it throws:


ERROR: In /data4/PVBoxLibTest/paraview/VTK/Common/DataModel/vtkAMRInformation.cxx, line 573
vtkAMRInformation (0x44210f0): Invalid grid description for a vtkUniformGrid


I have a feeling this might get beyond my paraview knowledge to fix.


One potential source of the problem -- what version of Visit are the other readers pulled from? I have the Boxlib files from the latest version, but looking at some of the other readers, they are from older versions.

The latest date I see in the copyright for existing readers is 2013 and looking through the Visit Release notes, the last release in 2013 says it was upgraded to use VTK-6.0.


Is it possible the bridge is based on Visit before that major VTK upgrade and I need to pull the reader code from a version earlier than that?


Thanks for your help. If I can't find something I know how to fix soon, I can create a merge request and see if anybody else can get it the rest of the way.


Tim

________________________________
From: Utkarsh Ayachit <utkarsh.ayachit at kitware.com<mailto:utkarsh.ayachit at kitware.com>>
Sent: Monday, August 29, 2016 12:17 PM
To: Gallagher, Timothy P
Cc: paraview at paraview.org<mailto:paraview at paraview.org>
Subject: Re: [Paraview] Status of BoxLib AMR reader

Tim,

It doesn't know what the class is. Multiple things could have gone wrong:
1. is there call to ADD_VISIT_READER() for the new reader?
2. does the case match between the XML's class="" and the name specified in 1?

If it makes it easier, create a MR on the https://gitlab.kitware.com/paraview/visitbridge repo with your changes, and I can do the necessary fixes.
[https://gitlab.kitware.com/uploads/project/avatar/12/VisitBridge_Icon__3_.png]<https://gitlab.kitware.com/paraview/visitbridge>

ParaView / VisItBridge<https://gitlab.kitware.com/paraview/visitbridge>
gitlab.kitware.com<http://gitlab.kitware.com>
Bridge between VisIt and ParaView to use VisIt readers in ParaView.


Utkarsh

On Mon, Aug 29, 2016 at 12:06 PM, Gallagher, Timothy P <tim.gallagher at gatech.edu<mailto:tim.gallagher at gatech.edu>> wrote:

Utkarash,


Thanks, I had added it to the xml file, but I didn't reconfigure (just rebuilt) so it didn't get added to the list.


I'm making some progress it seems, it is picking the right reader now. But it is crashing with a rather unhelpful message:


ERROR: In /data4/PVBoxLibTest/paraview/ParaViewCore/ServerImplementation/Core/vtkSIProxy.cxx, line 310
vtkSISourceProxy (0x3e87420): Failed to create vtkVisItBoxlib2DReader. Aborting for debugging purposes.


I thought compiling with a Debug build type would give more verbose messages, but it's the same.


Is there documentation or suggestions on debugging paraview? Is there a way to get more verbose output on why it isn't able to create the reader?


Thanks again,


Tim

________________________________
From: Utkarsh Ayachit <utkarsh.ayachit at kitware.com<mailto:utkarsh.ayachit at kitware.com>>
Sent: Monday, August 29, 2016 8:46 AM

To: Gallagher, Timothy P
Cc: paraview at paraview.org<mailto:paraview at paraview.org>
Subject: Re: [Paraview] Status of BoxLib AMR reader

Tim,

Did you also add it to visit_readers.xml [1]? The proxy definition should also have a  <hints> section like so [2].

Utkarsh

[1] https://gitlab.kitware.com/paraview/visitbridge/blob/master/databases/visit_readers.xml
[2] https://gitlab.kitware.com/paraview/visitbridge/blob/master/databases/visit_readers.xml#L2562-2565



On Fri, Aug 26, 2016 at 6:26 PM, Gallagher, Timothy P <tim.gallagher at gatech.edu<mailto:tim.gallagher at gatech.edu>> wrote:

I took a stab at adding the Boxlib reader from the visit source to the VisitBridge internal readers. I managed to get everything to compile and link, Paraview built fine, but I can't seem to figure out how to make Paraview aware the reader exists.


There isn't an option for Boxlib in the dropdown for the file type when I try to open a file, and it doesn't appear as an available reader when I try to select the file -- although all the others from the VisitBridge appear. I missed a configuration file somewhere to make the file loading aware of the reader.


Any suggestions on what I missed? I added a section in the Utilities/VisItBridge/databases/visit_readers.xml file, but that wasn't enough I guess.


Thanks,


Tim


________________________________
From: ParaView <paraview-bounces at paraview.org<mailto:paraview-bounces at paraview.org>> on behalf of Gallagher, Timothy P <tim.gallagher at gatech.edu<mailto:tim.gallagher at gatech.edu>>
Sent: Friday, August 26, 2016 11:53 AM
To: Utkarsh Ayachit

Cc: paraview at paraview.org<mailto:paraview at paraview.org>
Subject: Re: [Paraview] Status of BoxLib AMR reader


Hi Utkarsh,


I just checked with the latest head of the git repo and when I compile with the VisitBridge, there are no readers for BoxLib built.


This page lists it as supported: http://www.paraview.org/ParaView/index.php/VisIt_avt_Integration


But then this later one doesn't include it: http://www.paraview.org/Wiki/VisIt_Database_Bridge


I have a dataset for you, I will send it off-list.


Thanks,


Tim


________________________________
From: Utkarsh Ayachit <utkarsh.ayachit at kitware.com<mailto:utkarsh.ayachit at kitware.com>>
Sent: Friday, August 26, 2016 8:35 AM
To: Gallagher, Timothy P
Cc: paraview at paraview.org<mailto:paraview at paraview.org>
Subject: Re: [Paraview] Status of BoxLib AMR reader

Tim,

I am not exactly sure what's the status of the reader, but I can
certainly look it up. Do you have a sample dataset also to test that
it's working (or not)?

Utkarsh

On Thu, Aug 25, 2016 at 2:22 PM, Gallagher, Timothy P
<tim.gallagher at gatech.edu<mailto:tim.gallagher at gatech.edu>> wrote:
> Hi,
>
>
> Our code is moving away from traditional structured grids towards an AMR
> capability using BoxLib. That means, unfortunately, that all of the
> development we have done to make our code Paraview and CoProcessing friendly
> is not usable with the BoxLib file format.
>
>
> I have seen some information on various websites about using the VisitBridge
> to add the readers from Visit into Paraview, but when I build with it, the
> BoxLib reader was not included in the list of formats I could use for files
> -- even though it is listed online.
>
>
> Does anybody know what the status is of the reader in PV and if it is
> usable? Or is there a different format we can try to write out from our code
> that would be usable? I really don't want to lose the work we've done with
> PV and I would rather spend time writing code to get things working again
> for PV than learn to use new software!
>
>
> Thanks,
>
>
> Tim
>
>
> _______________________________________________
> Powered by www.kitware.com<http://www.kitware.com>
[http://www.kitware.com/img/Areas_Index_Home.jpg]<http://www.kitware.com/>

Kitware Inc. - leading edge, high-quality software<http://www.kitware.com/>
www.kitware.com<http://www.kitware.com>
Kitware's mission is to create state-of-the-art software products and services in visualization and data processing using advanced quality software methods and ...


>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Please keep messages on-topic and check the ParaView Wiki at:
> http://paraview.org/Wiki/ParaView
>
> Search the list archives at: http://markmail.org/search/?q=ParaView
>
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From wascott at sandia.gov  Tue Sep  6 18:39:44 2016
From: wascott at sandia.gov (Scott, W Alan)
Date: Tue, 6 Sep 2016 22:39:44 +0000
Subject: [Paraview] Axis grid
Message-ID: <a9a5ccff4e1743d6aa7089d5aa068806@ES01AMSNLNT.srn.sandia.gov>

A user needs to put an axis around one or more single parts (i.e., blocks or filter outputs).  Is this possible?  If not, we need to add this feature.  This is a showstopper for him with newer versions of ParaView.  An example is he wants to show an axis around the can part of can.exo.



Thanks,



Alan



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From Matthias.Zenker at erbe-med.com  Wed Sep  7 03:13:45 2016
From: Matthias.Zenker at erbe-med.com (Zenker, Dr. Matthias)
Date: Wed, 7 Sep 2016 07:13:45 +0000
Subject: [Paraview] :  Reload button in paraviw
Message-ID: <F9562F3B302F29479A203FC5AF9E3E050F9DFC3B@SERBE4I1.intra.erbe-med.de>

Hi Rahul,



check this post http://markmail.org/message/exxynsgishbvtngg  for some code permitting to get the functionality before the October release.



HTH,



Matthias





Date: Tue, 6 Sep 2016 16:00:15 +0530

From: Rahul Kumar Soni <rahulsoni at immt.res.in<mailto:rahulsoni at immt.res.in>>

To: ParaView <paraview at paraview.org<mailto:paraview at paraview.org>>, vtkusers at vtk.org<mailto:vtkusers at vtk.org>

Subject: [Paraview] Reload button in paraviw

Message-ID:

                <CA+PKs7dwggpGxwSWD47PUfkaoPTHW2xzHcKE+wgn65piLaAOZQ at mail.gmail.com<mailto:CA+PKs7dwggpGxwSWD47PUfkaoPTHW2xzHcKE+wgn65piLaAOZQ at mail.gmail.com>>

Content-Type: text/plain; charset="utf-8"



The particular feature discussed in following link is not available in the latest paraview. When can I expect this much awaited feature in the standard paraview. Is there a way to get it early.



https://urldefense.proofpoint.com/v2/url?u=https-3A__gitlab.kitware.com_paraview_paraview_merge-5Frequests_1000&d=DQICAg&c=7vND7vRFB1FzfxRXc-X80O-MJSZd5Q-IVyyYW-Ff2gY&r=3enlI3TuQDmO9BnMCnxq2Mfm4tAO6Z3_Ae1Yc57DMr4&m=li7IeOuR1ANenRgYX4r7Zqv7U0k6Qyzg2l33o0kXgGI&s=yCHb5MWXyCr0fpCUUaZ3-TTHn1W5UE9roIgQG3NJ_UE&e=

--

Regards



[image: photo]

*Rahul K Soni*

Scientist, Council of Scientific & Industrial Research

+91 674 237 9370 | +91 94790 58522 | +91 674 2567160 |

________________________________

Erbe Elektromedizin GmbH Firmensitz: 72072 Tuebingen Geschaeftsfuehrer: Christian O. Erbe, Reiner Thede Registergericht: Stuttgart HRB 380137

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From felipebordeu at gmail.com  Wed Sep  7 05:12:46 2016
From: felipebordeu at gmail.com (Felipe Bordeu)
Date: Wed, 7 Sep 2016 11:12:46 +0200
Subject: [Paraview] change background color based on a data variable?
In-Reply-To: <63B92F57-ED86-4B7E-AB51-08FDDAC37F82@email.arizona.edu>
References: <63B92F57-ED86-4B7E-AB51-08FDDAC37F82@email.arizona.edu>
Message-ID: <CAJbHkX_AOnj1N7q1vvBd7OzkP86=im_oF4CTci0eSi7HgvRQWw@mail.gmail.com>

You can use the animation view with a "Python Animation Track" script like
this:

def start_cue(self):

   self.t = 0


def tick(self):

   from paraview.simple import *

   renderView1 = GetActiveViewOrCreate('RenderView')

   renderView1.Background = [self.t, 0.42745098039215684, 0.023529411764705882]

   self.t = self.t+0.1


def end_cue(self): pass


of course you have to the script to you needs.

Felipe

2016-08-30 18:18 GMT+02:00 Hart, Cynthia Joyce - (cyndyb) <
cyndyb at email.arizona.edu>:

> Hi folks.  Another ignorant question.   (and Thank You to Burlen Loring
> for his assistance with my last question)
>
> I have created an animation of a time series of some months of several
> temperature sensors.  It is desired by the end user of this visualization,
> to show the diurnal cycle as the animation goes by, by changing the
> background color from blue to through to black as the days so by.  I can
> use the time values in the data table that contains my sensor data as a
> variable to determine a color by, but I don?t know what/or if there is, a
> filter to use to do this readily; that is, as a control of the background
> color.   If anyone can give me some direction, I?d appreciate it much.
>
>
>
> Thank you,
>
> Cynthia
>
>
>
> _______________________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at http://www.kitware.com/
> opensource/opensource.html
>
> Please keep messages on-topic and check the ParaView Wiki at:
> http://paraview.org/Wiki/ParaView
>
> Search the list archives at: http://markmail.org/search/?q=ParaView
>
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From utkarsh.ayachit at kitware.com  Wed Sep  7 07:27:48 2016
From: utkarsh.ayachit at kitware.com (Utkarsh Ayachit)
Date: Wed, 7 Sep 2016 07:27:48 -0400
Subject: [Paraview] Axis grid
In-Reply-To: <a9a5ccff4e1743d6aa7089d5aa068806@ES01AMSNLNT.srn.sandia.gov>
References: <a9a5ccff4e1743d6aa7089d5aa068806@ES01AMSNLNT.srn.sandia.gov>
Message-ID: <CADHSJjDyzFKDxiWtuxDKJNm6xjhyNsv+G5YZAzvySKtpHYkUew@mail.gmail.com>

Alan,

That's not possible currently. The implementation heavily relies on
the being "under" or "over" all dataset in the scene. This assumption
makes it possible to place 2D labels in 3D without having to worry
about labels showing through surfaces even when data is distributed
among ranks. Thus, supporting this will entail consider refactoring of
the Axis Grid.

Utkarsh

On Tue, Sep 6, 2016 at 6:39 PM, Scott, W Alan <wascott at sandia.gov> wrote:
> A user needs to put an axis around one or more single parts (i.e., blocks or
> filter outputs).  Is this possible?  If not, we need to add this feature.
> This is a showstopper for him with newer versions of ParaView.  An example
> is he wants to show an axis around the can part of can.exo.
>
>
>
> Thanks,
>
>
>
> Alan
>
>
>
>
>
>
> _______________________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Please keep messages on-topic and check the ParaView Wiki at:
> http://paraview.org/Wiki/ParaView
>
> Search the list archives at: http://markmail.org/search/?q=ParaView
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/paraview
>

From info at seoaachen.de  Wed Sep  7 08:17:32 2016
From: info at seoaachen.de (Daniel Zuidinga)
Date: Wed, 7 Sep 2016 14:17:32 +0200
Subject: [Paraview] Paraview Web on Ubuntu with gpu but without screen
Message-ID: <be5cafee-e245-427f-6568-3dffb0c5f15e@seoaachen.de>

Hi,

I try to get pvweb to run on my server without monitor (but intel 
graphics card). Seems not as easy as I thought. I run e.g. the visualizer:

/root/salome_meca/V2016/prerequisites/Paraview-v501_EDF/bin/pvpython 
/root/salome_meca/V2016/prerequisites/Paraview-v501_EDF/lib/paraview-5.0/site-packages/paraview/web/pv_web_visualizer.py

and I get the error:

terminate called after throwing an instance of 'Json::LogicError'
   what():  in Json::Value::find(key, end, found): requires objectValue 
or nullValue


any ideas?


From utkarsh.ayachit at kitware.com  Wed Sep  7 09:08:42 2016
From: utkarsh.ayachit at kitware.com (Utkarsh Ayachit)
Date: Wed, 7 Sep 2016 09:08:42 -0400
Subject: [Paraview] Status of BoxLib AMR reader
In-Reply-To: <CY1PR0701MB2058FD60B33B1C6BCCA733719DF90@CY1PR0701MB2058.namprd07.prod.outlook.com>
References: <CY1PR0701MB2058DA767925F078D7697F619DED0@CY1PR0701MB2058.namprd07.prod.outlook.com>
 <CADHSJjBZ2+dkxt-zCaMm1i-2YRCEfEA2x9njh=kRvEDsbWRwog@mail.gmail.com>
 <CY1PR0701MB205876961A89DA1389157B3B9DEC0@CY1PR0701MB2058.namprd07.prod.outlook.com>
 <CY1PR0701MB2058C1F7A05DE29385DFE5AF9DEC0@CY1PR0701MB2058.namprd07.prod.outlook.com>
 <CADHSJjDiKQruLPGw3cOBcjP9LSTyBkyPWtGJETWKmfnU0i4LWg@mail.gmail.com>
 <CY1PR0701MB2058273B5F97EC7DA780DCFE9DE10@CY1PR0701MB2058.namprd07.prod.outlook.com>
 <CADHSJjD=bOtc2SH7WMET+HxycP+TPF-eZ8YDev8_hmuKubDumw@mail.gmail.com>
 <CY1PR0701MB2058055C46034B39CFC609059DE10@CY1PR0701MB2058.namprd07.prod.outlook.com>
 <CY1PR0701MB205870806EF0B4D8EA415DD19DE10@CY1PR0701MB2058.namprd07.prod.outlook.com>
 <CADHSJjCtJ3GNQz_8YQuUYdmePFRqs43y4Qnyt0RavPPp57ksnQ@mail.gmail.com>
 <CY1PR0701MB2058FD60B33B1C6BCCA733719DF90@CY1PR0701MB2058.namprd07.prod.outlook.com>
Message-ID: <CADHSJjD5aLaXsS_YT0xP8xj6nCHpA5sNyy1EA=zJOfZxfpqMEA@mail.gmail.com>

Tim,
Sorry, no I didn't get a chance to look at it yet.

Utkarsh

On Tue, Sep 6, 2016 at 2:52 PM, Gallagher, Timothy P <
tim.gallagher at gatech.edu> wrote:

> Hi Utkarsh,
>
>
> Have you had a chance to take a look at this yet? I will have some time
> later this week to pick it back up -- just wanted to check if there was
> anything new about it before I dove back in.
>
>
> Thanks,
>
>
> Tim
>
>
> ------------------------------
> *From:* Utkarsh Ayachit <utkarsh.ayachit at kitware.com>
> *Sent:* Tuesday, August 30, 2016 7:51 AM
>
> *To:* Gallagher, Timothy P
> *Cc:* paraview at paraview.org
> *Subject:* Re: [Paraview] Status of BoxLib AMR reader
>
> Thanks, Tim. I'll take a look in next few days.
>
> Utkarsh
>
> On Mon, Aug 29, 2016 at 4:12 PM, Gallagher, Timothy P <
> tim.gallagher at gatech.edu> wrote:
>
>> I have to throw in the towel on this one for now and get back to some
>> other deadlines... but, I put what I have so far online and created a merge
>> request with information about the error and an example dataset attached.
>>
>>
>> Hopefully somebody better with VTK than I am can take a look and figure
>> out what I'm missing. I tried comparing the files for Chombo against the
>> original Visit source files to see if any special modifications were
>> required and none are (the only changes are HDF5 related). It looks like
>> the Chombo reader is from Visit 2.7.0 -- the Boxlib files I added are from
>> 2.10.3, but I tried it with the Boxlib reader from Visit 2.7.0 also and
>> it's the same issue.
>>
>>
>> If anybody has a chance to take a look, I'd appreciate it. Hopefully it's
>> something simple. If not, I'll try to pick it back up in a few days. I
>> apologize for the hacked CMakeLists to link against the library, I will fix
>> it to do it properly once everything else works!
>>
>> Tim
>>
>>
>> ------------------------------
>> *From:* ParaView <paraview-bounces at paraview.org> on behalf of Gallagher,
>> Timothy P <tim.gallagher at gatech.edu>
>> *Sent:* Monday, August 29, 2016 12:41 PM
>>
>> *To:* Utkarsh Ayachit
>> *Cc:* paraview at paraview.org
>> *Subject:* Re: [Paraview] Status of BoxLib AMR reader
>>
>>
>> Thanks for the quick response, the case didn't match between the two
>> files and that was the issue. I'm able to use the reader to select the file
>> and it sees the names of the variables in it properly, but when I hit Apply
>> it throws:
>>
>>
>> ERROR: In /data4/PVBoxLibTest/paraview/VTK/Common/DataModel/vtkAMRInformation.cxx,
>> line 573
>> vtkAMRInformation (0x44210f0): Invalid grid description for a
>> vtkUniformGrid
>>
>>
>> I have a feeling this might get beyond my paraview knowledge to fix.
>>
>>
>> One potential source of the problem -- what version of Visit are the
>> other readers pulled from? I have the Boxlib files from the latest version,
>> but looking at some of the other readers, they are from older versions.
>>
>> The latest date I see in the copyright for existing readers is 2013 and
>> looking through the Visit Release notes, the last release in 2013 says it
>> was upgraded to use VTK-6.0.
>>
>>
>> Is it possible the bridge is based on Visit before that major VTK upgrade
>> and I need to pull the reader code from a version earlier than that?
>>
>>
>> Thanks for your help. If I can't find something I know how to fix soon, I
>> can create a merge request and see if anybody else can get it the rest of
>> the way.
>>
>>
>> Tim
>>
>> ------------------------------
>> *From:* Utkarsh Ayachit <utkarsh.ayachit at kitware.com>
>> *Sent:* Monday, August 29, 2016 12:17 PM
>> *To:* Gallagher, Timothy P
>> *Cc:* paraview at paraview.org
>> *Subject:* Re: [Paraview] Status of BoxLib AMR reader
>>
>> Tim,
>>
>> It doesn't know what the class is. Multiple things could have gone wrong:
>> 1. is there call to ADD_VISIT_READER() for the new reader?
>> 2. does the case match between the XML's class="" and the name specified
>> in 1?
>>
>> If it makes it easier, create a MR on the https://gitlab.kitware.com
>> /paraview/visitbridge repo with your changes, and I can do the necessary
>> fixes.
>> <https://gitlab.kitware.com/paraview/visitbridge>
>> ParaView / VisItBridge <https://gitlab.kitware.com/paraview/visitbridge>
>> gitlab.kitware.com
>> Bridge between VisIt and ParaView to use VisIt readers in ParaView.
>>
>> Utkarsh
>>
>> On Mon, Aug 29, 2016 at 12:06 PM, Gallagher, Timothy P <
>> tim.gallagher at gatech.edu> wrote:
>>
>>> Utkarash,
>>>
>>>
>>> Thanks, I had added it to the xml file, but I didn't reconfigure (just
>>> rebuilt) so it didn't get added to the list.
>>>
>>>
>>> I'm making some progress it seems, it is picking the right reader now.
>>> But it is crashing with a rather unhelpful message:
>>>
>>>
>>> ERROR: In /data4/PVBoxLibTest/paraview/ParaViewCore/ServerImplementation/Core/vtkSIProxy.cxx,
>>> line 310
>>> vtkSISourceProxy (0x3e87420): Failed to create vtkVisItBoxlib2DReader.
>>> Aborting for debugging purposes.
>>>
>>> I thought compiling with a Debug build type would give more verbose
>>> messages, but it's the same.
>>>
>>>
>>> Is there documentation or suggestions on debugging paraview? Is there a
>>> way to get more verbose output on why it isn't able to create the reader?
>>>
>>>
>>> Thanks again,
>>>
>>>
>>> Tim
>>>
>>> ------------------------------
>>> *From:* Utkarsh Ayachit <utkarsh.ayachit at kitware.com>
>>> *Sent:* Monday, August 29, 2016 8:46 AM
>>>
>>> *To:* Gallagher, Timothy P
>>> *Cc:* paraview at paraview.org
>>> *Subject:* Re: [Paraview] Status of BoxLib AMR reader
>>>
>>> Tim,
>>>
>>> Did you also add it to visit_readers.xml [1]? The proxy definition
>>> should also have a  <hints> section like so [2].
>>>
>>> Utkarsh
>>>
>>> [1] https://gitlab.kitware.com/paraview/visitbridge/blob/mas
>>> ter/databases/visit_readers.xml
>>> [2] https://gitlab.kitware.com/paraview/visitbridge/blob/mas
>>> ter/databases/visit_readers.xml#L2562-2565
>>>
>>>
>>>
>>> On Fri, Aug 26, 2016 at 6:26 PM, Gallagher, Timothy P <
>>> tim.gallagher at gatech.edu> wrote:
>>>
>>>> I took a stab at adding the Boxlib reader from the visit source to the
>>>> VisitBridge internal readers. I managed to get everything to compile and
>>>> link, Paraview built fine, but I can't seem to figure out how to make
>>>> Paraview aware the reader exists.
>>>>
>>>>
>>>> There isn't an option for Boxlib in the dropdown for the file type when
>>>> I try to open a file, and it doesn't appear as an available reader when I
>>>> try to select the file -- although all the others from the VisitBridge
>>>> appear. I missed a configuration file somewhere to make the file loading
>>>> aware of the reader.
>>>>
>>>>
>>>> Any suggestions on what I missed? I added a section in the
>>>> Utilities/VisItBridge/databases/visit_readers.xml file, but that
>>>> wasn't enough I guess.
>>>>
>>>>
>>>> Thanks,
>>>>
>>>>
>>>> Tim
>>>>
>>>>
>>>> ------------------------------
>>>> *From:* ParaView <paraview-bounces at paraview.org> on behalf of
>>>> Gallagher, Timothy P <tim.gallagher at gatech.edu>
>>>> *Sent:* Friday, August 26, 2016 11:53 AM
>>>> *To:* Utkarsh Ayachit
>>>>
>>>> *Cc:* paraview at paraview.org
>>>> *Subject:* Re: [Paraview] Status of BoxLib AMR reader
>>>>
>>>>
>>>> Hi Utkarsh,
>>>>
>>>>
>>>> I just checked with the latest head of the git repo and when I compile
>>>> with the VisitBridge, there are no readers for BoxLib built.
>>>>
>>>>
>>>> This page lists it as supported: http://www.paraview.org/ParaVi
>>>> ew/index.php/VisIt_avt_Integration
>>>>
>>>>
>>>> But then this later one doesn't include it: http://www.paraview.org/Wi
>>>> ki/VisIt_Database_Bridge
>>>>
>>>>
>>>> I have a dataset for you, I will send it off-list.
>>>>
>>>>
>>>> Thanks,
>>>>
>>>>
>>>> Tim
>>>>
>>>>
>>>> ------------------------------
>>>> *From:* Utkarsh Ayachit <utkarsh.ayachit at kitware.com>
>>>> *Sent:* Friday, August 26, 2016 8:35 AM
>>>> *To:* Gallagher, Timothy P
>>>> *Cc:* paraview at paraview.org
>>>> *Subject:* Re: [Paraview] Status of BoxLib AMR reader
>>>>
>>>> Tim,
>>>>
>>>> I am not exactly sure what's the status of the reader, but I can
>>>> certainly look it up. Do you have a sample dataset also to test that
>>>> it's working (or not)?
>>>>
>>>> Utkarsh
>>>>
>>>> On Thu, Aug 25, 2016 at 2:22 PM, Gallagher, Timothy P
>>>> <tim.gallagher at gatech.edu> wrote:
>>>> > Hi,
>>>> >
>>>> >
>>>> > Our code is moving away from traditional structured grids towards an
>>>> AMR
>>>> > capability using BoxLib. That means, unfortunately, that all of the
>>>> > development we have done to make our code Paraview and CoProcessing
>>>> friendly
>>>> > is not usable with the BoxLib file format.
>>>> >
>>>> >
>>>> > I have seen some information on various websites about using the
>>>> VisitBridge
>>>> > to add the readers from Visit into Paraview, but when I build with
>>>> it, the
>>>> > BoxLib reader was not included in the list of formats I could use for
>>>> files
>>>> > -- even though it is listed online.
>>>> >
>>>> >
>>>> > Does anybody know what the status is of the reader in PV and if it is
>>>> > usable? Or is there a different format we can try to write out from
>>>> our code
>>>> > that would be usable? I really don't want to lose the work we've done
>>>> with
>>>> > PV and I would rather spend time writing code to get things working
>>>> again
>>>> > for PV than learn to use new software!
>>>> >
>>>> >
>>>> > Thanks,
>>>> >
>>>> >
>>>> > Tim
>>>> >
>>>> >
>>>> > _______________________________________________
>>>> > Powered by www.kitware.com
>>>> <http://www.kitware.com/>
>>>> Kitware Inc. - leading edge, high-quality software
>>>> <http://www.kitware.com/>
>>>> www.kitware.com
>>>> Kitware's mission is to create state-of-the-art software products and
>>>> services in visualization and data processing using advanced quality
>>>> software methods and ...
>>>>
>>>> >
>>>> > Visit other Kitware open-source projects at
>>>> > http://www.kitware.com/opensource/opensource.html
>>>> >
>>>> > Please keep messages on-topic and check the ParaView Wiki at:
>>>> > http://paraview.org/Wiki/ParaView
>>>> >
>>>> > Search the list archives at: http://markmail.org/search/?q=ParaView
>>>> >
>>>> > Follow this link to subscribe/unsubscribe:
>>>> > http://public.kitware.com/mailman/listinfo/paraview
>>>> >
>>>>
>>>
>>>
>>
>
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From scott.wittenburg at kitware.com  Wed Sep  7 12:05:12 2016
From: scott.wittenburg at kitware.com (Scott Wittenburg)
Date: Wed, 7 Sep 2016 10:05:12 -0600
Subject: [Paraview] Paraview Web on Ubuntu with gpu but without screen
In-Reply-To: <be5cafee-e245-427f-6568-3dffb0c5f15e@seoaachen.de>
References: <be5cafee-e245-427f-6568-3dffb0c5f15e@seoaachen.de>
Message-ID: <CAPiw4fA7uELp2d4-3sgAt353S7+6vgiyU0VyCMBY_siULJkXAw@mail.gmail.com>

Hi Daniel,

   I have several thoughts after reading your email, though I'm not sure
how helpful they may be.  First, the error you reported doesn't sound (to
me) like the typical error you might see when you do not have your graphics
environment configured properly.  I assume that even without a display you
are setting up an X server and making sure to set the DISPLAY environment
variable before running the script?  Even though you are not using EC2,
some of the information at the link below could pertain to your situation:

http://kitware.github.io/paraviewweb/docs/guides/graphics_on_ec2_g2.html

hopefully that gets you pointed in the right direction.

   Another thing to note: I don't believe that the pv_web_visualizer python
script is included in ParaView anymore, though I don't recall exactly when
that moved (it appears you are using version 5 or above).  Now the web side
of ParaView has moved into various other github repositories:

Core Libraries: https://github.com/Kitware/paraviewweb
Web Visualizer Application: https://github.com/Kitware/visualizer

   These days you will find the equivalent of the pv_web_visualizer.py
script in the above repo (located under "server/pvw-visualizer.py").

   However, if you do indeed have the python script in the location stated
in your email, then I'm not sure what could be causing the apparent json
error you mentioned.  Normally though, one might have provided some
arguments to that python script in the use case it seems you are targeting,
although perhaps you just left them out when composing your email.  For
example, if you did not provide a "--content" argument, specifying the path
to the static content you are serving, are you managing that another way?

   Feel free to post more information such as the complete command line you
are invoking, how you are connecting from your browser (assuming you get
that far), or perhaps more error output if there is any.

   Hope this helps.

Cheers,
Scott



On Wed, Sep 7, 2016 at 6:17 AM, Daniel Zuidinga <info at seoaachen.de> wrote:

> Hi,
>
> I try to get pvweb to run on my server without monitor (but intel graphics
> card). Seems not as easy as I thought. I run e.g. the visualizer:
>
> /root/salome_meca/V2016/prerequisites/Paraview-v501_EDF/bin/pvpython
> /root/salome_meca/V2016/prerequisites/Paraview-v501_EDF/lib/
> paraview-5.0/site-packages/paraview/web/pv_web_visualizer.py
>
> and I get the error:
>
> terminate called after throwing an instance of 'Json::LogicError'
>   what():  in Json::Value::find(key, end, found): requires objectValue or
> nullValue
>
>
> any ideas?
>
> _______________________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at http://www.kitware.com/opensou
> rce/opensource.html
>
> Please keep messages on-topic and check the ParaView Wiki at:
> http://paraview.org/Wiki/ParaView
>
> Search the list archives at: http://markmail.org/search/?q=ParaView
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/paraview
>
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From dave.demarle at kitware.com  Wed Sep  7 17:15:01 2016
From: dave.demarle at kitware.com (David E DeMarle)
Date: Wed, 7 Sep 2016 17:15:01 -0400
Subject: [Paraview] Please nominate ParaView for for the 2016 HPCwire
	Readers' Choice Awards
In-Reply-To: <CANjZAi_sm9363V3sUDijivg3pQLPXoOY3spgTWDDsp=tgr=ajQ@mail.gmail.com>
References: <CANjZAi_sm9363V3sUDijivg3pQLPXoOY3spgTWDDsp=tgr=ajQ@mail.gmail.com>
Message-ID: <CANjZAi9GPQ9uuUruMwDb5xKGuoOuvYwXYgbooBSXL8=BrWyvpw@mail.gmail.com>

Thank you to everyone who nominated ParaView for the HPCwire Readers?
Choice Awards.

The survey is now open for voting, and ParaView is included in the ?Best
HPC Visualization Product or Technology? category.? To vote for ParaView,
please visit https://www.hpcwire.com/2016-hpcwire-readers-choice-awards/.

Thank you for your continued support!

David E DeMarle
Kitware, Inc.
R&D Engineer
21 Corporate Drive
Clifton Park, NY 12065-8662
Phone: 518-881-4909

On Tue, Aug 2, 2016 at 11:54 AM, David E DeMarle <dave.demarle at kitware.com>
wrote:

> We would like to thank everyone who contributed to version 5.1.2 of
> ParaView. To acknowledge the growth of ParaView, please join us in
> nominating the fruit of our combined efforts for a 2016 HPCwire Readers?
> Award in the ?Best HPC Visualization Product or Technology? category.
>
> Nominations can be made at http://www.hpcwire.com/2015-
> hpcwire-readers-choice-awards. Thank you for your support!
>
> For reference, here are some recent updates
> <https://blog.kitware.com/paraview-5-1-0-release-notes/> made to ParaView:
>
>    - Enabled ray tracing through OSPRay
>    - Added ?Point Interpolation? filters
>    - Introduced the capability to render picture-in-picture visualizations
>    - Launched a welcome screen with a link to ?ParaView Getting Started
>    Guide?
>    - Improved ParaView Catalyst and Cinema for In-Situ processing at
>    extreme scales
>
> David E DeMarle
> Kitware, Inc.
> R&D Engineer
> 21 Corporate Drive
> Clifton Park, NY 12065-8662
> Phone: 518-881-4909
>
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From wascott at sandia.gov  Wed Sep  7 22:13:13 2016
From: wascott at sandia.gov (Scott, W Alan)
Date: Thu, 8 Sep 2016 02:13:13 +0000
Subject: [Paraview] FW: [EXT] RE: [EXTERNAL] EXODUS: How to find nodes that
 are common to more than 1	sideset
In-Reply-To: <CY1PR07MB2506079547F03FB6C6D00BBE9FF80@CY1PR07MB2506.namprd07.prod.outlook.com>
References: <CY1PR07MB250688F4283C26F2004A9E539FE50@CY1PR07MB2506.namprd07.prod.outlook.com>
 <e2cc81913627437a9dbed9a23ff87486@ES01AMSNLNT.srn.sandia.gov>
 <CY1PR07MB2506079547F03FB6C6D00BBE9FF80@CY1PR07MB2506.namprd07.prod.outlook.com>
Message-ID: <7ab5ed618bf54f96bbd01f716c46c9db@ES01AMSNLNT.srn.sandia.gov>

Ping?

From: Dennis Conklin [mailto:dennis_conklin at goodyear.com]
Sent: Wednesday, September 07, 2016 5:55 AM
To: Scott, W Alan <wascott at sandia.gov>
Subject: RE: [EXT] RE: [EXTERNAL] [Paraview] EXODUS: How to find nodes that are common to more than 1 sideset

Scott,

Nope, I haven't gotten any responses.   A more general question is how to access the sidesets within the Exodus reader - I remember how difficult it was to access block names and am wondering if this will be as non-intuitive as that was.

Dennis

From: Scott, W Alan [mailto:wascott at sandia.gov]
Sent: Tuesday, September 06, 2016 7:56 PM
To: Dennis Conklin <dennis_conklin at goodyear.com<mailto:dennis_conklin at goodyear.com>>
Subject: [EXT] RE: [EXTERNAL] [Paraview] EXODUS: How to find nodes that are common to more than 1 sideset

Ever get an answer?  I have no idea myself.  Maybe functionality that we need?

Alan

From: ParaView [mailto:paraview-bounces at paraview.org] On Behalf Of Dennis Conklin
Sent: Friday, September 02, 2016 8:09 AM
To: Paraview (paraview at paraview.org<mailto:paraview at paraview.org>) <paraview at paraview.org<mailto:paraview at paraview.org>>
Subject: [EXTERNAL] [Paraview] EXODUS: How to find nodes that are common to more than 1 sideset

All,

I want to search or query for nodes that are in more than 1 sideset, as common nodes drive Multi-Point Constraints crazy.  I don't have any great ideas.   Do any of you?

Thanks for any hints you may have.

Dennis


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From bjagrine at national-electric-coil.com  Wed Sep  7 22:08:34 2016
From: bjagrine at national-electric-coil.com (Boris Jagrine)
Date: Thu, 8 Sep 2016 02:08:34 +0000
Subject: [Paraview] Opening two .vtu files simultaneously
Message-ID: <86CBF863C3462B48B83B11B8C20E2CEB356136FA@NCOEXC10.NEC.LOCAL>

I am new to Paraview and will appreciate an answer to the following question:
Is it possible to open two separate .vtu files (linear elasticity) each with displacement analysis of a separate body so that the same color scale is used to display the displacements of the two bodies and make comparison obvious?
Thank you.
Boris

DISCLAIMER: This e-mail and any attachments to it contain confidential and proprietary material of NEC/RPI, its affiliates or agents, and is solely for the use of the intended recipient. Any review, use, disclosure, distribution or copying of this transmittal is prohibited except by or on behalf of the intended recipient. If you have received this transmittal in error, please notify the sender and destroy this e-mail and any attachments and all copies, whether electronic or printed.
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From andy.bauer at kitware.com  Wed Sep  7 22:48:26 2016
From: andy.bauer at kitware.com (Andy Bauer)
Date: Wed, 7 Sep 2016 22:48:26 -0400
Subject: [Paraview] Opening two .vtu files simultaneously
In-Reply-To: <86CBF863C3462B48B83B11B8C20E2CEB356136FA@NCOEXC10.NEC.LOCAL>
References: <86CBF863C3462B48B83B11B8C20E2CEB356136FA@NCOEXC10.NEC.LOCAL>
Message-ID: <CAMaOp+Hrw09O0o9+Lcxme+Y1bf-6G0WkzjSsd=nSSm9WHdbC1g@mail.gmail.com>

Hi Boris,

ParaView actually forces the same color scale for all pseudo-colored
objects in the render view, as long as the fields selected have the same
name (and possibly type). So in short answer, yes what you want is possible
and should be done automatically.

In the upper right corner of the view window there are buttons to split the
view either vertically or horizontally (choose Render View in this case in
the list of views in the newly created view window). You can do this and
then view the grid from each file in separate windows to help the
comparison. Also, if you right click on one of these views it will come up
with a "Link Camera..." button that you can click on. After doing this, you
can click on the other view window which will do view point/camera
manipulations like zoom, pan, rotate, etc. in both windows in sync so that
you can look at the two separate input files similarly in the two separate
windows.

Let us know if my answer isn't clear or if you have other questions.

Welcome to ParaView!
Andy

On Wed, Sep 7, 2016 at 10:08 PM, Boris Jagrine <
bjagrine at national-electric-coil.com> wrote:

> I am new to Paraview and will appreciate an answer to the following
> question:
>
> Is it possible to open two separate .vtu files (linear elasticity) each
> with displacement analysis of a separate body so that the same color scale
> is used to display the displacements of the two bodies and make comparison
> obvious?
>
> Thank you.
>
> Boris
>
> DISCLAIMER: This e-mail and any attachments to it contain confidential and
> proprietary material of NEC/RPI, its affiliates or agents, and is solely
> for the use of the intended recipient. Any review, use, disclosure,
> distribution or copying of this transmittal is prohibited except by or on
> behalf of the intended recipient. If you have received this transmittal in
> error, please notify the sender and destroy this e-mail and any attachments
> and all copies, whether electronic or printed.   ??
>
> _______________________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at http://www.kitware.com/
> opensource/opensource.html
>
> Please keep messages on-topic and check the ParaView Wiki at:
> http://paraview.org/Wiki/ParaView
>
> Search the list archives at: http://markmail.org/search/?q=ParaView
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/paraview
>
>
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From postgurke at web.de  Thu Sep  8 03:52:03 2016
From: postgurke at web.de (postgurke at web.de)
Date: Thu, 8 Sep 2016 09:52:03 +0200 (CEST)
Subject: [Paraview] Import Preset color scale only if not already loaded
Message-ID: <106326969.4071.1473321123621.JavaMail.open-xchange@app06.ox.hosteurope.de>

Hello All

I haven't been able to find a solution for this, so maybe someone can give me a
hint...:
I am loading data via a python script into ParaView (5.0) and want to color it
with a specific color scale. I can load this scale with the script and apply the
coloring as desired but if the scale is already loaded, it will then be loaded
twice (or more). What I would like to do is check if the scale is loaded and if
yes apply it, if not first load and then apply.
I tought, that try/except would be my friend here, but applying a preset that is
not loaded doesn't throw an error but uses the default Cool to Warm scale
instead... What is also somewhat strange: if I had the specific scale loaded in
a ParaView session, but removed it from the list of presets, ParaView can
somehow remember it nonetheless and shows the data correctly (i.e. not with the
Cool to Warm scale but the specific one). 
Does somebody have an idea how I can avoid having the specific scale loaded
multiple times and still have the python script always producing the correct
visualization of the data set?

Here is the code I was trying:
...
zLUT=GetColorTransferFunction(ts)
try: 
	zLUT.ApplyPreset(colorname,False)
except: 
	ImportPresets(filename=colorname+'.json')
	zLUT.ApplyPreset(colorname,False)
...


Thank you very much! 
Venke

From claire.guilbaud at cea.fr  Thu Sep  8 05:57:38 2016
From: claire.guilbaud at cea.fr (GUILBAUD Claire)
Date: Thu, 8 Sep 2016 11:57:38 +0200
Subject: [Paraview] paraview.5.1.renderingbackend.opengl on server and
 paraview.5.1.renderingbackend.opengl2 on client
In-Reply-To: <CACDyxREGqktAMVEm5OpeWOba_1aGVoCE-8NMcUSxpntFG1cL=Q@mail.gmail.com>
References: <CACDyxREGqktAMVEm5OpeWOba_1aGVoCE-8NMcUSxpntFG1cL=Q@mail.gmail.com>
Message-ID: <d5d98929-2c10-e0c7-11c5-d71d9fca103c@cea.fr>

Hi John,

It is written in the code that you can't have a client in OpenGL and a 
server in OpenGL2 on the server. But you can have a pvserver with mesa 
with backend opengl2.
When you build ParaView with Mesa, you have to choose a backend. This 
means that you must build 2 times ParaView for Mesa, one for each backend.
When running paraview (client), you have to choose the good pvserver 
(same backend than the client). Thus the hand shake strings should be 
the same.

Claire

From matthias at familie-sitte.org  Thu Sep  8 07:02:22 2016
From: matthias at familie-sitte.org (Matthias Sitte)
Date: Thu, 8 Sep 2016 13:02:22 +0200
Subject: [Paraview] offset for axis grid available?
Message-ID: <cf170925-77e3-433e-e135-10f2898cdedc@familie-sitte.org>

Is there an offset option for the axes grid? Specifically, I'm trying to 
annotate a subset of a rectilinear grid, but the origin of the axes grid 
is the origin of the original grid, not at the "new" origin.

Best, Matthias


From grothausmann.roman at mh-hannover.de  Thu Sep  8 06:36:40 2016
From: grothausmann.roman at mh-hannover.de (Grothausmann, Roman Dr.)
Date: Thu, 8 Sep 2016 12:36:40 +0200
Subject: [Paraview] Testing ITK/VTK/PV contributions with (kitware) Gitlab-CI
Message-ID: <b559f993-9283-7f14-b7ad-66eb85c5d52a@mh-hannover.de>

Dear mailing list members,


Just getting to know Gitlab-CI, I am wondering whether it is possible to test 
contributions to ITK/VTK/PV with Gitlab-CI from gitlab.com or 
gitlab.kitware.com. As far as I understand, this basically needs runners, in 
this case specific to ITK/VTK/PV. Since kitware has done CI even before the use 
of gitlab, I wonder if the former testing environments are available for use 
with Gitlab-CI and if so how to use them.
For example, none of my contributions to the ITK/VTK/Midas Journals got into the 
testing phase even though marked for testing during submission. So a possibility 
to use Gitlab-CI to test the compilation and to run the project test would be 
really great, especially for continued development and testing on other OSs.
Specifically, for e.g. testing my FacetAnalyser contribution 
(http://www.midasjournal.org/browse/publication/951 
https://gitlab.com/romangrothausmann/FacetAnalyser) I would need a runner 
environment with PV, VTK and ITK ideally for Linux, MacOS and Windows.

Thanks for any comments and hints.
Roman

-- 
Dr. Roman Grothausmann

Tomographie und Digitale Bildverarbeitung
Tomography and Digital Image Analysis

Institut f?r Funktionelle und Angewandte Anatomie, OE 4120
Medizinische Hochschule Hannover
Carl-Neuberg-Str. 1
D-30625 Hannover

Tel. +49 511 532-2900

From bjagrine at national-electric-coil.com  Thu Sep  8 07:15:14 2016
From: bjagrine at national-electric-coil.com (Boris Jagrine)
Date: Thu, 8 Sep 2016 11:15:14 +0000
Subject: [Paraview] Opening two .vtu files simultaneously
In-Reply-To: <CAMaOp+Hrw09O0o9+Lcxme+Y1bf-6G0WkzjSsd=nSSm9WHdbC1g@mail.gmail.com>
References: <86CBF863C3462B48B83B11B8C20E2CEB356136FA@NCOEXC10.NEC.LOCAL>
 <CAMaOp+Hrw09O0o9+Lcxme+Y1bf-6G0WkzjSsd=nSSm9WHdbC1g@mail.gmail.com>
Message-ID: <86CBF863C3462B48B83B11B8C20E2CEB356138B9@NCOEXC10.NEC.LOCAL>

Hi Andy,
Your answer is clear. I did what you suggested and it worked!
Thanks!
Boris

From: Andy Bauer [mailto:andy.bauer at kitware.com]
Sent: Wednesday, September 07, 2016 10:48 PM
To: Boris Jagrine
Cc: paraview at paraview.org
Subject: Re: [Paraview] Opening two .vtu files simultaneously

Hi Boris,
ParaView actually forces the same color scale for all pseudo-colored objects in the render view, as long as the fields selected have the same name (and possibly type). So in short answer, yes what you want is possible and should be done automatically.
In the upper right corner of the view window there are buttons to split the view either vertically or horizontally (choose Render View in this case in the list of views in the newly created view window). You can do this and then view the grid from each file in separate windows to help the comparison. Also, if you right click on one of these views it will come up with a "Link Camera..." button that you can click on. After doing this, you can click on the other view window which will do view point/camera manipulations like zoom, pan, rotate, etc. in both windows in sync so that you can look at the two separate input files similarly in the two separate windows.
Let us know if my answer isn't clear or if you have other questions.

Welcome to ParaView!
Andy

On Wed, Sep 7, 2016 at 10:08 PM, Boris Jagrine <bjagrine at national-electric-coil.com<mailto:bjagrine at national-electric-coil.com>> wrote:
I am new to Paraview and will appreciate an answer to the following question:
Is it possible to open two separate .vtu files (linear elasticity) each with displacement analysis of a separate body so that the same color scale is used to display the displacements of the two bodies and make comparison obvious?
Thank you.
Boris

DISCLAIMER: This e-mail and any attachments to it contain confidential and proprietary material of NEC/RPI, its affiliates or agents, and is solely for the use of the intended recipient. Any review, use, disclosure, distribution or copying of this transmittal is prohibited except by or on behalf of the intended recipient. If you have received this transmittal in error, please notify the sender and destroy this e-mail and any attachments and all copies, whether electronic or printed.   ??

_______________________________________________
Powered by www.kitware.com<http://www.kitware.com>

Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html

Please keep messages on-topic and check the ParaView Wiki at: http://paraview.org/Wiki/ParaView

Search the list archives at: http://markmail.org/search/?q=ParaView

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From utkarsh.ayachit at kitware.com  Thu Sep  8 07:21:12 2016
From: utkarsh.ayachit at kitware.com (Utkarsh Ayachit)
Date: Thu, 8 Sep 2016 07:21:12 -0400
Subject: [Paraview] paraview.5.1.renderingbackend.opengl on server and
 paraview.5.1.renderingbackend.opengl2 on client
In-Reply-To: <CACDyxREGqktAMVEm5OpeWOba_1aGVoCE-8NMcUSxpntFG1cL=Q@mail.gmail.com>
References: <CACDyxREGqktAMVEm5OpeWOba_1aGVoCE-8NMcUSxpntFG1cL=Q@mail.gmail.com>
Message-ID: <CADHSJjD_2mEXSeoGtoNO0O1T1LE_SOC3XgpO7CeSKM7nb9_y_g@mail.gmail.com>

> Is it true that I can?t use the classic rendering (old GL) on the backend
> with a GL 2 on the client?

John, as Claire said, no, you can't use classic rendering and GL2
together. Client/Server should have the same rendering mode.

> Is there a workaround or do I have to figure out
> how to build a more modern OS Mesa (which might just be a copy/paste from
> the aforementioned website?)?

This blog [1] describes how I built modern OSMesa. You can also use
the ParaView Superbuild's build script for clues on how Mesa is built.


[1] https://blog.kitware.com/messing-with-mesa-for-paraview-5-0vtk-7-0/
[2] https://gitlab.kitware.com/paraview/paraview-superbuild/blob/master/projects/unix/osmesa.cmake

From utkarsh.ayachit at kitware.com  Thu Sep  8 07:29:43 2016
From: utkarsh.ayachit at kitware.com (Utkarsh Ayachit)
Date: Thu, 8 Sep 2016 07:29:43 -0400
Subject: [Paraview] Import Preset color scale only if not already loaded
In-Reply-To: <106326969.4071.1473321123621.JavaMail.open-xchange@app06.ox.hosteurope.de>
References: <106326969.4071.1473321123621.JavaMail.open-xchange@app06.ox.hosteurope.de>
Message-ID: <CADHSJjDqpUO3YpN3yNngcMTG7AbJRUn-ytO4zby_UoQuzcsVsA@mail.gmail.com>

Something like following should do the trick:

def HasPreset(name):
     presets = servermanager.vtkSMTransferFunctionPresets()
     for i in range(presets.GetNumberOfPresets()):
         if presets.GetPresetName(i) == name:
             return True
     return False



On Thu, Sep 8, 2016 at 3:52 AM,  <postgurke at web.de> wrote:
> Hello All
>
> I haven't been able to find a solution for this, so maybe someone can give me a
> hint...:
> I am loading data via a python script into ParaView (5.0) and want to color it
> with a specific color scale. I can load this scale with the script and apply the
> coloring as desired but if the scale is already loaded, it will then be loaded
> twice (or more). What I would like to do is check if the scale is loaded and if
> yes apply it, if not first load and then apply.
> I tought, that try/except would be my friend here, but applying a preset that is
> not loaded doesn't throw an error but uses the default Cool to Warm scale
> instead... What is also somewhat strange: if I had the specific scale loaded in
> a ParaView session, but removed it from the list of presets, ParaView can
> somehow remember it nonetheless and shows the data correctly (i.e. not with the
> Cool to Warm scale but the specific one).
> Does somebody have an idea how I can avoid having the specific scale loaded
> multiple times and still have the python script always producing the correct
> visualization of the data set?
>
> Here is the code I was trying:
> ...
> zLUT=GetColorTransferFunction(ts)
> try:
>         zLUT.ApplyPreset(colorname,False)
> except:
>         ImportPresets(filename=colorname+'.json')
>         zLUT.ApplyPreset(colorname,False)
> ...
>
>
> Thank you very much!
> Venke
> _______________________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html
>
> Please keep messages on-topic and check the ParaView Wiki at: http://paraview.org/Wiki/ParaView
>
> Search the list archives at: http://markmail.org/search/?q=ParaView
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/paraview

From postgurke at web.de  Thu Sep  8 08:41:30 2016
From: postgurke at web.de (postgurke at web.de)
Date: Thu, 8 Sep 2016 14:41:30 +0200 (CEST)
Subject: [Paraview] Import Preset color scale only if not already loaded
In-Reply-To: <CADHSJjDqpUO3YpN3yNngcMTG7AbJRUn-ytO4zby_UoQuzcsVsA@mail.gmail.com>
References: <106326969.4071.1473321123621.JavaMail.open-xchange@app06.ox.hosteurope.de>
 <CADHSJjDqpUO3YpN3yNngcMTG7AbJRUn-ytO4zby_UoQuzcsVsA@mail.gmail.com>
Message-ID: <1487587166.5589.1473338490949.JavaMail.open-xchange@app06.ox.hosteurope.de>

... not just something like it, it is exactly the solution to my problem!
Thanks!! :)


> Utkarsh Ayachit <utkarsh.ayachit at kitware.com> hat am 8. September 2016 um
> 13:29 geschrieben:
> 
> 
> Something like following should do the trick:
> 
> def HasPreset(name):
>      presets = servermanager.vtkSMTransferFunctionPresets()
>      for i in range(presets.GetNumberOfPresets()):
>          if presets.GetPresetName(i) == name:
>              return True
>      return False
> 
> 
> 
> On Thu, Sep 8, 2016 at 3:52 AM,  <postgurke at web.de> wrote:
> > Hello All
> >
> > I haven't been able to find a solution for this, so maybe someone can give
> > me a
> > hint...:
> > I am loading data via a python script into ParaView (5.0) and want to color
> > it
> > with a specific color scale. I can load this scale with the script and apply
> > the
> > coloring as desired but if the scale is already loaded, it will then be
> > loaded
> > twice (or more). What I would like to do is check if the scale is loaded and
> > if
> > yes apply it, if not first load and then apply.
> > I tought, that try/except would be my friend here, but applying a preset
> > that is
> > not loaded doesn't throw an error but uses the default Cool to Warm scale
> > instead... What is also somewhat strange: if I had the specific scale loaded
> > in
> > a ParaView session, but removed it from the list of presets, ParaView can
> > somehow remember it nonetheless and shows the data correctly (i.e. not with
> > the
> > Cool to Warm scale but the specific one).
> > Does somebody have an idea how I can avoid having the specific scale loaded
> > multiple times and still have the python script always producing the correct
> > visualization of the data set?
> >
> > Here is the code I was trying:
> > ...
> > zLUT=GetColorTransferFunction(ts)
> > try:
> >         zLUT.ApplyPreset(colorname,False)
> > except:
> >         ImportPresets(filename=colorname+'.json')
> >         zLUT.ApplyPreset(colorname,False)
> > ...
> >
> >
> > Thank you very much!
> > Venke
> > _______________________________________________
> > Powered by www.kitware.com
> >
> > Visit other Kitware open-source projects at
> > http://www.kitware.com/opensource/opensource.html
> >
> > Please keep messages on-topic and check the ParaView Wiki at:
> > http://paraview.org/Wiki/ParaView
> >
> > Search the list archives at: http://markmail.org/search/?q=ParaView
> >
> > Follow this link to subscribe/unsubscribe:
> > http://public.kitware.com/mailman/listinfo/paraview

From utkarsh.ayachit at kitware.com  Thu Sep  8 08:41:41 2016
From: utkarsh.ayachit at kitware.com (Utkarsh Ayachit)
Date: Thu, 8 Sep 2016 08:41:41 -0400
Subject: [Paraview] offset for axis grid available?
In-Reply-To: <cf170925-77e3-433e-e135-10f2898cdedc@familie-sitte.org>
References: <cf170925-77e3-433e-e135-10f2898cdedc@familie-sitte.org>
Message-ID: <CADHSJjDAv_2mV1o834mw0X6aw7NSgvJDQHfRshhvHCUjnjJ6nA@mail.gmail.com>

Not sure I can reproduce this. If I apply "Extract Subset", the Axis
Grid does update to show the new subset (provided I turned off the
visibility of the original data).

On Thu, Sep 8, 2016 at 7:02 AM, Matthias Sitte
<matthias at familie-sitte.org> wrote:
> Is there an offset option for the axes grid? Specifically, I'm trying to
> annotate a subset of a rectilinear grid, but the origin of the axes grid is
> the origin of the original grid, not at the "new" origin.
>
> Best, Matthias
>
> _______________________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Please keep messages on-topic and check the ParaView Wiki at:
> http://paraview.org/Wiki/ParaView
>
> Search the list archives at: http://markmail.org/search/?q=ParaView
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/paraview

From info at seoaachen.de  Thu Sep  8 08:45:10 2016
From: info at seoaachen.de (Daniel Zuidinga)
Date: Thu, 8 Sep 2016 14:45:10 +0200
Subject: [Paraview] Paraview Web on Ubuntu with gpu but without screen
In-Reply-To: <CAPiw4fA7uELp2d4-3sgAt353S7+6vgiyU0VyCMBY_siULJkXAw@mail.gmail.com>
References: <be5cafee-e245-427f-6568-3dffb0c5f15e@seoaachen.de>
 <CAPiw4fA7uELp2d4-3sgAt353S7+6vgiyU0VyCMBY_siULJkXAw@mail.gmail.com>
Message-ID: <e5239654-0d51-54a8-ec67-91292b01b396@seoaachen.de>

Thanks for your long answer Scott.

seemed that I had a wrong x server configuration. I setup a new user and 
now it works. I think you can't use x or the paraview web stuff as a 
root user.

Am 07.09.2016 um 18:05 schrieb Scott Wittenburg:
> Hi Daniel,
>
>    I have several thoughts after reading your email, though I'm not 
> sure how helpful they may be.  First, the error you reported doesn't 
> sound (to me) like the typical error you might see when you do not 
> have your graphics environment configured properly.  I assume that 
> even without a display you are setting up an X server and making sure 
> to set the DISPLAY environment variable before running the script?  
> Even though you are not using EC2, some of the information at the link 
> below could pertain to your situation:
>
> http://kitware.github.io/paraviewweb/docs/guides/graphics_on_ec2_g2.html
>
> hopefully that gets you pointed in the right direction.
>
>    Another thing to note: I don't believe that the pv_web_visualizer 
> python script is included in ParaView anymore, though I don't recall 
> exactly when that moved (it appears you are using version 5 or 
> above).  Now the web side of ParaView has moved into various other 
> github repositories:
>
> Core Libraries: https://github.com/Kitware/paraviewweb
> Web Visualizer Application: https://github.com/Kitware/visualizer
>
>    These days you will find the equivalent of the pv_web_visualizer.py 
> script in the above repo (located under "server/pvw-visualizer.py").
>
>    However, if you do indeed have the python script in the location 
> stated in your email, then I'm not sure what could be causing the 
> apparent json error you mentioned.  Normally though, one might have 
> provided some arguments to that python script in the use case it seems 
> you are targeting, although perhaps you just left them out when 
> composing your email.  For example, if you did not provide a 
> "--content" argument, specifying the path to the static content you 
> are serving, are you managing that another way?
>
>    Feel free to post more information such as the complete command 
> line you are invoking, how you are connecting from your browser 
> (assuming you get that far), or perhaps more error output if there is any.
>
>    Hope this helps.
>
> Cheers,
> Scott
>
>
>
> On Wed, Sep 7, 2016 at 6:17 AM, Daniel Zuidinga <info at seoaachen.de 
> <mailto:info at seoaachen.de>> wrote:
>
>     Hi,
>
>     I try to get pvweb to run on my server without monitor (but intel
>     graphics card). Seems not as easy as I thought. I run e.g. the
>     visualizer:
>
>     /root/salome_meca/V2016/prerequisites/Paraview-v501_EDF/bin/pvpython
>     /root/salome_meca/V2016/prerequisites/Paraview-v501_EDF/lib/paraview-5.0/site-packages/paraview/web/pv_web_visualizer.py
>
>     and I get the error:
>
>     terminate called after throwing an instance of 'Json::LogicError'
>       what():  in Json::Value::find(key, end, found): requires
>     objectValue or nullValue
>
>
>     any ideas?
>
>     _______________________________________________
>     Powered by www.kitware.com <http://www.kitware.com>
>
>     Visit other Kitware open-source projects at
>     http://www.kitware.com/opensource/opensource.html
>     <http://www.kitware.com/opensource/opensource.html>
>
>     Please keep messages on-topic and check the ParaView Wiki at:
>     http://paraview.org/Wiki/ParaView <http://paraview.org/Wiki/ParaView>
>
>     Search the list archives at:
>     http://markmail.org/search/?q=ParaView
>     <http://markmail.org/search/?q=ParaView>
>
>     Follow this link to subscribe/unsubscribe:
>     http://public.kitware.com/mailman/listinfo/paraview
>     <http://public.kitware.com/mailman/listinfo/paraview>
>
>

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From utkarsh.ayachit at kitware.com  Thu Sep  8 08:48:28 2016
From: utkarsh.ayachit at kitware.com (Utkarsh Ayachit)
Date: Thu, 8 Sep 2016 08:48:28 -0400
Subject: [Paraview] EXODUS: How to find nodes that are common to more
 than 1 sideset
In-Reply-To: <CY1PR07MB250688F4283C26F2004A9E539FE50@CY1PR07MB2506.namprd07.prod.outlook.com>
References: <CY1PR07MB250688F4283C26F2004A9E539FE50@CY1PR07MB2506.namprd07.prod.outlook.com>
Message-ID: <CADHSJjCjyLvbQRdVD30nw+Kmzdf2Pz0yTz3VEDErM--OFotY7Q@mail.gmail.com>

Do you have a dataset that demonstrates this? It may be easier to
figure out what could work with a sample dataset at hand.

Utkarsh

On Fri, Sep 2, 2016 at 10:09 AM, Dennis Conklin
<dennis_conklin at goodyear.com> wrote:
> All,
>
>
>
> I want to search or query for nodes that are in more than 1 sideset, as
> common nodes drive Multi-Point Constraints crazy.  I don?t have any great
> ideas.   Do any of you?
>
>
>
> Thanks for any hints you may have.
>
>
>
> Dennis
>
>
>
>
>
>
> _______________________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Please keep messages on-topic and check the ParaView Wiki at:
> http://paraview.org/Wiki/ParaView
>
> Search the list archives at: http://markmail.org/search/?q=ParaView
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/paraview
>

From ben.boeckel at kitware.com  Thu Sep  8 09:14:17 2016
From: ben.boeckel at kitware.com (Ben Boeckel)
Date: Thu, 8 Sep 2016 09:14:17 -0400
Subject: [Paraview] [vtkusers] Testing ITK/VTK/PV contributions with
 (kitware) Gitlab-CI
In-Reply-To: <b559f993-9283-7f14-b7ad-66eb85c5d52a@mh-hannover.de>
References: <b559f993-9283-7f14-b7ad-66eb85c5d52a@mh-hannover.de>
Message-ID: <20160908131417.GB13993@megas.kitware.com>

On Thu, Sep 08, 2016 at 12:36:40 +0200, Grothausmann, Roman Dr. wrote:
> Just getting to know Gitlab-CI, I am wondering whether it is possible to test 
> contributions to ITK/VTK/PV with Gitlab-CI from gitlab.com or 
> gitlab.kitware.com. As far as I understand, this basically needs runners, in 
> this case specific to ITK/VTK/PV. Since kitware has done CI even before the use 
> of gitlab, I wonder if the former testing environments are available for use 
> with Gitlab-CI and if so how to use them.

We're (VTK and ParaView) using buildbot to manage our testing. The
number of settings we test across machines is hard to specify in YAML
files (machines also have different settings based on what you're
testing, e.g., load up a different compiler or Qt4 or Qt5 and the paths
they live in, etc.). We're working on improving the hardware situation
buildbot is currently in; things should be getting better over the next
few months on that front.

> For example, none of my contributions to the ITK/VTK/Midas Journals got into the 
> testing phase even though marked for testing during submission. So a possibility 
> to use Gitlab-CI to test the compilation and to run the project test would be 
> really great, especially for continued development and testing on other OSs.
> Specifically, for e.g. testing my FacetAnalyser contribution 
> (http://www.midasjournal.org/browse/publication/951 
> https://gitlab.com/romangrothausmann/FacetAnalyser) I would need a runner 
> environment with PV, VTK and ITK ideally for Linux, MacOS and Windows.

ITK is using Gerrit and Jenkins, not Gitlab.

--Ben

From dennis_conklin at goodyear.com  Thu Sep  8 09:00:50 2016
From: dennis_conklin at goodyear.com (Dennis Conklin)
Date: Thu, 8 Sep 2016 13:00:50 +0000
Subject: [Paraview] [EXT] Re: EXODUS: How to find nodes that are common
 to more than 1 sideset
In-Reply-To: <CADHSJjCjyLvbQRdVD30nw+Kmzdf2Pz0yTz3VEDErM--OFotY7Q@mail.gmail.com>
References: <CY1PR07MB250688F4283C26F2004A9E539FE50@CY1PR07MB2506.namprd07.prod.outlook.com>
 <CADHSJjCjyLvbQRdVD30nw+Kmzdf2Pz0yTz3VEDErM--OFotY7Q@mail.gmail.com>
Message-ID: <CY1PR07MB250643F813F72523725A7F5A9FFB0@CY1PR07MB2506.namprd07.prod.outlook.com>

Utkarsh,

This is funny, because I just spent 6 days laboriously eliminating all the common nodes on 4 different models.  I don't think I have any bad meshes left.  And if I did I would not be able to share them with the list.  

Really, I just need an example of how to access side sets (block(4) of Exodus Reader) in a Programmable Filter
As in output=self.GetOutput()    SideSets=output.GetBlock(4)

After that I'm lost as to how to identify SSet by ID (name?) and how to access the actual values in the SSet.  Comparing them to find common nodes would be fairly easy if I just understood how to get to the SSets.

Say I have SSet "1201" and SSet "1202" and I want to compare them to see if they have any common nodes - the hard part is finding the right SSets and getting the nodes in them.

I remember going through this a while back when needing to access Block Names and never would have figured it out on my own.

Dennis

-----Original Message-----
From: Utkarsh Ayachit [mailto:utkarsh.ayachit at kitware.com] 
Sent: Thursday, September 08, 2016 8:48 AM
To: Dennis Conklin <dennis_conklin at goodyear.com>
Cc: Paraview (paraview at paraview.org) <paraview at paraview.org>
Subject: [EXT] Re: [Paraview] EXODUS: How to find nodes that are common to more than 1 sideset

Do you have a dataset that demonstrates this? It may be easier to figure out what could work with a sample dataset at hand.

Utkarsh

On Fri, Sep 2, 2016 at 10:09 AM, Dennis Conklin <dennis_conklin at goodyear.com> wrote:
> All,
>
>
>
> I want to search or query for nodes that are in more than 1 sideset, 
> as common nodes drive Multi-Point Constraints crazy.  I don?t have any great
> ideas.   Do any of you?
>
>
>
> Thanks for any hints you may have.
>
>
>
> Dennis
>
>
>
>
>
>
> _______________________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at 
> http://www.kitware.com/opensource/opensource.html
>
> Please keep messages on-topic and check the ParaView Wiki at:
> http://paraview.org/Wiki/ParaView
>
> Search the list archives at: http://markmail.org/search/?q=ParaView
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/paraview
>

From matthias at familie-sitte.org  Thu Sep  8 14:01:48 2016
From: matthias at familie-sitte.org (Matthias Sitte)
Date: Thu, 8 Sep 2016 20:01:48 +0200
Subject: [Paraview] offset for axis grid available?
In-Reply-To: <CADHSJjDAv_2mV1o834mw0X6aw7NSgvJDQHfRshhvHCUjnjJ6nA@mail.gmail.com>
References: <cf170925-77e3-433e-e135-10f2898cdedc@familie-sitte.org>
 <CADHSJjDAv_2mV1o834mw0X6aw7NSgvJDQHfRshhvHCUjnjJ6nA@mail.gmail.com>
Message-ID: <8b628bb8-5f2f-5b61-f1f0-7c04d989a642@familie-sitte.org>

Well, the Axes Grid is updated, but the labels refer to the "old" full set.


What I want to achieve is the following: Take a grid 200x100. I want to 
display the subset [50,100]x[50,100] but with axes labeled from 
[0,50]x[0,50]. Is that possible?


Matthias

On 08/09/16 14:41, Utkarsh Ayachit wrote:
> Not sure I can reproduce this. If I apply "Extract Subset", the Axis
> Grid does update to show the new subset (provided I turned off the
> visibility of the original data).
>
> On Thu, Sep 8, 2016 at 7:02 AM, Matthias Sitte
> <matthias at familie-sitte.org> wrote:
>> Is there an offset option for the axes grid? Specifically, I'm trying to
>> annotate a subset of a rectilinear grid, but the origin of the axes grid is
>> the origin of the original grid, not at the "new" origin.
>>
>> Best, Matthias
>>
>> _______________________________________________
>> Powered by www.kitware.com
>>
>> Visit other Kitware open-source projects at
>> http://www.kitware.com/opensource/opensource.html
>>
>> Please keep messages on-topic and check the ParaView Wiki at:
>> http://paraview.org/Wiki/ParaView
>>
>> Search the list archives at: http://markmail.org/search/?q=ParaView
>>
>> Follow this link to subscribe/unsubscribe:
>> http://public.kitware.com/mailman/listinfo/paraview


From utkarsh.ayachit at kitware.com  Thu Sep  8 15:56:08 2016
From: utkarsh.ayachit at kitware.com (Utkarsh Ayachit)
Date: Thu, 8 Sep 2016 15:56:08 -0400
Subject: [Paraview] offset for axis grid available?
In-Reply-To: <8b628bb8-5f2f-5b61-f1f0-7c04d989a642@familie-sitte.org>
References: <cf170925-77e3-433e-e135-10f2898cdedc@familie-sitte.org>
 <CADHSJjDAv_2mV1o834mw0X6aw7NSgvJDQHfRshhvHCUjnjJ6nA@mail.gmail.com>
 <8b628bb8-5f2f-5b61-f1f0-7c04d989a642@familie-sitte.org>
Message-ID: <CADHSJjDNGAp9t1SC9AV7-QJaokoPjxCAKUi+r2dDXcCn-29xWg@mail.gmail.com>

Nope, that's not possible. You could move your data to 0,0 using the
"Translation" property on the Properties panel and then the labels
will do what you want.

On Thu, Sep 8, 2016 at 2:01 PM, Matthias Sitte
<matthias at familie-sitte.org> wrote:
> Well, the Axes Grid is updated, but the labels refer to the "old" full set.
>
>
> What I want to achieve is the following: Take a grid 200x100. I want to
> display the subset [50,100]x[50,100] but with axes labeled from
> [0,50]x[0,50]. Is that possible?
>
>
> Matthias
>
>
> On 08/09/16 14:41, Utkarsh Ayachit wrote:
>>
>> Not sure I can reproduce this. If I apply "Extract Subset", the Axis
>> Grid does update to show the new subset (provided I turned off the
>> visibility of the original data).
>>
>> On Thu, Sep 8, 2016 at 7:02 AM, Matthias Sitte
>> <matthias at familie-sitte.org> wrote:
>>>
>>> Is there an offset option for the axes grid? Specifically, I'm trying to
>>> annotate a subset of a rectilinear grid, but the origin of the axes grid
>>> is
>>> the origin of the original grid, not at the "new" origin.
>>>
>>> Best, Matthias
>>>
>>> _______________________________________________
>>> Powered by www.kitware.com
>>>
>>> Visit other Kitware open-source projects at
>>> http://www.kitware.com/opensource/opensource.html
>>>
>>> Please keep messages on-topic and check the ParaView Wiki at:
>>> http://paraview.org/Wiki/ParaView
>>>
>>> Search the list archives at: http://markmail.org/search/?q=ParaView
>>>
>>> Follow this link to subscribe/unsubscribe:
>>> http://public.kitware.com/mailman/listinfo/paraview
>
>
> _______________________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Please keep messages on-topic and check the ParaView Wiki at:
> http://paraview.org/Wiki/ParaView
>
> Search the list archives at: http://markmail.org/search/?q=ParaView
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/paraview

From dennis_conklin at goodyear.com  Thu Sep  8 14:32:14 2016
From: dennis_conklin at goodyear.com (Dennis Conklin)
Date: Thu, 8 Sep 2016 18:32:14 +0000
Subject: [Paraview] Is the PythonAnnotation documentation obsolete?
Message-ID: <CY1PR07MB25068EDA77910589D1DB0A959FFB0@CY1PR07MB2506.namprd07.prod.outlook.com>

All,

I have tried to use PythonAnnotation but it only seems to work properly with FieldVariables.

So for instance, with field variables  of REACTZ_901 and REACTZ_902, the following expressions work and display the  values as expected

REACTZ_901                                displays array of values for all timesteps
REACTZ_901[t_index]                 displays single number (no brackets)
Int(REACTZ_901)                          (error)
Int(REACTZ_901[t_index]            displays truncated integer value (no brackets)

To try to work with CellData I have made an ExtractSelection of a single Cell.  I have a Cell variable of FBFORCE1
I want to use PythonAnnotation to print out the FBFORCE1 for that cell over time (with formatting)

FBFORCE1                                      [VTKArray([154.2])]  shouldn't this have a value for each timestep?
FBFORCE1[t_index]                       (error)
FBFORCE1[0]                                  [ 154.2]
FBFORCE1[1]                                  (error)
Int(FBFORCE1)                                (error)
Int(FBFORCE1[0])                           (error)

2nd try - Ran PythonAnnotation on an entire file - many cells, with following results
FBFORCE1                                       VTKArray([ value1, value2 .........value_final]) - seems like 1 value per timestep (shouldn't there be array of # of cells by # of timesteps?

FBFORCE1[t_index]                       [131.4]  -  again- should be array of # of cells? Which cell is this
FBFORCE1[t_index][0]                   (error)
Int(FBFORCE1[t_index])                 error)

So it seems that Field Variables are numpy-friendly in that formatting works with them, while Cell Variables are still VTK Array variables and not numpy-friendly.

It's possible that I am completely missing something here, but it seems Cell Variables are not very useable in the PythonAnnotation.  Is there a way for me to Annotate with individual cell values, either by running PythonAnnotation on a single cell, or by manipulating the variables which are available in the filter?

At this point I don't know why Cell and Point Variables are included in the filter since I can only figure out how to use Field Variables

Thanks for any hints

Dennis
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From gtmasur at gmail.com  Fri Sep  9 02:43:49 2016
From: gtmasur at gmail.com (Gokce Tuba Masur)
Date: Fri, 9 Sep 2016 08:43:49 +0200
Subject: [Paraview] Paraview does not proceed
Message-ID: <CAKj1GeeL71wWYXeGPU552PV6huXBvu+V3b1eWY5+q2L5m9z9gA@mail.gmail.com>

Hello,

I have 12 meshes and I want to see the structure of them, so I have
constructed a constant function on those meshes and save the functions in
'for' loop with pvd extension.

I am able to visualize the first function but then when I click 'next'
button to proceed the next function, Paraview  stops and gives this error
message.

paraview:
/build/paraview-arsa8T/paraview-5.0.1+dfsg1/VTK/IO/XML/vtkXMLDataReader.cxx:302:
virtual void vtkXMLDataReader::SetupOutputData(): Assertion
`this->NumberOfPointArrays ==
this->PointDataArraySelection->GetNumberOfArraysEnabled()' failed.

I have uninstalled and intalled again but it didnt work. What am I supposed
to do to solve this issue?

Best,
Tuba
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From postgurke at web.de  Fri Sep  9 03:52:49 2016
From: postgurke at web.de (postgurke at web.de)
Date: Fri, 9 Sep 2016 09:52:49 +0200 (CEST)
Subject: [Paraview] Lock Data Range for multiple attributes
Message-ID: <166776580.5718.1473407569425.JavaMail.open-xchange@app08.ox.hosteurope.de>

Hello All

Sorry to bother you again... I seem to miss something wanting to fix color scale
ranges for objects with multiple attributes. 
For example: I have a vtk-Plane with associated velocity and density values that
I can choose for coloring. When I imported the object, I set
LUT.RescaleTransferFunction(min, max) and LUT.LockDataRange = 1 for both
attributes (with different min,max, of course). In the GUI everything looks fine
at first, but when I switch the coloring from one attribute to another, ParaView
seems to ignore the checked "Lock Data Range" but switches to some Min/Max found
in the data. Maybe I misunderstand the functionality of "Lock Data Range"? Is
this the expected behaviour? If yes, what could I do to really fix the min,max
to my own specification? (I also tried to use a preset color scale with my
desired min,max, but this does not change the behaviour either.) 

Thanks for your support and any ideas on this,
Venke

From simonwalkersamuel at gmail.com  Fri Sep  9 05:19:07 2016
From: simonwalkersamuel at gmail.com (Simon Walker-Samuel)
Date: Fri, 9 Sep 2016 10:19:07 +0100
Subject: [Paraview] Blood vessel network (spatial graph) visualisation
Message-ID: <b21d9037-24d1-ca76-89c3-1b9b55deedd3@gmail.com>

Hi,

I'm investigating how I might use ParaView to visualise large 3D spatial 
graphs (i.e. a spatial distribution of nodes connected by segments) that 
represent blood vessel networks in tumours. I usually use Amira or 
Imaris for this, but would much prefer to use an open source solution 
like ParaView. My current project aims to simulate blood flow and drug 
delivery to tumours, which has lots of potential for in-depth visualisation.

To start off with, I am trying to work out if it's possible to display 
this type of network in ParaView as connected tubes, with radii scaled 
by the size of the vessels. As I say, these datasets are large, 
typically with around 300k segments. If this kind of visualisation is 
available (or potentially could be developed), the next challenge would 
be to find a file format that could be use to import them.

My data is currently in Amira mesh (spatial graph) format, which 
consists of multiple fields that define 1) the 3D coordinates of the 
nodes, 2) connections (segments) between the nodes, 3) 3D coordinates 
defining the path of the segments and 4) scalar fields defining 
atrributes of the segments (e.g. vessel radius, blood flow, pressure, etc.).

I've searched unsuccessfully for Amira mesh readers (or the similar 
Duke-Southampton format), but perhaps this area has not yet been 
explored as an application for ParaView?

Any initial guidance would be much appreciated.

Best wishes,
Simon

From utkarsh.ayachit at kitware.com  Fri Sep  9 07:29:52 2016
From: utkarsh.ayachit at kitware.com (Utkarsh Ayachit)
Date: Fri, 9 Sep 2016 07:29:52 -0400
Subject: [Paraview] Blood vessel network (spatial graph) visualisation
In-Reply-To: <b21d9037-24d1-ca76-89c3-1b9b55deedd3@gmail.com>
References: <b21d9037-24d1-ca76-89c3-1b9b55deedd3@gmail.com>
Message-ID: <CADHSJjDM1ekc0fn9BRRwBk9smMrNZHUsrwJDU0UjqcogVzCm-w@mail.gmail.com>

Simon,

> To start off with, I am trying to work out if it's possible to display this
> type of network in ParaView as connected tubes, with radii scaled by the
> size of the vessels. As I say, these datasets are large, typically with
> around 300k segments. If this kind of visualisation is available (or
> potentially could be developed), the next challenge would be to find a file
> format that could be use to import them.

The most obvious choice is to use the "Tube" filter for a dataset that
comprises of line segments with radii specified as point-data. The
tube filter can be told to scale the radius based on any variable in
the data. For 300K segments, it may be fine, but if things get too
large fret not. We are looking into ways of doing the "tubing" in GPU
itself, so that's coming in the next release or two.

> My data is currently in Amira mesh (spatial graph) format, which consists of
> multiple fields that define 1) the 3D coordinates of the nodes, 2)
> connections (segments) between the nodes, 3) 3D coordinates defining the
> path of the segments and 4) scalar fields defining atrributes of the
> segments (e.g. vessel radius, blood flow, pressure, etc.).

AFAIK, ParaView currently doesn't support Amira mesh format. You have
multiple options,
1. You could use an already supported file format instead e.g. Legacy
VTK, VTK-XML, Xdmf etc. Both Legacy VTK and VTK-XML are simple enough
formats that should be reasonable for the size you mention.
2. Write your own reader using the Programmable Source. The ParaView
Guide [1] has a few examples to get you started.

Hope that helps get you started. As always, feel free to ask if you
have more questions.

Utkarsh


[1] http://www.paraview.org/paraview-guide/

From utkarsh.ayachit at kitware.com  Fri Sep  9 07:31:46 2016
From: utkarsh.ayachit at kitware.com (Utkarsh Ayachit)
Date: Fri, 9 Sep 2016 07:31:46 -0400
Subject: [Paraview] Paraview does not proceed
In-Reply-To: <CAKj1GeeL71wWYXeGPU552PV6huXBvu+V3b1eWY5+q2L5m9z9gA@mail.gmail.com>
References: <CAKj1GeeL71wWYXeGPU552PV6huXBvu+V3b1eWY5+q2L5m9z9gA@mail.gmail.com>
Message-ID: <CADHSJjA_8MKO7FFS_HtGSAXwSOWWmY+CgKfsYQUeAirwy-avrg@mail.gmail.com>

For whichever timestep ParaView fails, that timestep has incorrect
number of arrays. All datasets in a timeseries must have identical
arrays. It seems that's not the case with your data. You

On Fri, Sep 9, 2016 at 2:43 AM, Gokce Tuba Masur <gtmasur at gmail.com> wrote:
>
> Hello,
>
> I have 12 meshes and I want to see the structure of them, so I have
> constructed a constant function on those meshes and save the functions in
> 'for' loop with pvd extension.
>
> I am able to visualize the first function but then when I click 'next'
> button to proceed the next function, Paraview  stops and gives this error
> message.
>
> paraview:
> /build/paraview-arsa8T/paraview-5.0.1+dfsg1/VTK/IO/XML/vtkXMLDataReader.cxx:302:
> virtual void vtkXMLDataReader::SetupOutputData(): Assertion
> `this->NumberOfPointArrays ==
> this->PointDataArraySelection->GetNumberOfArraysEnabled()' failed.
>
> I have uninstalled and intalled again but it didnt work. What am I supposed
> to do to solve this issue?
>
> Best,
> Tuba
>
>
> _______________________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Please keep messages on-topic and check the ParaView Wiki at:
> http://paraview.org/Wiki/ParaView
>
> Search the list archives at: http://markmail.org/search/?q=ParaView
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/paraview
>

From labcorrea at gmail.com  Fri Sep  9 09:28:54 2016
From: labcorrea at gmail.com (=?UTF-8?B?TMO6Y2lvIENvcnLDqmE=?=)
Date: Fri, 9 Sep 2016 15:28:54 +0200
Subject: [Paraview] Questions about XMF - 3DCoRectMesh
Message-ID: <CAPJ5paXK2DqePt+bRXJGposT5ZvQ5x6DNDJ-A9cOeqvRv6=MPA@mail.gmail.com>

Hi everbody,

I have a stupid question about the XMF - 3DCoRectMesh...

I tried to build an "extruded rectangle" using this function (I attached
the files).

I asked for a 6 by 16 by 46 elements as you can see in the XMF file...

     <Topology TopologyType="3DCoRectMesh" Dimensions="7 17 47"/>
     <Geometry GeometryType="ORIGIN_DXDYDZ">
   <DataItem Name="origin" Format="XML" DataType="Float" Precision="8"
Dimensions="3">
             -0.6000000000
             -1.6000000000
             -4.6000000000

but when I open in Paraview (4.3.1 and 5.1.2) I found a 46 by 16 by 6
elements...

I tried also to look in: VTK/ThirdParty/xdmf3/vtkxdmf3/XdmfRegularGrid.cpp,
but I didn't found the reason to Paraview "change" the X axis by the Z axis.

Someone found the same thing? Or, where I made a mistake?

Regards,
-- 
Lucio
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From andrew.j.burns35.ctr at mail.mil  Fri Sep  9 10:15:03 2016
From: andrew.j.burns35.ctr at mail.mil (Burns, Andrew J CTR USARMY RDECOM ARL (US))
Date: Fri, 9 Sep 2016 14:15:03 +0000
Subject: [Paraview] [Non-DoD Source] Questions about XMF - 3DCoRectMesh
In-Reply-To: <CAPJ5paXK2DqePt+bRXJGposT5ZvQ5x6DNDJ-A9cOeqvRv6=MPA@mail.gmail.com>
References: <CAPJ5paXK2DqePt+bRXJGposT5ZvQ5x6DNDJ-A9cOeqvRv6=MPA@mail.gmail.com>
Message-ID: <DEE37B508E36B64285856EEA9FC0C337458FA6FC@UCOLHPTV.easf.csd.disa.mil>

We noticed this also, I believe the plan is to remove the flipping of dimension ordering. However, I am unsure on when that will occur.

Andrew Burns
Software Engineer | Leidos
Phone: 410-306-0409
ARL DSRC
andrew.j.burns35.ctr at mail.mil

-----Original Message-----
From: ParaView [mailto:paraview-bounces at paraview.org] On Behalf Of L?cio Corr?a
Sent: Friday, September 09, 2016 9:29 AM
To: paraview at paraview.org
Subject: [Non-DoD Source] [Paraview] Questions about XMF - 3DCoRectMesh

Hi everbody,

I have a stupid question about the XMF - 3DCoRectMesh...

I tried to build an "extruded rectangle" using this function (I attached the files).

I asked for a 6 by 16 by 46 elements as you can see in the XMF file...

     <Topology TopologyType="3DCoRectMesh" Dimensions="7 17 47"/>
     <Geometry GeometryType="ORIGIN_DXDYDZ">
   <DataItem Name="origin" Format="XML" DataType="Float" Precision="8" Dimensions="3">
             -0.6000000000
             -1.6000000000
             -4.6000000000

but when I open in Paraview (4.3.1 and 5.1.2) I found a 46 by 16 by 6 elements...

I tried also to look in: VTK/ThirdParty/xdmf3/vtkxdmf3/XdmfRegularGrid.cpp, but I didn't found the reason to Paraview "change" the X axis by the Z axis.

Someone found the same thing? Or, where I made a mistake?

Regards,
-- 

Lucio

From dkxls23 at gmail.com  Fri Sep  9 10:44:29 2016
From: dkxls23 at gmail.com (Armin Wehrfritz)
Date: Fri, 9 Sep 2016 17:44:29 +0300
Subject: [Paraview] [Non-DoD Source] Questions about XMF - 3DCoRectMesh
In-Reply-To: <DEE37B508E36B64285856EEA9FC0C337458FA6FC@UCOLHPTV.easf.csd.disa.mil>
References: <CAPJ5paXK2DqePt+bRXJGposT5ZvQ5x6DNDJ-A9cOeqvRv6=MPA@mail.gmail.com>
 <DEE37B508E36B64285856EEA9FC0C337458FA6FC@UCOLHPTV.easf.csd.disa.mil>
Message-ID: <81a6f694-ce62-c15a-fb12-622ba1344c9a@gmail.com>

This is apparently a "very very old bug" [1] and pops up every now and
then on this mailing-list. There was apparently a plan to fix this back
in 2009 [2], but I'm doubtful that this was done.

[1] http://public.kitware.com/pipermail/paraview/2014-September/032263.html
[2] http://public.kitware.com/pipermail/paraview/2009-May/012278.html

-Armin






On 09/09/2016 05:15 PM, Burns, Andrew J CTR USARMY RDECOM ARL (US) wrote:
> We noticed this also, I believe the plan is to remove the flipping of dimension ordering. However, I am unsure on when that will occur.
>
> Andrew Burns
> Software Engineer | Leidos
> Phone: 410-306-0409
> ARL DSRC
> andrew.j.burns35.ctr at mail.mil
>
> -----Original Message-----
> From: ParaView [mailto:paraview-bounces at paraview.org] On Behalf Of L?cio Corr?a
> Sent: Friday, September 09, 2016 9:29 AM
> To: paraview at paraview.org
> Subject: [Non-DoD Source] [Paraview] Questions about XMF - 3DCoRectMesh
>
> Hi everbody,
>
> I have a stupid question about the XMF - 3DCoRectMesh...
>
> I tried to build an "extruded rectangle" using this function (I attached the files).
>
> I asked for a 6 by 16 by 46 elements as you can see in the XMF file...
>
>      <Topology TopologyType="3DCoRectMesh" Dimensions="7 17 47"/>
>      <Geometry GeometryType="ORIGIN_DXDYDZ">
>    <DataItem Name="origin" Format="XML" DataType="Float" Precision="8" Dimensions="3">
>              -0.6000000000
>              -1.6000000000
>              -4.6000000000
>
> but when I open in Paraview (4.3.1 and 5.1.2) I found a 46 by 16 by 6 elements...
>
> I tried also to look in: VTK/ThirdParty/xdmf3/vtkxdmf3/XdmfRegularGrid.cpp, but I didn't found the reason to Paraview "change" the X axis by the Z axis.
>
> Someone found the same thing? Or, where I made a mistake?
>
> Regards,
>

From labcorrea at gmail.com  Fri Sep  9 10:46:20 2016
From: labcorrea at gmail.com (=?UTF-8?B?TMO6Y2lvIENvcnLDqmE=?=)
Date: Fri, 9 Sep 2016 16:46:20 +0200
Subject: [Paraview] [Non-DoD Source] Questions about XMF - 3DCoRectMesh
In-Reply-To: <81a6f694-ce62-c15a-fb12-622ba1344c9a@gmail.com>
References: <CAPJ5paXK2DqePt+bRXJGposT5ZvQ5x6DNDJ-A9cOeqvRv6=MPA@mail.gmail.com>
 <DEE37B508E36B64285856EEA9FC0C337458FA6FC@UCOLHPTV.easf.csd.disa.mil>
 <81a6f694-ce62-c15a-fb12-622ba1344c9a@gmail.com>
Message-ID: <CAPJ5paVWk+eHia2dJioW5fONA9nV=WpCeaXwVm_8zYbdaNVdZw@mail.gmail.com>

Thanks guys!


2016-09-09 16:44 GMT+02:00 Armin Wehrfritz <dkxls23 at gmail.com>:

> This is apparently a "very very old bug" [1] and pops up every now and
> then on this mailing-list. There was apparently a plan to fix this back
> in 2009 [2], but I'm doubtful that this was done.
>
> [1] http://public.kitware.com/pipermail/paraview/2014-September/
> 032263.html
> [2] http://public.kitware.com/pipermail/paraview/2009-May/012278.html
>
> -Armin
>
>
>
>
>
>
>
> On 09/09/2016 05:15 PM, Burns, Andrew J CTR USARMY RDECOM ARL (US) wrote:
>
>> We noticed this also, I believe the plan is to remove the flipping of
>> dimension ordering. However, I am unsure on when that will occur.
>>
>> Andrew Burns
>> Software Engineer | Leidos
>> Phone: 410-306-0409
>> ARL DSRC
>> andrew.j.burns35.ctr at mail.mil
>>
>> -----Original Message-----
>> From: ParaView [mailto:paraview-bounces at paraview.org] On Behalf Of L?cio
>> Corr?a
>> Sent: Friday, September 09, 2016 9:29 AM
>> To: paraview at paraview.org
>> Subject: [Non-DoD Source] [Paraview] Questions about XMF - 3DCoRectMesh
>>
>> Hi everbody,
>>
>> I have a stupid question about the XMF - 3DCoRectMesh...
>>
>> I tried to build an "extruded rectangle" using this function (I attached
>> the files).
>>
>> I asked for a 6 by 16 by 46 elements as you can see in the XMF file...
>>
>>      <Topology TopologyType="3DCoRectMesh" Dimensions="7 17 47"/>
>>      <Geometry GeometryType="ORIGIN_DXDYDZ">
>>    <DataItem Name="origin" Format="XML" DataType="Float" Precision="8"
>> Dimensions="3">
>>              -0.6000000000
>>              -1.6000000000
>>              -4.6000000000
>>
>> but when I open in Paraview (4.3.1 and 5.1.2) I found a 46 by 16 by 6
>> elements...
>>
>> I tried also to look in: VTK/ThirdParty/xdmf3/vtkxdmf3/XdmfRegularGrid.cpp,
>> but I didn't found the reason to Paraview "change" the X axis by the Z axis.
>>
>> Someone found the same thing? Or, where I made a mistake?
>>
>> Regards,
>>
>
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From utkarsh.ayachit at kitware.com  Fri Sep  9 10:53:44 2016
From: utkarsh.ayachit at kitware.com (Utkarsh Ayachit)
Date: Fri, 9 Sep 2016 10:53:44 -0400
Subject: [Paraview] Is the PythonAnnotation documentation obsolete?
In-Reply-To: <CY1PR07MB25068EDA77910589D1DB0A959FFB0@CY1PR07MB2506.namprd07.prod.outlook.com>
References: <CY1PR07MB25068EDA77910589D1DB0A959FFB0@CY1PR07MB2506.namprd07.prod.outlook.com>
Message-ID: <CADHSJjCw77KAvE+LyunMQELLEYLH5wMUjDDB+TeH_ZzcHdPRZQ@mail.gmail.com>

Dennis,

Python Annotation only works with what's available in the current
timestep. If you look at the "Field Data" in the SpreadSheet view,
you'll see that the Exodus reader puts out an array with values for
all timesteps for variables like REACTZ_901 and hence you can offset
into it using t_index irrespective of which timestep you are at.

For Point/Cell data, you have access to the field values for all
points/cells for the current timestep only. Thus, t_index doesn't make
much sense for those cases. For understanding how indexing works when
dealing with multblock datasets, I'd recommend reading Berk's blog
post [1].

Hope that helps.
Utkarsh

[1] https://blog.kitware.com/improved-vtk-numpy-integration-part-5/

On Thu, Sep 8, 2016 at 2:32 PM, Dennis Conklin
<dennis_conklin at goodyear.com> wrote:
> All,
>
>
>
> I have tried to use PythonAnnotation but it only seems to work properly with
> FieldVariables.
>
>
>
> So for instance, with field variables  of REACTZ_901 and REACTZ_902, the
> following expressions work and display the  values as expected
>
>
>
> REACTZ_901                                displays array of values for all
> timesteps
>
> REACTZ_901[t_index]                 displays single number (no brackets)
>
> Int(REACTZ_901)                          (error)
>
> Int(REACTZ_901[t_index]            displays truncated integer value (no
> brackets)
>
>
>
> To try to work with CellData I have made an ExtractSelection of a single
> Cell.  I have a Cell variable of FBFORCE1
>
> I want to use PythonAnnotation to print out the FBFORCE1 for that cell over
> time (with formatting)
>
>
>
> FBFORCE1                                      [VTKArray([154.2])]  shouldn?t
> this have a value for each timestep?
>
> FBFORCE1[t_index]                       (error)
>
> FBFORCE1[0]                                  [ 154.2]
>
> FBFORCE1[1]                                  (error)
>
> Int(FBFORCE1)                                (error)
>
> Int(FBFORCE1[0])                           (error)
>
>
>
> 2nd try ? Ran PythonAnnotation on an entire file ? many cells, with
> following results
>
> FBFORCE1                                       VTKArray([ value1, value2
> ???value_final]) ? seems like 1 value per timestep (shouldn?t there be array
> of # of cells by # of timesteps?
>
>
>
> FBFORCE1[t_index]                       [131.4]  -  again- should be array
> of # of cells? Which cell is this
>
> FBFORCE1[t_index][0]                   (error)
>
> Int(FBFORCE1[t_index])                 error)
>
>
>
> So it seems that Field Variables are numpy-friendly in that formatting works
> with them, while Cell Variables are still VTK Array variables and not
> numpy-friendly.
>
>
>
> It?s possible that I am completely missing something here, but it seems Cell
> Variables are not very useable in the PythonAnnotation.  Is there a way for
> me to Annotate with individual cell values, either by running
> PythonAnnotation on a single cell, or by manipulating the variables which
> are available in the filter?
>
>
>
> At this point I don?t know why Cell and Point Variables are included in the
> filter since I can only figure out how to use Field Variables
>
>
>
> Thanks for any hints
>
>
>
> Dennis
>
>
> _______________________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Please keep messages on-topic and check the ParaView Wiki at:
> http://paraview.org/Wiki/ParaView
>
> Search the list archives at: http://markmail.org/search/?q=ParaView
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/paraview
>

From andrew.j.burns35.ctr at mail.mil  Fri Sep  9 10:53:49 2016
From: andrew.j.burns35.ctr at mail.mil (Burns, Andrew J CTR USARMY RDECOM ARL (US))
Date: Fri, 9 Sep 2016 14:53:49 +0000
Subject: [Paraview] [Non-DoD Source] Questions about XMF - 3DCoRectMesh
In-Reply-To: <CAPJ5paVWk+eHia2dJioW5fONA9nV=WpCeaXwVm_8zYbdaNVdZw@mail.gmail.com>
References: <CAPJ5paXK2DqePt+bRXJGposT5ZvQ5x6DNDJ-A9cOeqvRv6=MPA@mail.gmail.com>
 <DEE37B508E36B64285856EEA9FC0C337458FA6FC@UCOLHPTV.easf.csd.disa.mil>
 <81a6f694-ce62-c15a-fb12-622ba1344c9a@gmail.com>
 <CAPJ5paVWk+eHia2dJioW5fONA9nV=WpCeaXwVm_8zYbdaNVdZw@mail.gmail.com>
Message-ID: <DEE37B508E36B64285856EEA9FC0C337458FA71C@UCOLHPTV.easf.csd.disa.mil>

Looking at the old error reports, it's an issue of differences in indexing in programming languages. I guess Paraview was initially designed with Fortran's output in mind?

-Andrew Burns

-----Original Message-----
From: L?cio Corr?a [mailto:labcorrea at gmail.com] 
Sent: Friday, September 09, 2016 10:46 AM
To: Armin Wehrfritz <dkxls23 at gmail.com>
Cc: Burns, Andrew J CTR USARMY RDECOM ARL (US) <andrew.j.burns35.ctr at mail.mil>; paraview at paraview.org
Subject: Re: [Paraview] [Non-DoD Source] Questions about XMF - 3DCoRectMesh

All active links contained in this email were disabled. Please verify the identity of the sender, and confirm the authenticity of all links contained within the message prior to copying and pasting the address to a Web browser. 


________________________________



Thanks guys!


2016-09-09 16:44 GMT+02:00 Armin Wehrfritz <dkxls23 at gmail.com < Caution-mailto:dkxls23 at gmail.com > >:


	This is apparently a "very very old bug" [1] and pops up every now and
	then on this mailing-list. There was apparently a plan to fix this back
	in 2009 [2], but I'm doubtful that this was done.
	
	[1] Caution-http://public.kitware.com/pipermail/paraview/2014-September/032263.html < Caution-http://public.kitware.com/pipermail/paraview/2014-September/032263.html > 
	[2] Caution-http://public.kitware.com/pipermail/paraview/2009-May/012278.html < Caution-http://public.kitware.com/pipermail/paraview/2009-May/012278.html > 
	
	-Armin







	On 09/09/2016 05:15 PM, Burns, Andrew J CTR USARMY RDECOM ARL (US) wrote:
	

		We noticed this also, I believe the plan is to remove the flipping of dimension ordering. However, I am unsure on when that will occur.
		
		Andrew Burns
		Software Engineer | Leidos
		Phone: 410-306-0409 < tel:410-306-0409 > 
		ARL DSRC
		andrew.j.burns35.ctr at mail.mil < Caution-mailto:andrew.j.burns35.ctr at mail.mil > 
		
		-----Original Message-----
		From: ParaView [Caution-mailto:paraview-bounces at paraview.org < Caution-mailto:paraview-bounces at paraview.org > ] On Behalf Of L?cio Corr?a
		Sent: Friday, September 09, 2016 9:29 AM
		To: paraview at paraview.org < Caution-mailto:paraview at paraview.org > 
		Subject: [Non-DoD Source] [Paraview] Questions about XMF - 3DCoRectMesh
		
		Hi everbody,
		
		I have a stupid question about the XMF - 3DCoRectMesh...
		
		I tried to build an "extruded rectangle" using this function (I attached the files).
		
		I asked for a 6 by 16 by 46 elements as you can see in the XMF file...
		
		     <Topology TopologyType="3DCoRectMesh" Dimensions="7 17 47"/>
		     <Geometry GeometryType="ORIGIN_DXDYDZ">
		   <DataItem Name="origin" Format="XML" DataType="Float" Precision="8" Dimensions="3">
		             -0.6000000000
		             -1.6000000000
		             -4.6000000000
		
		but when I open in Paraview (4.3.1 and 5.1.2) I found a 46 by 16 by 6 elements...
		
		I tried also to look in: VTK/ThirdParty/xdmf3/vtkxdmf3/XdmfRegularGrid.cpp, but I didn't found the reason to Paraview "change" the X axis by the Z axis.
		
		Someone found the same thing? Or, where I made a mistake?
		
		Regards,
		


From dennis_conklin at goodyear.com  Fri Sep  9 13:28:28 2016
From: dennis_conklin at goodyear.com (Dennis Conklin)
Date: Fri, 9 Sep 2016 17:28:28 +0000
Subject: [Paraview] [EXT] Re: Is the PythonAnnotation documentation
 obsolete?
In-Reply-To: <CADHSJjCw77KAvE+LyunMQELLEYLH5wMUjDDB+TeH_ZzcHdPRZQ@mail.gmail.com>
References: <CY1PR07MB25068EDA77910589D1DB0A959FFB0@CY1PR07MB2506.namprd07.prod.outlook.com>
 <CADHSJjCw77KAvE+LyunMQELLEYLH5wMUjDDB+TeH_ZzcHdPRZQ@mail.gmail.com>
Message-ID: <CY1PR07MB2506DB7E9ED33F32D05C496A9FFA0@CY1PR07MB2506.namprd07.prod.outlook.com>

Utkarsh,

Okay, thanks for that explanation.   I have some comments.

The documentation is very confusing and/or incomplete and misleading.   Hovering over the expression box produces a popup which makes it seem as though t-index is the way to access things.  No real distinction is made between Field, Cell and Point variables  

<<The expression is evaluated and the resulting scalar value or numpy array is added to the output as an array>>

What??  The expression is added to the row data, which I have never seen or used before.  And this is PythonAnnotation, not PythonCalculator - the object is to display it on the screen.   So why can I only format Field data on the screen?
"Vertical Force: %g" %REACTZ_901    works and outputs formatted, labelled text on screen because it is a Field Variable
"FBFORCE1: %g" %FBFORCE[0]    prints (error) to the screen because it is a cell variable.   What is the point of including cell and point variables into an Annotation filter in a way which makes it impossible to format the annotation?    I'm not able to think of a situation in which this is useful.  Perhaps I'm not creative enough.

I couldn't find an explanation of all of this anywhere in the documentation, so my title for this thread stands.   I think the documentation might be expanded a little.   And I would suggest a new name of PythonFieldVariableAnnotation.  I have used it to annotate Field Variables, but I don't know how I can use unlabeled, unformatted Cell or Point data annotations to add value to a picture or animation.

Re-reading this it seems harsher than I intended.   Just my disappointment at not being able to Annotate Cell Values.  I appreciate your support and explanations, I just would like to capture this information somewhere in the documentation.

Thanks again,

Dennis


-----Original Message-----
From: Utkarsh Ayachit [mailto:utkarsh.ayachit at kitware.com] 
Sent: Friday, September 09, 2016 10:54 AM
To: Dennis Conklin <dennis_conklin at goodyear.com>
Cc: Paraview (paraview at paraview.org) <paraview at paraview.org>
Subject: [EXT] Re: [Paraview] Is the PythonAnnotation documentation obsolete?

Dennis,

Python Annotation only works with what's available in the current timestep. If you look at the "Field Data" in the SpreadSheet view, you'll see that the Exodus reader puts out an array with values for all timesteps for variables like REACTZ_901 and hence you can offset into it using t_index irrespective of which timestep you are at.

For Point/Cell data, you have access to the field values for all points/cells for the current timestep only. Thus, t_index doesn't make much sense for those cases. For understanding how indexing works when dealing with multblock datasets, I'd recommend reading Berk's blog post [1].

Hope that helps.
Utkarsh

[1] https://blog.kitware.com/improved-vtk-numpy-integration-part-5/

On Thu, Sep 8, 2016 at 2:32 PM, Dennis Conklin <dennis_conklin at goodyear.com> wrote:
> All,
>
>
>
> I have tried to use PythonAnnotation but it only seems to work 
> properly with FieldVariables.
>
>
>
> So for instance, with field variables  of REACTZ_901 and REACTZ_902, 
> the following expressions work and display the  values as expected
>
>
>
> REACTZ_901                                displays array of values for all
> timesteps
>
> REACTZ_901[t_index]                 displays single number (no brackets)
>
> Int(REACTZ_901)                          (error)
>
> Int(REACTZ_901[t_index]            displays truncated integer value (no
> brackets)
>
>
>
> To try to work with CellData I have made an ExtractSelection of a 
> single Cell.  I have a Cell variable of FBFORCE1
>
> I want to use PythonAnnotation to print out the FBFORCE1 for that cell 
> over time (with formatting)
>
>
>
> FBFORCE1                                      [VTKArray([154.2])]  shouldn?t
> this have a value for each timestep?
>
> FBFORCE1[t_index]                       (error)
>
> FBFORCE1[0]                                  [ 154.2]
>
> FBFORCE1[1]                                  (error)
>
> Int(FBFORCE1)                                (error)
>
> Int(FBFORCE1[0])                           (error)
>
>
>
> 2nd try ? Ran PythonAnnotation on an entire file ? many cells, with 
> following results
>
> FBFORCE1                                       VTKArray([ value1, value2
> ???value_final]) ? seems like 1 value per timestep (shouldn?t there be 
> array of # of cells by # of timesteps?
>
>
>
> FBFORCE1[t_index]                       [131.4]  -  again- should be array
> of # of cells? Which cell is this
>
> FBFORCE1[t_index][0]                   (error)
>
> Int(FBFORCE1[t_index])                 error)
>
>
>
> So it seems that Field Variables are numpy-friendly in that formatting 
> works with them, while Cell Variables are still VTK Array variables 
> and not numpy-friendly.
>
>
>
> It?s possible that I am completely missing something here, but it 
> seems Cell Variables are not very useable in the PythonAnnotation.  Is 
> there a way for me to Annotate with individual cell values, either by 
> running PythonAnnotation on a single cell, or by manipulating the 
> variables which are available in the filter?
>
>
>
> At this point I don?t know why Cell and Point Variables are included 
> in the filter since I can only figure out how to use Field Variables
>
>
>
> Thanks for any hints
>
>
>
> Dennis
>
>
> _______________________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at 
> http://www.kitware.com/opensource/opensource.html
>
> Please keep messages on-topic and check the ParaView Wiki at:
> http://paraview.org/Wiki/ParaView
>
> Search the list archives at: http://markmail.org/search/?q=ParaView
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/paraview
>

From Saideep.Pavuluri at pet.hw.ac.uk  Fri Sep  9 13:28:44 2016
From: Saideep.Pavuluri at pet.hw.ac.uk (Saideep Pavuluri)
Date: Fri, 9 Sep 2016 17:28:44 +0000
Subject: [Paraview] Precise location of contours on boundaries
Message-ID: <E744507DCB192B45930918B1A2FF10312901B4F3@petmail.WIN.PET.HW.AC.UK>

Hi guys;

Is there a way to know the precise location of a contour on the boundaries (as shown in picture)? I use the  traditional tool "ruler", however when I have too many points to measure (as in the figure) by hand it gets complicated.

I tried using the integrate variables(selecting the contour) however, the block numbering isn't consistent and I particularly want values only at the boundaries. I am dealing with meniscus and it has a specific curvature based on flow.

Any advice here.

Thanks;
Saideep
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From utkarsh.ayachit at kitware.com  Fri Sep  9 14:40:21 2016
From: utkarsh.ayachit at kitware.com (Utkarsh Ayachit)
Date: Fri, 9 Sep 2016 14:40:21 -0400
Subject: [Paraview] [EXT] Re: Is the PythonAnnotation documentation
	obsolete?
In-Reply-To: <CY1PR07MB2506DB7E9ED33F32D05C496A9FFA0@CY1PR07MB2506.namprd07.prod.outlook.com>
References: <CY1PR07MB25068EDA77910589D1DB0A959FFB0@CY1PR07MB2506.namprd07.prod.outlook.com>
 <CADHSJjCw77KAvE+LyunMQELLEYLH5wMUjDDB+TeH_ZzcHdPRZQ@mail.gmail.com>
 <CY1PR07MB2506DB7E9ED33F32D05C496A9FFA0@CY1PR07MB2506.namprd07.prod.outlook.com>
Message-ID: <CADHSJjAH2s1UA4GJvnp-UuXyzeok1MoW3sr1mzL-9Vt3rpHnoQ@mail.gmail.com>

No objection there. I'd suggest reporting an issue for the same,
otherwise it's going to get lost and forgotten.

https://gitlab.kitware.com/paraview/paraview/issues

On Fri, Sep 9, 2016 at 1:28 PM, Dennis Conklin
<dennis_conklin at goodyear.com> wrote:
> Utkarsh,
>
> Okay, thanks for that explanation.   I have some comments.
>
> The documentation is very confusing and/or incomplete and misleading.   Hovering over the expression box produces a popup which makes it seem as though t-index is the way to access things.  No real distinction is made between Field, Cell and Point variables
>
> <<The expression is evaluated and the resulting scalar value or numpy array is added to the output as an array>>
>
> What??  The expression is added to the row data, which I have never seen or used before.  And this is PythonAnnotation, not PythonCalculator - the object is to display it on the screen.   So why can I only format Field data on the screen?
> "Vertical Force: %g" %REACTZ_901    works and outputs formatted, labelled text on screen because it is a Field Variable
> "FBFORCE1: %g" %FBFORCE[0]    prints (error) to the screen because it is a cell variable.   What is the point of including cell and point variables into an Annotation filter in a way which makes it impossible to format the annotation?    I'm not able to think of a situation in which this is useful.  Perhaps I'm not creative enough.
>
> I couldn't find an explanation of all of this anywhere in the documentation, so my title for this thread stands.   I think the documentation might be expanded a little.   And I would suggest a new name of PythonFieldVariableAnnotation.  I have used it to annotate Field Variables, but I don't know how I can use unlabeled, unformatted Cell or Point data annotations to add value to a picture or animation.
>
> Re-reading this it seems harsher than I intended.   Just my disappointment at not being able to Annotate Cell Values.  I appreciate your support and explanations, I just would like to capture this information somewhere in the documentation.
>
> Thanks again,
>
> Dennis
>
>
> -----Original Message-----
> From: Utkarsh Ayachit [mailto:utkarsh.ayachit at kitware.com]
> Sent: Friday, September 09, 2016 10:54 AM
> To: Dennis Conklin <dennis_conklin at goodyear.com>
> Cc: Paraview (paraview at paraview.org) <paraview at paraview.org>
> Subject: [EXT] Re: [Paraview] Is the PythonAnnotation documentation obsolete?
>
> Dennis,
>
> Python Annotation only works with what's available in the current timestep. If you look at the "Field Data" in the SpreadSheet view, you'll see that the Exodus reader puts out an array with values for all timesteps for variables like REACTZ_901 and hence you can offset into it using t_index irrespective of which timestep you are at.
>
> For Point/Cell data, you have access to the field values for all points/cells for the current timestep only. Thus, t_index doesn't make much sense for those cases. For understanding how indexing works when dealing with multblock datasets, I'd recommend reading Berk's blog post [1].
>
> Hope that helps.
> Utkarsh
>
> [1] https://blog.kitware.com/improved-vtk-numpy-integration-part-5/
>
> On Thu, Sep 8, 2016 at 2:32 PM, Dennis Conklin <dennis_conklin at goodyear.com> wrote:
>> All,
>>
>>
>>
>> I have tried to use PythonAnnotation but it only seems to work
>> properly with FieldVariables.
>>
>>
>>
>> So for instance, with field variables  of REACTZ_901 and REACTZ_902,
>> the following expressions work and display the  values as expected
>>
>>
>>
>> REACTZ_901                                displays array of values for all
>> timesteps
>>
>> REACTZ_901[t_index]                 displays single number (no brackets)
>>
>> Int(REACTZ_901)                          (error)
>>
>> Int(REACTZ_901[t_index]            displays truncated integer value (no
>> brackets)
>>
>>
>>
>> To try to work with CellData I have made an ExtractSelection of a
>> single Cell.  I have a Cell variable of FBFORCE1
>>
>> I want to use PythonAnnotation to print out the FBFORCE1 for that cell
>> over time (with formatting)
>>
>>
>>
>> FBFORCE1                                      [VTKArray([154.2])]  shouldn?t
>> this have a value for each timestep?
>>
>> FBFORCE1[t_index]                       (error)
>>
>> FBFORCE1[0]                                  [ 154.2]
>>
>> FBFORCE1[1]                                  (error)
>>
>> Int(FBFORCE1)                                (error)
>>
>> Int(FBFORCE1[0])                           (error)
>>
>>
>>
>> 2nd try ? Ran PythonAnnotation on an entire file ? many cells, with
>> following results
>>
>> FBFORCE1                                       VTKArray([ value1, value2
>> ???value_final]) ? seems like 1 value per timestep (shouldn?t there be
>> array of # of cells by # of timesteps?
>>
>>
>>
>> FBFORCE1[t_index]                       [131.4]  -  again- should be array
>> of # of cells? Which cell is this
>>
>> FBFORCE1[t_index][0]                   (error)
>>
>> Int(FBFORCE1[t_index])                 error)
>>
>>
>>
>> So it seems that Field Variables are numpy-friendly in that formatting
>> works with them, while Cell Variables are still VTK Array variables
>> and not numpy-friendly.
>>
>>
>>
>> It?s possible that I am completely missing something here, but it
>> seems Cell Variables are not very useable in the PythonAnnotation.  Is
>> there a way for me to Annotate with individual cell values, either by
>> running PythonAnnotation on a single cell, or by manipulating the
>> variables which are available in the filter?
>>
>>
>>
>> At this point I don?t know why Cell and Point Variables are included
>> in the filter since I can only figure out how to use Field Variables
>>
>>
>>
>> Thanks for any hints
>>
>>
>>
>> Dennis
>>
>>
>> _______________________________________________
>> Powered by www.kitware.com
>>
>> Visit other Kitware open-source projects at
>> http://www.kitware.com/opensource/opensource.html
>>
>> Please keep messages on-topic and check the ParaView Wiki at:
>> http://paraview.org/Wiki/ParaView
>>
>> Search the list archives at: http://markmail.org/search/?q=ParaView
>>
>> Follow this link to subscribe/unsubscribe:
>> http://public.kitware.com/mailman/listinfo/paraview
>>

From kmorel at sandia.gov  Fri Sep  9 15:35:08 2016
From: kmorel at sandia.gov (Moreland, Kenneth)
Date: Fri, 9 Sep 2016 19:35:08 +0000
Subject: [Paraview] Precise location of contours on boundaries
Message-ID: <87DF6962-19D8-4E58-8D1B-2FE472DB5F7A@sandia.gov>

Saideep,

This may or may not be what you are asking for, but you should be able to get the exact location of the contour on the boundaries by first extracting the boundary and then running the contours on the boundary. This will give you the contours on the boundary only.

How you get the boundary depends on the type of data you have. Based on the question and the image you provided, I am assuming that you are talking about contours on 2D data. If your 2D data is poly data, you can get the boundary by running the ?Feature Edges? filter and turning on the ?Boundary Edges? option (while turning off all the rest). If you have some other 2D data (such as an image), you can first convert it to poly data with the ?Extract Surface? filter and then follow the previous step of using the ?Feature Edges? filter. Then just run the contour filter on the result of the feature edges and that will give you the exact position of the contours on the boundaries. You can then open up a spreadsheet view to view the exact locations of those contours.

-Ken

From: ParaView <paraview-bounces at paraview.org> on behalf of Saideep Pavuluri <Saideep.Pavuluri at pet.hw.ac.uk>
Date: Friday, September 9, 2016 at 11:28 AM
To: "paraview at paraview.org" <paraview at paraview.org>
Subject: [EXTERNAL] [Paraview] Precise location of contours on boundaries

Hi guys;

Is there a way to know the precise location of a contour on the boundaries (as shown in picture)? I use the  traditional tool ?ruler?, however when I have too many points to measure (as in the figure) by hand it gets complicated.

I tried using the integrate variables(selecting the contour) however, the block numbering isn?t consistent and I particularly want values only at the boundaries. I am dealing with meniscus and it has a specific curvature based on flow.

Any advice here.

Thanks;
Saideep
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From dave.demarle at kitware.com  Sat Sep 10 07:53:49 2016
From: dave.demarle at kitware.com (David E DeMarle)
Date: Sat, 10 Sep 2016 07:53:49 -0400
Subject: [Paraview] ISC 2017 research paper submissions now open
Message-ID: <CANjZAi9bxT4TU4B-yrgjaLRpKT7C881Jjevnm=oEqkwJzD0EHQ@mail.gmail.com>

The call for submissions for ISC research paper sessions for 2017 is now
open. More information is located at:

https://www.hpcwire.com/off-the-wire/call-submissions-now-open-isc-2017-research-paper-sessions/?eid=328379665&bid=1522852
.

Best of luck with your research!

David E DeMarle
Kitware, Inc.
R&D Engineer
21 Corporate Drive
Clifton Park, NY 12065-8662
Phone: 518-881-4909
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From grothausmann.roman at mh-hannover.de  Mon Sep 12 05:49:35 2016
From: grothausmann.roman at mh-hannover.de (Grothausmann, Roman Dr.)
Date: Mon, 12 Sep 2016 11:49:35 +0200
Subject: [Paraview] [vtkusers] Testing ITK/VTK/PV contributions with
 (kitware) Gitlab-CI
In-Reply-To: <CAPf2UMRfLtz1Cd_kYy0uX3V3nA96F2BqGuNGn=zY6_wg_5mkEw@mail.gmail.com>
References: <b559f993-9283-7f14-b7ad-66eb85c5d52a@mh-hannover.de>
 <20160908131417.GB13993@megas.kitware.com>
 <CAPf2UMRfLtz1Cd_kYy0uX3V3nA96F2BqGuNGn=zY6_wg_5mkEw@mail.gmail.com>
Message-ID: <ddc193b4-0cc5-7cb5-4cd6-47c2409435ba@mh-hannover.de>

Many thanks Ben and D?enan for Your replies and pointing me to CircleCI. I see 
that testing contributions employing PV,VTK and ITK all together is rather 
challenging.

I wonder though why my pure VTK (PV) based contribution did not get tested when 
submitted to the VTK-Journal, e.g.
http://www.midasjournal.org/browse/publication/949

Is the testing the VTK/Midas Journals used to do not available any more?

Regards,
Roman

On 08/09/16 16:26, D?enan Zuki? wrote:
> Hi Roman,
>
> some of ITK's remote modules are using CircleCI for testing. Two recent examples
> are RLEImage <https://github.com/KitwareMedical/ITKRLEImage> and
> MorphologicalContourInterpolation
> <https://github.com/KitwareMedical/ITKMorphologicalContourInterpolation>. Of
> course, you should be familiar, or familiarize yourself with CircleCI
> <https://circleci.com/docs/configuration/>.
>
> Regards,
> D?enan
>
> On Thu, Sep 8, 2016 at 9:14 AM, Ben Boeckel <ben.boeckel at kitware.com
> <mailto:ben.boeckel at kitware.com>> wrote:
>
>     On Thu, Sep 08, 2016 at 12:36:40 +0200, Grothausmann, Roman Dr. wrote:
>     > Just getting to know Gitlab-CI, I am wondering whether it is possible to test
>     > contributions to ITK/VTK/PV with Gitlab-CI from gitlab.com <http://gitlab.com> or
>     > gitlab.kitware.com <http://gitlab.kitware.com>. As far as I understand, this
>     basically needs runners, in
>     > this case specific to ITK/VTK/PV. Since kitware has done CI even before the use
>     > of gitlab, I wonder if the former testing environments are available for use
>     > with Gitlab-CI and if so how to use them.
>
>     We're (VTK and ParaView) using buildbot to manage our testing. The
>     number of settings we test across machines is hard to specify in YAML
>     files (machines also have different settings based on what you're
>     testing, e.g., load up a different compiler or Qt4 or Qt5 and the paths
>     they live in, etc.). We're working on improving the hardware situation
>     buildbot is currently in; things should be getting better over the next
>     few months on that front.
>
>     > For example, none of my contributions to the ITK/VTK/Midas Journals got into the
>     > testing phase even though marked for testing during submission. So a possibility
>     > to use Gitlab-CI to test the compilation and to run the project test would be
>     > really great, especially for continued development and testing on other OSs.
>     > Specifically, for e.g. testing my FacetAnalyser contribution
>     > (http://www.midasjournal.org/browse/publication/951
>     <http://www.midasjournal.org/browse/publication/951>
>     > https://gitlab.com/romangrothausmann/FacetAnalyser
>     <https://gitlab.com/romangrothausmann/FacetAnalyser>) I would need a runner
>     > environment with PV, VTK and ITK ideally for Linux, MacOS and Windows.
>
>     ITK is using Gerrit and Jenkins, not Gitlab.
>
>     --Ben
>     _______________________________________________
>     Powered by www.kitware.com <http://www.kitware.com>
>
>     Visit other Kitware open-source projects at
>     http://www.kitware.com/opensource/opensource.html
>     <http://www.kitware.com/opensource/opensource.html>
>
>     Please keep messages on-topic and check the VTK FAQ at:
>     http://www.vtk.org/Wiki/VTK_FAQ <http://www.vtk.org/Wiki/VTK_FAQ>
>
>     Search the list archives at: http://markmail.org/search/?q=vtkusers
>     <http://markmail.org/search/?q=vtkusers>
>
>     Follow this link to subscribe/unsubscribe:
>     http://public.kitware.com/mailman/listinfo/vtkusers
>     <http://public.kitware.com/mailman/listinfo/vtkusers>
>
>

-- 
Dr. Roman Grothausmann

Tomographie und Digitale Bildverarbeitung
Tomography and Digital Image Analysis

Institut f?r Funktionelle und Angewandte Anatomie, OE 4120
Medizinische Hochschule Hannover
Carl-Neuberg-Str. 1
D-30625 Hannover

Tel. +49 511 532-2900

From utkarsh.ayachit at kitware.com  Mon Sep 12 09:29:53 2016
From: utkarsh.ayachit at kitware.com (Utkarsh Ayachit)
Date: Mon, 12 Sep 2016 09:29:53 -0400
Subject: [Paraview] Job Posting: Software Developer at Kitware
Message-ID: <CADHSJjA8zYDMiaWa9km5atBQJ05ntiAqhQjd23xMv+K28_xtXQ@mail.gmail.com>

Folks,

I wanted to draw your attention to this job posting:
https://www.smartrecruiters.com/kitware/90427842-software-developer

The posting itself is quite general and targets multiple teams, so I
figured I'd give a few more details on what our team is looking for.

We are the VTK, ParaView, VTK-m (and related technologies) team. If
you think you can make contributions to these projects on algorithms
or applications side, then certainly apply. At the same time, however,
if you are a systems guy or gal, with interests in the workings of
different computer systems including Crays, BlueGenes, with aptitude
for overcoming platform (and compiler) quirks, or are at home with
CMake scripts, then you may be a good match. If development workflows
is your thing: toying with testing systems like Buildbot, setting up
Git hooks and configurations to simplify development, etc, then this
job posting  may be of interest to you too.

We routinely work with various National (and Intentional) Labs to get
our tools built and deployed on the latest and greatest
super-computing system. If that's of interest to you, I'd strongly
encourage you to apply for this position. If you have any questions,
feel free to email me directly.

Look forward to hearing from you all.

Utkarsh

From andy.bauer at kitware.com  Mon Sep 12 10:31:25 2016
From: andy.bauer at kitware.com (Andy Bauer)
Date: Mon, 12 Sep 2016 10:31:25 -0400
Subject: [Paraview] [Paraview-developers] cmake error configuring
	catalyst project
In-Reply-To: <cfc6bdc1d866adfc01751b20180518a4.startmail@www.startmail.com>
References: <54a417a8e29114d0e57681fcc2cb76ce.startmail@www.startmail.com>
 <CAMaOp+GM+BsEHi3wM2YverxKqwPJ4h1drJ2KOFd1u3uK4CmyoQ@mail.gmail.com>
 <cfc6bdc1d866adfc01751b20180518a4.startmail@www.startmail.com>
Message-ID: <CAMaOp+HpxHqkzW9QG=wBx+rjLzxpWbrMaOUaDeZKH0CKg_ccnw@mail.gmail.com>

Hi Thomas,

Please keep the discussions on the mailing list.

As to your questions, I don't regularly build on Windows so I don't know
the answer. My suggestion would be to see if those libraries are available
in your build/install directory and if your proper environment is set to
find them. Maybe someone else can chime in here with better information.

Best,
Andy

On Mon, Sep 5, 2016 at 4:47 AM, <thomasblome at startmail.com> wrote:

> Hello,
>
> thank you for your quick reply. I had tried it first using the cmake-gui
> but then I followed your recommendation to use the shell script and now it
> works fine.
> Next thing I want to do is get the Catalyst "CxxFullExample" going. I
> generated a project file for that example using CMake. Only thing I had to
> do was to set the ParaView_DIR variable, that is to add the path to the
> ParaViewConfig.cmake file which I found in the bin-directory of Catalyst
> (C:\Kitware\Catalyst-v5.1.2\bin).
> Now I have got following questions:
>
> 1.) I try to run the example by calling CxxFullExample.exe in the debug
> folder by calling
>             CxxFullExample 2 C:\Users\Peripherie\Desktop\
> CxxFullExample\SampleScripts\feslicesript
>      from the windows cmd, where I specify the python script
> "feslicesript" as the second argument.
>      By doing so I get an error message saying that following three
> libraries are missing:
>             vtkPVPythonCatalyst-pv5.1.dll
>             vtkPVCatalyst-pv5.1.dll
>             vtkCommon-pv5.1.dll
>      Do I have to change some options in the cmake.sh script to include
> those libs?
> 2.) Do I have to install Paraview too, or is the Catalyst version I just
> installed sufficient to run the example?
>
> Kind regards
> Thomas
>
>
> Am Sonntag, 28. August 2016 13:06 schrieb Andy Bauer <
> andy.bauer at kitware.com>:
>
>
> Did you try the build directions at http://www.paraview.org/Wiki/
> Build_Directions? You'll want to use the cmake.sh script instead of the
> default CMake settings.
>
> On Sat, Aug 27, 2016 at 12:46 PM, <thomasblome at startmail.com> wrote:
>
> Hi,
>
> I downloaded the latest Catalyst edition (5.1.2) to build it on my Windows
> 10 system.
> In CMake I use default settings, but it starts complaining while
> configuring, displaying following error message:
>
>
> CMake Error at VTK/CMake/vtkModuleTop.cmake:59 (message):
> No such module "vtkGUISupportQt" needed by "vtkPVVTKExtensionsRendering"
> Call Stack (most recent call first):
> VTK/CMake/vtkModuleTop.cmake:75 (vtk_module_check)
> VTK/CMake/vtkModuleTop.cmake:75 (vtk_module_check)
> VTK/CMake/vtkModuleTop.cmake:82 (vtk_module_check)
> VTK/CMakeLists.txt:543 (include)
>
> Does anybody know how to fix that?
>
> Kind regards,
> Thomas
>
> _______________________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at http://www.kitware.com/
> opensource/opensource.html
>
> Search the list archives at: http://markmail.org/search/?q=
> Paraview-developers
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/paraview-developers
>
>
>
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From orion at cora.nwra.com  Mon Sep 12 12:11:44 2016
From: orion at cora.nwra.com (Orion Poplawski)
Date: Mon, 12 Sep 2016 10:11:44 -0600
Subject: [Paraview] ANN: ParaView 5.1.2 available for download
In-Reply-To: <CADHSJjB=zmCDoZhhoi-V9o3H4Mrqr=2-AnsN+t=cH1b6KUvm5Q@mail.gmail.com>
References: <CADHSJjB=zmCDoZhhoi-V9o3H4Mrqr=2-AnsN+t=cH1b6KUvm5Q@mail.gmail.com>
Message-ID: <00f81a2e-8fcc-dda7-9244-8a20086a4694@cora.nwra.com>

On 07/28/2016 08:55 AM, Utkarsh Ayachit wrote:
> Folks,
> 
> ParaView 5.1.2 is now available for download [1]. Please refer to the
> release notes on the Kitware blog [2]. As always, we look forward to
> your feedback [3].
> 
> Also stay tuned to the Kitware Blog [4] for upcoming features and
> enhancements to ParaView, ParaView Catalyst, ParaViewWeb and much
> more!
> 
> - ParaView Team
> 
> [1] http://www.paraview.org/download/
> [2] https://blog.kitware.com/paraview-5-1-2-release-notes/
> [3] http://paraview.uservoice.com
> [4] https://blog.kitware.com/tag/ParaView/

I'm hitting a problem with MPI builds that is preventing me from updating
paraview in Fedora.  See https://gitlab.kitware.com/paraview/paraview/issues/16814

-- 
Orion Poplawski
Technical Manager                     303-415-9701 x222
NWRA, Boulder/CoRA Office             FAX: 303-415-9702
3380 Mitchell Lane                       orion at nwra.com
Boulder, CO 80301                   http://www.nwra.com

From chrisneal at snumerics.com  Mon Sep 12 13:36:42 2016
From: chrisneal at snumerics.com (Christopher Neal)
Date: Mon, 12 Sep 2016 13:36:42 -0400
Subject: [Paraview] Catalyst osMesa rendering time
Message-ID: <BE7FEBAD-3DD0-4516-B69A-7568050FB2A3@snumerics.com>

Hi all,

 

I have compiled a version of ParaView with osMesa enabled. The version is 5.1.2 for ParaView. I?m running the CxxFullExample Catalyst example that is located in ParaView/Examples/Catalyst.


Operating system info

lsb_release ?a: 
LSB Version:???????? n/a

Distributor ID:???? openSUSE project

Description:???????? openSUSE 13.2 (Harlequin) (x86_64)

Release:??????????????? 13.2

Codename:?????????? Harlequin



I have added 1 additional script to the Catalyst example by using the ?CoProcessing? button in ParaView to generate a Catalyst script that just exports a .png of an isometric view of the geometry. When I run the example, the operating system seems to freeze up completely in my login session i.e. windows can not be clicked, nothing at all can be done with the exception of moving the mouse around on the screen. It stays frozen like this for about 2 minutes before a window pops up that says ?Paraview(batch)?. In the window is the isometric view and the window updates to show the geometry at every timestep that the example outputs an image at. The Catalyst script does seem to execute fine and outputs image files for each frame that I requested, but it is soooo slow for some reason.

Is this the expected behavior of running Catalyst with an osMesa build? I thought that ?os? stood for ?off-screen?, which I interpreted as there being no screen display component to the rendering. Have I done something wrong with compiling ParaView with osMesa? Is Catalyst supposed to completely lock up the session until a window pops up?? 

I would love to hear from other users of Catalyst to hear about the experiences of running Catalyst.


Thank you,

Chris Neal

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From andy.bauer at kitware.com  Mon Sep 12 14:39:41 2016
From: andy.bauer at kitware.com (Andy Bauer)
Date: Mon, 12 Sep 2016 14:39:41 -0400
Subject: [Paraview] Catalyst osMesa rendering time
In-Reply-To: <BE7FEBAD-3DD0-4516-B69A-7568050FB2A3@snumerics.com>
References: <BE7FEBAD-3DD0-4516-B69A-7568050FB2A3@snumerics.com>
Message-ID: <CAMaOp+HDga=x=TKmq6S+WDAE9AvrCwx61P3c1Pb+ERUuFX1NfA@mail.gmail.com>

Hi Chris,

It sounds like you didn't properly build ParaView with offscreen rendering.
Can  you share your CMakeCache.txt from your build? I'm guessing VTK_USE_X,
VTK_USE_OFFSCREEN or some other thing didn't get set properly.

Andy

On Mon, Sep 12, 2016 at 1:36 PM, Christopher Neal <chrisneal at snumerics.com>
wrote:

> Hi all,
>
>
>
> I have compiled a version of ParaView with osMesa enabled. The version is
> 5.1.2 for ParaView. I?m running the CxxFullExample Catalyst example that is
> located in ParaView/Examples/Catalyst.
>
> *Operating system info*
>
> lsb_release ?a:
> LSB Version:         n/a
>
> Distributor ID:     openSUSE project
>
> Description:         openSUSE 13.2 (Harlequin) (x86_64)
>
> Release:                13.2
>
> Codename:           Harlequin
>
>
>
> I have added 1 additional script to the Catalyst example by using the
> ?CoProcessing? button in ParaView to generate a Catalyst script that just
> exports a .png of an isometric view of the geometry. When I run the
> example, the operating system seems to freeze up completely in my login
> session i.e. windows can not be clicked, nothing at all can be done with
> the exception of moving the mouse around on the screen. It stays frozen
> like this for about 2 minutes before a window pops up that says
> ?Paraview(batch)?. In the window is the isometric view and the window
> updates to show the geometry at every timestep that the example outputs an
> image at. The Catalyst script does seem to execute fine and outputs image
> files for each frame that I requested, but it is soooo slow for some reason.
>
> Is this the expected behavior of running Catalyst with an osMesa build? I
> thought that ?os? stood for ?off-screen?, which I interpreted as there
> being no screen display component to the rendering. Have I done something
> wrong with compiling ParaView with osMesa? Is Catalyst supposed to
> completely lock up the session until a window pops up?
>
> I would love to hear from other users of Catalyst to hear about the
> experiences of running Catalyst.
>
>
> Thank you,
>
> Chris Neal
>
> _______________________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at http://www.kitware.com/
> opensource/opensource.html
>
> Please keep messages on-topic and check the ParaView Wiki at:
> http://paraview.org/Wiki/ParaView
>
> Search the list archives at: http://markmail.org/search/?q=ParaView
>
> Follow this link to subscribe/unsubscribe:
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>
>
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From chrisneal at snumerics.com  Mon Sep 12 15:00:15 2016
From: chrisneal at snumerics.com (Christopher Neal)
Date: Mon, 12 Sep 2016 15:00:15 -0400
Subject: [Paraview] Catalyst osMesa rendering time
In-Reply-To: <CAMaOp+HDga=x=TKmq6S+WDAE9AvrCwx61P3c1Pb+ERUuFX1NfA@mail.gmail.com>
References: <BE7FEBAD-3DD0-4516-B69A-7568050FB2A3@snumerics.com>
 <CAMaOp+HDga=x=TKmq6S+WDAE9AvrCwx61P3c1Pb+ERUuFX1NfA@mail.gmail.com>
Message-ID: <DDC524AE-CAF3-4818-B3C1-D44ACC408204@snumerics.com>

Thanks Andy,

The file is quite large, so I have attached it.


I tried to follow the process that is explained at(http://www.paraview.org/Wiki/ParaView/ParaView_And_Mesa_3D) so I made a shell script that contains all of the arguments passed to cmake. It is shown below.

 

 

#!/bin/bash

 

cmake \

? -DCMAKE_SOURCE_DIR:PATH=/home/neal/software/ParaView_osMesa/Source \

? -DCMAKE_INSTALL_PREFIX:PATH=/home/neal/software/ParaView_osMesa/build \

? -DCMAKE_BUILD_TYPE:STRING=Release \

? -DCMAKE_SKIP_INSTALL_RPATH:BOOL=YES \

? -DBUILD_TESTING:BOOL=OFF \

? -DPARAVIEW_BUILD_QT_GUI:BOOL=OFF \

? -DVTK_RENDERING_BACKEND=OpenGL2 \

? -DPARAVIEW_USE_MPI:BOOL=ON \

? -DPARAVIEW_ENABLE_PYTHON:BOOL=ON \

? -DPARAVIEW_INSTALL_DEVELOPMENT_FILES:BOOL=ON \

? -DPARAVIEW_BUILD_CATALYST_ADAPTERS:BOOL=ON \

? -DPARAVIEW_BUILD_PLUGIN_AnalyzeNIfTIIO:BOOL=FALSE \

? -DPARAVIEW_BUILD_PLUGIN_ArrowGlyph:BOOL=FALSE \

? -DPARAVIEW_BUILD_PLUGIN_CDIReader:BOOL=FALSE \

? -DPARAVIEW_BUILD_PLUGIN_EyeDomeLighting:BOOL=FALSE \

? -DPARAVIEW_BUILD_PLUGIN_GMVReader:BOOL=FALSE \

 ?-DPARAVIEW_BUILD_PLUGIN_GeodesicMeasurement:BOOL=FALSE \

? -DPARAVIEW_BUILD_PLUGIN_H5PartReader:BOOL=FALSE \

? -DPARAVIEW_BUILD_PLUGIN_InSituExodus:BOOL=FALSE \

? -DPARAVIEW_BUILD_PLUGIN_MantaView:BOOL=FALSE \

? -DPARAVIEW_BUILD_PLUGIN_Moments:BOOL=FALSE \

? -DPARAVIEW_BUILD_PLUGIN_NonOrthogonalSource:BOOL=FALSE \

? -DPARAVIEW_BUILD_PLUGIN_PacMan:BOOL=FALSE \

? -DPARAVIEW_BUILD_PLUGIN_PointSprite:BOOL=FALSE \

? -DPARAVIEW_BUILD_PLUGIN_RGBZView:BOOL=FALSE \

? -DPARAVIEW_BUILD_PLUGIN_SLACTools:BOOL=FALSE \

 ?-DPARAVIEW_BUILD_PLUGIN_SciberQuestToolKit:BOOL=FALSE \

? -DPARAVIEW_BUILD_PLUGIN_SierraPlotTools:BOOL=FALSE \

? -DPARAVIEW_BUILD_PLUGIN_StreamingParticles:BOOL=FALSE \

? -DPARAVIEW_BUILD_PLUGIN_SurfaceLIC:BOOL=FALSE \

? -DPARAVIEW_BUILD_PLUGIN_UncertaintyRendering:BOOL=FALSE \

? -DPARAVIEW_BUILD_PLUGIN_AcceleratedAlgorithms:BOOL=OFF \

? -DVTK_USE_CXX11_FEATURES:BOOL=ON \

? -DVTK_USE_X:BOOL=OFF \

? -DOPENGL_INCLUDE_DIR:PATH=/home/neal/software/Mesa/build/include \

? -DOPENGL_gl_LIBRARY:PATH=/home/neal/software/Mesa/build/lib64/libOSMesa.so \

? -DOPENGL_glu_LIBRARY:PATH=/home/neal/software/Mesa/build/lib64/libGLU.so \

? -DVTK_OPENGL_HAS_OSMESA:BOOL=ON \

? -DOSMESA_INCLUDE_DIR:PATH=/home/neal/software/Mesa/build/include \

? -DOSMESA_LIBRARY:PATH=/home/neal/software/Mesa/build/lib64/libOSMesa.so? /home/neal/software/ParaView_osMesa/Source

 

make -j20

#make -j20 install

 

 


-Chris

 

From: Andy Bauer <andy.bauer at kitware.com>
Date: Monday, September 12, 2016 at 2:39 PM
To: Christopher Neal <chrisneal at snumerics.com>
Cc: Benson Muite via ParaView <paraview at paraview.org>
Subject: Re: [Paraview] Catalyst osMesa rendering time

 

Hi Chris,

It sounds like you didn't properly build ParaView with offscreen rendering. Can  you share your CMakeCache.txt from your build? I'm guessing VTK_USE_X, VTK_USE_OFFSCREEN or some other thing didn't get set properly.

Andy

 

On Mon, Sep 12, 2016 at 1:36 PM, Christopher Neal <chrisneal at snumerics.com> wrote:

Hi all,

 

I have compiled a version of ParaView with osMesa enabled. The version is 5.1.2 for ParaView. I?m running the CxxFullExample Catalyst example that is located in ParaView/Examples/Catalyst.

Operating system info

lsb_release ?a: 
LSB Version:         n/a

Distributor ID:     openSUSE project

Description:         openSUSE 13.2 (Harlequin) (x86_64)

Release:                13.2

Codename:           Harlequin



I have added 1 additional script to the Catalyst example by using the ?CoProcessing? button in ParaView to generate a Catalyst script that just exports a .png of an isometric view of the geometry. When I run the example, the operating system seems to freeze up completely in my login session i.e. windows can not be clicked, nothing at all can be done with the exception of moving the mouse around on the screen. It stays frozen like this for about 2 minutes before a window pops up that says ?Paraview(batch)?. In the window is the isometric view and the window updates to show the geometry at every timestep that the example outputs an image at. The Catalyst script does seem to execute fine and outputs image files for each frame that I requested, but it is soooo slow for some reason.

Is this the expected behavior of running Catalyst with an osMesa build? I thought that ?os? stood for ?off-screen?, which I interpreted as there being no screen display component to the rendering. Have I done something wrong with compiling ParaView with osMesa? Is Catalyst supposed to completely lock up the session until a window pops up?  

I would love to hear from other users of Catalyst to hear about the experiences of running Catalyst.


Thank you,

Chris Neal


_______________________________________________
Powered by www.kitware.com

Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html

Please keep messages on-topic and check the ParaView Wiki at: http://paraview.org/Wiki/ParaView

Search the list archives at: http://markmail.org/search/?q=ParaView

Follow this link to subscribe/unsubscribe:
http://public.kitware.com/mailman/listinfo/paraview

 

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From andy.bauer at kitware.com  Mon Sep 12 15:20:31 2016
From: andy.bauer at kitware.com (Andy Bauer)
Date: Mon, 12 Sep 2016 15:20:31 -0400
Subject: [Paraview] Catalyst osMesa rendering time
In-Reply-To: <DDC524AE-CAF3-4818-B3C1-D44ACC408204@snumerics.com>
References: <BE7FEBAD-3DD0-4516-B69A-7568050FB2A3@snumerics.com>
 <CAMaOp+HDga=x=TKmq6S+WDAE9AvrCwx61P3c1Pb+ERUuFX1NfA@mail.gmail.com>
 <DDC524AE-CAF3-4818-B3C1-D44ACC408204@snumerics.com>
Message-ID: <CAMaOp+FBNkGwGfwHd6JmW_BXAeatiLD52Hs1g_Lm90OBDTRoCg@mail.gmail.com>

I think the missing item is that you need to set VTK_USE_OFFSCREEN to ON.

On Mon, Sep 12, 2016 at 3:00 PM, Christopher Neal <chrisneal at snumerics.com>
wrote:

> Thanks Andy,
>
> The file is quite large, so I have attached it.
>
> I tried to follow the process that is explained at(
> http://www.paraview.org/Wiki/ParaView/ParaView_And_Mesa_3D) so I made a
> shell script that contains all of the arguments passed to cmake. It is
> shown below.
>
>
>
>
>
> #!/bin/bash
>
>
>
> cmake \
>
>   -DCMAKE_SOURCE_DIR:PATH=/home/neal/software/ParaView_osMesa/Source \
>
>   -DCMAKE_INSTALL_PREFIX:PATH=/home/neal/software/ParaView_osMesa/build \
>
>   -DCMAKE_BUILD_TYPE:STRING=Release \
>
>   -DCMAKE_SKIP_INSTALL_RPATH:BOOL=YES \
>
>   -DBUILD_TESTING:BOOL=OFF \
>
>   -DPARAVIEW_BUILD_QT_GUI:BOOL=OFF \
>
>   -DVTK_RENDERING_BACKEND=OpenGL2 \
>
>   -DPARAVIEW_USE_MPI:BOOL=ON \
>
>   -DPARAVIEW_ENABLE_PYTHON:BOOL=ON \
>
>   -DPARAVIEW_INSTALL_DEVELOPMENT_FILES:BOOL=ON \
>
>   -DPARAVIEW_BUILD_CATALYST_ADAPTERS:BOOL=ON \
>
>   -DPARAVIEW_BUILD_PLUGIN_AnalyzeNIfTIIO:BOOL=FALSE \
>
>   -DPARAVIEW_BUILD_PLUGIN_ArrowGlyph:BOOL=FALSE \
>
>   -DPARAVIEW_BUILD_PLUGIN_CDIReader:BOOL=FALSE \
>
>   -DPARAVIEW_BUILD_PLUGIN_EyeDomeLighting:BOOL=FALSE \
>
>   -DPARAVIEW_BUILD_PLUGIN_GMVReader:BOOL=FALSE \
>
>  -DPARAVIEW_BUILD_PLUGIN_GeodesicMeasurement:BOOL=FALSE \
>
>   -DPARAVIEW_BUILD_PLUGIN_H5PartReader:BOOL=FALSE \
>
>   -DPARAVIEW_BUILD_PLUGIN_InSituExodus:BOOL=FALSE \
>
>   -DPARAVIEW_BUILD_PLUGIN_MantaView:BOOL=FALSE \
>
>   -DPARAVIEW_BUILD_PLUGIN_Moments:BOOL=FALSE \
>
>   -DPARAVIEW_BUILD_PLUGIN_NonOrthogonalSource:BOOL=FALSE \
>
>   -DPARAVIEW_BUILD_PLUGIN_PacMan:BOOL=FALSE \
>
>   -DPARAVIEW_BUILD_PLUGIN_PointSprite:BOOL=FALSE \
>
>   -DPARAVIEW_BUILD_PLUGIN_RGBZView:BOOL=FALSE \
>
>   -DPARAVIEW_BUILD_PLUGIN_SLACTools:BOOL=FALSE \
>
>  -DPARAVIEW_BUILD_PLUGIN_SciberQuestToolKit:BOOL=FALSE \
>
>   -DPARAVIEW_BUILD_PLUGIN_SierraPlotTools:BOOL=FALSE \
>
>   -DPARAVIEW_BUILD_PLUGIN_StreamingParticles:BOOL=FALSE \
>
>   -DPARAVIEW_BUILD_PLUGIN_SurfaceLIC:BOOL=FALSE \
>
>   -DPARAVIEW_BUILD_PLUGIN_UncertaintyRendering:BOOL=FALSE \
>
>   -DPARAVIEW_BUILD_PLUGIN_AcceleratedAlgorithms:BOOL=OFF \
>
>   -DVTK_USE_CXX11_FEATURES:BOOL=ON \
>
>   -DVTK_USE_X:BOOL=OFF \
>
>   -DOPENGL_INCLUDE_DIR:PATH=/home/neal/software/Mesa/build/include \
>
>   -DOPENGL_gl_LIBRARY:PATH=/home/neal/software/Mesa/build/lib64/libOSMesa.so
> \
>
>   -DOPENGL_glu_LIBRARY:PATH=/home/neal/software/Mesa/build/lib64/libGLU.so
> \
>
>   -DVTK_OPENGL_HAS_OSMESA:BOOL=ON \
>
>   -DOSMESA_INCLUDE_DIR:PATH=/home/neal/software/Mesa/build/include \
>
>   -DOSMESA_LIBRARY:PATH=/home/neal/software/Mesa/build/lib64/libOSMesa.so
> /home/neal/software/ParaView_osMesa/Source
>
>
>
> make -j20
>
> #make -j20 install
>
>
>
>
>
>
> -Chris
>
>
>
> *From: *Andy Bauer <andy.bauer at kitware.com>
> *Date: *Monday, September 12, 2016 at 2:39 PM
> *To: *Christopher Neal <chrisneal at snumerics.com>
> *Cc: *Benson Muite via ParaView <paraview at paraview.org>
> *Subject: *Re: [Paraview] Catalyst osMesa rendering time
>
>
>
> Hi Chris,
>
> It sounds like you didn't properly build ParaView with offscreen
> rendering. Can  you share your CMakeCache.txt from your build? I'm guessing
> VTK_USE_X, VTK_USE_OFFSCREEN or some other thing didn't get set properly.
>
> Andy
>
>
>
> On Mon, Sep 12, 2016 at 1:36 PM, Christopher Neal <chrisneal at snumerics.com>
> wrote:
>
> Hi all,
>
>
>
> I have compiled a version of ParaView with osMesa enabled. The version is
> 5.1.2 for ParaView. I?m running the CxxFullExample Catalyst example that is
> located in ParaView/Examples/Catalyst.
>
> *Operating system info*
>
> lsb_release ?a:
> LSB Version:         n/a
>
> Distributor ID:     openSUSE project
>
> Description:         openSUSE 13.2 (Harlequin) (x86_64)
>
> Release:                13.2
>
> Codename:           Harlequin
>
>
>
> I have added 1 additional script to the Catalyst example by using the
> ?CoProcessing? button in ParaView to generate a Catalyst script that just
> exports a .png of an isometric view of the geometry. When I run the
> example, the operating system seems to freeze up completely in my login
> session i.e. windows can not be clicked, nothing at all can be done with
> the exception of moving the mouse around on the screen. It stays frozen
> like this for about 2 minutes before a window pops up that says
> ?Paraview(batch)?. In the window is the isometric view and the window
> updates to show the geometry at every timestep that the example outputs an
> image at. The Catalyst script does seem to execute fine and outputs image
> files for each frame that I requested, but it is soooo slow for some reason.
>
> Is this the expected behavior of running Catalyst with an osMesa build? I
> thought that ?os? stood for ?off-screen?, which I interpreted as there
> being no screen display component to the rendering. Have I done something
> wrong with compiling ParaView with osMesa? Is Catalyst supposed to
> completely lock up the session until a window pops up?
>
> I would love to hear from other users of Catalyst to hear about the
> experiences of running Catalyst.
>
>
> Thank you,
>
> Chris Neal
>
>
> _______________________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at http://www.kitware.com/
> opensource/opensource.html
>
> Please keep messages on-topic and check the ParaView Wiki at:
> http://paraview.org/Wiki/ParaView
>
> Search the list archives at: http://markmail.org/search/?q=ParaView
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/paraview
>
>
>
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From chrisneal at snumerics.com  Mon Sep 12 15:37:08 2016
From: chrisneal at snumerics.com (Christopher Neal)
Date: Mon, 12 Sep 2016 15:37:08 -0400
Subject: [Paraview] Catalyst osMesa rendering time
In-Reply-To: <CAMaOp+FBNkGwGfwHd6JmW_BXAeatiLD52Hs1g_Lm90OBDTRoCg@mail.gmail.com>
References: <BE7FEBAD-3DD0-4516-B69A-7568050FB2A3@snumerics.com>
 <CAMaOp+HDga=x=TKmq6S+WDAE9AvrCwx61P3c1Pb+ERUuFX1NfA@mail.gmail.com>
 <DDC524AE-CAF3-4818-B3C1-D44ACC408204@snumerics.com>
 <CAMaOp+FBNkGwGfwHd6JmW_BXAeatiLD52Hs1g_Lm90OBDTRoCg@mail.gmail.com>
Message-ID: <AE9D5AC6-1FC5-4960-AAF5-B5C8AC978035@snumerics.com>

That?s what I thought when I read your reply, so I did a rebuild with that option included just to be safe. I rebuilt the example using the ParaView build that had the VTK_USE_ONSCREEN set to ON, and it still is creating a window on the screen when I run the example. For reference the new configuration script that I used is shown below with the change highlighted in bold. I have also attached the CMakeCache.txt for the newest build.


cmake \

? -DCMAKE_SOURCE_DIR:PATH=/home/neal/software/ParaView_osMesa/Source \

? -DCMAKE_INSTALL_PREFIX:PATH=/home/neal/software/ParaView_osMesa/build \

? -DCMAKE_BUILD_TYPE:STRING=Release \

? -DCMAKE_SKIP_INSTALL_RPATH:BOOL=YES \

? -DBUILD_TESTING:BOOL=OFF \

? -DPARAVIEW_BUILD_QT_GUI:BOOL=OFF \

? -DVTK_RENDERING_BACKEND=OpenGL2 \

? -DPARAVIEW_USE_MPI:BOOL=ON \

? -DPARAVIEW_ENABLE_PYTHON:BOOL=ON \

? -DPARAVIEW_INSTALL_DEVELOPMENT_FILES:BOOL=ON \

? -DPARAVIEW_BUILD_CATALYST_ADAPTERS:BOOL=ON \

 

? -DPARAVIEW_BUILD_PLUGIN_AnalyzeNIfTIIO:BOOL=FALSE \

? -DPARAVIEW_BUILD_PLUGIN_ArrowGlyph:BOOL=FALSE \

? -DPARAVIEW_BUILD_PLUGIN_CDIReader:BOOL=FALSE \

? -DPARAVIEW_BUILD_PLUGIN_EyeDomeLighting:BOOL=FALSE \

? -DPARAVIEW_BUILD_PLUGIN_GMVReader:BOOL=FALSE \

? -DPARAVIEW_BUILD_PLUGIN_GeodesicMeasurement:BOOL=FALSE \

? -DPARAVIEW_BUILD_PLUGIN_H5PartReader:BOOL=FALSE \

? -DPARAVIEW_BUILD_PLUGIN_InSituExodus:BOOL=FALSE \

? -DPARAVIEW_BUILD_PLUGIN_MantaView:BOOL=FALSE \

? -DPARAVIEW_BUILD_PLUGIN_Moments:BOOL=FALSE \

? -DPARAVIEW_BUILD_PLUGIN_NonOrthogonalSource:BOOL=FALSE \

? -DPARAVIEW_BUILD_PLUGIN_PacMan:BOOL=FALSE \

? -DPARAVIEW_BUILD_PLUGIN_PointSprite:BOOL=FALSE \

? -DPARAVIEW_BUILD_PLUGIN_RGBZView:BOOL=FALSE \

? -DPARAVIEW_BUILD_PLUGIN_SLACTools:BOOL=FALSE \

? -DPARAVIEW_BUILD_PLUGIN_SciberQuestToolKit:BOOL=FALSE \

? -DPARAVIEW_BUILD_PLUGIN_SierraPlotTools:BOOL=FALSE \

? -DPARAVIEW_BUILD_PLUGIN_StreamingParticles:BOOL=FALSE \

? -DPARAVIEW_BUILD_PLUGIN_SurfaceLIC:BOOL=FALSE \

? -DPARAVIEW_BUILD_PLUGIN_UncertaintyRendering:BOOL=FALSE \

? -DPARAVIEW_BUILD_PLUGIN_AcceleratedAlgorithms:BOOL=OFF \

 

? -DVTK_USE_CXX11_FEATURES:BOOL=ON \

? -DVTK_USE_X:BOOL=OFF \

? -DVTK_USE_OFFSCREEN:BOOL=ON \

? -DOPENGL_INCLUDE_DIR:PATH=/home/neal/software/Mesa/build/include \

? -DOPENGL_gl_LIBRARY:PATH=/home/neal/software/Mesa/build/lib64/libOSMesa.so \

? -DOPENGL_glu_LIBRARY:PATH=/home/neal/software/Mesa/build/lib64/libGLU.so \

? -DVTK_OPENGL_HAS_OSMESA:BOOL=ON \

? -DOSMESA_INCLUDE_DIR:PATH=/home/neal/software/Mesa/build/include \

? -DOSMESA_LIBRARY:PATH=/home/neal/software/Mesa/build/lib64/libOSMesa.so? /home/neal/software/ParaView_osMesa/Source

 

make -j20

#make -j20 install

 

 


-Chris

 

From: Andy Bauer <andy.bauer at kitware.com>
Date: Monday, September 12, 2016 at 3:20 PM
To: Christopher Neal <chrisneal at snumerics.com>
Cc: Benson Muite via ParaView <paraview at paraview.org>
Subject: Re: [Paraview] Catalyst osMesa rendering time

 

I think the missing item is that you need to set VTK_USE_OFFSCREEN to ON.

 

On Mon, Sep 12, 2016 at 3:00 PM, Christopher Neal <chrisneal at snumerics.com> wrote:

Thanks Andy,

The file is quite large, so I have attached it.

I tried to follow the process that is explained at(http://www.paraview.org/Wiki/ParaView/ParaView_And_Mesa_3D) so I made a shell script that contains all of the arguments passed to cmake. It is shown below.

 

 

#!/bin/bash

 

cmake \

  -DCMAKE_SOURCE_DIR:PATH=/home/neal/software/ParaView_osMesa/Source \

  -DCMAKE_INSTALL_PREFIX:PATH=/home/neal/software/ParaView_osMesa/build \

  -DCMAKE_BUILD_TYPE:STRING=Release \

  -DCMAKE_SKIP_INSTALL_RPATH:BOOL=YES \

  -DBUILD_TESTING:BOOL=OFF \

  -DPARAVIEW_BUILD_QT_GUI:BOOL=OFF \

  -DVTK_RENDERING_BACKEND=OpenGL2 \

  -DPARAVIEW_USE_MPI:BOOL=ON \

  -DPARAVIEW_ENABLE_PYTHON:BOOL=ON \

  -DPARAVIEW_INSTALL_DEVELOPMENT_FILES:BOOL=ON \

  -DPARAVIEW_BUILD_CATALYST_ADAPTERS:BOOL=ON \

  -DPARAVIEW_BUILD_PLUGIN_AnalyzeNIfTIIO:BOOL=FALSE \

  -DPARAVIEW_BUILD_PLUGIN_ArrowGlyph:BOOL=FALSE \

  -DPARAVIEW_BUILD_PLUGIN_CDIReader:BOOL=FALSE \

  -DPARAVIEW_BUILD_PLUGIN_EyeDomeLighting:BOOL=FALSE \

  -DPARAVIEW_BUILD_PLUGIN_GMVReader:BOOL=FALSE \

 -DPARAVIEW_BUILD_PLUGIN_GeodesicMeasurement:BOOL=FALSE \

  -DPARAVIEW_BUILD_PLUGIN_H5PartReader:BOOL=FALSE \

  -DPARAVIEW_BUILD_PLUGIN_InSituExodus:BOOL=FALSE \

  -DPARAVIEW_BUILD_PLUGIN_MantaView:BOOL=FALSE \

  -DPARAVIEW_BUILD_PLUGIN_Moments:BOOL=FALSE \

  -DPARAVIEW_BUILD_PLUGIN_NonOrthogonalSource:BOOL=FALSE \

  -DPARAVIEW_BUILD_PLUGIN_PacMan:BOOL=FALSE \

  -DPARAVIEW_BUILD_PLUGIN_PointSprite:BOOL=FALSE \

  -DPARAVIEW_BUILD_PLUGIN_RGBZView:BOOL=FALSE \

  -DPARAVIEW_BUILD_PLUGIN_SLACTools:BOOL=FALSE \

 -DPARAVIEW_BUILD_PLUGIN_SciberQuestToolKit:BOOL=FALSE \

  -DPARAVIEW_BUILD_PLUGIN_SierraPlotTools:BOOL=FALSE \

  -DPARAVIEW_BUILD_PLUGIN_StreamingParticles:BOOL=FALSE \

  -DPARAVIEW_BUILD_PLUGIN_SurfaceLIC:BOOL=FALSE \

  -DPARAVIEW_BUILD_PLUGIN_UncertaintyRendering:BOOL=FALSE \

  -DPARAVIEW_BUILD_PLUGIN_AcceleratedAlgorithms:BOOL=OFF \

  -DVTK_USE_CXX11_FEATURES:BOOL=ON \

  -DVTK_USE_X:BOOL=OFF \

  -DOPENGL_INCLUDE_DIR:PATH=/home/neal/software/Mesa/build/include \

  -DOPENGL_gl_LIBRARY:PATH=/home/neal/software/Mesa/build/lib64/libOSMesa.so \

  -DOPENGL_glu_LIBRARY:PATH=/home/neal/software/Mesa/build/lib64/libGLU.so \

  -DVTK_OPENGL_HAS_OSMESA:BOOL=ON \

  -DOSMESA_INCLUDE_DIR:PATH=/home/neal/software/Mesa/build/include \

  -DOSMESA_LIBRARY:PATH=/home/neal/software/Mesa/build/lib64/libOSMesa.so  /home/neal/software/ParaView_osMesa/Source

 

make -j20

#make -j20 install

 

 


-Chris

 

From: Andy Bauer <andy.bauer at kitware.com>
Date: Monday, September 12, 2016 at 2:39 PM
To: Christopher Neal <chrisneal at snumerics.com>
Cc: Benson Muite via ParaView <paraview at paraview.org>
Subject: Re: [Paraview] Catalyst osMesa rendering time

 

Hi Chris,

It sounds like you didn't properly build ParaView with offscreen rendering. Can  you share your CMakeCache.txt from your build? I'm guessing VTK_USE_X, VTK_USE_OFFSCREEN or some other thing didn't get set properly.

Andy

 

On Mon, Sep 12, 2016 at 1:36 PM, Christopher Neal <chrisneal at snumerics.com> wrote:

Hi all,

 

I have compiled a version of ParaView with osMesa enabled. The version is 5.1.2 for ParaView. I?m running the CxxFullExample Catalyst example that is located in ParaView/Examples/Catalyst.

Operating system info

lsb_release ?a: 
LSB Version:         n/a

Distributor ID:     openSUSE project

Description:         openSUSE 13.2 (Harlequin) (x86_64)

Release:                13.2

Codename:           Harlequin



I have added 1 additional script to the Catalyst example by using the ?CoProcessing? button in ParaView to generate a Catalyst script that just exports a .png of an isometric view of the geometry. When I run the example, the operating system seems to freeze up completely in my login session i.e. windows can not be clicked, nothing at all can be done with the exception of moving the mouse around on the screen. It stays frozen like this for about 2 minutes before a window pops up that says ?Paraview(batch)?. In the window is the isometric view and the window updates to show the geometry at every timestep that the example outputs an image at. The Catalyst script does seem to execute fine and outputs image files for each frame that I requested, but it is soooo slow for some reason.

Is this the expected behavior of running Catalyst with an osMesa build? I thought that ?os? stood for ?off-screen?, which I interpreted as there being no screen display component to the rendering. Have I done something wrong with compiling ParaView with osMesa? Is Catalyst supposed to completely lock up the session until a window pops up?  

I would love to hear from other users of Catalyst to hear about the experiences of running Catalyst.


Thank you,

Chris Neal


_______________________________________________
Powered by www.kitware.com

Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html

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From chrisneal at snumerics.com  Mon Sep 12 16:47:55 2016
From: chrisneal at snumerics.com (Christopher Neal)
Date: Mon, 12 Sep 2016 16:47:55 -0400
Subject: [Paraview] Catalyst osMesa rendering time
In-Reply-To: <CAMaOp+FBNkGwGfwHd6JmW_BXAeatiLD52Hs1g_Lm90OBDTRoCg@mail.gmail.com>
References: <BE7FEBAD-3DD0-4516-B69A-7568050FB2A3@snumerics.com>
 <CAMaOp+HDga=x=TKmq6S+WDAE9AvrCwx61P3c1Pb+ERUuFX1NfA@mail.gmail.com>
 <DDC524AE-CAF3-4818-B3C1-D44ACC408204@snumerics.com>
 <CAMaOp+FBNkGwGfwHd6JmW_BXAeatiLD52Hs1g_Lm90OBDTRoCg@mail.gmail.com>
Message-ID: <4991EDE5-10A4-40C4-AFFC-36E59A0A5687@snumerics.com>

Hey Andy,

 

I should have also noted that I was using Mesa 9.2.2 for my build.? I found a blog post by Utkarsh where he talks about building ParaView with osMesa enabled (https://blog.kitware.com/messing-with-mesa-for-paraview-5-0vtk-7-0/ ) . It looks like he was using a newer version of Mesa, so I downloaded 12.0.2, and I will try again using that.

-Chris

 

From: Andy Bauer <andy.bauer at kitware.com>
Date: Monday, September 12, 2016 at 3:20 PM
To: Christopher Neal <chrisneal at snumerics.com>
Cc: Benson Muite via ParaView <paraview at paraview.org>
Subject: Re: [Paraview] Catalyst osMesa rendering time

 

I think the missing item is that you need to set VTK_USE_OFFSCREEN to ON.

 

On Mon, Sep 12, 2016 at 3:00 PM, Christopher Neal <chrisneal at snumerics.com> wrote:

Thanks Andy,

The file is quite large, so I have attached it.

I tried to follow the process that is explained at(http://www.paraview.org/Wiki/ParaView/ParaView_And_Mesa_3D) so I made a shell script that contains all of the arguments passed to cmake. It is shown below.

 

 

#!/bin/bash

 

cmake \

  -DCMAKE_SOURCE_DIR:PATH=/home/neal/software/ParaView_osMesa/Source \

  -DCMAKE_INSTALL_PREFIX:PATH=/home/neal/software/ParaView_osMesa/build \

  -DCMAKE_BUILD_TYPE:STRING=Release \

  -DCMAKE_SKIP_INSTALL_RPATH:BOOL=YES \

  -DBUILD_TESTING:BOOL=OFF \

  -DPARAVIEW_BUILD_QT_GUI:BOOL=OFF \

  -DVTK_RENDERING_BACKEND=OpenGL2 \

  -DPARAVIEW_USE_MPI:BOOL=ON \

  -DPARAVIEW_ENABLE_PYTHON:BOOL=ON \

  -DPARAVIEW_INSTALL_DEVELOPMENT_FILES:BOOL=ON \

  -DPARAVIEW_BUILD_CATALYST_ADAPTERS:BOOL=ON \

  -DPARAVIEW_BUILD_PLUGIN_AnalyzeNIfTIIO:BOOL=FALSE \

  -DPARAVIEW_BUILD_PLUGIN_ArrowGlyph:BOOL=FALSE \

  -DPARAVIEW_BUILD_PLUGIN_CDIReader:BOOL=FALSE \

  -DPARAVIEW_BUILD_PLUGIN_EyeDomeLighting:BOOL=FALSE \

  -DPARAVIEW_BUILD_PLUGIN_GMVReader:BOOL=FALSE \

 -DPARAVIEW_BUILD_PLUGIN_GeodesicMeasurement:BOOL=FALSE \

  -DPARAVIEW_BUILD_PLUGIN_H5PartReader:BOOL=FALSE \

  -DPARAVIEW_BUILD_PLUGIN_InSituExodus:BOOL=FALSE \

  -DPARAVIEW_BUILD_PLUGIN_MantaView:BOOL=FALSE \

  -DPARAVIEW_BUILD_PLUGIN_Moments:BOOL=FALSE \

  -DPARAVIEW_BUILD_PLUGIN_NonOrthogonalSource:BOOL=FALSE \

  -DPARAVIEW_BUILD_PLUGIN_PacMan:BOOL=FALSE \

  -DPARAVIEW_BUILD_PLUGIN_PointSprite:BOOL=FALSE \

  -DPARAVIEW_BUILD_PLUGIN_RGBZView:BOOL=FALSE \

  -DPARAVIEW_BUILD_PLUGIN_SLACTools:BOOL=FALSE \

 -DPARAVIEW_BUILD_PLUGIN_SciberQuestToolKit:BOOL=FALSE \

  -DPARAVIEW_BUILD_PLUGIN_SierraPlotTools:BOOL=FALSE \

  -DPARAVIEW_BUILD_PLUGIN_StreamingParticles:BOOL=FALSE \

  -DPARAVIEW_BUILD_PLUGIN_SurfaceLIC:BOOL=FALSE \

  -DPARAVIEW_BUILD_PLUGIN_UncertaintyRendering:BOOL=FALSE \

  -DPARAVIEW_BUILD_PLUGIN_AcceleratedAlgorithms:BOOL=OFF \

  -DVTK_USE_CXX11_FEATURES:BOOL=ON \

  -DVTK_USE_X:BOOL=OFF \

  -DOPENGL_INCLUDE_DIR:PATH=/home/neal/software/Mesa/build/include \

  -DOPENGL_gl_LIBRARY:PATH=/home/neal/software/Mesa/build/lib64/libOSMesa.so \

  -DOPENGL_glu_LIBRARY:PATH=/home/neal/software/Mesa/build/lib64/libGLU.so \

  -DVTK_OPENGL_HAS_OSMESA:BOOL=ON \

  -DOSMESA_INCLUDE_DIR:PATH=/home/neal/software/Mesa/build/include \

  -DOSMESA_LIBRARY:PATH=/home/neal/software/Mesa/build/lib64/libOSMesa.so  /home/neal/software/ParaView_osMesa/Source

 

make -j20

#make -j20 install

 

 


-Chris

 

From: Andy Bauer <andy.bauer at kitware.com>
Date: Monday, September 12, 2016 at 2:39 PM
To: Christopher Neal <chrisneal at snumerics.com>
Cc: Benson Muite via ParaView <paraview at paraview.org>
Subject: Re: [Paraview] Catalyst osMesa rendering time

 

Hi Chris,

It sounds like you didn't properly build ParaView with offscreen rendering. Can  you share your CMakeCache.txt from your build? I'm guessing VTK_USE_X, VTK_USE_OFFSCREEN or some other thing didn't get set properly.

Andy

 

On Mon, Sep 12, 2016 at 1:36 PM, Christopher Neal <chrisneal at snumerics.com> wrote:

Hi all,

 

I have compiled a version of ParaView with osMesa enabled. The version is 5.1.2 for ParaView. I?m running the CxxFullExample Catalyst example that is located in ParaView/Examples/Catalyst.

Operating system info

lsb_release ?a: 
LSB Version:         n/a

Distributor ID:     openSUSE project

Description:         openSUSE 13.2 (Harlequin) (x86_64)

Release:                13.2

Codename:           Harlequin



I have added 1 additional script to the Catalyst example by using the ?CoProcessing? button in ParaView to generate a Catalyst script that just exports a .png of an isometric view of the geometry. When I run the example, the operating system seems to freeze up completely in my login session i.e. windows can not be clicked, nothing at all can be done with the exception of moving the mouse around on the screen. It stays frozen like this for about 2 minutes before a window pops up that says ?Paraview(batch)?. In the window is the isometric view and the window updates to show the geometry at every timestep that the example outputs an image at. The Catalyst script does seem to execute fine and outputs image files for each frame that I requested, but it is soooo slow for some reason.

Is this the expected behavior of running Catalyst with an osMesa build? I thought that ?os? stood for ?off-screen?, which I interpreted as there being no screen display component to the rendering. Have I done something wrong with compiling ParaView with osMesa? Is Catalyst supposed to completely lock up the session until a window pops up?  

I would love to hear from other users of Catalyst to hear about the experiences of running Catalyst.


Thank you,

Chris Neal


_______________________________________________
Powered by www.kitware.com

Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html

Please keep messages on-topic and check the ParaView Wiki at: http://paraview.org/Wiki/ParaView

Search the list archives at: http://markmail.org/search/?q=ParaView

Follow this link to subscribe/unsubscribe:
http://public.kitware.com/mailman/listinfo/paraview

 

 

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From stephane at fujielectric.com  Tue Sep 13 04:29:07 2016
From: stephane at fujielectric.com (=?UTF-8?B?c3RlcGhhbmXjg7Pjg4njg7PjgrAg44Oh44OV44Kh44ON?=)
Date: Tue, 13 Sep 2016 17:29:07 +0900
Subject: [Paraview] PCL plugin and ParaviewTango PLugin
Message-ID: <CADLMsL7h4Q8VckLzr+qKAz+qzxQYAyFArVgit9wWQxgRh_cbBA@mail.gmail.com>

Hello,

I would like to know if one or both of the plugins mentioned in the message
subject can be used in win7/Paraview 5.1.2.
If yes, are there pre-built available?
If no, any plan to resurrect those plugins???

Thanks

Ndong-Mefane Stephane, Dr.Eng
Basic Design Sec.
Steam Turbine Dept.
Kawasaki Factory

Fuji Electric Co., Ltd
1-1, Tanabeshinden, Kawasaki-ku,
Kawasaki-city 210-9530, Japan
Phone: +81-44-329-2155
Fax: +81-44-329-2394
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From chrisneal at snumerics.com  Tue Sep 13 11:35:12 2016
From: chrisneal at snumerics.com (Christopher Neal)
Date: Tue, 13 Sep 2016 11:35:12 -0400
Subject: [Paraview] Catalyst osMesa rendering time
In-Reply-To: <4991EDE5-10A4-40C4-AFFC-36E59A0A5687@snumerics.com>
References: <BE7FEBAD-3DD0-4516-B69A-7568050FB2A3@snumerics.com>
 <CAMaOp+HDga=x=TKmq6S+WDAE9AvrCwx61P3c1Pb+ERUuFX1NfA@mail.gmail.com>
 <DDC524AE-CAF3-4818-B3C1-D44ACC408204@snumerics.com>
 <CAMaOp+FBNkGwGfwHd6JmW_BXAeatiLD52Hs1g_Lm90OBDTRoCg@mail.gmail.com>
 <4991EDE5-10A4-40C4-AFFC-36E59A0A5687@snumerics.com>
Message-ID: <192F3735-4D5A-4734-81F5-7FBB25A925A7@snumerics.com>

Hi Andy,

 

It appears that the changes to the cmake configuration file haven?t been able to prevent the opening of a window onscreen, nor has changing the Mesa version to 12.0.2 done anything to change the runtime behavior. I want to back up and make sure I?m not doing something wrong when running Catalyst. Do I need to change any steps in my process of running a code that has been instrumented to use Catalyst? i.e. Do I need to add any additional arguments or change the catalyst python scripts in any way to tell it ?to use offscreen rendering?

Thank you,

Chris

 

 

From: ParaView <paraview-bounces at paraview.org> on behalf of Christopher Neal <chrisneal at snumerics.com>
Date: Monday, September 12, 2016 at 4:47 PM
To: Andy Bauer <andy.bauer at kitware.com>
Cc: Benson Muite via ParaView <paraview at paraview.org>
Subject: Re: [Paraview] Catalyst osMesa rendering time

 

Hey Andy,

 

I should have also noted that I was using Mesa 9.2.2 for my build.  I found a blog post by Utkarsh where he talks about building ParaView with osMesa enabled (https://blog.kitware.com/messing-with-mesa-for-paraview-5-0vtk-7-0/ ) . It looks like he was using a newer version of Mesa, so I downloaded 12.0.2, and I will try again using that.

-Chris

 

From: Andy Bauer <andy.bauer at kitware.com>
Date: Monday, September 12, 2016 at 3:20 PM
To: Christopher Neal <chrisneal at snumerics.com>
Cc: Benson Muite via ParaView <paraview at paraview.org>
Subject: Re: [Paraview] Catalyst osMesa rendering time

 

I think the missing item is that you need to set VTK_USE_OFFSCREEN to ON.

 

On Mon, Sep 12, 2016 at 3:00 PM, Christopher Neal <chrisneal at snumerics.com> wrote:

Thanks Andy,

The file is quite large, so I have attached it.

I tried to follow the process that is explained at(http://www.paraview.org/Wiki/ParaView/ParaView_And_Mesa_3D) so I made a shell script that contains all of the arguments passed to cmake. It is shown below.

 

 

#!/bin/bash

 

cmake \

  -DCMAKE_SOURCE_DIR:PATH=/home/neal/software/ParaView_osMesa/Source \

  -DCMAKE_INSTALL_PREFIX:PATH=/home/neal/software/ParaView_osMesa/build \

  -DCMAKE_BUILD_TYPE:STRING=Release \

  -DCMAKE_SKIP_INSTALL_RPATH:BOOL=YES \

  -DBUILD_TESTING:BOOL=OFF \

  -DPARAVIEW_BUILD_QT_GUI:BOOL=OFF \

  -DVTK_RENDERING_BACKEND=OpenGL2 \

  -DPARAVIEW_USE_MPI:BOOL=ON \

  -DPARAVIEW_ENABLE_PYTHON:BOOL=ON \

  -DPARAVIEW_INSTALL_DEVELOPMENT_FILES:BOOL=ON \

  -DPARAVIEW_BUILD_CATALYST_ADAPTERS:BOOL=ON \

  -DPARAVIEW_BUILD_PLUGIN_AnalyzeNIfTIIO:BOOL=FALSE \

  -DPARAVIEW_BUILD_PLUGIN_ArrowGlyph:BOOL=FALSE \

  -DPARAVIEW_BUILD_PLUGIN_CDIReader:BOOL=FALSE \

  -DPARAVIEW_BUILD_PLUGIN_EyeDomeLighting:BOOL=FALSE \

  -DPARAVIEW_BUILD_PLUGIN_GMVReader:BOOL=FALSE \

 -DPARAVIEW_BUILD_PLUGIN_GeodesicMeasurement:BOOL=FALSE \

  -DPARAVIEW_BUILD_PLUGIN_H5PartReader:BOOL=FALSE \

  -DPARAVIEW_BUILD_PLUGIN_InSituExodus:BOOL=FALSE \

  -DPARAVIEW_BUILD_PLUGIN_MantaView:BOOL=FALSE \

  -DPARAVIEW_BUILD_PLUGIN_Moments:BOOL=FALSE \

  -DPARAVIEW_BUILD_PLUGIN_NonOrthogonalSource:BOOL=FALSE \

  -DPARAVIEW_BUILD_PLUGIN_PacMan:BOOL=FALSE \

  -DPARAVIEW_BUILD_PLUGIN_PointSprite:BOOL=FALSE \

  -DPARAVIEW_BUILD_PLUGIN_RGBZView:BOOL=FALSE \

  -DPARAVIEW_BUILD_PLUGIN_SLACTools:BOOL=FALSE \

 -DPARAVIEW_BUILD_PLUGIN_SciberQuestToolKit:BOOL=FALSE \

  -DPARAVIEW_BUILD_PLUGIN_SierraPlotTools:BOOL=FALSE \

  -DPARAVIEW_BUILD_PLUGIN_StreamingParticles:BOOL=FALSE \

  -DPARAVIEW_BUILD_PLUGIN_SurfaceLIC:BOOL=FALSE \

  -DPARAVIEW_BUILD_PLUGIN_UncertaintyRendering:BOOL=FALSE \

  -DPARAVIEW_BUILD_PLUGIN_AcceleratedAlgorithms:BOOL=OFF \

  -DVTK_USE_CXX11_FEATURES:BOOL=ON \

  -DVTK_USE_X:BOOL=OFF \

  -DOPENGL_INCLUDE_DIR:PATH=/home/neal/software/Mesa/build/include \

  -DOPENGL_gl_LIBRARY:PATH=/home/neal/software/Mesa/build/lib64/libOSMesa.so \

  -DOPENGL_glu_LIBRARY:PATH=/home/neal/software/Mesa/build/lib64/libGLU.so \

  -DVTK_OPENGL_HAS_OSMESA:BOOL=ON \

  -DOSMESA_INCLUDE_DIR:PATH=/home/neal/software/Mesa/build/include \

  -DOSMESA_LIBRARY:PATH=/home/neal/software/Mesa/build/lib64/libOSMesa.so  /home/neal/software/ParaView_osMesa/Source

 

make -j20

#make -j20 install

 

 


-Chris

 

From: Andy Bauer <andy.bauer at kitware.com>
Date: Monday, September 12, 2016 at 2:39 PM
To: Christopher Neal <chrisneal at snumerics.com>
Cc: Benson Muite via ParaView <paraview at paraview.org>
Subject: Re: [Paraview] Catalyst osMesa rendering time

 

Hi Chris,

It sounds like you didn't properly build ParaView with offscreen rendering. Can  you share your CMakeCache.txt from your build? I'm guessing VTK_USE_X, VTK_USE_OFFSCREEN or some other thing didn't get set properly.

Andy

 

On Mon, Sep 12, 2016 at 1:36 PM, Christopher Neal <chrisneal at snumerics.com> wrote:

Hi all,

 

I have compiled a version of ParaView with osMesa enabled. The version is 5.1.2 for ParaView. I?m running the CxxFullExample Catalyst example that is located in ParaView/Examples/Catalyst.

Operating system info

lsb_release ?a: 
LSB Version:         n/a

Distributor ID:     openSUSE project

Description:         openSUSE 13.2 (Harlequin) (x86_64)

Release:                13.2

Codename:           Harlequin



I have added 1 additional script to the Catalyst example by using the ?CoProcessing? button in ParaView to generate a Catalyst script that just exports a .png of an isometric view of the geometry. When I run the example, the operating system seems to freeze up completely in my login session i.e. windows can not be clicked, nothing at all can be done with the exception of moving the mouse around on the screen. It stays frozen like this for about 2 minutes before a window pops up that says ?Paraview(batch)?. In the window is the isometric view and the window updates to show the geometry at every timestep that the example outputs an image at. The Catalyst script does seem to execute fine and outputs image files for each frame that I requested, but it is soooo slow for some reason.

Is this the expected behavior of running Catalyst with an osMesa build? I thought that ?os? stood for ?off-screen?, which I interpreted as there being no screen display component to the rendering. Have I done something wrong with compiling ParaView with osMesa? Is Catalyst supposed to completely lock up the session until a window pops up?  

I would love to hear from other users of Catalyst to hear about the experiences of running Catalyst.


Thank you,

Chris Neal


_______________________________________________
Powered by www.kitware.com

Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html

Please keep messages on-topic and check the ParaView Wiki at: http://paraview.org/Wiki/ParaView

Search the list archives at: http://markmail.org/search/?q=ParaView

Follow this link to subscribe/unsubscribe:
http://public.kitware.com/mailman/listinfo/paraview

 

 

_______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Please keep messages on-topic and check the ParaView Wiki at: http://paraview.org/Wiki/ParaView Search the list archives at: http://markmail.org/search/?q=ParaView Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/paraview 

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From stephen.wornom at inria.fr  Wed Sep 14 07:11:54 2016
From: stephen.wornom at inria.fr (Stephen Wornom)
Date: Wed, 14 Sep 2016 13:11:54 +0200 (CEST)
Subject: [Paraview] PV 4.10 how to locate x, y,
	z for negative pressure at a point
In-Reply-To: <622981634.661823.1473851351668.JavaMail.zimbra@inria.fr>
Message-ID: <1543783073.662734.1473851514798.JavaMail.zimbra@inria.fr>

PV information shows a negative pressure, how can I locate the coordinates where the negative pressure occurs? 
I hope my question is clear. 
Thanks, 
Stephen 
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From mathieu.westphal at kitware.com  Wed Sep 14 08:26:56 2016
From: mathieu.westphal at kitware.com (Mathieu Westphal)
Date: Wed, 14 Sep 2016 14:26:56 +0200
Subject: [Paraview] PV 4.10 how to locate x, y,
 z for negative pressure at a point
In-Reply-To: <1543783073.662734.1473851514798.JavaMail.zimbra@inria.fr>
References: <622981634.661823.1473851351668.JavaMail.zimbra@inria.fr>
 <1543783073.662734.1473851514798.JavaMail.zimbra@inria.fr>
Message-ID: <CAC2t4USxDX11T4VrbGssVyvORkLfyoAqZQvX0UfiY+YgDM5dnw@mail.gmail.com>

Hello
With
Edit->FindData

you will be able to write a simple query to find the cells or points where
this happens.

Regards,



Mathieu Westphal

On Wed, Sep 14, 2016 at 1:11 PM, Stephen Wornom <stephen.wornom at inria.fr>
wrote:

> PV information shows a negative pressure, how can I locate the coordinates
> where the negative pressure occurs?
> I hope my question is clear.
> Thanks,
> Stephen
>
> _______________________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at http://www.kitware.com/
> opensource/opensource.html
>
> Please keep messages on-topic and check the ParaView Wiki at:
> http://paraview.org/Wiki/ParaView
>
> Search the list archives at: http://markmail.org/search/?q=ParaView
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/paraview
>
>
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From chrisneal at snumerics.com  Wed Sep 14 12:44:56 2016
From: chrisneal at snumerics.com (Christopher Neal)
Date: Wed, 14 Sep 2016 12:44:56 -0400
Subject: [Paraview] Building Paraview with OSMESA
Message-ID: <6FF58A1E-71E6-409F-A365-8456DD4D03EE@snumerics.com>

Hi All,

 

I?ve been trying to compile a version of ParaView that uses osMesa. I?ve tried to follow the process that is explained on the wiki (http://www.paraview.org/Wiki/ParaView/ParaView_And_Mesa_3D ), but I haven?t been able to get ParaView to render offscreen. I don?t have build errors, but when I run something that saves a screenshot I still see a window pop up on my screen. Would anyone be willing to share their configuration script/command that they use for compiling ParaView with osMESA?? 

Also ? If I have a python script that creates a screenshot of some geometry, do I need to edit it in any way before running it with a version of ParaView that uses osMesa? Or is all of that handled behind the scenes?


Thank you,

Chris N

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From richard.c.angelini.civ at mail.mil  Wed Sep 14 13:24:56 2016
From: richard.c.angelini.civ at mail.mil (Angelini, Richard C (Rick) CIV USARMY RDECOM ARL (US))
Date: Wed, 14 Sep 2016 17:24:56 +0000
Subject: [Paraview] [Non-DoD Source]  Building Paraview with OSMESA
In-Reply-To: <6FF58A1E-71E6-409F-A365-8456DD4D03EE@snumerics.com>
References: <6FF58A1E-71E6-409F-A365-8456DD4D03EE@snumerics.com>
Message-ID: <D3FEFF9C.2D5F0%Richard.C.Angelini.CIV@mail.mil>

Stupid question ? when you start up the pvserver process, are you passing it
the ??use-offscreen-rendering? flag?

mpirun ?np 8 pvserver ?use-offscreen-rendering ??.

What?s your build platform?  I have lots and lots of build scripts I can
share!   

________________________________
Rick Angelini
USArmy Research Laboratory
CISD/HPC Architectures Team
Phone:  410-278-6266

From:  ParaView <paraview-bounces at paraview.org> on behalf of Christopher
Neal <chrisneal at snumerics.com>
Date:  Wednesday, September 14, 2016 at 12:44 PM
To:  Benson Muite via ParaView <paraview at paraview.org>
Subject:  [Non-DoD Source] [Paraview] Building Paraview with OSMESA

All active links contained in this email were disabled. Please verify the
identity of the sender, and confirm the authenticity of all links contained
within the message prior to copying and pasting the address to a Web
browser. 




Hi All,
 
I?ve been trying to compile a version of ParaView that uses osMesa. I?ve
tried to follow the process that is explained on the wiki
(Caution-http://www.paraview.org/Wiki/ParaView/ParaView_And_Mesa_3D <
Caution-http://www.paraview.org/Wiki/ParaView/ParaView_And_Mesa_3D >  ), but
I haven?t been able to get ParaView to render offscreen. I don?t have build
errors, but when I run something that saves a screenshot I still see a
window pop up on my screen. Would anyone be willing to share their
configuration script/command that they use for compiling ParaView with
osMESA?  

Also ? If I have a python script that creates a screenshot of some geometry,
do I need to edit it in any way before running it with a version of ParaView
that uses osMesa? Or is all of that handled behind the scenes?


Thank you,
Chris N


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From chrisneal at snumerics.com  Wed Sep 14 13:44:27 2016
From: chrisneal at snumerics.com (Christopher Neal)
Date: Wed, 14 Sep 2016 13:44:27 -0400
Subject: [Paraview] [Non-DoD Source]  Building Paraview with OSMESA
In-Reply-To: <D3FEFF9C.2D5F0%Richard.C.Angelini.CIV@mail.mil>
References: <6FF58A1E-71E6-409F-A365-8456DD4D03EE@snumerics.com>
 <D3FEFF9C.2D5F0%Richard.C.Angelini.CIV@mail.mil>
Message-ID: <4E32C24E-0A43-4DDB-86BE-2007B2475729@snumerics.com>

Thanks Rick!

I?m running OpenSuse 13.2 64bit. I?m not explicitly starting a pvserver, because I?m running one of the C++ Catalyst examples, which is located at ParaView/Examples/Catalyst/CxxFullExample. That is mainly what is confusing me. I?m not sure if I built ParaView with osMesa incorrectly, or if that Catalyst example is somehow just telling ParaView ?Hey, don?t use the offscreen rendering stuff, just go ahead and keep rendering to the screen.?

I?m thinking that I should be able to test the offscreen rendering capability independently of that Catalyst example by generating a Python trace of a pipeline that creates an image output, and the running it with a command like:
pvserver ?use-offscreen-rendering TestScript.py

 

From: "Angelini, Richard C (Rick) CIV USARMY RDECOM ARL (US)" <richard.c.angelini.civ at mail.mil>
Date: Wednesday, September 14, 2016 at 1:24 PM
To: Christopher Neal <chrisneal at snumerics.com>, Benson Muite via ParaView <paraview at paraview.org>
Subject: Re: [Non-DoD Source] [Paraview] Building Paraview with OSMESA

 

Stupid question ? when you start up the pvserver process, are you passing it the ??use-offscreen-rendering? flag?    

 

mpirun ?np 8 pvserver ?use-offscreen-rendering ??.

 

What?s your build platform?  I have lots and lots of build scripts I can share!   

 

________________________________

Rick Angelini

USArmy Research Laboratory

CISD/HPC Architectures Team

Phone:  410-278-6266

 

From: ParaView <paraview-bounces at paraview.org> on behalf of Christopher Neal <chrisneal at snumerics.com>
Date: Wednesday, September 14, 2016 at 12:44 PM
To: Benson Muite via ParaView <paraview at paraview.org>
Subject: [Non-DoD Source] [Paraview] Building Paraview with OSMESA

 

All active links contained in this email were disabled. Please verify the identity of the sender, and confirm the authenticity of all links contained within the message prior to copying and pasting the address to a Web browser. 

 

Hi All,

 

I?ve been trying to compile a version of ParaView that uses osMesa. I?ve tried to follow the process that is explained on the wiki (Caution-http://www.paraview.org/Wiki/ParaView/ParaView_And_Mesa_3D < Caution-http://www.paraview.org/Wiki/ParaView/ParaView_And_Mesa_3D >  ), but I haven?t been able to get ParaView to render offscreen. I don?t have build errors, but when I run something that saves a screenshot I still see a window pop up on my screen. Would anyone be willing to share their configuration script/command that they use for compiling ParaView with osMESA?  

Also ? If I have a python script that creates a screenshot of some geometry, do I need to edit it in any way before running it with a version of ParaView that uses osMesa? Or is all of that handled behind the scenes?


Thank you,

Chris N

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From richard.c.angelini.civ at mail.mil  Wed Sep 14 14:28:02 2016
From: richard.c.angelini.civ at mail.mil (Angelini, Richard C (Rick) CIV USARMY RDECOM ARL (US))
Date: Wed, 14 Sep 2016 18:28:02 +0000
Subject: [Paraview] [Non-DoD Source]  Building Paraview with OSMESA
In-Reply-To: <4E32C24E-0A43-4DDB-86BE-2007B2475729@snumerics.com>
References: <6FF58A1E-71E6-409F-A365-8456DD4D03EE@snumerics.com>
 <D3FEFF9C.2D5F0%Richard.C.Angelini.CIV@mail.mil>
 <4E32C24E-0A43-4DDB-86BE-2007B2475729@snumerics.com>
Message-ID: <D3FF0DE5.2D5FF%Richard.C.Angelini.CIV@mail.mil>

Chris - Yeah, so I?m also not sure how Catalyst might be firing this up.
Here?s an example OS_Mesa/cmake command used on one of our generic RHEL6
systems.   With this build, we throw the ??use-offscreen-rendering? flag
when we fire up the pvserver.    I think that the critical flags are
?osmesa=ON, mesa=OFF, qt=OFF? ?..   Can you use your current build in a
traditional client-server configuration to verify that the OS_Mesa is built
correctly?      That might make it easier to narrow down to a build issue or
a Catalyst issue.   Just a thought.




cmake 
-DCMAKE_INSTALL_PREFIX:PATH=${HOME}/pv/${paraview_version}${build_extension}
\
-Ddownload_location=`pwd`/../Downloads \
-DParaView_FROM_GIT=OFF \
-DParaView_URL=`pwd`/../Downloads/ParaView-v${paraview_version}-source.tar.g
z \
-DCMAKE_BUILD_TYPE=Release \
-DENABLE_boost=ON \
-DBoost_NO_BOOST_CMAKE:BOOL=ON \
-DENABLE_visitbridge:BOOL=ON \
-DENABLE_cgns=ON \
-DENABLE_ffmpeg=ON \
-DENABLE_hdf5=ON \
-DENABLE_matplotlib=ON \
-DENABLE_osmesa=ON \
-DENABLE_mesa=OFF \
-DPARAVIEW_RENDERING_BACKEND:STRING=OpenGL2 \
-DENABLE_mpi=ON \
-DUSE_SYSTEM_mpi=ON \
-DENABLE_numpy=ON \
-DENABLE_paraview=ON \
-DENABLE_python=ON \
-DENABLE_qt=OFF \
-DENABLE_silo=ON \
-DENABLE_szip=ON \
-Dqt_DISABLE_WEBKIT=ON \
-DMPI_CXX_LIBRARIES:STRING="-L${MPI_HOME}/lib -lmpi_cxx -ldl" \
-DMPI_C_LIBRARIES:STRING="-L${MPI_HOME}/lib -lmpi -ldl" \
-DMPI_LIBRARY:FILEPATH="-L${MPI_HOME}/lib -lmpi_cxx -ldl" \
../Source
________________________________
Rick Angelini
USArmy Research Laboratory
CISD/HPC Architectures Team
Phone:  410-278-6266

From:  Christopher Neal <chrisneal at snumerics.com> on behalf of Christopher
Neal <chrisneal at snumerics.com>
Date:  Wednesday, September 14, 2016 at 1:44 PM
To:  Rick Angelini <Richard.C.Angelini.CIV at mail.mil>, Benson Muite via
ParaView <paraview at paraview.org>
Subject:  Re: [Non-DoD Source] [Paraview] Building Paraview with OSMESA

All active links contained in this email were disabled. Please verify the
identity of the sender, and confirm the authenticity of all links contained
within the message prior to copying and pasting the address to a Web
browser. 




Thanks Rick!

I?m running OpenSuse 13.2 64bit. I?m not explicitly starting a pvserver,
because I?m running one of the C++ Catalyst examples, which is located at
ParaView/Examples/Catalyst/CxxFullExample. That is mainly what is confusing
me. I?m not sure if I built ParaView with osMesa incorrectly, or if that
Catalyst example is somehow just telling ParaView ?Hey, don?t use the
offscreen rendering stuff, just go ahead and keep rendering to the screen.?

I?m thinking that I should be able to test the offscreen rendering
capability independently of that Catalyst example by generating a Python
trace of a pipeline that creates an image output, and the running it with a
command like:
pvserver ?use-offscreen-rendering TestScript.py
 

From: "Angelini, Richard C (Rick) CIV USARMY RDECOM ARL (US)"
<richard.c.angelini.civ at mail.mil>
Date: Wednesday, September 14, 2016 at 1:24 PM
To: Christopher Neal <chrisneal at snumerics.com>, Benson Muite via ParaView
<paraview at paraview.org>
Subject: Re: [Non-DoD Source] [Paraview] Building Paraview with OSMESA

 

Stupid question ? when you start up the pvserver process, are you passing it
the ??use-offscreen-rendering? flag?

 

mpirun ?np 8 pvserver ?use-offscreen-rendering ??.

 

What?s your build platform?  I have lots and lots of build scripts I can
share!   

 

________________________________

Rick Angelini

USArmy Research Laboratory

CISD/HPC Architectures Team

Phone:  410-278-6266

 

From: ParaView <paraview-bounces at paraview.org <
Caution-mailto:paraview-bounces at paraview.org > > on behalf of Christopher
Neal <chrisneal at snumerics.com < Caution-mailto:chrisneal at snumerics.com > >
Date: Wednesday, September 14, 2016 at 12:44 PM
To: Benson Muite via ParaView <paraview at paraview.org <
Caution-mailto:paraview at paraview.org > >
Subject: [Non-DoD Source] [Paraview] Building Paraview with OSMESA

 

All active links contained in this email were disabled. Please verify the
identity of the sender, and confirm the authenticity of all links contained
within the message prior to copying and pasting the address to a Web
browser. 


 
Hi All,
 
I?ve been trying to compile a version of ParaView that uses osMesa. I?ve
tried to follow the process that is explained on the wiki
(Caution-Caution-http://www.paraview.org/Wiki/ParaView/ParaView_And_Mesa_3D
< Caution-http://www.paraview.org/Wiki/ParaView/ParaView_And_Mesa_3D >  <
Caution-Caution-http://www.paraview.org/Wiki/ParaView/ParaView_And_Mesa_3D <
Caution-http://www.paraview.org/Wiki/ParaView/ParaView_And_Mesa_3D >  >  ),
but I haven?t been able to get ParaView to render offscreen. I don?t have
build errors, but when I run something that saves a screenshot I still see a
window pop up on my screen. Would anyone be willing to share their
configuration script/command that they use for compiling ParaView with
osMESA?  

Also ? If I have a python script that creates a screenshot of some geometry,
do I need to edit it in any way before running it with a version of ParaView
that uses osMesa? Or is all of that handled behind the scenes?


Thank you,
Chris N


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From andy.bauer at kitware.com  Wed Sep 14 14:53:28 2016
From: andy.bauer at kitware.com (Andy Bauer)
Date: Wed, 14 Sep 2016 14:53:28 -0400
Subject: [Paraview] [Non-DoD Source] Building Paraview with OSMESA
In-Reply-To: <D3FF0DE5.2D5FF%Richard.C.Angelini.CIV@mail.mil>
References: <6FF58A1E-71E6-409F-A365-8456DD4D03EE@snumerics.com>
 <D3FEFF9C.2D5F0%Richard.C.Angelini.CIV@mail.mil>
 <4E32C24E-0A43-4DDB-86BE-2007B2475729@snumerics.com>
 <D3FF0DE5.2D5FF%Richard.C.Angelini.CIV@mail.mil>
Message-ID: <CAMaOp+ExmHL+NHEJT+orNiOGnFkHp+PHgeEftkqMEP969JCasw@mail.gmail.com>

Hi Rick,

This CMake script is for the superbuild, correct?

That's definitely the way to go for OS Mesa as it builds the proper version
of OS Mesa for you. The superbuild stuff is at
https://gitlab.kitware.com/paraview/paraview-superbuild.

Chris, if you have an NVIDIA card with a fairly new driver what I would
recommend is using NVIDIA's EGL drivers. There's more information on that
at
https://blog.kitware.com/off-screen-rendering-through-the-native-platform-interface-egl/
.

Best,
andy

On Wed, Sep 14, 2016 at 2:28 PM, Angelini, Richard C (Rick) CIV USARMY
RDECOM ARL (US) <richard.c.angelini.civ at mail.mil> wrote:

> Chris - Yeah, so I?m also not sure how Catalyst might be firing this up.
> Here?s an example OS_Mesa/cmake command used on one of our generic RHEL6
> systems.   With this build, we throw the ??use-offscreen-rendering? flag
> when we fire up the pvserver.    I think that the critical flags are
> ?osmesa=ON, mesa=OFF, qt=OFF? ?..   Can you use your current build in a
> traditional client-server configuration to verify that the OS_Mesa is built
> correctly?      That might make it easier to narrow down to a build issue
> or a Catalyst issue.   Just a thought.
>
>
>
>
> cmake -DCMAKE_INSTALL_PREFIX:PATH=${HOME}/pv/${paraview_version}${build_extension}
> \
> -Ddownload_location=`pwd`/../Downloads \
> -DParaView_FROM_GIT=OFF \
> -DParaView_URL=`pwd`/../Downloads/ParaView-v${
> paraview_version}-source.tar.gz \
> -DCMAKE_BUILD_TYPE=Release \
> -DENABLE_boost=ON \
> -DBoost_NO_BOOST_CMAKE:BOOL=ON \
> -DENABLE_visitbridge:BOOL=ON \
> -DENABLE_cgns=ON \
> -DENABLE_ffmpeg=ON \
> -DENABLE_hdf5=ON \
> -DENABLE_matplotlib=ON \
> -DENABLE_osmesa=ON \
> -DENABLE_mesa=OFF \
> -DPARAVIEW_RENDERING_BACKEND:STRING=OpenGL2 \
> -DENABLE_mpi=ON \
> -DUSE_SYSTEM_mpi=ON \
> -DENABLE_numpy=ON \
> -DENABLE_paraview=ON \
> -DENABLE_python=ON \
> -DENABLE_qt=OFF \
> -DENABLE_silo=ON \
> -DENABLE_szip=ON \
> -Dqt_DISABLE_WEBKIT=ON \
> -DMPI_CXX_LIBRARIES:STRING="-L${MPI_HOME}/lib -lmpi_cxx -ldl" \
> -DMPI_C_LIBRARIES:STRING="-L${MPI_HOME}/lib -lmpi -ldl" \
> -DMPI_LIBRARY:FILEPATH="-L${MPI_HOME}/lib -lmpi_cxx -ldl" \
> ../Source
> ________________________________
> Rick Angelini
> USArmy Research Laboratory
> CISD/HPC Architectures Team
> Phone:  410-278-6266
>
> From: Christopher Neal <chrisneal at snumerics.com> on behalf of Christopher
> Neal <chrisneal at snumerics.com>
> Date: Wednesday, September 14, 2016 at 1:44 PM
> To: Rick Angelini <Richard.C.Angelini.CIV at mail.mil>, Benson Muite via
> ParaView <paraview at paraview.org>
> Subject: Re: [Non-DoD Source] [Paraview] Building Paraview with OSMESA
>
> All active links contained in this email were disabled. Please verify the
> identity of the sender, and confirm the authenticity of all links contained
> within the message prior to copying and pasting the address to a Web
> browser.
>
> ------------------------------
>
>
> Thanks Rick!
>
> I?m running OpenSuse 13.2 64bit. I?m not explicitly starting a pvserver,
> because I?m running one of the C++ Catalyst examples, which is located at
> ParaView/Examples/Catalyst/CxxFullExample. That is mainly what is
> confusing me. I?m not sure if I built ParaView with osMesa incorrectly, or
> if that Catalyst example is somehow just telling ParaView ?Hey, don?t use
> the offscreen rendering stuff, just go ahead and keep rendering to the
> screen.?
>
> I?m thinking that I should be able to test the offscreen rendering
> capability independently of that Catalyst example by generating a Python
> trace of a pipeline that creates an image output, and the running it with a
> command like:
> pvserver ?use-offscreen-rendering TestScript.py
>
>
>
> *From: *"Angelini, Richard C (Rick) CIV USARMY RDECOM ARL (US)" <
> richard.c.angelini.civ at mail.mil>
> *Date: *Wednesday, September 14, 2016 at 1:24 PM
> *To: *Christopher Neal <chrisneal at snumerics.com>, Benson Muite via
> ParaView <paraview at paraview.org>
> *Subject: *Re: [Non-DoD Source] [Paraview] Building Paraview with OSMESA
>
>
>
> Stupid question ? when you start up the pvserver process, are you passing
> it the ??use-offscreen-rendering? flag?
>
>
>
> mpirun ?np 8 pvserver ?use-offscreen-rendering ??.
>
>
>
> What?s your build platform?  I have lots and lots of build scripts I can
> share!
>
>
>
> ________________________________
>
> Rick Angelini
>
> USArmy Research Laboratory
>
> CISD/HPC Architectures Team
>
> Phone:  410-278-6266
>
>
>
> *From: *ParaView <paraview-bounces at paraview.org < Caution-mailto:paraview-
> bounces at paraview.org <paraview-bounces at paraview.org> > > on behalf of
> Christopher Neal <chrisneal at snumerics.com < Caution-mailto:chrisneal@
> snumerics.com <chrisneal at snumerics.com> > >
> *Date: *Wednesday, September 14, 2016 at 12:44 PM
> *To: *Benson Muite via ParaView <paraview at paraview.org < Caution-
> mailto:paraview at paraview.org <paraview at paraview.org> > >
> *Subject: *[Non-DoD Source] [Paraview] Building Paraview with OSMESA
>
>
>
> All active links contained in this email were disabled. Please verify the
> identity of the sender, and confirm the authenticity of all links contained
> within the message prior to copying and pasting the address to a Web
> browser.
> ------------------------------
>
>
>
> Hi All,
>
>
>
> I?ve been trying to compile a version of ParaView that uses osMesa. I?ve
> tried to follow the process that is explained on the wiki (Caution-Caution-
> http://www.paraview.org/Wiki/ParaView/ParaView_And_Mesa_3D < Caution-
> http://www.paraview.org/Wiki/ParaView/ParaView_And_Mesa_3D >  < Caution-
> Caution-http://www.paraview.org/Wiki/ParaView/ParaView_And_Mesa_3D
>  < Caution-http://www.paraview.org/Wiki/ParaView/ParaView_And_Mesa_3D >  >
> ), but I haven?t been able to get ParaView to render offscreen. I don?t
> have build errors, but when I run something that saves a screenshot I still
> see a window pop up on my screen. Would anyone be willing to share their
> configuration script/command that they use for compiling ParaView with
> osMESA?
>
> Also ? If I have a python script that creates a screenshot of some
> geometry, do I need to edit it in any way before running it with a version
> of ParaView that uses osMesa? Or is all of that handled behind the scenes?
>
>
> Thank you,
>
> Chris N
>
> _______________________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at http://www.kitware.com/
> opensource/opensource.html
>
> Please keep messages on-topic and check the ParaView Wiki at:
> http://paraview.org/Wiki/ParaView
>
> Search the list archives at: http://markmail.org/search/?q=ParaView
>
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>
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From chrisneal at snumerics.com  Wed Sep 14 15:13:24 2016
From: chrisneal at snumerics.com (Christopher Neal)
Date: Wed, 14 Sep 2016 15:13:24 -0400
Subject: [Paraview] [Non-DoD Source] Building Paraview with OSMESA
In-Reply-To: <CAMaOp+ExmHL+NHEJT+orNiOGnFkHp+PHgeEftkqMEP969JCasw@mail.gmail.com>
References: <6FF58A1E-71E6-409F-A365-8456DD4D03EE@snumerics.com>
 <D3FEFF9C.2D5F0%Richard.C.Angelini.CIV@mail.mil>
 <4E32C24E-0A43-4DDB-86BE-2007B2475729@snumerics.com>
 <D3FF0DE5.2D5FF%Richard.C.Angelini.CIV@mail.mil>
 <CAMaOp+ExmHL+NHEJT+orNiOGnFkHp+PHgeEftkqMEP969JCasw@mail.gmail.com>
Message-ID: <FA3B5DB1-EEE2-4C4F-B49D-C196EBB90D2D@snumerics.com>

Thanks Andy,

 

I?m set on trying to get a build that doesn?t use a graphics card, because the nodes on Nasa?s Plieades cluster don?t have GPUs, so running a code with Catalyst would not work on that machine.

I?ll give the superbuild a shot with Rick?s configuration script.

Thanks,

Chris N

 

From: Andy Bauer <andy.bauer at kitware.com>
Date: Wednesday, September 14, 2016 at 2:53 PM
To: "Angelini, Richard C (Rick) CIV USARMY RDECOM ARL (US)" <richard.c.angelini.civ at mail.mil>
Cc: Christopher Neal <chrisneal at snumerics.com>, Benson Muite via ParaView <paraview at paraview.org>
Subject: Re: [Paraview] [Non-DoD Source] Building Paraview with OSMESA

 

Hi Rick,

This CMake script is for the superbuild, correct?

That's definitely the way to go for OS Mesa as it builds the proper version of OS Mesa for you. The superbuild stuff is at https://gitlab.kitware.com/paraview/paraview-superbuild.

Chris, if you have an NVIDIA card with a fairly new driver what I would recommend is using NVIDIA's EGL drivers. There's more information on that at https://blog.kitware.com/off-screen-rendering-through-the-native-platform-interface-egl/.

Best,

andy

 

On Wed, Sep 14, 2016 at 2:28 PM, Angelini, Richard C (Rick) CIV USARMY RDECOM ARL (US) <richard.c.angelini.civ at mail.mil> wrote:

Chris - Yeah, so I?m also not sure how Catalyst might be firing this up.   Here?s an example OS_Mesa/cmake command used on one of our generic RHEL6 systems.   With this build, we throw the ??use-offscreen-rendering? flag when we fire up the pvserver.    I think that the critical flags are ?osmesa=ON, mesa=OFF, qt=OFF? ?..   Can you use your current build in a traditional client-server configuration to verify that the OS_Mesa is built correctly?      That might make it easier to narrow down to a build issue or a Catalyst issue.   Just a thought.

 

 

 

 

cmake -DCMAKE_INSTALL_PREFIX:PATH=${HOME}/pv/${paraview_version}${build_extension} \

-Ddownload_location=`pwd`/../Downloads \

-DParaView_FROM_GIT=OFF \

-DParaView_URL=`pwd`/../Downloads/ParaView-v${paraview_version}-source.tar.gz \

-DCMAKE_BUILD_TYPE=Release \

-DENABLE_boost=ON \

-DBoost_NO_BOOST_CMAKE:BOOL=ON \

-DENABLE_visitbridge:BOOL=ON \

-DENABLE_cgns=ON \

-DENABLE_ffmpeg=ON \

-DENABLE_hdf5=ON \

-DENABLE_matplotlib=ON \

-DENABLE_osmesa=ON \

-DENABLE_mesa=OFF \

-DPARAVIEW_RENDERING_BACKEND:STRING=OpenGL2 \

-DENABLE_mpi=ON \

-DUSE_SYSTEM_mpi=ON \

-DENABLE_numpy=ON \

-DENABLE_paraview=ON \

-DENABLE_python=ON \

-DENABLE_qt=OFF \

-DENABLE_silo=ON \

-DENABLE_szip=ON \

-Dqt_DISABLE_WEBKIT=ON \

-DMPI_CXX_LIBRARIES:STRING="-L${MPI_HOME}/lib -lmpi_cxx -ldl" \

-DMPI_C_LIBRARIES:STRING="-L${MPI_HOME}/lib -lmpi -ldl" \

-DMPI_LIBRARY:FILEPATH="-L${MPI_HOME}/lib -lmpi_cxx -ldl" \

../Source

________________________________

Rick Angelini

USArmy Research Laboratory

CISD/HPC Architectures Team

Phone:  410-278-6266

 

From: Christopher Neal <chrisneal at snumerics.com> on behalf of Christopher Neal <chrisneal at snumerics.com>
Date: Wednesday, September 14, 2016 at 1:44 PM
To: Rick Angelini <Richard.C.Angelini.CIV at mail.mil>, Benson Muite via ParaView <paraview at paraview.org>
Subject: Re: [Non-DoD Source] [Paraview] Building Paraview with OSMESA

 

All active links contained in this email were disabled. Please verify the identity of the sender, and confirm the authenticity of all links contained within the message prior to copying and pasting the address to a Web browser. 

 

Thanks Rick!

I?m running OpenSuse 13.2 64bit. I?m not explicitly starting a pvserver, because I?m running one of the C++ Catalyst examples, which is located at ParaView/Examples/Catalyst/CxxFullExample. That is mainly what is confusing me. I?m not sure if I built ParaView with osMesa incorrectly, or if that Catalyst example is somehow just telling ParaView ?Hey, don?t use the offscreen rendering stuff, just go ahead and keep rendering to the screen.?

I?m thinking that I should be able to test the offscreen rendering capability independently of that Catalyst example by generating a Python trace of a pipeline that creates an image output, and the running it with a command like:
pvserver ?use-offscreen-rendering TestScript.py

 

From: "Angelini, Richard C (Rick) CIV USARMY RDECOM ARL (US)" <richard.c.angelini.civ at mail.mil>
Date: Wednesday, September 14, 2016 at 1:24 PM
To: Christopher Neal <chrisneal at snumerics.com>, Benson Muite via ParaView <paraview at paraview.org>
Subject: Re: [Non-DoD Source] [Paraview] Building Paraview with OSMESA

 

Stupid question ? when you start up the pvserver process, are you passing it the ??use-offscreen-rendering? flag?    

 

mpirun ?np 8 pvserver ?use-offscreen-rendering ??.

 

What?s your build platform?  I have lots and lots of build scripts I can share!   

 

________________________________

Rick Angelini

USArmy Research Laboratory

CISD/HPC Architectures Team

Phone:  410-278-6266

 

From: ParaView <paraview-bounces at paraview.org < Caution-mailto:paraview-bounces at paraview.org > > on behalf of Christopher Neal <chrisneal at snumerics.com < Caution-mailto:chrisneal at snumerics.com > >
Date: Wednesday, September 14, 2016 at 12:44 PM
To: Benson Muite via ParaView <paraview at paraview.org < Caution-mailto:paraview at paraview.org > >
Subject: [Non-DoD Source] [Paraview] Building Paraview with OSMESA

 

All active links contained in this email were disabled. Please verify the identity of the sender, and confirm the authenticity of all links contained within the message prior to copying and pasting the address to a Web browser. 

 

Hi All,

 

I?ve been trying to compile a version of ParaView that uses osMesa. I?ve tried to follow the process that is explained on the wiki (Caution-Caution-http://www.paraview.org/Wiki/ParaView/ParaView_And_Mesa_3D < Caution-http://www.paraview.org/Wiki/ParaView/ParaView_And_Mesa_3D >  < Caution-Caution-http://www.paraview.org/Wiki/ParaView/ParaView_And_Mesa_3D < Caution-http://www.paraview.org/Wiki/ParaView/ParaView_And_Mesa_3D >  >  ), but I haven?t been able to get ParaView to render offscreen. I don?t have build errors, but when I run something that saves a screenshot I still see a window pop up on my screen. Would anyone be willing to share their configuration script/command that they use for compiling ParaView with osMESA?  

Also ? If I have a python script that creates a screenshot of some geometry, do I need to edit it in any way before running it with a version of ParaView that uses osMesa? Or is all of that handled behind the scenes?


Thank you,

Chris N


_______________________________________________
Powered by www.kitware.com

Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html

Please keep messages on-topic and check the ParaView Wiki at: http://paraview.org/Wiki/ParaView

Search the list archives at: http://markmail.org/search/?q=ParaView

Follow this link to subscribe/unsubscribe:
http://public.kitware.com/mailman/listinfo/paraview

 

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From dennis_conklin at goodyear.com  Wed Sep 14 15:46:16 2016
From: dennis_conklin at goodyear.com (Dennis Conklin)
Date: Wed, 14 Sep 2016 19:46:16 +0000
Subject: [Paraview] Anyone know of a reader for SAT (Saved As Text) files,
 which are Spatial (ACIS) geometry format
Message-ID: <CY1PR07MB250629B0507FAD199984D0D39FF10@CY1PR07MB2506.namprd07.prod.outlook.com>

This format:

http://paulbourke.net/dataformats/sat/sat.pdf
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From chrisneal at snumerics.com  Wed Sep 14 16:11:21 2016
From: chrisneal at snumerics.com (Christopher Neal)
Date: Wed, 14 Sep 2016 16:11:21 -0400
Subject: [Paraview] [Non-DoD Source]  Building Paraview with OSMESA
In-Reply-To: <D3FF0DE5.2D5FF%Richard.C.Angelini.CIV@mail.mil>
References: <6FF58A1E-71E6-409F-A365-8456DD4D03EE@snumerics.com>
 <D3FEFF9C.2D5F0%Richard.C.Angelini.CIV@mail.mil>
 <4E32C24E-0A43-4DDB-86BE-2007B2475729@snumerics.com>
 <D3FF0DE5.2D5FF%Richard.C.Angelini.CIV@mail.mil>
Message-ID: <11773A37-3F2C-44A3-B9E8-7ACCF6DB080E@snumerics.com>

Rick - ?I?ve never compiled the Superbuild version of ParaView before. I?m following that Wiki page for the Superbuild.? I have a directory with the following structure:

build??? Downloads??? ParaViewSuperbuild

I downloaded the 5.1.0 version of the Superbuild from the Gitlab website, and I put the .tar.gz file into the ?Downloads? folder.? I independently cloned the Superbuild from Github for version 5.1.0 into the ?ParaViewSuperbuild? directory. From the ?build? directory I will execute the configuration command that you provided.? I just want to be sure what ?/Source? means in your configuration script. Where does that point to exactly?? Should I point it to ?../ParaViewSuperbuild??


Thank you,

Chris Neal

 

 

From: "Angelini, Richard C (Rick) CIV USARMY RDECOM ARL (US)" <richard.c.angelini.civ at mail.mil>
Date: Wednesday, September 14, 2016 at 2:28 PM
To: Christopher Neal <chrisneal at snumerics.com>, Benson Muite via ParaView <paraview at paraview.org>
Subject: Re: [Non-DoD Source] [Paraview] Building Paraview with OSMESA

 

Chris - Yeah, so I?m also not sure how Catalyst might be firing this up.   Here?s an example OS_Mesa/cmake command used on one of our generic RHEL6 systems.   With this build, we throw the ??use-offscreen-rendering? flag when we fire up the pvserver.    I think that the critical flags are ?osmesa=ON, mesa=OFF, qt=OFF? ?..   Can you use your current build in a traditional client-server configuration to verify that the OS_Mesa is built correctly?      That might make it easier to narrow down to a build issue or a Catalyst issue.   Just a thought.

 

 

 

 

cmake -DCMAKE_INSTALL_PREFIX:PATH=${HOME}/pv/${paraview_version}${build_extension} \

-Ddownload_location=`pwd`/../Downloads \

-DParaView_FROM_GIT=OFF \

-DParaView_URL=`pwd`/../Downloads/ParaView-v${paraview_version}-source.tar.gz \

-DCMAKE_BUILD_TYPE=Release \

-DENABLE_boost=ON \

-DBoost_NO_BOOST_CMAKE:BOOL=ON \

-DENABLE_visitbridge:BOOL=ON \

-DENABLE_cgns=ON \

-DENABLE_ffmpeg=ON \

-DENABLE_hdf5=ON \

-DENABLE_matplotlib=ON \

-DENABLE_osmesa=ON \

-DENABLE_mesa=OFF \

-DPARAVIEW_RENDERING_BACKEND:STRING=OpenGL2 \

-DENABLE_mpi=ON \

-DUSE_SYSTEM_mpi=ON \

-DENABLE_numpy=ON \

-DENABLE_paraview=ON \

-DENABLE_python=ON \

-DENABLE_qt=OFF \

-DENABLE_silo=ON \

-DENABLE_szip=ON \

-Dqt_DISABLE_WEBKIT=ON \

-DMPI_CXX_LIBRARIES:STRING="-L${MPI_HOME}/lib -lmpi_cxx -ldl" \

-DMPI_C_LIBRARIES:STRING="-L${MPI_HOME}/lib -lmpi -ldl" \

-DMPI_LIBRARY:FILEPATH="-L${MPI_HOME}/lib -lmpi_cxx -ldl" \

../Source

________________________________

Rick Angelini

USArmy Research Laboratory

CISD/HPC Architectures Team

Phone:  410-278-6266

 

From: Christopher Neal <chrisneal at snumerics.com> on behalf of Christopher Neal <chrisneal at snumerics.com>
Date: Wednesday, September 14, 2016 at 1:44 PM
To: Rick Angelini <Richard.C.Angelini.CIV at mail.mil>, Benson Muite via ParaView <paraview at paraview.org>
Subject: Re: [Non-DoD Source] [Paraview] Building Paraview with OSMESA

 

All active links contained in this email were disabled. Please verify the identity of the sender, and confirm the authenticity of all links contained within the message prior to copying and pasting the address to a Web browser. 

 

Thanks Rick!

I?m running OpenSuse 13.2 64bit. I?m not explicitly starting a pvserver, because I?m running one of the C++ Catalyst examples, which is located at ParaView/Examples/Catalyst/CxxFullExample. That is mainly what is confusing me. I?m not sure if I built ParaView with osMesa incorrectly, or if that Catalyst example is somehow just telling ParaView ?Hey, don?t use the offscreen rendering stuff, just go ahead and keep rendering to the screen.?

I?m thinking that I should be able to test the offscreen rendering capability independently of that Catalyst example by generating a Python trace of a pipeline that creates an image output, and the running it with a command like:
pvserver ?use-offscreen-rendering TestScript.py

 

From: "Angelini, Richard C (Rick) CIV USARMY RDECOM ARL (US)" <richard.c.angelini.civ at mail.mil>
Date: Wednesday, September 14, 2016 at 1:24 PM
To: Christopher Neal <chrisneal at snumerics.com>, Benson Muite via ParaView <paraview at paraview.org>
Subject: Re: [Non-DoD Source] [Paraview] Building Paraview with OSMESA

 

Stupid question ? when you start up the pvserver process, are you passing it the ??use-offscreen-rendering? flag?    

 

mpirun ?np 8 pvserver ?use-offscreen-rendering ??.

 

What?s your build platform?  I have lots and lots of build scripts I can share!   

 

________________________________

Rick Angelini

USArmy Research Laboratory

CISD/HPC Architectures Team

Phone:  410-278-6266

 

From: ParaView <paraview-bounces at paraview.org < Caution-mailto:paraview-bounces at paraview.org > > on behalf of Christopher Neal <chrisneal at snumerics.com < Caution-mailto:chrisneal at snumerics.com > >
Date: Wednesday, September 14, 2016 at 12:44 PM
To: Benson Muite via ParaView <paraview at paraview.org < Caution-mailto:paraview at paraview.org > >
Subject: [Non-DoD Source] [Paraview] Building Paraview with OSMESA

 

All active links contained in this email were disabled. Please verify the identity of the sender, and confirm the authenticity of all links contained within the message prior to copying and pasting the address to a Web browser. 

 

Hi All,

 

I?ve been trying to compile a version of ParaView that uses osMesa. I?ve tried to follow the process that is explained on the wiki (Caution-Caution-http://www.paraview.org/Wiki/ParaView/ParaView_And_Mesa_3D < Caution-http://www.paraview.org/Wiki/ParaView/ParaView_And_Mesa_3D >  < Caution-Caution-http://www.paraview.org/Wiki/ParaView/ParaView_And_Mesa_3D < Caution-http://www.paraview.org/Wiki/ParaView/ParaView_And_Mesa_3D >  >  ), but I haven?t been able to get ParaView to render offscreen. I don?t have build errors, but when I run something that saves a screenshot I still see a window pop up on my screen. Would anyone be willing to share their configuration script/command that they use for compiling ParaView with osMESA?  

Also ? If I have a python script that creates a screenshot of some geometry, do I need to edit it in any way before running it with a version of ParaView that uses osMesa? Or is all of that handled behind the scenes?


Thank you,

Chris N

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From postgurke at web.de  Thu Sep 15 03:44:04 2016
From: postgurke at web.de (postgurke at web.de)
Date: Thu, 15 Sep 2016 09:44:04 +0200 (CEST)
Subject: [Paraview] Lock Data Range for multiple attributes
In-Reply-To: <166776580.5718.1473407569425.JavaMail.open-xchange@app08.ox.hosteurope.de>
References: <166776580.5718.1473407569425.JavaMail.open-xchange@app08.ox.hosteurope.de>
Message-ID: <1122471505.23385.1473925444617.JavaMail.open-xchange@app05.ox.hosteurope.de>

Hello

Does nobody have a solution for this, or am I missing something obvious? 
The only thing I can do to fix the color ranges is separate the file into
multiple objects, but as one can only look at one at a time anyways (as they are
at the same location, obviously) and our model already contains a lot of
objects, this is rather bothersome...

Cheers
Venke



> postgurke at web.de hat am 9. September 2016 um 09:52 geschrieben:
> 
> 
> Hello All
> 
> Sorry to bother you again... I seem to miss something wanting to fix color
> scale
> ranges for objects with multiple attributes. 
> For example: I have a vtk-Plane with associated velocity and density values
> that
> I can choose for coloring. When I imported the object, I set
> LUT.RescaleTransferFunction(min, max) and LUT.LockDataRange = 1 for both
> attributes (with different min,max, of course). In the GUI everything looks
> fine
> at first, but when I switch the coloring from one attribute to another,
> ParaView
> seems to ignore the checked "Lock Data Range" but switches to some Min/Max
> found
> in the data. Maybe I misunderstand the functionality of "Lock Data Range"? Is
> this the expected behaviour? If yes, what could I do to really fix the min,max
> to my own specification? (I also tried to use a preset color scale with my
> desired min,max, but this does not change the behaviour either.) 
> 
> Thanks for your support and any ideas on this,
> Venke
> _______________________________________________
> Powered by www.kitware.com
> 
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
> 
> Please keep messages on-topic and check the ParaView Wiki at:
> http://paraview.org/Wiki/ParaView
> 
> Search the list archives at: http://markmail.org/search/?q=ParaView
> 
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/paraview

From mathieu.westphal at kitware.com  Thu Sep 15 04:46:41 2016
From: mathieu.westphal at kitware.com (Mathieu Westphal)
Date: Thu, 15 Sep 2016 10:46:41 +0200
Subject: [Paraview] Lock Data Range for multiple attributes
In-Reply-To: <1122471505.23385.1473925444617.JavaMail.open-xchange@app05.ox.hosteurope.de>
References: <166776580.5718.1473407569425.JavaMail.open-xchange@app08.ox.hosteurope.de>
 <1122471505.23385.1473925444617.JavaMail.open-xchange@app05.ox.hosteurope.de>
Message-ID: <CAC2t4UTb6tRxnDWWgV2VrV8A6k_RR6fO5o9tWs+MRbHojbhY+A@mail.gmail.com>

Hello

There is an easy work around for this. Do not use the lock range feature,
but add lookup table point on the data value you want to lock.
See attached pvsm, locked data are RTData and Results.




Mathieu Westphal

On Thu, Sep 15, 2016 at 9:44 AM, <postgurke at web.de> wrote:

> Hello
>
> Does nobody have a solution for this, or am I missing something obvious?
> The only thing I can do to fix the color ranges is separate the file into
> multiple objects, but as one can only look at one at a time anyways (as
> they are
> at the same location, obviously) and our model already contains a lot of
> objects, this is rather bothersome...
>
> Cheers
> Venke
>
>
>
> > postgurke at web.de hat am 9. September 2016 um 09:52 geschrieben:
> >
> >
> > Hello All
> >
> > Sorry to bother you again... I seem to miss something wanting to fix
> color
> > scale
> > ranges for objects with multiple attributes.
> > For example: I have a vtk-Plane with associated velocity and density
> values
> > that
> > I can choose for coloring. When I imported the object, I set
> > LUT.RescaleTransferFunction(min, max) and LUT.LockDataRange = 1 for both
> > attributes (with different min,max, of course). In the GUI everything
> looks
> > fine
> > at first, but when I switch the coloring from one attribute to another,
> > ParaView
> > seems to ignore the checked "Lock Data Range" but switches to some
> Min/Max
> > found
> > in the data. Maybe I misunderstand the functionality of "Lock Data
> Range"? Is
> > this the expected behaviour? If yes, what could I do to really fix the
> min,max
> > to my own specification? (I also tried to use a preset color scale with
> my
> > desired min,max, but this does not change the behaviour either.)
> >
> > Thanks for your support and any ideas on this,
> > Venke
> > _______________________________________________
> > Powered by www.kitware.com
> >
> > Visit other Kitware open-source projects at
> > http://www.kitware.com/opensource/opensource.html
> >
> > Please keep messages on-topic and check the ParaView Wiki at:
> > http://paraview.org/Wiki/ParaView
> >
> > Search the list archives at: http://markmail.org/search/?q=ParaView
> >
> > Follow this link to subscribe/unsubscribe:
> > http://public.kitware.com/mailman/listinfo/paraview
> _______________________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at http://www.kitware.com/
> opensource/opensource.html
>
> Please keep messages on-topic and check the ParaView Wiki at:
> http://paraview.org/Wiki/ParaView
>
> Search the list archives at: http://markmail.org/search/?q=ParaView
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/paraview
>
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From postgurke at web.de  Thu Sep 15 05:30:14 2016
From: postgurke at web.de (postgurke at web.de)
Date: Thu, 15 Sep 2016 11:30:14 +0200 (CEST)
Subject: [Paraview] Lock Data Range for multiple attributes
In-Reply-To: <CAC2t4UTb6tRxnDWWgV2VrV8A6k_RR6fO5o9tWs+MRbHojbhY+A@mail.gmail.com>
References: <166776580.5718.1473407569425.JavaMail.open-xchange@app08.ox.hosteurope.de>
 <1122471505.23385.1473925444617.JavaMail.open-xchange@app05.ox.hosteurope.de>
 <CAC2t4UTb6tRxnDWWgV2VrV8A6k_RR6fO5o9tWs+MRbHojbhY+A@mail.gmail.com>
Message-ID: <370580332.24090.1473931814940.JavaMail.open-xchange@app05.ox.hosteurope.de>

Hello Mathieu

Thank you for your answer. Unfortunately I don't quite understand :(. I tried to
duplicate the first and last point of LUT.RGBPoints (which are initially correct
before I look at a different attribute and switch back) - but this does not do
the trick. Sorry, I am not used to reading from State-Files. Do you have a short
explanation what you did in either the Paraview python shell or GUI to achieve
this?

Cheers
Venke

 

> Mathieu Westphal <mathieu.westphal at kitware.com> hat am 15. September 2016 um
> 10:46 geschrieben:
> 
> 
> Hello
> 
> There is an easy work around for this. Do not use the lock range feature,
> but add lookup table point on the data value you want to lock.
> See attached pvsm, locked data are RTData and Results.
> 
> 
> 
> 
> Mathieu Westphal
> 
> On Thu, Sep 15, 2016 at 9:44 AM, <postgurke at web.de> wrote:
> 
> > Hello
> >
> > Does nobody have a solution for this, or am I missing something obvious?
> > The only thing I can do to fix the color ranges is separate the file into
> > multiple objects, but as one can only look at one at a time anyways (as
> > they are
> > at the same location, obviously) and our model already contains a lot of
> > objects, this is rather bothersome...
> >
> > Cheers
> > Venke
> >
> >
> >
> > > postgurke at web.de hat am 9. September 2016 um 09:52 geschrieben:
> > >
> > >
> > > Hello All
> > >
> > > Sorry to bother you again... I seem to miss something wanting to fix
> > color
> > > scale
> > > ranges for objects with multiple attributes.
> > > For example: I have a vtk-Plane with associated velocity and density
> > values
> > > that
> > > I can choose for coloring. When I imported the object, I set
> > > LUT.RescaleTransferFunction(min, max) and LUT.LockDataRange = 1 for both
> > > attributes (with different min,max, of course). In the GUI everything
> > looks
> > > fine
> > > at first, but when I switch the coloring from one attribute to another,
> > > ParaView
> > > seems to ignore the checked "Lock Data Range" but switches to some
> > Min/Max
> > > found
> > > in the data. Maybe I misunderstand the functionality of "Lock Data
> > Range"? Is
> > > this the expected behaviour? If yes, what could I do to really fix the
> > min,max
> > > to my own specification? (I also tried to use a preset color scale with
> > my
> > > desired min,max, but this does not change the behaviour either.)
> > >
> > > Thanks for your support and any ideas on this,
> > > Venke
> > > _______________________________________________
> > > Powered by www.kitware.com
> > >
> > > Visit other Kitware open-source projects at
> > > http://www.kitware.com/opensource/opensource.html
> > >
> > > Please keep messages on-topic and check the ParaView Wiki at:
> > > http://paraview.org/Wiki/ParaView
> > >
> > > Search the list archives at: http://markmail.org/search/?q=ParaView
> > >
> > > Follow this link to subscribe/unsubscribe:
> > > http://public.kitware.com/mailman/listinfo/paraview
> > _______________________________________________
> > Powered by www.kitware.com
> >
> > Visit other Kitware open-source projects at http://www.kitware.com/
> > opensource/opensource.html
> >
> > Please keep messages on-topic and check the ParaView Wiki at:
> > http://paraview.org/Wiki/ParaView
> >
> > Search the list archives at: http://markmail.org/search/?q=ParaView
> >
> > Follow this link to subscribe/unsubscribe:
> > http://public.kitware.com/mailman/listinfo/paraview
> >

From mathieu.westphal at kitware.com  Thu Sep 15 06:03:39 2016
From: mathieu.westphal at kitware.com (Mathieu Westphal)
Date: Thu, 15 Sep 2016 12:03:39 +0200
Subject: [Paraview] Lock Data Range for multiple attributes
In-Reply-To: <370580332.24090.1473931814940.JavaMail.open-xchange@app05.ox.hosteurope.de>
References: <166776580.5718.1473407569425.JavaMail.open-xchange@app08.ox.hosteurope.de>
 <1122471505.23385.1473925444617.JavaMail.open-xchange@app05.ox.hosteurope.de>
 <CAC2t4UTb6tRxnDWWgV2VrV8A6k_RR6fO5o9tWs+MRbHojbhY+A@mail.gmail.com>
 <370580332.24090.1473931814940.JavaMail.open-xchange@app05.ox.hosteurope.de>
Message-ID: <CAC2t4UQOiKoHQQrHg6BvPJmXkn51rh3ZrYUoFuCaek1Cskgwnw@mail.gmail.com>

Hello Venke,

Sure, here is the process to set up the lookuptable correctly with the gui:
 - Open ParaView
 - Open your data
 - Color with the data you want to "lock"
 - Show the Color Map Editor ( Right Click on toolbar, Color Map Editor)
- Click on the cogwheel to show advanced options
- Click on the dot on the color line (below the graph) to remove all data
point except the minimum and maximum
- Click on the color line (below the graph) to add two datapoint
approximativally around the locked range you want to set
- Set the correct value for the data point you just added in the table
- Copy the RGB color of the minimum and maximum into your locked range

Done

A side effect is the scalar bar does not show the information you want, but
the color on the mesh are correct.
In Any case, the "Lock Data Range" option should work, but it doesn't, so
it looks like a bug to me.


Regards,


Mathieu Westphal

On Thu, Sep 15, 2016 at 11:30 AM, <postgurke at web.de> wrote:

> Hello Mathieu
>
> Thank you for your answer. Unfortunately I don't quite understand :(. I
> tried to
> duplicate the first and last point of LUT.RGBPoints (which are initially
> correct
> before I look at a different attribute and switch back) - but this does
> not do
> the trick. Sorry, I am not used to reading from State-Files. Do you have a
> short
> explanation what you did in either the Paraview python shell or GUI to
> achieve
> this?
>
> Cheers
> Venke
>
>
>
> > Mathieu Westphal <mathieu.westphal at kitware.com> hat am 15. September
> 2016 um
> > 10:46 geschrieben:
> >
> >
> > Hello
> >
> > There is an easy work around for this. Do not use the lock range feature,
> > but add lookup table point on the data value you want to lock.
> > See attached pvsm, locked data are RTData and Results.
> >
> >
> >
> >
> > Mathieu Westphal
> >
> > On Thu, Sep 15, 2016 at 9:44 AM, <postgurke at web.de> wrote:
> >
> > > Hello
> > >
> > > Does nobody have a solution for this, or am I missing something
> obvious?
> > > The only thing I can do to fix the color ranges is separate the file
> into
> > > multiple objects, but as one can only look at one at a time anyways (as
> > > they are
> > > at the same location, obviously) and our model already contains a lot
> of
> > > objects, this is rather bothersome...
> > >
> > > Cheers
> > > Venke
> > >
> > >
> > >
> > > > postgurke at web.de hat am 9. September 2016 um 09:52 geschrieben:
> > > >
> > > >
> > > > Hello All
> > > >
> > > > Sorry to bother you again... I seem to miss something wanting to fix
> > > color
> > > > scale
> > > > ranges for objects with multiple attributes.
> > > > For example: I have a vtk-Plane with associated velocity and density
> > > values
> > > > that
> > > > I can choose for coloring. When I imported the object, I set
> > > > LUT.RescaleTransferFunction(min, max) and LUT.LockDataRange = 1 for
> both
> > > > attributes (with different min,max, of course). In the GUI everything
> > > looks
> > > > fine
> > > > at first, but when I switch the coloring from one attribute to
> another,
> > > > ParaView
> > > > seems to ignore the checked "Lock Data Range" but switches to some
> > > Min/Max
> > > > found
> > > > in the data. Maybe I misunderstand the functionality of "Lock Data
> > > Range"? Is
> > > > this the expected behaviour? If yes, what could I do to really fix
> the
> > > min,max
> > > > to my own specification? (I also tried to use a preset color scale
> with
> > > my
> > > > desired min,max, but this does not change the behaviour either.)
> > > >
> > > > Thanks for your support and any ideas on this,
> > > > Venke
> > > > _______________________________________________
> > > > Powered by www.kitware.com
> > > >
> > > > Visit other Kitware open-source projects at
> > > > http://www.kitware.com/opensource/opensource.html
> > > >
> > > > Please keep messages on-topic and check the ParaView Wiki at:
> > > > http://paraview.org/Wiki/ParaView
> > > >
> > > > Search the list archives at: http://markmail.org/search/?q=ParaView
> > > >
> > > > Follow this link to subscribe/unsubscribe:
> > > > http://public.kitware.com/mailman/listinfo/paraview
> > > _______________________________________________
> > > Powered by www.kitware.com
> > >
> > > Visit other Kitware open-source projects at http://www.kitware.com/
> > > opensource/opensource.html
> > >
> > > Please keep messages on-topic and check the ParaView Wiki at:
> > > http://paraview.org/Wiki/ParaView
> > >
> > > Search the list archives at: http://markmail.org/search/?q=ParaView
> > >
> > > Follow this link to subscribe/unsubscribe:
> > > http://public.kitware.com/mailman/listinfo/paraview
> > >
>
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From postgurke at web.de  Thu Sep 15 06:41:19 2016
From: postgurke at web.de (postgurke at web.de)
Date: Thu, 15 Sep 2016 12:41:19 +0200 (CEST)
Subject: [Paraview] Lock Data Range for multiple attributes
In-Reply-To: <CAC2t4UQOiKoHQQrHg6BvPJmXkn51rh3ZrYUoFuCaek1Cskgwnw@mail.gmail.com>
References: <166776580.5718.1473407569425.JavaMail.open-xchange@app08.ox.hosteurope.de>
 <1122471505.23385.1473925444617.JavaMail.open-xchange@app05.ox.hosteurope.de>
 <CAC2t4UTb6tRxnDWWgV2VrV8A6k_RR6fO5o9tWs+MRbHojbhY+A@mail.gmail.com>
 <370580332.24090.1473931814940.JavaMail.open-xchange@app05.ox.hosteurope.de>
 <CAC2t4UQOiKoHQQrHg6BvPJmXkn51rh3ZrYUoFuCaek1Cskgwnw@mail.gmail.com>
Message-ID: <1726767132.24462.1473936079227.JavaMail.open-xchange@app05.ox.hosteurope.de>

Mathieu

Thank you so much! 
It seems that I can have other color values in between the min/max (so I don't
have to remove all the dots), but the scale must contain the min/max contained
in the attribute data as limits. I now understand what you meant in your
previous e-mail... 
Yes, the color bar is not optimal, but right now I care more for a consistent
coloring of all objects. 

Maybe the Lock Data Range function could be made to work in this scenario as
well in a future PV version. That would still be very helpful :).

Thanks again
Venke





> Mathieu Westphal <mathieu.westphal at kitware.com> hat am 15. September 2016 um
> 12:03 geschrieben:
> 
> 
> Hello Venke,
> 
> Sure, here is the process to set up the lookuptable correctly with the gui:
>  - Open ParaView
>  - Open your data
>  - Color with the data you want to "lock"
>  - Show the Color Map Editor ( Right Click on toolbar, Color Map Editor)
> - Click on the cogwheel to show advanced options
> - Click on the dot on the color line (below the graph) to remove all data
> point except the minimum and maximum
> - Click on the color line (below the graph) to add two datapoint
> approximativally around the locked range you want to set
> - Set the correct value for the data point you just added in the table
> - Copy the RGB color of the minimum and maximum into your locked range
> 
> Done
> 
> A side effect is the scalar bar does not show the information you want, but
> the color on the mesh are correct.
> In Any case, the "Lock Data Range" option should work, but it doesn't, so
> it looks like a bug to me.
> 
> 
> Regards,
> 
> 
> Mathieu Westphal
> 
> On Thu, Sep 15, 2016 at 11:30 AM, <postgurke at web.de> wrote:
> 
> > Hello Mathieu
> >
> > Thank you for your answer. Unfortunately I don't quite understand :(. I
> > tried to
> > duplicate the first and last point of LUT.RGBPoints (which are initially
> > correct
> > before I look at a different attribute and switch back) - but this does
> > not do
> > the trick. Sorry, I am not used to reading from State-Files. Do you have a
> > short
> > explanation what you did in either the Paraview python shell or GUI to
> > achieve
> > this?
> >
> > Cheers
> > Venke
> >
> >
> >
> > > Mathieu Westphal <mathieu.westphal at kitware.com> hat am 15. September
> > 2016 um
> > > 10:46 geschrieben:
> > >
> > >
> > > Hello
> > >
> > > There is an easy work around for this. Do not use the lock range feature,
> > > but add lookup table point on the data value you want to lock.
> > > See attached pvsm, locked data are RTData and Results.
> > >
> > >
> > >
> > >
> > > Mathieu Westphal
> > >
> > > On Thu, Sep 15, 2016 at 9:44 AM, <postgurke at web.de> wrote:
> > >
> > > > Hello
> > > >
> > > > Does nobody have a solution for this, or am I missing something
> > obvious?
> > > > The only thing I can do to fix the color ranges is separate the file
> > into
> > > > multiple objects, but as one can only look at one at a time anyways (as
> > > > they are
> > > > at the same location, obviously) and our model already contains a lot
> > of
> > > > objects, this is rather bothersome...
> > > >
> > > > Cheers
> > > > Venke
> > > >
> > > >
> > > >
> > > > > postgurke at web.de hat am 9. September 2016 um 09:52 geschrieben:
> > > > >
> > > > >
> > > > > Hello All
> > > > >
> > > > > Sorry to bother you again... I seem to miss something wanting to fix
> > > > color
> > > > > scale
> > > > > ranges for objects with multiple attributes.
> > > > > For example: I have a vtk-Plane with associated velocity and density
> > > > values
> > > > > that
> > > > > I can choose for coloring. When I imported the object, I set
> > > > > LUT.RescaleTransferFunction(min, max) and LUT.LockDataRange = 1 for
> > both
> > > > > attributes (with different min,max, of course). In the GUI everything
> > > > looks
> > > > > fine
> > > > > at first, but when I switch the coloring from one attribute to
> > another,
> > > > > ParaView
> > > > > seems to ignore the checked "Lock Data Range" but switches to some
> > > > Min/Max
> > > > > found
> > > > > in the data. Maybe I misunderstand the functionality of "Lock Data
> > > > Range"? Is
> > > > > this the expected behaviour? If yes, what could I do to really fix
> > the
> > > > min,max
> > > > > to my own specification? (I also tried to use a preset color scale
> > with
> > > > my
> > > > > desired min,max, but this does not change the behaviour either.)
> > > > >
> > > > > Thanks for your support and any ideas on this,
> > > > > Venke
> > > > > _______________________________________________
> > > > > Powered by www.kitware.com
> > > > >
> > > > > Visit other Kitware open-source projects at
> > > > > http://www.kitware.com/opensource/opensource.html
> > > > >
> > > > > Please keep messages on-topic and check the ParaView Wiki at:
> > > > > http://paraview.org/Wiki/ParaView
> > > > >
> > > > > Search the list archives at: http://markmail.org/search/?q=ParaView
> > > > >
> > > > > Follow this link to subscribe/unsubscribe:
> > > > > http://public.kitware.com/mailman/listinfo/paraview
> > > > _______________________________________________
> > > > Powered by www.kitware.com
> > > >
> > > > Visit other Kitware open-source projects at http://www.kitware.com/
> > > > opensource/opensource.html
> > > >
> > > > Please keep messages on-topic and check the ParaView Wiki at:
> > > > http://paraview.org/Wiki/ParaView
> > > >
> > > > Search the list archives at: http://markmail.org/search/?q=ParaView
> > > >
> > > > Follow this link to subscribe/unsubscribe:
> > > > http://public.kitware.com/mailman/listinfo/paraview
> > > >
> >

From andy.bauer at kitware.com  Thu Sep 15 13:01:29 2016
From: andy.bauer at kitware.com (Andy Bauer)
Date: Thu, 15 Sep 2016 13:01:29 -0400
Subject: [Paraview] FW:  Exporting Run Selection Query results to ASCI,
 Word or Excel
In-Reply-To: <86CBF863C3462B48B83B11B8C20E2CEB356164D7@NCOEXC10.NEC.LOCAL>
References: <86CBF863C3462B48B83B11B8C20E2CEB356164D7@NCOEXC10.NEC.LOCAL>
Message-ID: <CAMaOp+Gem3TuFfyQ4GggkspyUoHPdA=gbN1dZi6yA3peTi3W5Q@mail.gmail.com>

Hi Boris,

Please keep the conversations on the mailing list so that everyone can
participate.

As for your question, I don't know the answer.

Best,
Andy

On Mon, Sep 12, 2016 at 9:38 AM, Boris Jagrine <
bjagrine at national-electric-coil.com> wrote:

> Hello Andy,
>
> You solved one of my problems. Thanks a lot. Here is another one.
>
> Is it possible to convert to ASCI or other text file and record the Run
> Selection Query results or plotted curves?
>
> Your help will be appreciated.
>
> Boris
>
>
>
> *From:* Boris Jagrine
> *Sent:* Thursday, September 08, 2016 7:15 AM
> *To:* 'Andy Bauer'
> *Cc:* paraview at paraview.org
> *Subject:* RE: [Paraview] Opening two .vtu files simultaneously
>
>
>
> Hi Andy,
>
> Your answer is clear. I did what you suggested and it worked!
>
> Thanks!
>
> Boris
>
>
>
> *From:* Andy Bauer [mailto:andy.bauer at kitware.com]
> *Sent:* Wednesday, September 07, 2016 10:48 PM
> *To:* Boris Jagrine
> *Cc:* paraview at paraview.org
> *Subject:* Re: [Paraview] Opening two .vtu files simultaneously
>
>
>
> Hi Boris,
>
> ParaView actually forces the same color scale for all pseudo-colored
> objects in the render view, as long as the fields selected have the same
> name (and possibly type). So in short answer, yes what you want is possible
> and should be done automatically.
>
> In the upper right corner of the view window there are buttons to split
> the view either vertically or horizontally (choose Render View in this case
> in the list of views in the newly created view window). You can do this and
> then view the grid from each file in separate windows to help the
> comparison. Also, if you right click on one of these views it will come up
> with a "Link Camera..." button that you can click on. After doing this, you
> can click on the other view window which will do view point/camera
> manipulations like zoom, pan, rotate, etc. in both windows in sync so that
> you can look at the two separate input files similarly in the two separate
> windows.
>
> Let us know if my answer isn't clear or if you have other questions.
>
>
>
> Welcome to ParaView!
>
> Andy
>
>
>
> On Wed, Sep 7, 2016 at 10:08 PM, Boris Jagrine <
> bjagrine at national-electric-coil.com> wrote:
>
> I am new to Paraview and will appreciate an answer to the following
> question:
>
> Is it possible to open two separate .vtu files (linear elasticity) each
> with displacement analysis of a separate body so that the same color scale
> is used to display the displacements of the two bodies and make comparison
> obvious?
>
> Thank you.
>
> Boris
>
>
> DISCLAIMER: This e-mail and any attachments to it contain confidential and
> proprietary material of NEC/RPI, its affiliates or agents, and is solely
> for the use of the intended recipient. Any review, use, disclosure,
> distribution or copying of this transmittal is prohibited except by or on
> behalf of the intended recipient. If you have received this transmittal in
> error, please notify the sender and destroy this e-mail and any attachments
> and all copies, whether electronic or printed.   ??
>
>
> _______________________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at http://www.kitware.com/
> opensource/opensource.html
>
> Please keep messages on-topic and check the ParaView Wiki at:
> http://paraview.org/Wiki/ParaView
>
> Search the list archives at: http://markmail.org/search/?q=ParaView
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/paraview
>
>
>
> DISCLAIMER: This e-mail and any attachments to it contain confidential and
> proprietary material of NEC/RPI, its affiliates or agents, and is solely
> for the use of the intended recipient. Any review, use, disclosure,
> distribution or copying of this transmittal is prohibited except by or on
> behalf of the intended recipient. If you have received this transmittal in
> error, please notify the sender and destroy this e-mail and any attachments
> and all copies, whether electronic or printed.   ??
>
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From will.schroeder at kitware.com  Thu Sep 15 13:54:58 2016
From: will.schroeder at kitware.com (Will Schroeder)
Date: Thu, 15 Sep 2016 13:54:58 -0400
Subject: [Paraview] VTK Textbook and User's Guide now available for download
Message-ID: <CAEiDrtVi8dBP_5jNd6fs1kmyiS0VtzxJk0ZVSyzk89fpuvHouQ@mail.gmail.com>

Kitware is releasing the VTK Textbook and VTK User's Guide for PDF
download. Follow the links below to a landing page where you can buy a
printed version, or download a PDF.

Longer term, the plan is to convert these books to LaTeX (from Framemaker)
and place the content into an open repository. The first step is to mostly
duplicate what exists now; eventually we have the ambitious goal to
completely rewrite / recombine / rethink the books. For example, using
VTK.js (under development now) to offer web interaction with examples etc.
We can certainly use the talents of the community to take this challenge
on, so if you are interested please let me know.

The Visualization Toolkit An Object-Oriented Approach to 3D Graphics (4th
ed.)
http://www.vtk.org/vtk-textbook/
pdf: http://www.kitware.com/products/books/VTKTextbook.pdf

*The VTK User?s Guide*
http://www.vtk.org/vtk-users-guide/
pdf: http://www.kitware.com/products/books/VTKUsersGuide.pdf

Best, please let me know if there are issues or concerns.
W

-- 
William J. Schroeder, PhD
Kitware, Inc. - Building the World's Technical Computing Software
28 Corporate Drive
Clifton Park, NY 12065
will.schroeder at kitware.com
http://www.kitware.com
(518) 881-4902
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From nawijn at gmail.com  Thu Sep 15 14:58:04 2016
From: nawijn at gmail.com (Marco Nawijn)
Date: Thu, 15 Sep 2016 20:58:04 +0200
Subject: [Paraview] Anyone know of a reader for SAT (Saved As Text)
 files, which are Spatial (ACIS) geometry format
In-Reply-To: <CY1PR07MB250629B0507FAD199984D0D39FF10@CY1PR07MB2506.namprd07.prod.outlook.com>
References: <CY1PR07MB250629B0507FAD199984D0D39FF10@CY1PR07MB2506.namprd07.prod.outlook.com>
Message-ID: <CA+pnd0mVBnpCfjGww5m7gEA7SBMJpXECbQQnbBhQHr8A8iyGjw@mail.gmail.com>

Hi Dennis,

I doubt there will be a native Paraview/VTK reader voor SAT. If you want
a geometric representation of your CAD model in Paraview, for example
to create an overlay of your simulation data over the geometry, I think
your best bet is to create an STL file. I have had success with this when
overlaying finite element and digital image correlation data over a
CAD model in Paraview.

I am not aware of a free opensource CAD package that can read SAT.
FreeCAD (based on OpenCascade) cannot. OpenCascade does provide
a paid for extension that can read SAT files. Also, are you aware of
cadexchanger (http://cadexchanger.com)? Ofcourse the standard CAD
systems like SolidWorks, CATIA, SolidEdge etc. can do the conversion
too (you might need a separate license for this).

Marco
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From stephen.wornom at inria.fr  Fri Sep 16 10:02:55 2016
From: stephen.wornom at inria.fr (Stephen Wornom)
Date: Fri, 16 Sep 2016 16:02:55 +0200 (CEST)
Subject: [Paraview] PV 4.10 how to locate x, y,
 z for negative pressure at a point
In-Reply-To: <CAC2t4USxDX11T4VrbGssVyvORkLfyoAqZQvX0UfiY+YgDM5dnw@mail.gmail.com>
References: <622981634.661823.1473851351668.JavaMail.zimbra@inria.fr>
 <1543783073.662734.1473851514798.JavaMail.zimbra@inria.fr>
 <CAC2t4USxDX11T4VrbGssVyvORkLfyoAqZQvX0UfiY+YgDM5dnw@mail.gmail.com>
Message-ID: <1741096731.1558011.1474034575638.JavaMail.zimbra@inria.fr>

Thanks Mattieu, 
iformation shows my data range for pressure 
-1106.5 15.3889 
PV does not give the id or cell number 
run query selection is blank so I put 
-1106.5get no hits 
Need I enter pressure some where? 
Thanks, 
Stephen 

----- Original Message -----

> From: "Mathieu Westphal" <mathieu.westphal at kitware.com>
> To: "Stephen Wornom" <stephen.wornom at inria.fr>
> Cc: "ParaView list" <paraview at paraview.org>, "Emmanuelle"
> <emmanuelle.itam at univ-montp2.fr>
> Sent: Wednesday, September 14, 2016 2:26:56 PM
> Subject: Re: [Paraview] PV 4.10 how to locate x, y, z for negative pressure
> at a point

> Hello
> With
> Edit->FindData

> you will be able to write a simple query to find the cells or points where
> this happens.

> Regards,

> Mathieu Westphal

> On Wed, Sep 14, 2016 at 1:11 PM, Stephen Wornom < stephen.wornom at inria.fr >
> wrote:

> > PV information shows a negative pressure, how can I locate the coordinates
> > where the negative pressure occurs?
> 
> > I hope my question is clear.
> 
> > Thanks,
> 
> > Stephen
> 

> > _______________________________________________
> 
> > Powered by www.kitware.com
> 

> > Visit other Kitware open-source projects at
> > http://www.kitware.com/opensource/opensource.html
> 

> > Please keep messages on-topic and check the ParaView Wiki at:
> > http://paraview.org/Wiki/ParaView
> 

> > Search the list archives at: http://markmail.org/search/?q=ParaView
> 

> > Follow this link to subscribe/unsubscribe:
> 
> > http://public.kitware.com/mailman/listinfo/paraview
> 
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From mathieu.westphal at kitware.com  Fri Sep 16 12:32:33 2016
From: mathieu.westphal at kitware.com (Mathieu Westphal)
Date: Fri, 16 Sep 2016 18:32:33 +0200
Subject: [Paraview] PV 4.10 how to locate x, y,
 z for negative pressure at a point
In-Reply-To: <1741096731.1558011.1474034575638.JavaMail.zimbra@inria.fr>
References: <622981634.661823.1473851351668.JavaMail.zimbra@inria.fr>
 <1543783073.662734.1473851514798.JavaMail.zimbra@inria.fr>
 <CAC2t4USxDX11T4VrbGssVyvORkLfyoAqZQvX0UfiY+YgDM5dnw@mail.gmail.com>
 <1741096731.1558011.1474034575638.JavaMail.zimbra@inria.fr>
Message-ID: <CAC2t4UTJ0mgkNHr8cAaTrsngHPFJrUF31hMT-qsqDAwUk-5trA@mail.gmail.com>

Hello

is it CellData or PointData ?

Mathieu Westphal

On Fri, Sep 16, 2016 at 4:02 PM, Stephen Wornom <stephen.wornom at inria.fr>
wrote:

> Thanks Mattieu,
> iformation shows my data range for pressure
> -1106.5   15.3889
> PV does not give the id or cell number
> run query selection is blank so I put
> -1106.5get no hits
> Need I enter pressure some where?
> Thanks,
> Stephen
>
>
>
> ------------------------------
>
> *From: *"Mathieu Westphal" <mathieu.westphal at kitware.com>
> *To: *"Stephen Wornom" <stephen.wornom at inria.fr>
> *Cc: *"ParaView list" <paraview at paraview.org>, "Emmanuelle" <
> emmanuelle.itam at univ-montp2.fr>
> *Sent: *Wednesday, September 14, 2016 2:26:56 PM
> *Subject: *Re: [Paraview] PV 4.10 how to locate x, y, z for negative
> pressure at a point
>
>
> Hello
> With
> Edit->FindData
>
> you will be able to write a simple query to find the cells or points where
> this happens.
>
> Regards,
>
>
>
> Mathieu Westphal
>
> On Wed, Sep 14, 2016 at 1:11 PM, Stephen Wornom <stephen.wornom at inria.fr>
> wrote:
>
>> PV information shows a negative pressure, how can I locate the
>> coordinates where the negative pressure occurs?
>> I hope my question is clear.
>> Thanks,
>> Stephen
>>
>> _______________________________________________
>> Powered by www.kitware.com
>>
>> Visit other Kitware open-source projects at http://www.kitware.com/
>> opensource/opensource.html
>>
>> Please keep messages on-topic and check the ParaView Wiki at:
>> http://paraview.org/Wiki/ParaView
>>
>> Search the list archives at: http://markmail.org/search/?q=ParaView
>>
>> Follow this link to subscribe/unsubscribe:
>> http://public.kitware.com/mailman/listinfo/paraview
>>
>>
>
>
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From weiliu620 at gmail.com  Fri Sep 16 13:35:03 2016
From: weiliu620 at gmail.com (Wei Liu)
Date: Fri, 16 Sep 2016 13:35:03 -0400
Subject: [Paraview] axis order for vector field
Message-ID: <CAJoKFkQwK_BA_A8cCWqJsiM1T1g6R2_44f74wjt_g9vSWvhJ+w@mail.gmail.com>

Hi paraview users,

I hope this is a simple question. I'm trying to visualize a 3D vector
field, and wonder what is the format of the data. I have a .nrrd file with
header like:

dimension: 4
space: left-posterior-superior
sizes: 3 256 256 130

paraview seems not load the data correctly, because it only show a single
slice no matter what 'representation' I choose.

Then I use unu tool (for nrrd file) to permute the dimension order and now
the size is: [256 256 130 3]. I loaded the data into paraview and can see
3D cube.  I guess I can use arrow glyph to visualize the vector at each
voxel? But I couldn't make it work. The arrow always point to same
direction.

I may need to read the document more carefully, but is there an simple
instruction for vector image visualization (3D volume image where each
voxel is a vector)?

Thank your for your help .
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From chrisneal at snumerics.com  Fri Sep 16 13:10:40 2016
From: chrisneal at snumerics.com (Christopher Neal)
Date: Fri, 16 Sep 2016 13:10:40 -0400
Subject: [Paraview] Catalyst osMesa rendering time
In-Reply-To: <CAMaOp+FBNkGwGfwHd6JmW_BXAeatiLD52Hs1g_Lm90OBDTRoCg@mail.gmail.com>
References: <BE7FEBAD-3DD0-4516-B69A-7568050FB2A3@snumerics.com>
 <CAMaOp+HDga=x=TKmq6S+WDAE9AvrCwx61P3c1Pb+ERUuFX1NfA@mail.gmail.com>
 <DDC524AE-CAF3-4818-B3C1-D44ACC408204@snumerics.com>
 <CAMaOp+FBNkGwGfwHd6JmW_BXAeatiLD52Hs1g_Lm90OBDTRoCg@mail.gmail.com>
Message-ID: <534999D2-55A7-4B50-A99D-AC16EBE19EB9@snumerics.com>

Hi Andy,

Thank you for all of the guidance that you have provided for compiling the osMesa version of ParaView. I think there must be a gap in my understanding that is causing me to implement/interpret your instructions incorrectly. My goal is to be able to run a code that makes calls to the Catalyst adaptor in order to generate .png output images of a domain for each timestep. The nodes that the code runs on do not have graphics cards, so I?m looking for a way to have the VTK library generate the images without resorting to calls to a GPU for rendering. That is what the ParaView build with osMesa is supposed to do right? It seems exceedingly difficult to get ParaView to compile osMesa, because even though I instruct the cmake configuration to use Mesa, it seems to disregard my request and continue to run by opening windows for generating the images. I don?t get compiler errors, so I suppose it just tosses out the osMesa stuff and compiles in the default way?

I apologize for the verbose post. I feel like Bill Murray in Groundhog Day in that I keep making changes to try to get ParaView to operate with osMesa, and I always end up back where I started with ParaView creating windows and causing my code to crash. I?m trying the superbuild, but that is currently failing to compile for reasons that I haven?t quite been able to figure out.

-Chris

 

From: Andy Bauer <andy.bauer at kitware.com>
Date: Monday, September 12, 2016 at 3:20 PM
To: Christopher Neal <chrisneal at snumerics.com>
Cc: Benson Muite via ParaView <paraview at paraview.org>
Subject: Re: [Paraview] Catalyst osMesa rendering time

 

I think the missing item is that you need to set VTK_USE_OFFSCREEN to ON.

 

On Mon, Sep 12, 2016 at 3:00 PM, Christopher Neal <chrisneal at snumerics.com> wrote:

Thanks Andy,

The file is quite large, so I have attached it.

I tried to follow the process that is explained at(http://www.paraview.org/Wiki/ParaView/ParaView_And_Mesa_3D) so I made a shell script that contains all of the arguments passed to cmake. It is shown below.

 

 

#!/bin/bash

 

cmake \

  -DCMAKE_SOURCE_DIR:PATH=/home/neal/software/ParaView_osMesa/Source \

  -DCMAKE_INSTALL_PREFIX:PATH=/home/neal/software/ParaView_osMesa/build \

  -DCMAKE_BUILD_TYPE:STRING=Release \

  -DCMAKE_SKIP_INSTALL_RPATH:BOOL=YES \

  -DBUILD_TESTING:BOOL=OFF \

  -DPARAVIEW_BUILD_QT_GUI:BOOL=OFF \

  -DVTK_RENDERING_BACKEND=OpenGL2 \

  -DPARAVIEW_USE_MPI:BOOL=ON \

  -DPARAVIEW_ENABLE_PYTHON:BOOL=ON \

  -DPARAVIEW_INSTALL_DEVELOPMENT_FILES:BOOL=ON \

  -DPARAVIEW_BUILD_CATALYST_ADAPTERS:BOOL=ON \

  -DPARAVIEW_BUILD_PLUGIN_AnalyzeNIfTIIO:BOOL=FALSE \

  -DPARAVIEW_BUILD_PLUGIN_ArrowGlyph:BOOL=FALSE \

  -DPARAVIEW_BUILD_PLUGIN_CDIReader:BOOL=FALSE \

  -DPARAVIEW_BUILD_PLUGIN_EyeDomeLighting:BOOL=FALSE \

  -DPARAVIEW_BUILD_PLUGIN_GMVReader:BOOL=FALSE \

 -DPARAVIEW_BUILD_PLUGIN_GeodesicMeasurement:BOOL=FALSE \

  -DPARAVIEW_BUILD_PLUGIN_H5PartReader:BOOL=FALSE \

  -DPARAVIEW_BUILD_PLUGIN_InSituExodus:BOOL=FALSE \

  -DPARAVIEW_BUILD_PLUGIN_MantaView:BOOL=FALSE \

  -DPARAVIEW_BUILD_PLUGIN_Moments:BOOL=FALSE \

  -DPARAVIEW_BUILD_PLUGIN_NonOrthogonalSource:BOOL=FALSE \

  -DPARAVIEW_BUILD_PLUGIN_PacMan:BOOL=FALSE \

  -DPARAVIEW_BUILD_PLUGIN_PointSprite:BOOL=FALSE \

  -DPARAVIEW_BUILD_PLUGIN_RGBZView:BOOL=FALSE \

  -DPARAVIEW_BUILD_PLUGIN_SLACTools:BOOL=FALSE \

 -DPARAVIEW_BUILD_PLUGIN_SciberQuestToolKit:BOOL=FALSE \

  -DPARAVIEW_BUILD_PLUGIN_SierraPlotTools:BOOL=FALSE \

  -DPARAVIEW_BUILD_PLUGIN_StreamingParticles:BOOL=FALSE \

  -DPARAVIEW_BUILD_PLUGIN_SurfaceLIC:BOOL=FALSE \

  -DPARAVIEW_BUILD_PLUGIN_UncertaintyRendering:BOOL=FALSE \

  -DPARAVIEW_BUILD_PLUGIN_AcceleratedAlgorithms:BOOL=OFF \

  -DVTK_USE_CXX11_FEATURES:BOOL=ON \

  -DVTK_USE_X:BOOL=OFF \

  -DOPENGL_INCLUDE_DIR:PATH=/home/neal/software/Mesa/build/include \

  -DOPENGL_gl_LIBRARY:PATH=/home/neal/software/Mesa/build/lib64/libOSMesa.so \

  -DOPENGL_glu_LIBRARY:PATH=/home/neal/software/Mesa/build/lib64/libGLU.so \

  -DVTK_OPENGL_HAS_OSMESA:BOOL=ON \

  -DOSMESA_INCLUDE_DIR:PATH=/home/neal/software/Mesa/build/include \

  -DOSMESA_LIBRARY:PATH=/home/neal/software/Mesa/build/lib64/libOSMesa.so  /home/neal/software/ParaView_osMesa/Source

 

make -j20

#make -j20 install

 

 


-Chris

 

From: Andy Bauer <andy.bauer at kitware.com>
Date: Monday, September 12, 2016 at 2:39 PM
To: Christopher Neal <chrisneal at snumerics.com>
Cc: Benson Muite via ParaView <paraview at paraview.org>
Subject: Re: [Paraview] Catalyst osMesa rendering time

 

Hi Chris,

It sounds like you didn't properly build ParaView with offscreen rendering. Can  you share your CMakeCache.txt from your build? I'm guessing VTK_USE_X, VTK_USE_OFFSCREEN or some other thing didn't get set properly.

Andy

 

On Mon, Sep 12, 2016 at 1:36 PM, Christopher Neal <chrisneal at snumerics.com> wrote:

Hi all,

 

I have compiled a version of ParaView with osMesa enabled. The version is 5.1.2 for ParaView. I?m running the CxxFullExample Catalyst example that is located in ParaView/Examples/Catalyst.

Operating system info

lsb_release ?a: 
LSB Version:         n/a

Distributor ID:     openSUSE project

Description:         openSUSE 13.2 (Harlequin) (x86_64)

Release:                13.2

Codename:           Harlequin



I have added 1 additional script to the Catalyst example by using the ?CoProcessing? button in ParaView to generate a Catalyst script that just exports a .png of an isometric view of the geometry. When I run the example, the operating system seems to freeze up completely in my login session i.e. windows can not be clicked, nothing at all can be done with the exception of moving the mouse around on the screen. It stays frozen like this for about 2 minutes before a window pops up that says ?Paraview(batch)?. In the window is the isometric view and the window updates to show the geometry at every timestep that the example outputs an image at. The Catalyst script does seem to execute fine and outputs image files for each frame that I requested, but it is soooo slow for some reason.

Is this the expected behavior of running Catalyst with an osMesa build? I thought that ?os? stood for ?off-screen?, which I interpreted as there being no screen display component to the rendering. Have I done something wrong with compiling ParaView with osMesa? Is Catalyst supposed to completely lock up the session until a window pops up?  

I would love to hear from other users of Catalyst to hear about the experiences of running Catalyst.


Thank you,

Chris Neal


_______________________________________________
Powered by www.kitware.com

Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html

Please keep messages on-topic and check the ParaView Wiki at: http://paraview.org/Wiki/ParaView

Search the list archives at: http://markmail.org/search/?q=ParaView

Follow this link to subscribe/unsubscribe:
http://public.kitware.com/mailman/listinfo/paraview

 

 

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From utkarsh.ayachit at kitware.com  Fri Sep 16 21:19:00 2016
From: utkarsh.ayachit at kitware.com (Utkarsh Ayachit)
Date: Fri, 16 Sep 2016 21:19:00 -0400
Subject: [Paraview] axis order for vector field
In-Reply-To: <CAJoKFkQwK_BA_A8cCWqJsiM1T1g6R2_44f74wjt_g9vSWvhJ+w@mail.gmail.com>
References: <CAJoKFkQwK_BA_A8cCWqJsiM1T1g6R2_44f74wjt_g9vSWvhJ+w@mail.gmail.com>
Message-ID: <CADHSJjBck8G6RvYt09jqvVRUsS-XPpLBZCRpsDkptZaUze10Og@mail.gmail.com>

Can you share the sample dataset? That'll make it easier to provide
some options.

Utkarsh

On Fri, Sep 16, 2016 at 1:35 PM, Wei Liu <weiliu620 at gmail.com> wrote:
> Hi paraview users,
>
> I hope this is a simple question. I'm trying to visualize a 3D vector field,
> and wonder what is the format of the data. I have a .nrrd file with header
> like:
>
> dimension: 4
> space: left-posterior-superior
> sizes: 3 256 256 130
>
> paraview seems not load the data correctly, because it only show a single
> slice no matter what 'representation' I choose.
>
> Then I use unu tool (for nrrd file) to permute the dimension order and now
> the size is: [256 256 130 3]. I loaded the data into paraview and can see 3D
> cube.  I guess I can use arrow glyph to visualize the vector at each voxel?
> But I couldn't make it work. The arrow always point to same direction.
>
> I may need to read the document more carefully, but is there an simple
> instruction for vector image visualization (3D volume image where each voxel
> is a vector)?
>
> Thank your for your help .
>
> _______________________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Please keep messages on-topic and check the ParaView Wiki at:
> http://paraview.org/Wiki/ParaView
>
> Search the list archives at: http://markmail.org/search/?q=ParaView
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/paraview
>

From fdkong.jd at gmail.com  Sun Sep 18 16:01:36 2016
From: fdkong.jd at gmail.com (Fande Kong)
Date: Sun, 18 Sep 2016 14:01:36 -0600
Subject: [Paraview] wall shear stress
Message-ID: <CAN5Wd-+edXj4B44BvuQASk+4gkotgve47NeCMBQA9Ow49sBxHA@mail.gmail.com>

Hi Developers,

I am solving an incompressible Navier-Stokes equations, and I have
solutions for the velocity (u)  and the pressure (p). Is it possible to
show the wall shear stress in paraview using the velocity?


Fande Kong,
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From david.thompson at kitware.com  Sun Sep 18 19:39:18 2016
From: david.thompson at kitware.com (David Thompson)
Date: Sun, 18 Sep 2016 19:39:18 -0400
Subject: [Paraview] wall shear stress
In-Reply-To: <CAN5Wd-+edXj4B44BvuQASk+4gkotgve47NeCMBQA9Ow49sBxHA@mail.gmail.com>
References: <CAN5Wd-+edXj4B44BvuQASk+4gkotgve47NeCMBQA9Ow49sBxHA@mail.gmail.com>
Message-ID: <F970B861-7090-485B-AB61-706EE1007A31@kitware.com>

Hi Fande,

You should be able to use the gradient filter to compute the velocity gradient and examine the component of the gradient normal to the wall. That will be proportional to the shear stress at the wall. Is the wall aligned with a coordinate axis? If not, you will need to extract the wall surface and generate normal vectors, then dot the gradient with the normal vectors.

    David

> On Sep 18, 2016, at 16:01, Fande Kong <fdkong.jd at gmail.com> wrote:
> 
> Hi Developers,
> 
> I am solving an incompressible Navier-Stokes equations, and I have solutions for the velocity (u)  and the pressure (p). Is it possible to show the wall shear stress in paraview using the velocity?  
> 
> 
> Fande Kong,
> _______________________________________________
> Powered by www.kitware.com
> 
> Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html
> 
> Please keep messages on-topic and check the ParaView Wiki at: http://paraview.org/Wiki/ParaView
> 
> Search the list archives at: http://markmail.org/search/?q=ParaView
> 
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/paraview
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From dave.demarle at kitware.com  Sun Sep 18 20:09:01 2016
From: dave.demarle at kitware.com (David E DeMarle)
Date: Sun, 18 Sep 2016 20:09:01 -0400
Subject: [Paraview] wall shear stress
In-Reply-To: <F970B861-7090-485B-AB61-706EE1007A31@kitware.com>
References: <CAN5Wd-+edXj4B44BvuQASk+4gkotgve47NeCMBQA9Ow49sBxHA@mail.gmail.com>
 <F970B861-7090-485B-AB61-706EE1007A31@kitware.com>
Message-ID: <CANjZAi8WdJkRTM+LXjG496tGgrESddtQ5PPwFHfWipnP_3R63Q@mail.gmail.com>

This topic comes up pretty often. We should automate the above.


David E DeMarle
Kitware, Inc.
R&D Engineer
21 Corporate Drive
Clifton Park, NY 12065-8662
Phone: 518-881-4909

On Sun, Sep 18, 2016 at 7:39 PM, David Thompson <david.thompson at kitware.com>
wrote:

> Hi Fande,
>
> You should be able to use the gradient filter to compute the velocity
> gradient and examine the component of the gradient normal to the wall. That
> will be proportional to the shear stress at the wall. Is the wall aligned
> with a coordinate axis? If not, you will need to extract the wall surface
> and generate normal vectors, then dot the gradient with the normal vectors.
>
>     David
>
> On Sep 18, 2016, at 16:01, Fande Kong <fdkong.jd at gmail.com> wrote:
>
> Hi Developers,
>
> I am solving an incompressible Navier-Stokes equations, and I have
> solutions for the velocity (u)  and the pressure (p). Is it possible to
> show the wall shear stress in paraview using the velocity?
>
>
> Fande Kong,
>
> _______________________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at http://www.kitware.com/
> opensource/opensource.html
>
> Please keep messages on-topic and check the ParaView Wiki at:
> http://paraview.org/Wiki/ParaView
>
> Search the list archives at: http://markmail.org/search/?q=ParaView
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/paraview
>
>
> _______________________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at http://www.kitware.com/
> opensource/opensource.html
>
> Please keep messages on-topic and check the ParaView Wiki at:
> http://paraview.org/Wiki/ParaView
>
> Search the list archives at: http://markmail.org/search/?q=ParaView
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/paraview
>
>
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From fdkong.jd at gmail.com  Sun Sep 18 20:54:35 2016
From: fdkong.jd at gmail.com (Fande Kong)
Date: Sun, 18 Sep 2016 18:54:35 -0600
Subject: [Paraview] wall shear stress
In-Reply-To: <F970B861-7090-485B-AB61-706EE1007A31@kitware.com>
References: <CAN5Wd-+edXj4B44BvuQASk+4gkotgve47NeCMBQA9Ow49sBxHA@mail.gmail.com>
 <F970B861-7090-485B-AB61-706EE1007A31@kitware.com>
Message-ID: <CAN5Wd-JOr9_q3DAee2R2yhLoguD-Ddhk3XfC9E3hkOZewifjww@mail.gmail.com>

Hi David,

Thanks very much for your reply. I am a new paraview user. Could you
possibly show me more details? Some documentations on each of these steps?

On Sun, Sep 18, 2016 at 5:39 PM, David Thompson <david.thompson at kitware.com>
wrote:

> Hi Fande,
>
> You should be able to use the gradient filter to compute the velocity
> gradient and examine the component of the gradient normal to the wall. That
> will be proportional to the shear stress at the wall. Is the wall aligned
> with a coordinate axis?
>

No, the wall is not aligned with a coordinate axis.  In fact, the geometry
is very complex. It is a pulmonary artery tree with several generations.

Thanks,

Fande,


> If not, you will need to extract the wall surface and generate normal
> vectors, then dot the gradient with the normal vectors.
>
>     David
>
> On Sep 18, 2016, at 16:01, Fande Kong <fdkong.jd at gmail.com> wrote:
>
> Hi Developers,
>
> I am solving an incompressible Navier-Stokes equations, and I have
> solutions for the velocity (u)  and the pressure (p). Is it possible to
> show the wall shear stress in paraview using the velocity?
>
>
> Fande Kong,
>
> _______________________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at http://www.kitware.com/
> opensource/opensource.html
>
> Please keep messages on-topic and check the ParaView Wiki at:
> http://paraview.org/Wiki/ParaView
>
> Search the list archives at: http://markmail.org/search/?q=ParaView
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/paraview
>
>
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From taylorbrennen731 at gmail.com  Mon Sep 19 00:13:51 2016
From: taylorbrennen731 at gmail.com (Brennen Taylor)
Date: Mon, 19 Sep 2016 09:43:51 +0530
Subject: [Paraview] How to merge .vtk files to visualize the result in
	Paraview
Message-ID: <CABxKrcqZasUk9V0=8dO1mL3z3-rWaHyJXVAN=QmXrmMUqsnXGA@mail.gmail.com>

Dear All,

I am using Paraview in order to visualize the result produced by parallel
program.
Each processor currently outputs its own .vtk files , which corresponsd to
the value of the fields in the domain.

I would like to know if there is a way of merging these .vtk files into one
.vtk file so that I can visualize using Paraview.



Thanks in advance !!

Best ,

Brennen
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From chrisneal at snumerics.com  Mon Sep 19 13:59:54 2016
From: chrisneal at snumerics.com (Christopher Neal)
Date: Mon, 19 Sep 2016 13:59:54 -0400
Subject: [Paraview] How to merge .vtk files to visualize the result in
 Paraview
In-Reply-To: <CABxKrcqZasUk9V0=8dO1mL3z3-rWaHyJXVAN=QmXrmMUqsnXGA@mail.gmail.com>
References: <CABxKrcqZasUk9V0=8dO1mL3z3-rWaHyJXVAN=QmXrmMUqsnXGA@mail.gmail.com>
Message-ID: <05938075-9942-461D-9146-3AC9616868A8@snumerics.com>

Hey Brennen,

I?m not an expert at Paraview?s IO system, but I believe that individual .vtk files would have to be opened individually i.e. Paraview cannot stitch the .vtk files together.? If you want to be able to open a single file and have the data for each processor?s output file be shown in one coherent data set, then I think you should look into the parallel xml file format that Paraview uses.

A PDF of VTK file formats (XML format is on page 11 of the document): http://www.vtk.org/wp-content/uploads/2015/04/file-formats.pdf


There is probably a better way to do this, but this is what I would do.
1.) Write a paraview python script to first convert all of the .vtk files to the newer xml format.? See: http://stackoverflow.com/questions/26158599/how-to-convert-vtk-legacy-files-to-vtu-format

??????????????? You will have to use the correct writer to write the proper XML file format for your data set type ? See page 12 of that file-formats pdf that I posted above to see what types exist for the datasets

2.) Let?s assume your data is unstructured. You will now have data for each sub-domain written to a bunch of .vtu files. One .vtu file per processor, just like the .vtk files. ?You can stitch all of these files together by using the parallel file format that VTK supports ( see page 16 of that pdf ). You just need to write out a .pvtu file that essentially just has a list containing the name of every .vtu file.

3.) Paraview should be able to open this new .pvtu file and display all of the data for all of the sub-domains.

Again, your xml file type might be .vti, .vtp, etc. depending on the data type that is being written to the .vtk files, structured, image, poly, etc.

Hope this helps. If anyone has a more straightforward solution please share it.


Best regards,

Chris Neal

 

 

From: ParaView <paraview-bounces at paraview.org> on behalf of Brennen Taylor <taylorbrennen731 at gmail.com>
Date: Monday, September 19, 2016 at 12:13 AM
To: <paraview at paraview.org>
Subject: [Paraview] How to merge .vtk files to visualize the result in Paraview

 

Dear All,

 

I am using Paraview in order to visualize the result produced by parallel program. 

Each processor currently outputs its own .vtk files , which corresponsd to the value of the fields in the domain.

 

I would like to know if there is a way of merging these .vtk files into one .vtk file so that I can visualize using Paraview.

 

 

 

Thanks in advance !!

 

Best ,

 

Brennen

_______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Please keep messages on-topic and check the ParaView Wiki at: http://paraview.org/Wiki/ParaView Search the list archives at: http://markmail.org/search/?q=ParaView Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/paraview 

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From e.a.hereth at gmail.com  Mon Sep 19 15:35:13 2016
From: e.a.hereth at gmail.com (Ethan Hereth)
Date: Mon, 19 Sep 2016 19:35:13 +0000
Subject: [Paraview] How to merge .vtk files to visualize the result in
	Paraview
In-Reply-To: <05938075-9942-461D-9146-3AC9616868A8@snumerics.com>
References: <CABxKrcqZasUk9V0=8dO1mL3z3-rWaHyJXVAN=QmXrmMUqsnXGA@mail.gmail.com>
 <05938075-9942-461D-9146-3AC9616868A8@snumerics.com>
Message-ID: <CACoCd8dyQLehKLKg9=BO12Y7oHNB_NjdK90FwBBM-cvozP7iPw@mail.gmail.com>

Furthermore, if you end up opening them all individually in paraview, you
can select all of the input files in Pipeline Browser and then run the
Group Datasets filter on them. This is a poor man's solution I think, but
in a pinch it works well.

Cheers!

Ethan Alan

On Mon, Sep 19, 2016 at 2:32 PM Christopher Neal <chrisneal at snumerics.com>
wrote:

> Hey Brennen,
>
> I?m not an expert at Paraview?s IO system, but I believe that individual
> .vtk files would have to be opened individually i.e. Paraview cannot stitch
> the .vtk files together.  If you want to be able to open a single file and
> have the data for each processor?s output file be shown in one coherent
> data set, then I think you should look into the parallel xml file format
> that Paraview uses.
>
> A PDF of VTK file formats (XML format is on page 11 of the document):
> http://www.vtk.org/wp-content/uploads/2015/04/file-formats.pdf
>
>
> There is probably a better way to do this, but this is what I would do.
> 1.) Write a paraview python script to first convert all of the .vtk files
> to the newer xml format.  See:
> http://stackoverflow.com/questions/26158599/how-to-convert-vtk-legacy-files-to-vtu-format
>
>                 You will have to use the correct writer to write the
> proper XML file format for your data set type ? See page 12 of that
> file-formats pdf that I posted above to see what types exist for the
> datasets
>
> 2.) Let?s assume your data is unstructured. You will now have data for
> each sub-domain written to a bunch of .vtu files. One .vtu file per
> processor, just like the .vtk files.  You can stitch all of these files
> together by using the parallel file format that VTK supports ( see page 16
> of that pdf ). You just need to write out a .pvtu file that essentially
> just has a list containing the name of every .vtu file.
>
> 3.) Paraview should be able to open this new .pvtu file and display all of
> the data for all of the sub-domains.
>
> Again, your xml file type might be .vti, .vtp, etc. depending on the data
> type that is being written to the .vtk files, structured, image, poly, etc.
>
> Hope this helps. If anyone has a more straightforward solution please
> share it.
>
> Best regards,
>
> Chris Neal
>
>
>
>
>
> *From: *ParaView <paraview-bounces at paraview.org> on behalf of Brennen
> Taylor <taylorbrennen731 at gmail.com>
> *Date: *Monday, September 19, 2016 at 12:13 AM
> *To: *<paraview at paraview.org>
> *Subject: *[Paraview] How to merge .vtk files to visualize the result in
> Paraview
>
>
>
> Dear All,
>
>
>
> I am using Paraview in order to visualize the result produced by parallel
> program.
>
> Each processor currently outputs its own .vtk files , which corresponsd to
> the value of the fields in the domain.
>
>
>
> I would like to know if there is a way of merging these .vtk files into
> one .vtk file so that I can visualize using Paraview.
>
>
>
>
>
>
>
> Thanks in advance !!
>
>
>
> Best ,
>
>
>
> Brennen
>
> _______________________________________________ Powered by www.kitware.com
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html Please keep messages
> on-topic and check the ParaView Wiki at: http://paraview.org/Wiki/ParaView
> Search the list archives at: http://markmail.org/search/?q=ParaView
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/paraview
> _______________________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Please keep messages on-topic and check the ParaView Wiki at:
> http://paraview.org/Wiki/ParaView
>
> Search the list archives at: http://markmail.org/search/?q=ParaView
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/paraview
>
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From dl826 at cornell.edu  Mon Sep 19 22:20:41 2016
From: dl826 at cornell.edu (dl826 at cornell.edu)
Date: Mon, 19 Sep 2016 22:20:41 -0400
Subject: [Paraview] Function JOIN of XDMF in Paraview
Message-ID: <57e09cfa.515b240a.59f3d.1f74@mx.google.com>

Hi?
I am now working on a project which needs the use of JOIN function in xdmf to concatenate the data from multiple h5 files and visualize those files in Paraview. I have created a small trial to test this JOIN function. I create two h5 files, each of which contains two points of a unit square. For each point, I assign a value to it as its attribute. Then I write one xdmf file, which uses function JOIN to concatenate the dataset from two h5 files. But when I load my xdmf file into Paraview, Paraview just crashes directly.  This is the xdmf file I have written:

<?xml version="1.0" encoding="utf-8"?>
<Xdmf xmlns:xi="http://www.w3.org/2001/XInclude" Version="2.97">
  <Domain>
    <Grid Name="Grid">
      <Geometry Type="XY">
        <DataItem ItemType="Function" Function="JOIN($0 ; $1)">
          <DataItem DataType="Float" Dimensions="2 2" Format="HDF" Precision="4">EvolvingSquare_01.h5:Coordinates</DataItem>
	  <DataItem DataType="Float" Dimensions="2 2" Format="HDF" Precision="4">EvolvingSquare_02.h5:Coordinates</DataItem>     
        </DataItem>
      </Geometry>
      <Topology TopologyType="2DSMesh" NumberOfElements="4 2"/> 
      <Attribute Center="Node" Name="Attributes" Type="None">
        <DataItem ItemType="Function" Function="JOIN($0 ; $1)">   
          <DataItem DataType="Float" Dimensions="2" Format="HDF" Precision="8">EvolvingSquare_01.h5:Attributes</DataItem>
          <DataItem DataType="Float" Dimensions="2" Format="HDF" Precision="8">EvolvingSquare_02.h5:Attributes</DataItem>
        </DataItem>
      </Attribute>
    </Grid>
  </Domain>
</Xdmf>

To avoid the problem of h5 file itself, I have also written two separate xdmf files for each h5 file and load each xdmf file separately into Paraview. I can successfully load these two h5 files separately into Paraview, so the problem might no be my h5 files. Can anyone help me with this problem? Are there any mistakes of my ways of using JOIN function in xdmf? 
Thanks

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From tim.gallagher at gatech.edu  Mon Sep 19 22:50:49 2016
From: tim.gallagher at gatech.edu (Gallagher, Timothy P)
Date: Tue, 20 Sep 2016 02:50:49 +0000
Subject: [Paraview] Function JOIN of XDMF in Paraview
In-Reply-To: <BN6PR07MB3012A1C7A7A59C8538E8679C9DF70@BN6PR07MB3012.namprd07.prod.outlook.com>
References: <57e09cfa.515b240a.59f3d.1f74@mx.google.com>,
 <BN6PR07MB3012A1C7A7A59C8538E8679C9DF70@BN6PR07MB3012.namprd07.prod.outlook.com>
Message-ID: <BN6PR07MB3012F358956060782D4F4D9D9DF70@BN6PR07MB3012.namprd07.prod.outlook.com>

Maybe to be more clear (because there are some differences in the grid definition in some other places), here is what our full grid definition looks like:


           <Grid GridType="Uniform" Name="Domain_00001">
                <Topology Dimensions="8 47 373 3" TopologyType="3DSMesh" />
                <Geometry GeometryType="XYZ" Units="m">
                        <DataItem Dimensions="8 47 373 3" Function="JOIN($0, $1, $2)" ItemType="Function">
                            <DataItem Dimensions="8 47 373" Format="HDF" NumberType="Float" Precision="8">&gridpath;/grid.h5:/Domain_00001/x</DataItem>
                            <DataItem Dimensions="8 47 373" Format="HDF" NumberType="Float" Precision="8">&gridpath;/grid.h5:/Domain_00001/y</DataItem>
                            <DataItem Dimensions="8 47 373" Format="HDF" NumberType="Float" Precision="8">&gridpath;/grid.h5:/Domain_00001/z</DataItem>
                        </DataItem>
                    </DataItem>
                </Geometry>
            </Grid>


The first difference is the 2DSMesh in yours instead of the 3DSMesh in mine. But we also use Dimensions in the Topology tag (instead of the NumberOfElements). We also interleave our coordinates (that's what the comma does) instead of appending the arrays (that's what the semicolon does) in the JOIN.


I would skip the attribute for now and focus on getting the format correct for the coordinates, and then look at the attribute. We also use the JOIN to create velocity vectors from individual arrays and it follows the same format as the grid coordinates.


Tim

________________________________
From: Gallagher, Timothy P
Sent: Monday, September 19, 2016 10:41 PM
To: dl826 at cornell.edu; paraview at paraview.org
Subject: Re: [Paraview] Function JOIN of XDMF in Paraview


The thing that jumps out at me is missing the Dimensions tag on the function itself. For instance, we create our grids as:


                        <DataItem Dimensions="8 47 373 3" Function="JOIN($0, $1, $2)" ItemType="Function">
                            <DataItem Dimensions="8 47 373" Format="HDF" NumberType="Float" Precision="8">grid.h5:/Domain_00001/x</DataItem>
                            <DataItem Dimensions="8 47 373" Format="HDF" NumberType="Float" Precision="8">grid.h5:/Domain_00001/y</DataItem>
                            <DataItem Dimensions="8 47 373" Format="HDF" NumberType="Float" Precision="8">grid.h5:/Domain_00001/z</DataItem>
                        </DataItem>


We also use a comma between the JOIN, not a semicolon -- not sure if that matters or not.


If you change your JOIN to look like:


        <DataItem Dimensions="2 2 2" ItemType="Function" Function="JOIN($0, $1)">

          <DataItem DataType="Float" Dimensions="2 2" Format="HDF" Precision="4">EvolvingSquare_01.h5:Coordinates</DataItem>

          <DataItem DataType="Float" Dimensions="2 2" Format="HDF" Precision="4">EvolvingSquare_02.h5:Coordinates</DataItem>

        </DataItem>


does that fix the problem?


Tim

________________________________
From: ParaView <paraview-bounces at paraview.org> on behalf of dl826 at cornell.edu <dl826 at cornell.edu>
Sent: Monday, September 19, 2016 10:20 PM
To: paraview at paraview.org
Subject: [Paraview] Function JOIN of XDMF in Paraview


Hi?

I am now working on a project which needs the use of JOIN function in xdmf to concatenate the data from multiple h5 files and visualize those files in Paraview. I have created a small trial to test this JOIN function. I create two h5 files, each of which contains two points of a unit square. For each point, I assign a value to it as its attribute. Then I write one xdmf file, which uses function JOIN to concatenate the dataset from two h5 files. But when I load my xdmf file into Paraview, Paraview just crashes directly.  This is the xdmf file I have written:



<?xml version="1.0" encoding="utf-8"?>

<Xdmf xmlns:xi="http://www.w3.org/2001/XInclude" Version="2.97">

  <Domain>

    <Grid Name="Grid">

      <Geometry Type="XY">

        <DataItem ItemType="Function" Function="JOIN($0 ; $1)">

          <DataItem DataType="Float" Dimensions="2 2" Format="HDF" Precision="4">EvolvingSquare_01.h5:Coordinates</DataItem>

     <DataItem DataType="Float" Dimensions="2 2" Format="HDF" Precision="4">EvolvingSquare_02.h5:Coordinates</DataItem>

        </DataItem>

      </Geometry>

      <Topology TopologyType="2DSMesh" NumberOfElements="4 2"/>

      <Attribute Center="Node" Name="Attributes" Type="None">

        <DataItem ItemType="Function" Function="JOIN($0 ; $1)">

          <DataItem DataType="Float" Dimensions="2" Format="HDF" Precision="8">EvolvingSquare_01.h5:Attributes</DataItem>

          <DataItem DataType="Float" Dimensions="2" Format="HDF" Precision="8">EvolvingSquare_02.h5:Attributes</DataItem>

        </DataItem>

      </Attribute>

    </Grid>

  </Domain>

</Xdmf>



To avoid the problem of h5 file itself, I have also written two separate xdmf files for each h5 file and load each xdmf file separately into Paraview. I can successfully load these two h5 files separately into Paraview, so the problem might no be my h5 files. Can anyone help me with this problem? Are there any mistakes of my ways of using JOIN function in xdmf?

Thanks


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From tim.gallagher at gatech.edu  Mon Sep 19 22:41:56 2016
From: tim.gallagher at gatech.edu (Gallagher, Timothy P)
Date: Tue, 20 Sep 2016 02:41:56 +0000
Subject: [Paraview] Function JOIN of XDMF in Paraview
In-Reply-To: <57e09cfa.515b240a.59f3d.1f74@mx.google.com>
References: <57e09cfa.515b240a.59f3d.1f74@mx.google.com>
Message-ID: <BN6PR07MB3012A1C7A7A59C8538E8679C9DF70@BN6PR07MB3012.namprd07.prod.outlook.com>

The thing that jumps out at me is missing the Dimensions tag on the function itself. For instance, we create our grids as:


                        <DataItem Dimensions="8 47 373 3" Function="JOIN($0, $1, $2)" ItemType="Function">
                            <DataItem Dimensions="8 47 373" Format="HDF" NumberType="Float" Precision="8">grid.h5:/Domain_00001/x</DataItem>
                            <DataItem Dimensions="8 47 373" Format="HDF" NumberType="Float" Precision="8">grid.h5:/Domain_00001/y</DataItem>
                            <DataItem Dimensions="8 47 373" Format="HDF" NumberType="Float" Precision="8">grid.h5:/Domain_00001/z</DataItem>
                        </DataItem>


We also use a comma between the JOIN, not a semicolon -- not sure if that matters or not.


If you change your JOIN to look like:


        <DataItem Dimensions="2 2 2" ItemType="Function" Function="JOIN($0, $1)">

          <DataItem DataType="Float" Dimensions="2 2" Format="HDF" Precision="4">EvolvingSquare_01.h5:Coordinates</DataItem>

          <DataItem DataType="Float" Dimensions="2 2" Format="HDF" Precision="4">EvolvingSquare_02.h5:Coordinates</DataItem>

        </DataItem>


does that fix the problem?


Tim

________________________________
From: ParaView <paraview-bounces at paraview.org> on behalf of dl826 at cornell.edu <dl826 at cornell.edu>
Sent: Monday, September 19, 2016 10:20 PM
To: paraview at paraview.org
Subject: [Paraview] Function JOIN of XDMF in Paraview


Hi,

I am now working on a project which needs the use of JOIN function in xdmf to concatenate the data from multiple h5 files and visualize those files in Paraview. I have created a small trial to test this JOIN function. I create two h5 files, each of which contains two points of a unit square. For each point, I assign a value to it as its attribute. Then I write one xdmf file, which uses function JOIN to concatenate the dataset from two h5 files. But when I load my xdmf file into Paraview, Paraview just crashes directly.  This is the xdmf file I have written:



<?xml version="1.0" encoding="utf-8"?>

<Xdmf xmlns:xi="http://www.w3.org/2001/XInclude" Version="2.97">

  <Domain>

    <Grid Name="Grid">

      <Geometry Type="XY">

        <DataItem ItemType="Function" Function="JOIN($0 ; $1)">

          <DataItem DataType="Float" Dimensions="2 2" Format="HDF" Precision="4">EvolvingSquare_01.h5:Coordinates</DataItem>

     <DataItem DataType="Float" Dimensions="2 2" Format="HDF" Precision="4">EvolvingSquare_02.h5:Coordinates</DataItem>

        </DataItem>

      </Geometry>

      <Topology TopologyType="2DSMesh" NumberOfElements="4 2"/>

      <Attribute Center="Node" Name="Attributes" Type="None">

        <DataItem ItemType="Function" Function="JOIN($0 ; $1)">

          <DataItem DataType="Float" Dimensions="2" Format="HDF" Precision="8">EvolvingSquare_01.h5:Attributes</DataItem>

          <DataItem DataType="Float" Dimensions="2" Format="HDF" Precision="8">EvolvingSquare_02.h5:Attributes</DataItem>

        </DataItem>

      </Attribute>

    </Grid>

  </Domain>

</Xdmf>



To avoid the problem of h5 file itself, I have also written two separate xdmf files for each h5 file and load each xdmf file separately into Paraview. I can successfully load these two h5 files separately into Paraview, so the problem might no be my h5 files. Can anyone help me with this problem? Are there any mistakes of my ways of using JOIN function in xdmf?

Thanks


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From victorsv at gmail.com  Tue Sep 20 09:13:23 2016
From: victorsv at gmail.com (victor sv)
Date: Tue, 20 Sep 2016 15:13:23 +0200
Subject: [Paraview] PV5.0 crash when I trying to open the xmf file !
In-Reply-To: <CADHSJjD02NLL0bYMePJYnt3u0sh0_KcfHEwFjh2xoKGf2roQWQ@mail.gmail.com>
References: <loom.20160301T170410-921@post.gmane.org>
 <CADHSJjD02NLL0bYMePJYnt3u0sh0_KcfHEwFjh2xoKGf2roQWQ@mail.gmail.com>
Message-ID: <CA+Wz_Fwu-3wgnuNHjzsrzkiE+-5x4CPioJUDvgQw=CT1z98rqw@mail.gmail.com>

Dear Utkarsh,

only FYI, I'm experience the same problem with Paraview version 5.0.1
downloaded from the Ubuntu 16.04 repositories.

Like Hadrien, i didn't have any problem opening XDMFv2 files with Paraview
v4 releases.

Thank you,
V?ctor



2016-03-16 15:57 GMT+01:00 Utkarsh Ayachit <utkarsh.ayachit at kitware.com>:

> Hadrien,
>
> Something's not exactly right with the build of ParaView you're using.
> When I try to open the dataset with 5.0.0 binaries from paraview.org,
> it opens fine when "Xdmf Reader"  is selected in the Select Reader
> dialog (fails with Xdmf3 Reader).
>
> Can you try the binaries from paraview.org to confirm?
>
> Thanks
> Utkarsh
>
> On Tue, Mar 1, 2016 at 11:07 AM, hadrien calmet <hadrien.calmet at bsc.es>
> wrote:
> > Hello everyone,
> >
> > When I open the xmf file (metadata of my .h5) PV5.0 crash !
> >
> > ERROR: In
> > /build/paraview-BGG4vx/paraview-5.0.0+dfsg1/ParaViewCore/
> > ServerImplementation/Core/vtkSIProxy.cxx,
> > line 310
> > vtkSISourceProxy (0x3264b90): Failed to create vtkXdmfReader.
> > Aborting for debugging purposes.
> >
> > Aborted
> >
> > With PV 4.3 I opened the .xmf without trouble.
> > With PV 4.4 I opened the .xmf with some extra setting, I had to put Xdmf
> > Reader.
> >
> > Someone can tell me what I have to change to open these files with PV 5.0
> >
> > Sorry I tried to copy paste the xmf file but the site don't want, top
> posting ?
> >
> > Thank you very much
> >
> >
> >
> > _______________________________________________
> > Powered by www.kitware.com
> >
> > Visit other Kitware open-source projects at http://www.kitware.com/
> opensource/opensource.html
> >
> > Please keep messages on-topic and check the ParaView Wiki at:
> http://paraview.org/Wiki/ParaView
> >
> > Search the list archives at: http://markmail.org/search/?q=ParaView
> >
> > Follow this link to subscribe/unsubscribe:
> > http://public.kitware.com/mailman/listinfo/paraview
> _______________________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at http://www.kitware.com/
> opensource/opensource.html
>
> Please keep messages on-topic and check the ParaView Wiki at:
> http://paraview.org/Wiki/ParaView
>
> Search the list archives at: http://markmail.org/search/?q=ParaView
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/paraview
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From utkarsh.ayachit at kitware.com  Tue Sep 20 15:37:16 2016
From: utkarsh.ayachit at kitware.com (Utkarsh Ayachit)
Date: Tue, 20 Sep 2016 15:37:16 -0400
Subject: [Paraview] ParaView Release Plan
Message-ID: <CADHSJjA0zvV+dPZXnGxRQ1tHgGrL=W138w7Vkxjp9B-ZxfV0bg@mail.gmail.com>

Folks,

To make it easier for deployment and planning for various ParaView
dependent projects, we are planning to adopt a timely release plan for
ParaView starting with 5.2.

The principles are simple:

1. We will have 2 planned releases per year. One before SC (Oct/Nov)
and another one before ISC (May/June).
2. Unplanned or off-cycle releases may happen between these two
planned releases as needed.

For planned releases, the release cycle will be as follows:

1. When a release is planned, a fixed date will be announced as the
date when the first RCs will be tagged.
2. A no-later-than date will also be announced for the final release
at the same time. Barring exceptional cases, the final release will
happen on or before that date.

With this is mind, here are the planned dates for the upcoming releases.

Codename: SC-16
RC Date: Oct 07, 2016
Final release no later than: Nov 04, 2016

Codename: SciDAC-17
RC Date: Feb 03, 2017
Final release no later than: March 03, 2017

Codename: ISC-17
RC Date: May 01, 2017
Final release no later than: June 09, 2017

We're using codenames, instead of version numbers to not have to
update the milestones if we need to have another unplanned release at
any time.

As you can see, the SciDAC-17 release is one of the off-cycle release
for next year and does not affect the two planned releases codenamed
SC-16 and ISC-17.

For up-to-date information on these, see the
https://gitlab.kitware.com/paraview/paraview/milestones

Thoughts? Comments?

Utkarsh

From wascott at sandia.gov  Tue Sep 20 15:47:42 2016
From: wascott at sandia.gov (Scott, W Alan)
Date: Tue, 20 Sep 2016 19:47:42 +0000
Subject: [Paraview] [EXTERNAL]  ParaView Release Plan
In-Reply-To: <CADHSJjA0zvV+dPZXnGxRQ1tHgGrL=W138w7Vkxjp9B-ZxfV0bg@mail.gmail.com>
References: <CADHSJjA0zvV+dPZXnGxRQ1tHgGrL=W138w7Vkxjp9B-ZxfV0bg@mail.gmail.com>
Message-ID: <3ff4b46cda934baa9e9604fedbf6b22d@ES01AMSNLNT.srn.sandia.gov>

Good plan.  Makes a lot of sense.

Alan



-----Original Message-----
From: ParaView [mailto:paraview-bounces at paraview.org] On Behalf Of Utkarsh Ayachit
Sent: Tuesday, September 20, 2016 1:37 PM
To: ParaView <paraview at paraview.org>
Subject: [EXTERNAL] [Paraview] ParaView Release Plan

Folks,

To make it easier for deployment and planning for various ParaView dependent projects, we are planning to adopt a timely release plan for ParaView starting with 5.2.

The principles are simple:

1. We will have 2 planned releases per year. One before SC (Oct/Nov) and another one before ISC (May/June).
2. Unplanned or off-cycle releases may happen between these two planned releases as needed.

For planned releases, the release cycle will be as follows:

1. When a release is planned, a fixed date will be announced as the date when the first RCs will be tagged.
2. A no-later-than date will also be announced for the final release at the same time. Barring exceptional cases, the final release will happen on or before that date.

With this is mind, here are the planned dates for the upcoming releases.

Codename: SC-16
RC Date: Oct 07, 2016
Final release no later than: Nov 04, 2016

Codename: SciDAC-17
RC Date: Feb 03, 2017
Final release no later than: March 03, 2017

Codename: ISC-17
RC Date: May 01, 2017
Final release no later than: June 09, 2017

We're using codenames, instead of version numbers to not have to update the milestones if we need to have another unplanned release at any time.

As you can see, the SciDAC-17 release is one of the off-cycle release for next year and does not affect the two planned releases codenamed
SC-16 and ISC-17.

For up-to-date information on these, see the https://gitlab.kitware.com/paraview/paraview/milestones

Thoughts? Comments?

Utkarsh
_______________________________________________
Powered by www.kitware.com

Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html

Please keep messages on-topic and check the ParaView Wiki at: http://paraview.org/Wiki/ParaView

Search the list archives at: http://markmail.org/search/?q=ParaView

Follow this link to subscribe/unsubscribe:
http://public.kitware.com/mailman/listinfo/paraview

From Simon.Praetorius at tu-dresden.de  Wed Sep 21 04:53:15 2016
From: Simon.Praetorius at tu-dresden.de (Simon Praetorius)
Date: Wed, 21 Sep 2016 08:53:15 +0000
Subject: [Paraview] old issue: using timeseries stored in a vtk xml file
In-Reply-To: <20160920171049.Horde.F3MMLuIH9ta_S4fSALQRUvC@mail.zih.tu-dresden.de>
Message-ID: <20160921085315.Horde.u2qd1QGji7nwtpaLDXcScPe@mail.zih.tu-dresden.de>

Hi,

In the year 2007 there was an issue on the issue-tracker (ID #5542)
about storing a timeseries of data in a single vtk xml file, e.g.
when you have many timesteps with a non-changing mesh. Exactly this
problem I stepped over yesterday, tried the example file in the "fixed"
issue and found out that it is not possible (any more (?)). Is this
feature remove from the vtk reader? Or just from paraview? Is there
an alternative way of storing multiple timestep data-sets while
storing the mesh only once?

Best,
Simon




-- 
Dr. Simon Praetorius
Institut f?r Wissenschaftliches Rechnen
Fachrichtung Mathematik
Technische Universit?t Dresden
Tel.: TUD-42377
Mail: simon.praetorius at tu-dresden.de
Web: www.math.tu-dresden.de/~spraetor
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From utkarsh.ayachit at kitware.com  Wed Sep 21 09:21:15 2016
From: utkarsh.ayachit at kitware.com (Utkarsh Ayachit)
Date: Wed, 21 Sep 2016 09:21:15 -0400
Subject: [Paraview] old issue: using timeseries stored in a vtk xml file
In-Reply-To: <20160921085315.Horde.u2qd1QGji7nwtpaLDXcScPe@mail.zih.tu-dresden.de>
References: <20160920171049.Horde.F3MMLuIH9ta_S4fSALQRUvC@mail.zih.tu-dresden.de>
 <20160921085315.Horde.u2qd1QGji7nwtpaLDXcScPe@mail.zih.tu-dresden.de>
Message-ID: <CADHSJjDcpjGSg6jZJ=zQZAxG8p_AAR-9pKp+oVOqM7yKk9zzNw@mail.gmail.com>

Simon,

If it's not working anymore, I am afraid it's broken in VTK reader
itself, not just ParaView. ParaView doesn't dictate these things, the
reader decides how to such things are handled. It would be great if
you can report an issue on the bug tracker with a sample dataset, if
possible.

Utkarsh

On Wed, Sep 21, 2016 at 4:53 AM, Simon Praetorius
<Simon.Praetorius at tu-dresden.de> wrote:
> Hi,
>
> In the year 2007 there was an issue on the issue-tracker (ID #5542)
> about storing a timeseries of data in a single vtk xml file, e.g.
> when you have many timesteps with a non-changing mesh. Exactly this
> problem I stepped over yesterday, tried the example file in the "fixed"
> issue and found out that it is not possible (any more (?)). Is this
> feature remove from the vtk reader? Or just from paraview? Is there
> an alternative way of storing multiple timestep data-sets while
> storing the mesh only once?
>
> Best,
> Simon
>
>
>
>
> --
> Dr. Simon Praetorius
> Institut f?r Wissenschaftliches Rechnen
> Fachrichtung Mathematik
> Technische Universit?t Dresden
> Tel.: TUD-42377
> Mail: simon.praetorius at tu-dresden.de
> Web: www.math.tu-dresden.de/~spraetor
>
> _______________________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Please keep messages on-topic and check the ParaView Wiki at:
> http://paraview.org/Wiki/ParaView
>
> Search the list archives at: http://markmail.org/search/?q=ParaView
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/paraview
>

From mdorier at anl.gov  Wed Sep 21 09:27:41 2016
From: mdorier at anl.gov (Dorier, Matthieu)
Date: Wed, 21 Sep 2016 13:27:41 +0000
Subject: [Paraview] Catalyst: dump everything in C++
Message-ID: <37142D5FC373A846ACE4F75AA11EA84D4CA4C4BE@DITKA.anl.gov>

Hi,

In general the way we create python scripts for a Catalyst-enabled simulation is by first running the simulation with a Python script that writes the data into files, then do offline analysis on those files and export a python script representing the analysis tasks to be done in situ.

I was wondering if, instead of using a Python script for writing all the data into file, an equivalent C++ code was available, and how such a code would be integrated into a Catalyst-enabled simulation? Or maybe just with VTK once the adaptors are written for the simulation's data?

Thanks,

Matthieu
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From andy.bauer at kitware.com  Wed Sep 21 10:25:36 2016
From: andy.bauer at kitware.com (Andy Bauer)
Date: Wed, 21 Sep 2016 10:25:36 -0400
Subject: [Paraview] Catalyst: dump everything in C++
In-Reply-To: <37142D5FC373A846ACE4F75AA11EA84D4CA4C4BE@DITKA.anl.gov>
References: <37142D5FC373A846ACE4F75AA11EA84D4CA4C4BE@DITKA.anl.gov>
Message-ID: <CAMaOp+H7oXRuJJS14LTufOiB_tWCZiwYmAOb43Ys2Uw0Ov9wgA@mail.gmail.com>

Hi Matthieu,

You can indeed use Catalyst without Python. There are two examples in the
Examples/Catalyst subdirectory of the source tree to do that. They are
CxxVTKPipelineExample and CxxPVSMPipelineExample. I wouldn't recommend this
method as the Python route is much simpler. Several people have thought
about avoiding the Python interface and generally come around to its
flexibility (both ease in creating new Catalyst output as well as making
changes without having to recompile code).

In my opinion, if you're not doing image output the C++ route is manageable
without too much difficulty. For image output there's a lot of things which
need to be set in order to get all the lookup tables, data ranges, camera
angle, etc. that can get quite complex. If you look at a GUI generated
Catalyst script for data extract output and compare it to image output
you'll easily see the difference in the complexity. Also, Cinema output is
Python driven so that wouldn't be available through a C++ pipeline.

Now that I've gone through all of this, is there a specific reason why
you're looking to avoid Python?

Best,
Andy

On Wed, Sep 21, 2016 at 9:27 AM, Dorier, Matthieu <mdorier at anl.gov> wrote:

> Hi,
>
> In general the way we create python scripts for a Catalyst-enabled
> simulation is by first running the simulation with a Python script that
> writes the data into files, then do offline analysis on those files and
> export a python script representing the analysis tasks to be done in situ.
>
> I was wondering if, instead of using a Python script for writing all the
> data into file, an equivalent C++ code was available, and how such a code
> would be integrated into a Catalyst-enabled simulation? Or maybe just with
> VTK once the adaptors are written for the simulation's data?
>
> Thanks,
>
> Matthieu
>
> _______________________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at http://www.kitware.com/
> opensource/opensource.html
>
> Please keep messages on-topic and check the ParaView Wiki at:
> http://paraview.org/Wiki/ParaView
>
> Search the list archives at: http://markmail.org/search/?q=ParaView
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/paraview
>
>
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From lokman.rahmani at irisa.fr  Wed Sep 21 10:33:28 2016
From: lokman.rahmani at irisa.fr (Lokman Rahmani)
Date: Wed, 21 Sep 2016 16:33:28 +0200 (CEST)
Subject: [Paraview] Catalyst: dump everything in C++
In-Reply-To: <CAMaOp+H7oXRuJJS14LTufOiB_tWCZiwYmAOb43Ys2Uw0Ov9wgA@mail.gmail.com>
References: <37142D5FC373A846ACE4F75AA11EA84D4CA4C4BE@DITKA.anl.gov>
 <CAMaOp+H7oXRuJJS14LTufOiB_tWCZiwYmAOb43Ys2Uw0Ov9wgA@mail.gmail.com>
Message-ID: <2124046656.2406370.1474468408075.JavaMail.zimbra@irisa.fr>

Thanks Andy, I was not aware of the examples. 

Best, 
Lokman 
================================ 

----- Mail original -----

> De: "Andy Bauer" <andy.bauer at kitware.com>
> ?: "Matthieu Dorier" <mdorier at anl.gov>
> Cc: "ParaView Mailing List ?[paraview at paraview.org]?" <paraview at paraview.org>
> Envoy?: Mercredi 21 Septembre 2016 16:25:36
> Objet: Re: [Paraview] Catalyst: dump everything in C++

> Hi Matthieu,

> You can indeed use Catalyst without Python. There are two examples in the
> Examples/Catalyst subdirectory of the source tree to do that. They are
> CxxVTKPipelineExample and CxxPVSMPipelineExample. I wouldn't recommend this
> method as the Python route is much simpler. Several people have thought
> about avoiding the Python interface and generally come around to its
> flexibility (both ease in creating new Catalyst output as well as making
> changes without having to recompile code).

> In my opinion, if you're not doing image output the C++ route is manageable
> without too much difficulty. For image output there's a lot of things which
> need to be set in order to get all the lookup tables, data ranges, camera
> angle, etc. that can get quite complex. If you look at a GUI generated
> Catalyst script for data extract output and compare it to image output
> you'll easily see the difference in the complexity. Also, Cinema output is
> Python driven so that wouldn't be available through a C++ pipeline.

> Now that I've gone through all of this, is there a specific reason why you're
> looking to avoid Python?

> Best,
> Andy

> On Wed, Sep 21, 2016 at 9:27 AM, Dorier, Matthieu < mdorier at anl.gov > wrote:

> > Hi,
> 

> > In general the way we create python scripts for a Catalyst-enabled
> > simulation
> > is by first running the simulation with a Python script that writes the
> > data
> > into files, then do offline analysis on those files and export a python
> > script representing the analysis tasks to be done in situ.
> 

> > I was wondering if, instead of using a Python script for writing all the
> > data
> > into file, an equivalent C++ code was available, and how such a code would
> > be integrated into a Catalyst-enabled simulation? Or maybe just with VTK
> > once the adaptors are written for the simulation's data?
> 

> > Thanks,
> 

> > Matthieu
> 

> > _______________________________________________
> 
> > Powered by www.kitware.com
> 

> > Visit other Kitware open-source projects at
> > http://www.kitware.com/opensource/opensource.html
> 

> > Please keep messages on-topic and check the ParaView Wiki at:
> > http://paraview.org/Wiki/ParaView
> 

> > Search the list archives at: http://markmail.org/search/?q=ParaView
> 

> > Follow this link to subscribe/unsubscribe:
> 
> > http://public.kitware.com/mailman/listinfo/paraview
> 

> _______________________________________________
> Powered by www.kitware.com

> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html

> Please keep messages on-topic and check the ParaView Wiki at:
> http://paraview.org/Wiki/ParaView

> Search the list archives at: http://markmail.org/search/?q=ParaView

> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/paraview
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From mdorier at anl.gov  Wed Sep 21 10:41:21 2016
From: mdorier at anl.gov (Dorier, Matthieu)
Date: Wed, 21 Sep 2016 14:41:21 +0000
Subject: [Paraview] Catalyst: dump everything in C++
In-Reply-To: <2124046656.2406370.1474468408075.JavaMail.zimbra@irisa.fr>
References: <37142D5FC373A846ACE4F75AA11EA84D4CA4C4BE@DITKA.anl.gov>
 <CAMaOp+H7oXRuJJS14LTufOiB_tWCZiwYmAOb43Ys2Uw0Ov9wgA@mail.gmail.com>,
 <2124046656.2406370.1474468408075.JavaMail.zimbra@irisa.fr>
Message-ID: <37142D5FC373A846ACE4F75AA11EA84D4CA4C516@DITKA.anl.gov>

Hi,

The reason I would like a C++ pipeline is that I have a simulation that has several available output formats (HDF5, etc.) and I would like to make VTK one of the possible formats. Since the simulation is instrumented with Catalyst, it would be easy to just use a Python script building a pipeline that just output the data, but I'd like to avoid having to carry around a Python script that the user may forget to copy in his working directory when the simulation is launched. I'd find it cleaner to have this particular pipeline setup in C++.

Thanks,

Matthieu

________________________________
From: Lokman Rahmani [lokman.rahmani at irisa.fr]
Sent: Wednesday, September 21, 2016 9:33 AM
To: Andy Bauer
Cc: Dorier, Matthieu; ParaView Mailing List ?[paraview at paraview.org]?
Subject: Re: [Paraview] Catalyst: dump everything in C++

Thanks Andy, I was not aware of the examples.

Best,
Lokman
================================


________________________________
De: "Andy Bauer" <andy.bauer at kitware.com>
?: "Matthieu Dorier" <mdorier at anl.gov>
Cc: "ParaView Mailing List ?[paraview at paraview.org]?" <paraview at paraview.org>
Envoy?: Mercredi 21 Septembre 2016 16:25:36
Objet: Re: [Paraview] Catalyst: dump everything in C++

Hi Matthieu,

You can indeed use Catalyst without Python. There are two examples in the Examples/Catalyst subdirectory of the source tree to do that. They are CxxVTKPipelineExample and CxxPVSMPipelineExample. I wouldn't recommend this method as the Python route is much simpler. Several people have thought about avoiding the Python interface and generally come around to its flexibility (both ease in creating new Catalyst output as well as making changes without having to recompile code).

In my opinion, if you're not doing image output the C++ route is manageable without too much difficulty. For image output there's a lot of things which need to be set in order to get all the lookup tables, data ranges, camera angle, etc. that can get quite complex. If you look at a GUI generated Catalyst script for data extract output and compare it to image output you'll easily see the difference in the complexity. Also, Cinema output is Python driven so that wouldn't be available through a C++ pipeline.

Now that I've gone through all of this, is there a specific reason why you're looking to avoid Python?

Best,
Andy

On Wed, Sep 21, 2016 at 9:27 AM, Dorier, Matthieu <mdorier at anl.gov<mailto:mdorier at anl.gov>> wrote:
Hi,

In general the way we create python scripts for a Catalyst-enabled simulation is by first running the simulation with a Python script that writes the data into files, then do offline analysis on those files and export a python script representing the analysis tasks to be done in situ.

I was wondering if, instead of using a Python script for writing all the data into file, an equivalent C++ code was available, and how such a code would be integrated into a Catalyst-enabled simulation? Or maybe just with VTK once the adaptors are written for the simulation's data?

Thanks,

Matthieu

_______________________________________________
Powered by www.kitware.com<http://www.kitware.com>

Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html

Please keep messages on-topic and check the ParaView Wiki at: http://paraview.org/Wiki/ParaView

Search the list archives at: http://markmail.org/search/?q=ParaView

Follow this link to subscribe/unsubscribe:
http://public.kitware.com/mailman/listinfo/paraview



_______________________________________________
Powered by www.kitware.com

Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html

Please keep messages on-topic and check the ParaView Wiki at: http://paraview.org/Wiki/ParaView

Search the list archives at: http://markmail.org/search/?q=ParaView

Follow this link to subscribe/unsubscribe:
http://public.kitware.com/mailman/listinfo/paraview

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From lokman.rahmani at irisa.fr  Wed Sep 21 10:29:28 2016
From: lokman.rahmani at irisa.fr (Lokman Rahmani)
Date: Wed, 21 Sep 2016 16:29:28 +0200 (CEST)
Subject: [Paraview] Catalyst: dump everything in C++
In-Reply-To: <37142D5FC373A846ACE4F75AA11EA84D4CA4C4BE@DITKA.anl.gov>
References: <37142D5FC373A846ACE4F75AA11EA84D4CA4C4BE@DITKA.anl.gov>
Message-ID: <1807618493.2404032.1474468168503.JavaMail.zimbra@irisa.fr>

Hi Matthieu! 

I investigated the same question recently, here is what I found so far. 

In Catalyst/CoProcessing the python script is used to create a vtk pipeline 

--------- 
vtkNew<vtkCPPythonScriptPipeline> pipeline; 
pipeline->Initialize(scriptPath) 
--------- 

This pipeline will be passed to vtk processor that will do the CoPorcessing by executing the pipeline 

------ 
vtkCPProcessor* Processor = vtkCPProcessor::New(); 
Processor->Initialize(); 
Processor->AddPipeline(pipeline.GetPointer()); 
Processor->CcProcess(...) 
------ 

checking the souce code of VtkCPProcessor ( https://gitlab.kitware.com/paraview/paraview/blob/master/CoProcessing/Catalyst/vtkCPProcessor.h ) 

---- 

/// Add in a pipeline that is externally configured. Returns 1 if /// successful and 0 otherwise. virtual int AddPipeline ( vtkCPPipeline * pipeline ); 
------- 

a vtkCPProcessor object can add a pipeline of any class extending the vtkCPPipeline (which is a an abstract class) 

Beside of the official python implementation ( https://gitlab.kitware.com/paraview/paraview/blob/master/CoProcessing/PythonCatalyst/vtkCPPythonScriptPipeline.h ) I am not aware of any other implementation. 

Otherwise, you can to implement your own implementation (which looks very time consuming ...). 
http://www.vtk.org/Wiki/VTK/Tutorials/New_Pipeline 

Hope this helps. 

I'll be interested if some one is aware of any c++ implementation of the pipeline. 

Best, 
Lokman 

================================ 

----- Mail original -----

> De: "Matthieu Dorier" <mdorier at anl.gov>
> ?: "ParaView Mailing List ?[paraview at paraview.org]?" <paraview at paraview.org>
> Envoy?: Mercredi 21 Septembre 2016 15:27:41
> Objet: [Paraview] Catalyst: dump everything in C++

> Hi,

> In general the way we create python scripts for a Catalyst-enabled simulation
> is by first running the simulation with a Python script that writes the data
> into files, then do offline analysis on those files and export a python
> script representing the analysis tasks to be done in situ.

> I was wondering if, instead of using a Python script for writing all the data
> into file, an equivalent C++ code was available, and how such a code would
> be integrated into a Catalyst-enabled simulation? Or maybe just with VTK
> once the adaptors are written for the simulation's data?

> Thanks,

> Matthieu

> _______________________________________________
> Powered by www.kitware.com

> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html

> Please keep messages on-topic and check the ParaView Wiki at:
> http://paraview.org/Wiki/ParaView

> Search the list archives at: http://markmail.org/search/?q=ParaView

> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/paraview
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From andy.bauer at kitware.com  Wed Sep 21 10:55:16 2016
From: andy.bauer at kitware.com (Andy Bauer)
Date: Wed, 21 Sep 2016 10:55:16 -0400
Subject: [Paraview] Catalyst: dump everything in C++
In-Reply-To: <1807618493.2404032.1474468168503.JavaMail.zimbra@irisa.fr>
References: <37142D5FC373A846ACE4F75AA11EA84D4CA4C4BE@DITKA.anl.gov>
 <1807618493.2404032.1474468168503.JavaMail.zimbra@irisa.fr>
Message-ID: <CAMaOp+HgPaQ_X6=Poa-0ko6j00crQAfY2mTHPj0p3npVeidAvQ@mail.gmail.com>

Hi Matthieu,

That makes complete sense. I've thought about putting in a C++ Catalyst
pipeline in the main source code that could be used to just write out the
data at some prescribed file name and frequency but haven't forced myself
to do it. It gets slightly more complicated when dealing with multiple
inputs. In the Examples/Catalyst/SampleScripts subdirectory of the source
code there are two Python scripts that can be used to write out the full
grid, gridwriter.py and allinputsgridwriter.py.

If you create a C++ script to do that and want to have it added into
ParaView, I can help with that. Otherwise, I'll get to it eventually...

Cheers,
Andy


On Wed, Sep 21, 2016 at 10:29 AM, Lokman Rahmani <lokman.rahmani at irisa.fr>
wrote:

> Hi Matthieu!
>
> I investigated the same question recently, here is what I found so far.
>
> In Catalyst/CoProcessing the python script is used to create a vtk pipeline
>
> ---------
> vtkNew<vtkCPPythonScriptPipeline> pipeline;
>
> pipeline->Initialize(scriptPath)
> ---------
>
> This pipeline will be passed to vtk processor that will do the
> CoPorcessing by executing the pipeline
>
> ------
> vtkCPProcessor* Processor = vtkCPProcessor::New();
>
> Processor->Initialize();
> Processor->AddPipeline(pipeline.GetPointer());
> Processor->CcProcess(...)
> ------
>
> checking the souce code of VtkCPProcessor (https://gitlab.kitware.com/
> paraview/paraview/blob/master/CoProcessing/Catalyst/vtkCPProcessor.h)
>
> ----
>
>   /// Add in a pipeline that is externally configured. Returns 1 if  /// successful and 0 otherwise.  virtual int AddPipeline(vtkCPPipeline* pipeline);
>
> -------
>
> a vtkCPProcessor object can add a pipeline of any class extending the
> vtkCPPipeline (which is a an abstract class)
>
> Beside of the official python implementation (https://gitlab.kitware.com/
> paraview/paraview/blob/master/CoProcessing/PythonCatalyst/
> vtkCPPythonScriptPipeline.h) I am not aware of any other implementation.
>
> Otherwise, you can to implement your own implementation (which looks very
> time consuming ...).
> http://www.vtk.org/Wiki/VTK/Tutorials/New_Pipeline
>
> Hope this helps.
>
> I'll be interested if some one is aware of any c++ implementation of the
> pipeline.
>
> Best,
> Lokman
>
> ================================
>
>
> ------------------------------
>
> *De: *"Matthieu Dorier" <mdorier at anl.gov>
> *?: *"ParaView Mailing List ?[paraview at paraview.org]?" <
> paraview at paraview.org>
> *Envoy?: *Mercredi 21 Septembre 2016 15:27:41
> *Objet: *[Paraview] Catalyst: dump everything in C++
>
>
> Hi,
>
> In general the way we create python scripts for a Catalyst-enabled
> simulation is by first running the simulation with a Python script that
> writes the data into files, then do offline analysis on those files and
> export a python script representing the analysis tasks to be done in situ.
>
> I was wondering if, instead of using a Python script for writing all the
> data into file, an equivalent C++ code was available, and how such a code
> would be integrated into a Catalyst-enabled simulation? Or maybe just with
> VTK once the adaptors are written for the simulation's data?
>
> Thanks,
>
> Matthieu
>
> _______________________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at http://www.kitware.com/
> opensource/opensource.html
>
> Please keep messages on-topic and check the ParaView Wiki at:
> http://paraview.org/Wiki/ParaView
>
> Search the list archives at: http://markmail.org/search/?q=ParaView
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/paraview
>
>
>
> _______________________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at http://www.kitware.com/
> opensource/opensource.html
>
> Please keep messages on-topic and check the ParaView Wiki at:
> http://paraview.org/Wiki/ParaView
>
> Search the list archives at: http://markmail.org/search/?q=ParaView
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/paraview
>
>
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From Simon.Praetorius at tu-dresden.de  Wed Sep 21 11:06:24 2016
From: Simon.Praetorius at tu-dresden.de (Simon Praetorius)
Date: Wed, 21 Sep 2016 15:06:24 +0000
Subject: [Paraview] old issue: using timeseries stored in a vtk xml file
In-Reply-To: <CADHSJjDcpjGSg6jZJ=zQZAxG8p_AAR-9pKp+oVOqM7yKk9zzNw@mail.gmail.com>
References: <20160920171049.Horde.F3MMLuIH9ta_S4fSALQRUvC@mail.zih.tu-dresden.de>
 <20160921085315.Horde.u2qd1QGji7nwtpaLDXcScPe@mail.zih.tu-dresden.de>
 <CADHSJjDcpjGSg6jZJ=zQZAxG8p_AAR-9pKp+oVOqM7yKk9zzNw@mail.gmail.com>
Message-ID: <20160921150624.Horde.4eFhzHVvsGb9e1PSbRbGY6b@mail.zih.tu-dresden.de>

Yes, it seems to be kind of a VTK bug, since the corresponding .vtu  
file can be created by a VTK test  
(IO/XML/Testing/Cxx/TestXMLCInterface.c) but not read back by  
VTLXMLUnstructuredGridReader (e.g. Examples/IO/Cxx/DumpXMLFile.cxx)

I will submit a report to the VTK mailinglist somehow.

Simon


Zitat von Utkarsh Ayachit <utkarsh.ayachit at kitware.com>:

> Simon,
>
> If it's not working anymore, I am afraid it's broken in VTK reader
> itself, not just ParaView. ParaView doesn't dictate these things, the
> reader decides how to such things are handled. It would be great if
> you can report an issue on the bug tracker with a sample dataset, if
> possible.
>
> Utkarsh
>
> On Wed, Sep 21, 2016 at 4:53 AM, Simon Praetorius
> <Simon.Praetorius at tu-dresden.de> wrote:
>> Hi,
>>
>> In the year 2007 there was an issue on the issue-tracker (ID #5542)
>> about storing a timeseries of data in a single vtk xml file, e.g.
>> when you have many timesteps with a non-changing mesh. Exactly this
>> problem I stepped over yesterday, tried the example file in the "fixed"
>> issue and found out that it is not possible (any more (?)). Is this
>> feature remove from the vtk reader? Or just from paraview? Is there
>> an alternative way of storing multiple timestep data-sets while
>> storing the mesh only once?
>>
>> Best,
>> Simon
>>
>>
>>
>>
>> --
>> Dr. Simon Praetorius
>> Institut f?r Wissenschaftliches Rechnen
>> Fachrichtung Mathematik
>> Technische Universit?t Dresden
>> Tel.: TUD-42377
>> Mail: simon.praetorius at tu-dresden.de
>> Web: www.math.tu-dresden.de/~spraetor
>>
>> _______________________________________________
>> Powered by www.kitware.com
>>
>> Visit other Kitware open-source projects at
>> http://www.kitware.com/opensource/opensource.html
>>
>> Please keep messages on-topic and check the ParaView Wiki at:
>> http://paraview.org/Wiki/ParaView
>>
>> Search the list archives at: http://markmail.org/search/?q=ParaView
>>
>> Follow this link to subscribe/unsubscribe:
>> http://public.kitware.com/mailman/listinfo/paraview
>>



-- 
Dr. Simon Praetorius
Institut f?r Wissenschaftliches Rechnen
Fachrichtung Mathematik
Technische Universit?t Dresden
Tel.: TUD-42377
Mail: simon.praetorius at tu-dresden.de
Web: www.math.tu-dresden.de/~spraetor
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From dave.demarle at kitware.com  Wed Sep 21 14:42:45 2016
From: dave.demarle at kitware.com (David E DeMarle)
Date: Wed, 21 Sep 2016 14:42:45 -0400
Subject: [Paraview] pvbatch hangs when enabling OSPRay
In-Reply-To: <CA+G-nc7xeiXVJ-=dtkb=Te=OPrUOmjbCd7PEVUFRzUThmFbm4g@mail.gmail.com>
References: <CA+G-nc7xeiXVJ-=dtkb=Te=OPrUOmjbCd7PEVUFRzUThmFbm4g@mail.gmail.com>
Message-ID: <CANjZAi-4FuUDFboVb2iDOFsyC7uZ-svuY5_r3NS5xSoysgXHJw@mail.gmail.com>

Ben,

I am not able to reproduce this locally. Can you file an issue to help me
keep track of it on ParaView's new gitlab issue tracker?

https://gitlab.kitware.com/paraview/paraview/issues


David E DeMarle
Kitware, Inc.
R&D Engineer
21 Corporate Drive
Clifton Park, NY 12065-8662
Phone: 518-881-4909

On Thu, Aug 4, 2016 at 3:24 PM, Benjam?n Hern?ndez <benjha at gmail.com> wrote:

> Hello,
>
> I've compiled Paraview 5.1 with multithreaded mpi and ospray (with OpenMP)
> support using the next  modules:
>
>   1) gcc/4.8.2            5) xalt/0.5.3           9) szip/2.1
>  13) boost/1.61.0
>   2) openmpi/1.8.4_mtm    6) DefApps             10) hdf5/1.8.11
> 14) libtool/2.4.2
>   3) PE-gnu/4.8.2-1.8.4   7) qt4/4.8.5           11) mxml/2.9
>  15) git/1.8.0.2
>   4) lustredu/1.4         8) python/2.7.9        12) adios/1.9.0
> 16) cmake/3.5.2
>
>
> and wrote a python script that loads a  vtu file  and renders it as glyph
> particles.
>
> When running pvbatch in one node it works fine, I can visualize and save
> images. However, when running pvbatch with mpi the script just hangs in the
> line  that enables OSPRay:
>
> oSPRayRendered3DView1.EnableOSPRay = 1
>
>
> I am using the next mpi  commands with no success:
>
> mpirun -npernode 16 pvbatch  --mpi --use-offscreen-rendering myscript
> inputfile.vtu outputimage.png
>
> mpirun -np 13 --map-by ppr:1:socket:pe=16 pvbatch  --mpi
> --use-offscreen-rendering myscript inputfile.vtu outputimage.png
>
>
> I did a simpler script that does the following:
>
> #### import the simple module from the paraview
> from paraview.simple import *
> #### disable automatic camera reset on 'Show'
> paraview.simple._DisableFirstRenderCameraReset()
>
> # set active view
> SetActiveView(None)
> CreateLayout('Layout #1')
>
> # Create a new 'Render View'
> print "Creating render view"
> renderView1 = CreateView('RenderView')
> renderView1.ViewSize = [11520, 3240]
> renderView1.CameraPosition = [0.0, 0.0, 6.69]
> renderView1.CameraFocalPoint = [0.0, 0.0, 0.0]
> renderView1.CameraViewUp = [0.0, 1.0, 0.0]
> renderView1.CameraViewAngle = 30.0
> renderView1.CameraParallelScale = 1.73
> renderView1.Background = [0.32, 0.34, 0.43]
> print "Before Enabling OSPRay"
> renderView1.EnableOSPRay = 1
> print "After Enabling OSPRay"
> renderView1.Shadows = 1
> renderView1.AmbientSamples = 4
> renderView1.SamplesPerPixel = 8
> renderView1.MaxFrames = 1
> renderView1.LightScale = 1.0
>
> print "Done!"
>
>
> #### saving camera placements for all active views
>
> # current camera placement for renderView1
> renderView1.CameraPosition = [148.48492741767512, 106.10239872416838,
> -28480.984448300518]
> renderView1.CameraFocalPoint = [137.62326776804608, 95.85538889348155,
> -28593.41405565134]
> renderView1.CameraViewUp = [-0.529722197084864, 0.8477698001026378,
> -0.02609137691878691]
> renderView1.CameraParallelScale = 19159.165918040744
>
>
>
> but it  never reaches the print "After Enabling OSPRay" line
>
>
>
> Any advice will be appreciated,
>
>
>
> Benjamin Hernandez
> OLCF
> Oak Ridge National Laboratory
>
>
> _______________________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at http://www.kitware.com/
> opensource/opensource.html
>
> Please keep messages on-topic and check the ParaView Wiki at:
> http://paraview.org/Wiki/ParaView
>
> Search the list archives at: http://markmail.org/search/?q=ParaView
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/paraview
>
>
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From benjha at gmail.com  Thu Sep 22 10:49:25 2016
From: benjha at gmail.com (=?UTF-8?B?QmVuamFtw61uIEhlcm7DoW5kZXo=?=)
Date: Thu, 22 Sep 2016 10:49:25 -0400
Subject: [Paraview] pvbatch hangs when enabling OSPRay
In-Reply-To: <CANjZAi-4FuUDFboVb2iDOFsyC7uZ-svuY5_r3NS5xSoysgXHJw@mail.gmail.com>
References: <CA+G-nc7xeiXVJ-=dtkb=Te=OPrUOmjbCd7PEVUFRzUThmFbm4g@mail.gmail.com>
 <CANjZAi-4FuUDFboVb2iDOFsyC7uZ-svuY5_r3NS5xSoysgXHJw@mail.gmail.com>
Message-ID: <CA+G-nc5UbCyK05Xf0MfMM8xz2VzfO4L2g-U9UkP750F65r_jKA@mail.gmail.com>

Sure Dave,

I forget to mention I found no problems when running paraview GUI and
ospray renderer in an interactive session in the cluster.

Regards,



On Wed, Sep 21, 2016 at 2:42 PM, David E DeMarle
<dave.demarle at kitware.com> wrote:
> Ben,
>
> I am not able to reproduce this locally. Can you file an issue to help me
> keep track of it on ParaView's new gitlab issue tracker?
>
> https://gitlab.kitware.com/paraview/paraview/issues
>
>
> David E DeMarle
> Kitware, Inc.
> R&D Engineer
> 21 Corporate Drive
> Clifton Park, NY 12065-8662
> Phone: 518-881-4909
>
> On Thu, Aug 4, 2016 at 3:24 PM, Benjam?n Hern?ndez <benjha at gmail.com> wrote:
>>
>> Hello,
>>
>> I've compiled Paraview 5.1 with multithreaded mpi and ospray (with OpenMP)
>> support using the next  modules:
>>
>>   1) gcc/4.8.2            5) xalt/0.5.3           9) szip/2.1
>> 13) boost/1.61.0
>>   2) openmpi/1.8.4_mtm    6) DefApps             10) hdf5/1.8.11
>> 14) libtool/2.4.2
>>   3) PE-gnu/4.8.2-1.8.4   7) qt4/4.8.5           11) mxml/2.9
>> 15) git/1.8.0.2
>>   4) lustredu/1.4         8) python/2.7.9        12) adios/1.9.0
>> 16) cmake/3.5.2
>>
>>
>> and wrote a python script that loads a  vtu file  and renders it as glyph
>> particles.
>>
>> When running pvbatch in one node it works fine, I can visualize and save
>> images. However, when running pvbatch with mpi the script just hangs in the
>> line  that enables OSPRay:
>>
>> oSPRayRendered3DView1.EnableOSPRay = 1
>>
>>
>> I am using the next mpi  commands with no success:
>>
>> mpirun -npernode 16 pvbatch  --mpi --use-offscreen-rendering myscript
>> inputfile.vtu outputimage.png
>>
>> mpirun -np 13 --map-by ppr:1:socket:pe=16 pvbatch  --mpi
>> --use-offscreen-rendering myscript inputfile.vtu outputimage.png
>>
>>
>> I did a simpler script that does the following:
>>
>> #### import the simple module from the paraview
>> from paraview.simple import *
>> #### disable automatic camera reset on 'Show'
>> paraview.simple._DisableFirstRenderCameraReset()
>>
>> # set active view
>> SetActiveView(None)
>> CreateLayout('Layout #1')
>>
>> # Create a new 'Render View'
>> print "Creating render view"
>> renderView1 = CreateView('RenderView')
>> renderView1.ViewSize = [11520, 3240]
>> renderView1.CameraPosition = [0.0, 0.0, 6.69]
>> renderView1.CameraFocalPoint = [0.0, 0.0, 0.0]
>> renderView1.CameraViewUp = [0.0, 1.0, 0.0]
>> renderView1.CameraViewAngle = 30.0
>> renderView1.CameraParallelScale = 1.73
>> renderView1.Background = [0.32, 0.34, 0.43]
>> print "Before Enabling OSPRay"
>> renderView1.EnableOSPRay = 1
>> print "After Enabling OSPRay"
>> renderView1.Shadows = 1
>> renderView1.AmbientSamples = 4
>> renderView1.SamplesPerPixel = 8
>> renderView1.MaxFrames = 1
>> renderView1.LightScale = 1.0
>>
>> print "Done!"
>>
>>
>> #### saving camera placements for all active views
>>
>> # current camera placement for renderView1
>> renderView1.CameraPosition = [148.48492741767512, 106.10239872416838,
>> -28480.984448300518]
>> renderView1.CameraFocalPoint = [137.62326776804608, 95.85538889348155,
>> -28593.41405565134]
>> renderView1.CameraViewUp = [-0.529722197084864, 0.8477698001026378,
>> -0.02609137691878691]
>> renderView1.CameraParallelScale = 19159.165918040744
>>
>>
>>
>> but it  never reaches the print "After Enabling OSPRay" line
>>
>>
>>
>> Any advice will be appreciated,
>>
>>
>>
>> Benjamin Hernandez
>> OLCF
>> Oak Ridge National Laboratory
>>
>>
>> _______________________________________________
>> Powered by www.kitware.com
>>
>> Visit other Kitware open-source projects at
>> http://www.kitware.com/opensource/opensource.html
>>
>> Please keep messages on-topic and check the ParaView Wiki at:
>> http://paraview.org/Wiki/ParaView
>>
>> Search the list archives at: http://markmail.org/search/?q=ParaView
>>
>> Follow this link to subscribe/unsubscribe:
>> http://public.kitware.com/mailman/listinfo/paraview
>>
>



-- 
---
---
B HDz
benjha at gmail.com

From chuck.atkins at kitware.com  Fri Sep 23 15:05:03 2016
From: chuck.atkins at kitware.com (Chuck Atkins)
Date: Fri, 23 Sep 2016 15:05:03 -0400
Subject: [Paraview] Which Compilers and Operating Systems to you require for
	VTK and / ParaView?
Message-ID: <CAOXZzG6zhq=vhNeP_2H_hgdiHQht2pvgC6JFnLXQ2nRjf-X_Xw@mail.gmail.com>

We're trying to identify where we may have gaps in our testing
infrastructure for both VTK and ParaView and how to prioritize filling
those gaps. Certain compilers like GCC and Intel on Linux or Visual Studio
on Windows will essentially always be supported with issues addressed
ASAP.  Others, however, sometimes come and go depending on available
testing resources, licensing, customer demand, etc.

Please take a brief moment to let us know which operating systems and
compilers are important to howe you use VTK and ParaView from a testing and
support standpoint.  The survey is very brief and should only take a minute
or two.

Note: If you are a current support customer with specific critical
requirements, please feel free to email me off-list.

https://docs.google.com/forms/d/e/1FAIpQLSczYSEWMr90ywhTg1jLg2u6JWVNRh6zUzCLeFPRnc_Qyc13dg/viewform

Thank you.

----------
Chuck Atkins
Staff R&D Engineer, Scientific Computing
Kitware, Inc.
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From Stefan.Melber at DLR.de  Mon Sep 26 01:11:29 2016
From: Stefan.Melber at DLR.de (Stefan Melber)
Date: Mon, 26 Sep 2016 07:11:29 +0200
Subject: [Paraview] Combination of polygonal-data and unstructured grid?
Message-ID: <e883554e-4476-f8c6-755c-549d1e5449a2@DLR.de>

Hi,

i have a question how to create volume data with complex shaped 
elements. An example of the "problem" is using the sphere-source and cut 
the resulting sphere you will get only the shell (because polydata is 
surface-data!) but not the enclosed volume. On the other side using 
unstructured grid data (e.g. for a box) and cut this one you will get 
the shell and the volume.

My problem is now i have a set of complex shaped volumes (dual-grid 
data) which cannot be found in the list of cell types for unstructured 
grid data. Therefore i use the polygonal data and color each cell with 
one color. Of course for further analysis (e.g. integration of the cell 
volumes, volume gradient and so on) i need a way to give a set of 
(closed surface) poly-data elements a kind connection to form a volume 
to handle them together.

Is there a way to perform this task?

      Stefan


================================================================

                      _/ *Dr. Stefan Melber-Wilkending*
                    _/_/
                  _/  _/             Deutsches Zentrum f?r Luft-
          _/_/_/_/_/_/_/_/_/_/         und Raumfahrt e.V. (DLR)
        _/    _/    _/    _/
      _/    _/    _/    _/             German Aerospace Center
    _/_/_/_/_/_/_/_/_/_/              Institute of Aerodynamics
          _/  _/  _      _               and Flow Technology
          _/_/   | \ |  |_|           Transport Aircraft Branch
          _/     |_/ |_ | \
                                          Lilienthalplatz 7
  Fields of activities:                  38108 Braunschweig
                                              Germany
  o Numerical Windtunnel Simulation
  o Aero-Acoustic Windtunnel Design    Phone : +49 531/295-2836
  o Numerical Optimization             Fax. .: +49 531/295-2914
  o Visualization Techniques
  o High-Lift Aerodynamics           Email : Stefan.Melber at DLR.de
  o Glider-Aerodynamics              Web ..: http://www.dlr.de/AS

================================================================

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From frank.albina at sauber-motorsport.com  Mon Sep 26 04:55:37 2016
From: frank.albina at sauber-motorsport.com (Albina, Frank)
Date: Mon, 26 Sep 2016 10:55:37 +0200
Subject: [Paraview] Paraview v5.1.2: SurfaceLIC & software rendering issues
Message-ID: <4373b551-40c8-44ca-8b27-9106bceac88c@srvcli01.spe-ch-md9.net>

Dear all,

I have downloaded from the paraview.org the latest binaries for Linux of ParaView v5.1.2. My main purpose is to make use of ParaView with software rendering in a clustered environment without GPU and, as such, I have been going through my small benchmark on a generic F1 car.

This what I have found so far when generating a SurfaceLIC representation on the whole car surface in batch mode.

Using pvbatch -mesa-llvm works fine. This is one of the produced images for reference:
[cid:image001.jpg at 01D217E4.08171B00]
Using 4 cores to perform the same task (with the same script) with mpiexec -np 4 pvbatch --mesa-llvm shows a good speed-up but the background is black instead of white (although view.Backgound = [1,1,1] is set explicitely), as shown hereafter:

[cid:image002.jpg at 01D217E4.08171B00]

On the same server (Intel Xeon ES-2650 v3), the CPU is AVX2 capable, so I tried also the same script with pvbatch --mesa-swr-avx2. The image background is corrupted with leftover frames apparently, as shown hereafter:

[cid:image003.jpg at 01D217E4.08171B00]
Was this behavior to be expected?

Please let me know if there is any interest in providing with my benchmark.

Frank Albina


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From frank.albina at sauber-motorsport.com  Mon Sep 26 05:17:14 2016
From: frank.albina at sauber-motorsport.com (Albina, Frank)
Date: Mon, 26 Sep 2016 11:17:14 +0200
Subject: [Paraview] Building ParaView v5.1.2 on Linux from source with
 support for GPU and SWR.
Message-ID: <591d7e7c-08d5-4787-8703-d90fd2be1bdb@srvcli01.spe-ch-md9.net>

Dear all,
after having downloaded last week the latest ParaView release (v5.1.2) for Linux, I have found out that the binary version has the following folder structure in lib/paraview-5.1:
mesa-llvm
|-- libGL.so -> libGL.so.1
|-- libGL.so.1 -> libGL.so.1.5
|-- libGL.so.1.5
|-- libOSMesa.so -> libOSMesa.so.8
|-- libOSMesa.so.8 -> libOSMesa.so.8.0.0
`-- libOSMesa.so.8.0.0
mesa-swr-avx
|-- libGL.so -> libGL.so.1
|-- libGL.so.1 -> libGL.so.1.5
|-- libGL.so.1.5
|-- libOSMesa.so -> libOSMesa.so.8
|-- libOSMesa.so.8 -> libOSMesa.so.8.0.0
`-- libOSMesa.so.8.0.0
mesa-swr-avx2
|-- libGL.so -> libGL.so.1
|-- libGL.so.1 -> libGL.so.1.5
|-- libGL.so.1.5
|-- libOSMesa.so -> libOSMesa.so.8
|-- libOSMesa.so.8 -> libOSMesa.so.8.0.0
`-- libOSMesa.so.8.0.0
Which is an elegant way of providing a binary package for GPU and non-GPU architectures at the same time.
Hence my question: How do I build ParaView v5.1.2 from source to have the same folder structure so that I have one version for GPU and software rendering? I understand that swr-avx(2) should be also available from Mesa v12.x. Is there anything I'd need to consider / take care of before building the different OSMesa libraries with LLVM / OpenSWR?
Frank Albina


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From benson_muite at yahoo.com  Mon Sep 26 05:17:27 2016
From: benson_muite at yahoo.com (Benson Muite)
Date: Mon, 26 Sep 2016 12:17:27 +0300
Subject: [Paraview] Paraview v5.1.2: SurfaceLIC & software rendering
 issues
In-Reply-To: <4373b551-40c8-44ca-8b27-9106bceac88c@srvcli01.spe-ch-md9.net>
References: <4373b551-40c8-44ca-8b27-9106bceac88c@srvcli01.spe-ch-md9.net>
Message-ID: <4c88d331-ce16-b8d1-6fe4-269df9877947@yahoo.com>

Hi,

Is the benchmark available? Would be interested in looking at this if 
possible to get example code.

Regards,

Benson


On 09/26/2016 11:55 AM, Albina, Frank wrote:
>
> Dear all,
>
> I have downloaded from the paraview.org the latest binaries for Linux 
> of ParaView v5.1.2. My main purpose is to make use of ParaView with 
> software rendering in a clustered environment without GPU and, as 
> such, I have been going through my small benchmark on a generic F1 car.
>
> This what I have found so far when generating a SurfaceLIC 
> representation on the whole car surface in batch mode.
>
> Using pvbatch ?mesa-llvm works fine. This is one of the produced 
> images for reference:
>
> Using 4 cores to perform the same task (with the same script) with 
> mpiexec ?np 4 pvbatch --mesa-llvm shows a good speed-up but the 
> background is black instead of white (although view.Backgound = 
> [1,1,1] is set explicitely), as shown hereafter:
>
> On the same server (Intel Xeon ES-2650 v3), the CPU is AVX2 capable, 
> so I tried also the same script with pvbatch --mesa-swr-avx2. The 
> image background is corrupted with leftover frames apparently, as 
> shown hereafter:
>
> Was this behavior to be expected?
>
> Please let me know if there is any interest in providing with my 
> benchmark.
>
> *Frank Albina*
>
>
>
> _______________________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html
>
> Please keep messages on-topic and check the ParaView Wiki at: http://paraview.org/Wiki/ParaView
>
> Search the list archives at: http://markmail.org/search/?q=ParaView
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/paraview

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From frank.albina at sauber-motorsport.com  Mon Sep 26 05:22:26 2016
From: frank.albina at sauber-motorsport.com (Albina, Frank)
Date: Mon, 26 Sep 2016 11:22:26 +0200
Subject: [Paraview] Paraview v5.1.2: SurfaceLIC & software rendering
 issues
In-Reply-To: <4c88d331-ce16-b8d1-6fe4-269df9877947@yahoo.com>
References: <4373b551-40c8-44ca-8b27-9106bceac88c@srvcli01.spe-ch-md9.net>
 <4c88d331-ce16-b8d1-6fe4-269df9877947@yahoo.com>
Message-ID: <a4c51f72-f684-4bbf-871d-ba4fb5002935@srvcli01.spe-ch-md9.net>

Benson,

do you need the data and the example code, or only the example code?

Frank.

From: Benson Muite [mailto:benson_muite at yahoo.com]
Sent: Montag, 26. September 2016 11:17
To: Albina, Frank; paraview at paraview.org
Cc: Del Citto, Francesco
Subject: Re: [Paraview] Paraview v5.1.2: SurfaceLIC & software rendering issues


Hi,

Is the benchmark available? Would be interested in looking at this if possible to get example code.

Regards,

Benson

On 09/26/2016 11:55 AM, Albina, Frank wrote:
Dear all,

I have downloaded from the paraview.org the latest binaries for Linux of ParaView v5.1.2. My main purpose is to make use of ParaView with software rendering in a clustered environment without GPU and, as such, I have been going through my small benchmark on a generic F1 car.

This what I have found so far when generating a SurfaceLIC representation on the whole car surface in batch mode.

Using pvbatch -mesa-llvm works fine. This is one of the produced images for reference:
[cid:image001.jpg at 01D217E8.426FCB40]
Using 4 cores to perform the same task (with the same script) with mpiexec -np 4 pvbatch --mesa-llvm shows a good speed-up but the background is black instead of white (although view.Backgound = [1,1,1] is set explicitely), as shown hereafter:

[cid:image002.jpg at 01D217E8.426FCB40]

On the same server (Intel Xeon ES-2650 v3), the CPU is AVX2 capable, so I tried also the same script with pvbatch --mesa-swr-avx2. The image background is corrupted with leftover frames apparently, as shown hereafter:

[cid:image003.jpg at 01D217E8.426FCB40]
Was this behavior to be expected?

Please let me know if there is any interest in providing with my benchmark.

Frank Albina







_______________________________________________

Powered by www.kitware.com<http://www.kitware.com>



Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html



Please keep messages on-topic and check the ParaView Wiki at: http://paraview.org/Wiki/ParaView



Search the list archives at: http://markmail.org/search/?q=ParaView



Follow this link to subscribe/unsubscribe:

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From benson_muite at yahoo.com  Mon Sep 26 05:30:07 2016
From: benson_muite at yahoo.com (Benson Muite)
Date: Mon, 26 Sep 2016 12:30:07 +0300
Subject: [Paraview] Paraview v5.1.2: SurfaceLIC & software rendering
 issues
In-Reply-To: <a4c51f72-f684-4bbf-871d-ba4fb5002935@srvcli01.spe-ch-md9.net>
References: <4373b551-40c8-44ca-8b27-9106bceac88c@srvcli01.spe-ch-md9.net>
 <4c88d331-ce16-b8d1-6fe4-269df9877947@yahoo.com>
 <a4c51f72-f684-4bbf-871d-ba4fb5002935@srvcli01.spe-ch-md9.net>
Message-ID: <645f8026-6a09-d096-feeb-f8248f71f408@yahoo.com>

Both would be great if possible.


On 09/26/2016 12:22 PM, Albina, Frank wrote:
>
> Benson,
>
> do you need the data and the example code, or only the example code?
>
> Frank.
>
> *From:*Benson Muite [mailto:benson_muite at yahoo.com]
> *Sent:* Montag, 26. September 2016 11:17
> *To:* Albina, Frank; paraview at paraview.org
> *Cc:* Del Citto, Francesco
> *Subject:* Re: [Paraview] Paraview v5.1.2: SurfaceLIC & software 
> rendering issues
>
> Hi,
>
> Is the benchmark available? Would be interested in looking at this if 
> possible to get example code.
>
> Regards,
>
> Benson
>
> On 09/26/2016 11:55 AM, Albina, Frank wrote:
>
>     Dear all,
>
>     I have downloaded from the paraview.org the latest binaries for
>     Linux of ParaView v5.1.2. My main purpose is to make use of
>     ParaView with software rendering in a clustered environment
>     without GPU and, as such, I have been going through my small
>     benchmark on a generic F1 car.
>
>     This what I have found so far when generating a SurfaceLIC
>     representation on the whole car surface in batch mode.
>
>     Using pvbatch ?mesa-llvm works fine. This is one of the produced
>     images for reference:
>
>     Using 4 cores to perform the same task (with the same script) with
>     mpiexec ?np 4 pvbatch --mesa-llvm shows a good speed-up but the
>     background is black instead of white (although view.Backgound =
>     [1,1,1] is set explicitely), as shown hereafter:
>
>     On the same server (Intel Xeon ES-2650 v3), the CPU is AVX2
>     capable, so I tried also the same script with pvbatch
>     --mesa-swr-avx2. The image background is corrupted with leftover
>     frames apparently, as shown hereafter:
>
>     Was this behavior to be expected?
>
>     Please let me know if there is any interest in providing with my
>     benchmark.
>
>     *Frank Albina*
>
>
>
>
>
>     _______________________________________________
>
>     Powered bywww.kitware.com <http://www.kitware.com>
>
>     Visit other Kitware open-source projects athttp://www.kitware.com/opensource/opensource.html
>
>     Please keep messages on-topic and check the ParaView Wiki at:http://paraview.org/Wiki/ParaView
>
>     Search the list archives at:http://markmail.org/search/?q=ParaView
>
>     Follow this link to subscribe/unsubscribe:
>
>     http://public.kitware.com/mailman/listinfo/paraview
>

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From dkxls23 at gmail.com  Mon Sep 26 06:16:23 2016
From: dkxls23 at gmail.com (Armin Wehrfritz)
Date: Mon, 26 Sep 2016 13:16:23 +0300
Subject: [Paraview] Combination of polygonal-data and unstructured grid?
In-Reply-To: <e883554e-4476-f8c6-755c-549d1e5449a2@DLR.de>
References: <e883554e-4476-f8c6-755c-549d1e5449a2@DLR.de>
Message-ID: <9d42f4ef-1082-6004-85ef-0457cb649bef@gmail.com>

Hi Stefan,

If I understand your problem correctly, then you are looking for
polyhedral cells (i.e. N face cells, where each face is a M edge
polygon). Polyhedral cells are commonly used in Computational Fluid
Dynamics codes, as e.g. OpenFOAM, and VTK/ParaView support them already
for quite some time (i.e. since around 2010), see [1] for more details.

> My problem is now i have a set of complex shaped volumes (dual-grid
> data) which cannot be found in the list of cell types for
> unstructured grid data. Therefore i use the polygonal data and color
> each cell with one color. Of course for further analysis (e.g.
> integration of the cell volumes, volume gradient and so on) i need a
> way to give a set of (closed surface) poly-data elements a kind
> connection to form a volume to handle them together.
In which file format do you store your data?

For example, the unstructured VTK XML format [2] has support for
polyhedral cells. An alternative would be the XDMF file format [3] to
which I recently added polyhedral cell support [4,5]. Please note that
the latest release versions of VTK (7.0) or ParaView (5.1) don't support
the polyhedral cells in XDMF yet, but the nightly builds and the
upcoming releases (i.e. VTK 7.1 and ParaView 5.2) will have this feature.

Cheers,
Armin


[1] http://www.vtk.org/Wiki/VTK/Polyhedron_Support
[2] http://www.vtk.org/Wiki/VTK_XML_Formats
[3] http://www.xdmf.org
[4] 
https://gitlab.kitware.com/xdmf/xdmf/commit/0a9fbd0590dff8a677c86754169cd2ccd72fe4b1
[5] 
https://gitlab.kitware.com/vtk/vtk/commit/802c9b61de28e560c2659d2af76660bbb49c68be


-- 
Armin Wehrfritz, Dipl.-Ing. (M.Sc.)
Aalto University, School of Engineering
Department of Mechanical Engineering
PO Box 14300
FI-00076 Aalto, Finland
+358 50 4340607
armin.wehrfritz at aalto.fi
https://people.aalto.fi/armin_wehrfritz

From frank.albina at sauber-motorsport.com  Mon Sep 26 08:23:56 2016
From: frank.albina at sauber-motorsport.com (Albina, Frank)
Date: Mon, 26 Sep 2016 14:23:56 +0200
Subject: [Paraview] Paraview v5.1.2: SurfaceLIC & software rendering
 issues
In-Reply-To: <645f8026-6a09-d096-feeb-f8248f71f408@yahoo.com>
References: <4373b551-40c8-44ca-8b27-9106bceac88c@srvcli01.spe-ch-md9.net>
 <4c88d331-ce16-b8d1-6fe4-269df9877947@yahoo.com>
 <a4c51f72-f684-4bbf-871d-ba4fb5002935@srvcli01.spe-ch-md9.net>
 <645f8026-6a09-d096-feeb-f8248f71f408@yahoo.com>
Message-ID: <6ef5223d-6810-4e0a-a78a-180bec4cad14@srvcli01.spe-ch-md9.net>

Benson,
I won't be able to provide you with the dataset you are requesting since the IP is protected. I might be able to provide it to Kitware for debugging purposes with the condition of not distributing it to any third parties. However, I can access your request to share the benchmarking code.
Please find attached the code I am using for my benchmark.
Hope you will find it useful.
Nonetheless, I would it useful if someone could point me towards a resolution of the issue I reported in my original email.
Regards,
Frank.
From: Benson Muite [mailto:benson_muite at yahoo.com]
Sent: Montag, 26. September 2016 11:30
To: Albina, Frank; paraview at paraview.org
Cc: Del Citto, Francesco
Subject: Re: [Paraview] Paraview v5.1.2: SurfaceLIC & software rendering issues


Both would be great if possible.

On 09/26/2016 12:22 PM, Albina, Frank wrote:
Benson,

do you need the data and the example code, or only the example code?

Frank.

From: Benson Muite [mailto:benson_muite at yahoo.com]
Sent: Montag, 26. September 2016 11:17
To: Albina, Frank; paraview at paraview.org<mailto:paraview at paraview.org>
Cc: Del Citto, Francesco
Subject: Re: [Paraview] Paraview v5.1.2: SurfaceLIC & software rendering issues


Hi,

Is the benchmark available? Would be interested in looking at this if possible to get example code.

Regards,

Benson

On 09/26/2016 11:55 AM, Albina, Frank wrote:
Dear all,

I have downloaded from the paraview.org the latest binaries for Linux of ParaView v5.1.2. My main purpose is to make use of ParaView with software rendering in a clustered environment without GPU and, as such, I have been going through my small benchmark on a generic F1 car.

This what I have found so far when generating a SurfaceLIC representation on the whole car surface in batch mode.

Using pvbatch -mesa-llvm works fine. This is one of the produced images for reference:
[cid:image001.jpg at 01D21801.1883A400]
Using 4 cores to perform the same task (with the same script) with mpiexec -np 4 pvbatch --mesa-llvm shows a good speed-up but the background is black instead of white (although view.Backgound = [1,1,1] is set explicitely), as shown hereafter:

[cid:image002.jpg at 01D21801.1883A400]

On the same server (Intel Xeon ES-2650 v3), the CPU is AVX2 capable, so I tried also the same script with pvbatch --mesa-swr-avx2. The image background is corrupted with leftover frames apparently, as shown hereafter:

[cid:image003.jpg at 01D21801.1883A400]
Was this behavior to be expected?

Please let me know if there is any interest in providing with my benchmark.

Frank Albina









_______________________________________________

Powered by www.kitware.com<http://www.kitware.com>



Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html



Please keep messages on-topic and check the ParaView Wiki at: http://paraview.org/Wiki/ParaView



Search the list archives at: http://markmail.org/search/?q=ParaView



Follow this link to subscribe/unsubscribe:

http://public.kitware.com/mailman/listinfo/paraview


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From seongmo.yeon at gmail.com  Mon Sep 26 09:05:31 2016
From: seongmo.yeon at gmail.com (SeongMo Yeon)
Date: Mon, 26 Sep 2016 22:05:31 +0900
Subject: [Paraview] x3d export issue : only transform nodes exists in x3d
Message-ID: <1743124c-f5c8-7738-7505-34271d3a0e65@gmail.com>

Hi,

I am trying to postprocess OpenFOAM results with paraview and export a 
scene into x3d format.

OpenFOAM results are in remote server and I have to use paraview 
client/server to work with them.

After reading the results with OpenFOAM reader and postprocessing them, 
the scene is exported into x3d format and I found that the file has only 
<Transform node ... /> without any vertices, faces, etc.. Am I doing 
something wrong?

FYI, I am using ParaView 5.1.2.


-- x3d file contents goes below

<?xml version="1.0" encoding ="UTF-8"?>

<X3D profile="Immersive" version="3.0">
   <head>
     <meta name="filename" content="/home/seongmo/Desktop/sece.x3d"/>
     <meta name="generator" content="Visualization ToolKit X3D exporter 
v0.9.1"/>
     <meta name="numberofelements" content="25"/>
   </head>
   <Scene>
     <Background skyColor="0.32 0.34 0.43"/>
     <Viewpoint fieldOfView="0.523599" position="-0.0179753 3.71721 
1.2599" description="Default View" orientation="0.974067 0.214559 
0.0718191 -1.34581" centerOfRotation="0.5 0.5 0.5"/>
     <NavigationInfo type='"EXAMINE" "FLY" "ANY"' speed="4" 
headlight="true"/>
     <DirectionalLight ambientIntensity="1" intensity="0" color="1 1 1"/>
     <Transform DEF="ROOT" translation="0 0 0">
       <DirectionalLight direction="-0.111619 -0.766044 -0.633022" 
color="1 0.97232 0.90222" intensity="0.75" on="true"/>
       <DirectionalLight direction="0.0449435 0.965926 -0.254887" 
color="0.90824 0.93314 1" intensity="0.25" on="true"/>
       <DirectionalLight direction="-0.939693 0 0.34202" color="0.9998 
0.9998 0.9998" intensity="0.214286" on="true"/>
       <DirectionalLight direction="0.939693 0 0.34202" color="0.9998 
0.9998 0.9998" intensity="0.214286" on="true"/>
       <Transform translation="0 0 0" rotation="0 0 1 -0" scale="1 1 1"/>
       <Transform translation="0 0 0" rotation="0 0 1 -0" scale="1 1 1"/>
     </Transform>
   </Scene>
</X3D>



-- 
Seong Mo Yeon
IIHR - Hydroscience & Engineering
College of Engineering, University of Iowa
Iowa City, IA 52242 USA

E-mail : seongmo.yeon at gmail.com
Tel :
--------------------------------------------------------
Fluctuat nec mergitur


From Matthias.Zenker at erbe-med.com  Mon Sep 26 09:11:05 2016
From: Matthias.Zenker at erbe-med.com (Zenker, Dr. Matthias)
Date: Mon, 26 Sep 2016 13:11:05 +0000
Subject: [Paraview] save filter result
Message-ID: <F9562F3B302F29479A203FC5AF9E3E050F9E3BDA@SERBE4I1.intra.erbe-med.de>

Hi,

I want to visualize the gradient of a potential, calculated in 3D, on a slice, with some coputours. My workflow is:


*         Open dataset (vtu),

*         apply "gradient of unstructured dataset" filter,

*         apply calculator to compute the magnitude of the gradient,

*         apply slice filter,

*         apply contour filter.
Since it takes some time to calculate gradient, magnitude and extract the slice, I would like to save the result in a file so that I can open it instantaneously later. How do I do that? If I just use "save data", ParaView saves all the data, including the initial potential values, which gives a huge file. Is there a way to just save the result of the calculator, or better, of the slice filter?
I have tried with the extract selection filter, but I seem not to manage to extract the results I want. How can I do that?

Thanks for a hint,

Matthias
________________________________

Erbe Elektromedizin GmbH Firmensitz: 72072 Tuebingen Geschaeftsfuehrer: Christian O. Erbe, Reiner Thede Registergericht: Stuttgart HRB 380137

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From benson_muite at yahoo.com  Mon Sep 26 09:16:02 2016
From: benson_muite at yahoo.com (Benson Muite)
Date: Mon, 26 Sep 2016 16:16:02 +0300
Subject: [Paraview] Paraview v5.1.2: SurfaceLIC & software rendering
 issues
In-Reply-To: <6ef5223d-6810-4e0a-a78a-180bec4cad14@srvcli01.spe-ch-md9.net>
References: <4373b551-40c8-44ca-8b27-9106bceac88c@srvcli01.spe-ch-md9.net>
 <4c88d331-ce16-b8d1-6fe4-269df9877947@yahoo.com>
 <a4c51f72-f684-4bbf-871d-ba4fb5002935@srvcli01.spe-ch-md9.net>
 <645f8026-6a09-d096-feeb-f8248f71f408@yahoo.com>
 <6ef5223d-6810-4e0a-a78a-180bec4cad14@srvcli01.spe-ch-md9.net>
Message-ID: <608793f2-58b1-273c-1c97-664f5db4c5bf@yahoo.com>

Frank,

Will see if can generate an example data set, in case am able to do so, 
can I redistribute the file (in particular would like to show several 
students how some of these parallel computing packages are used in 
industry)? Line 640 makes it difficult to re-distribute.

Benson

On 09/26/2016 03:23 PM, Albina, Frank wrote:
>
> Benson,
>
> I won?t be able to provide you with the dataset you are requesting 
> since the IP is protected. I might be able to provide it to Kitware 
> for debugging purposes with the condition of not distributing it to 
> any third parties. However, I can access your request to share the 
> benchmarking code.
>
> Please find attached the code I am using for my benchmark.
>
> Hope you will find it useful.
>
> Nonetheless, I would it useful if someone could point me towards a 
> resolution of the issue I reported in my original email.
>
> Regards,
>
> Frank.
>
> *From:*Benson Muite [mailto:benson_muite at yahoo.com]
> *Sent:* Montag, 26. September 2016 11:30
> *To:* Albina, Frank; paraview at paraview.org
> *Cc:* Del Citto, Francesco
> *Subject:* Re: [Paraview] Paraview v5.1.2: SurfaceLIC & software 
> rendering issues
>
> Both would be great if possible.
>
> On 09/26/2016 12:22 PM, Albina, Frank wrote:
>
>     Benson,
>
>     do you need the data and the example code, or only the example code?
>
>     Frank.
>
>     *From:*Benson Muite [mailto:benson_muite at yahoo.com]
>     *Sent:* Montag, 26. September 2016 11:17
>     *To:* Albina, Frank; paraview at paraview.org
>     <mailto:paraview at paraview.org>
>     *Cc:* Del Citto, Francesco
>     *Subject:* Re: [Paraview] Paraview v5.1.2: SurfaceLIC & software
>     rendering issues
>
>     Hi,
>
>     Is the benchmark available? Would be interested in looking at this
>     if possible to get example code.
>
>     Regards,
>
>     Benson
>
>     On 09/26/2016 11:55 AM, Albina, Frank wrote:
>
>         Dear all,
>
>         I have downloaded from the paraview.org the latest binaries
>         for Linux of ParaView v5.1.2. My main purpose is to make use
>         of ParaView with software rendering in a clustered environment
>         without GPU and, as such, I have been going through my small
>         benchmark on a generic F1 car.
>
>         This what I have found so far when generating a SurfaceLIC
>         representation on the whole car surface in batch mode.
>
>         Using pvbatch ?mesa-llvm works fine. This is one of the
>         produced images for reference:
>
>         Using 4 cores to perform the same task (with the same script)
>         with mpiexec ?np 4 pvbatch --mesa-llvm shows a good speed-up
>         but the background is black instead of white (although
>         view.Backgound = [1,1,1] is set explicitely), as shown hereafter:
>
>         On the same server (Intel Xeon ES-2650 v3), the CPU is AVX2
>         capable, so I tried also the same script with pvbatch
>         --mesa-swr-avx2. The image background is corrupted with
>         leftover frames apparently, as shown hereafter:
>
>         Was this behavior to be expected?
>
>         Please let me know if there is any interest in providing with
>         my benchmark.
>
>         *Frank Albina*
>
>
>
>
>
>
>
>         _______________________________________________
>
>         Powered bywww.kitware.com <http://www.kitware.com>
>
>           
>
>         Visit other Kitware open-source projects athttp://www.kitware.com/opensource/opensource.html
>
>           
>
>         Please keep messages on-topic and check the ParaView Wiki at:http://paraview.org/Wiki/ParaView
>
>           
>
>         Search the list archives at:http://markmail.org/search/?q=ParaView
>
>           
>
>         Follow this link to subscribe/unsubscribe:
>
>         http://public.kitware.com/mailman/listinfo/paraview
>

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From andy.bauer at kitware.com  Mon Sep 26 09:22:01 2016
From: andy.bauer at kitware.com (Andy Bauer)
Date: Mon, 26 Sep 2016 09:22:01 -0400
Subject: [Paraview] save filter result
In-Reply-To: <F9562F3B302F29479A203FC5AF9E3E050F9E3BDA@SERBE4I1.intra.erbe-med.de>
References: <F9562F3B302F29479A203FC5AF9E3E050F9E3BDA@SERBE4I1.intra.erbe-med.de>
Message-ID: <CAMaOp+F57qMAcK7FYOHjmoxjnBQPayon7uH3ULai0DLU6QbNxQ@mail.gmail.com>

Do you have the Slice filter highlighted in the GUI when you save the data
set? That's the proper way to just save out the results from that filter
and not the others. Also, you can use the Pass Arrays filter to selectively
choose which arrays you want to pass through the pipeline.

On Mon, Sep 26, 2016 at 9:11 AM, Zenker, Dr. Matthias <
Matthias.Zenker at erbe-med.com> wrote:

> Hi,
>
>
>
> I want to visualize the gradient of a potential, calculated in 3D, on a
> slice, with some coputours. My workflow is:
>
>
>
> ?         Open dataset (vtu),
>
> ?         apply ?gradient of unstructured dataset? filter,
>
> ?         apply calculator to compute the magnitude of the gradient,
>
> ?         apply slice filter,
>
> ?         apply contour filter.
>
> Since it takes some time to calculate gradient, magnitude and extract the
> slice, I would like to save the result in a file so that I can open it
> instantaneously later. How do I do that? If I just use ?save data?,
> ParaView saves all the data, including the initial potential values, which
> gives a huge file. Is there a way to just save the result of the
> calculator, or better, of the slice filter?
>
> I have tried with the extract selection filter, but I seem not to manage
> to extract the results I want. How can I do that?
>
>
>
> Thanks for a hint,
>
>
>
> Matthias
> ------------------------------
>
> Erbe Elektromedizin GmbH Firmensitz: 72072 Tuebingen Geschaeftsfuehrer:
> Christian O. Erbe, Reiner Thede Registergericht: Stuttgart HRB 380137
>
>
> _______________________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at http://www.kitware.com/
> opensource/opensource.html
>
> Please keep messages on-topic and check the ParaView Wiki at:
> http://paraview.org/Wiki/ParaView
>
> Search the list archives at: http://markmail.org/search/?q=ParaView
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/paraview
>
>
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From dave.demarle at kitware.com  Mon Sep 26 09:37:17 2016
From: dave.demarle at kitware.com (David E DeMarle)
Date: Mon, 26 Sep 2016 09:37:17 -0400
Subject: [Paraview] Building ParaView v5.1.2 on Linux from source with
 support for GPU and SWR.
In-Reply-To: <591d7e7c-08d5-4787-8703-d90fd2be1bdb@srvcli01.spe-ch-md9.net>
References: <591d7e7c-08d5-4787-8703-d90fd2be1bdb@srvcli01.spe-ch-md9.net>
Message-ID: <CANjZAi-m+7tU0U5piT-FszDTNbJdDkyZ6hs3Yue-rOwi2B8eog@mail.gmail.com>

I recommend the ParaView superbuild. All of the incantations that we use to
setup and build paraview, mesa and the rest of our dependencies are written
down and maintained there.

https://gitlab.kitware.com/paraview/paraview-superbuild

We've used it for our Desktop binaries for years, and more and more often
we use it for our HPC installs as well.

David E DeMarle
Kitware, Inc.
R&D Engineer
21 Corporate Drive
Clifton Park, NY 12065-8662
Phone: 518-881-4909

On Mon, Sep 26, 2016 at 5:17 AM, Albina, Frank <
frank.albina at sauber-motorsport.com> wrote:

> Dear all,
>
> after having downloaded last week the latest ParaView release (v5.1.2) for
> Linux, I have found out that the binary version has the following folder
> structure in lib/paraview-5.1:
>
> *mesa-llvm*
>
> |-- *libGL.so* -> libGL.so.1
>
> |-- *libGL.so.1 *-> libGL.so.1.5
>
> |-- libGL.so.1.5
>
> |-- *libOSMesa.so* -> libOSMesa.so.8
>
> |-- *libOSMesa.so.8* -> libOSMesa.so.8.0.0
>
> `-- libOSMesa.so.8.0.0
>
> *mesa-swr-avx*
>
> |-- *libGL.so* -> libGL.so.1
>
> |-- *libGL.so.1* -> libGL.so.1.5
>
> |-- libGL.so.1.5
>
> |-- *libOSMesa.so* -> libOSMesa.so.8
>
> |-- *libOSMesa.so.8* -> libOSMesa.so.8.0.0
>
> `-- libOSMesa.so.8.0.0
>
> *mesa-swr-avx2*
>
> |-- *libGL.so* -> libGL.so.1
>
> |-- *libGL.so.1 *-> libGL.so.1.5
>
> |-- libGL.so.1.5
>
> |-- *libOSMesa.so* -> libOSMesa.so.8
>
> |-- *libOSMesa.so.8* -> libOSMesa.so.8.0.0
>
> `-- libOSMesa.so.8.0.0
>
> Which is an elegant way of providing a binary package for GPU and non-GPU
> architectures at the same time.
>
> Hence my question: How do I build ParaView v5.1.2 from source to have the
> same folder structure so that I have one version for GPU and software
> rendering? I understand that swr-avx(2) should be also available from Mesa
> v12.x. Is there anything I?d need to consider / take care of before
> building the different OSMesa libraries with LLVM / OpenSWR?
>
> *Frank Albina*
>
>
>
> _______________________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at http://www.kitware.com/opensou
> rce/opensource.html
>
> Please keep messages on-topic and check the ParaView Wiki at:
> http://paraview.org/Wiki/ParaView
>
> Search the list archives at: http://markmail.org/search/?q=ParaView
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/paraview
>
>
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From frank.albina at sauber-motorsport.com  Mon Sep 26 09:42:43 2016
From: frank.albina at sauber-motorsport.com (Albina, Frank)
Date: Mon, 26 Sep 2016 15:42:43 +0200
Subject: [Paraview] Building ParaView v5.1.2 on Linux from source with
 support for GPU and SWR.
In-Reply-To: <CANjZAi-m+7tU0U5piT-FszDTNbJdDkyZ6hs3Yue-rOwi2B8eog@mail.gmail.com>
References: <591d7e7c-08d5-4787-8703-d90fd2be1bdb@srvcli01.spe-ch-md9.net>
 <CANjZAi-m+7tU0U5piT-FszDTNbJdDkyZ6hs3Yue-rOwi2B8eog@mail.gmail.com>
Message-ID: <98b353c4-1c35-47a8-808b-e37fa0385776@srvcli01.spe-ch-md9.net>

Hi David!

Thanks for the swift feedback. As I have been compiling ParaView from source for at least the last 6 years, it never came to my mind trying out the super-build. ?

I?ll try it out and report if I find myself stuck.

By the way, which CMake version do you recommend for building ParaView v5.1.2 from the git repository?

Best regards,

Frank.

From: David E DeMarle [mailto:dave.demarle at kitware.com]
Sent: Montag, 26. September 2016 15:37
To: Albina, Frank
Cc: paraview at paraview.org; Del Citto, Francesco
Subject: Re: [Paraview] Building ParaView v5.1.2 on Linux from source with support for GPU and SWR.

I recommend the ParaView superbuild. All of the incantations that we use to setup and build paraview, mesa and the rest of our dependencies are written down and maintained there.

https://gitlab.kitware.com/paraview/paraview-superbuild
We've used it for our Desktop binaries for years, and more and more often we use it for our HPC installs as well.

David E DeMarle
Kitware, Inc.
R&D Engineer
21 Corporate Drive
Clifton Park, NY 12065-8662
Phone: 518-881-4909<tel:518-881-4909>

On Mon, Sep 26, 2016 at 5:17 AM, Albina, Frank <frank.albina at sauber-motorsport.com<mailto:frank.albina at sauber-motorsport.com>> wrote:
Dear all,
after having downloaded last week the latest ParaView release (v5.1.2) for Linux, I have found out that the binary version has the following folder structure in lib/paraview-5.1:
mesa-llvm
|-- libGL.so -> libGL.so.1
|-- libGL.so.1 -> libGL.so.1.5
|-- libGL.so.1.5
|-- libOSMesa.so -> libOSMesa.so.8
|-- libOSMesa.so.8 -> libOSMesa.so.8.0.0
`-- libOSMesa.so.8.0.0
mesa-swr-avx
|-- libGL.so -> libGL.so.1
|-- libGL.so.1 -> libGL.so.1.5
|-- libGL.so.1.5
|-- libOSMesa.so -> libOSMesa.so.8
|-- libOSMesa.so.8 -> libOSMesa.so.8.0.0
`-- libOSMesa.so.8.0.0
mesa-swr-avx2
|-- libGL.so -> libGL.so.1
|-- libGL.so.1 -> libGL.so.1.5
|-- libGL.so.1.5
|-- libOSMesa.so -> libOSMesa.so.8
|-- libOSMesa.so.8 -> libOSMesa.so.8.0.0
`-- libOSMesa.so.8.0.0
Which is an elegant way of providing a binary package for GPU and non-GPU architectures at the same time.
Hence my question: How do I build ParaView v5.1.2 from source to have the same folder structure so that I have one version for GPU and software rendering? I understand that swr-avx(2) should be also available from Mesa v12.x. Is there anything I?d need to consider / take care of before building the different OSMesa libraries with LLVM / OpenSWR?
Frank Albina


_______________________________________________
Powered by www.kitware.com<http://www.kitware.com>

Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html

Please keep messages on-topic and check the ParaView Wiki at: http://paraview.org/Wiki/ParaView

Search the list archives at: http://markmail.org/search/?q=ParaView

Follow this link to subscribe/unsubscribe:
http://public.kitware.com/mailman/listinfo/paraview

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From dave.demarle at kitware.com  Mon Sep 26 09:48:49 2016
From: dave.demarle at kitware.com (David E DeMarle)
Date: Mon, 26 Sep 2016 09:48:49 -0400
Subject: [Paraview] Building ParaView v5.1.2 on Linux from source with
 support for GPU and SWR.
In-Reply-To: <98b353c4-1c35-47a8-808b-e37fa0385776@srvcli01.spe-ch-md9.net>
References: <591d7e7c-08d5-4787-8703-d90fd2be1bdb@srvcli01.spe-ch-md9.net>
 <CANjZAi-m+7tU0U5piT-FszDTNbJdDkyZ6hs3Yue-rOwi2B8eog@mail.gmail.com>
 <98b353c4-1c35-47a8-808b-e37fa0385776@srvcli01.spe-ch-md9.net>
Message-ID: <CANjZAi-RTCXFQqLnrw0izaX_OQwvR0iHqym7nTCiWuevyE9wvQ@mail.gmail.com>

3.3


David E DeMarle
Kitware, Inc.
R&D Engineer
21 Corporate Drive
Clifton Park, NY 12065-8662
Phone: 518-881-4909

On Mon, Sep 26, 2016 at 9:42 AM, Albina, Frank <
frank.albina at sauber-motorsport.com> wrote:

> Hi David!
>
>
>
> Thanks for the swift feedback. As I have been compiling ParaView from
> source for at least the last 6 years, it never came to my mind trying out
> the super-build. ?
>
>
>
> I?ll try it out and report if I find myself stuck.
>
>
>
> By the way, which CMake version do you recommend for building ParaView
> v5.1.2 from the git repository?
>
>
>
> Best regards,
>
>
> Frank.
>
>
>
> *From:* David E DeMarle [mailto:dave.demarle at kitware.com]
> *Sent:* Montag, 26. September 2016 15:37
> *To:* Albina, Frank
> *Cc:* paraview at paraview.org; Del Citto, Francesco
> *Subject:* Re: [Paraview] Building ParaView v5.1.2 on Linux from source
> with support for GPU and SWR.
>
>
>
> I recommend the ParaView superbuild. All of the incantations that we use
> to setup and build paraview, mesa and the rest of our dependencies are
> written down and maintained there.
>
> https://gitlab.kitware.com/paraview/paraview-superbuild
>
> We've used it for our Desktop binaries for years, and more and more often
> we use it for our HPC installs as well.
>
>
> David E DeMarle
> Kitware, Inc.
> R&D Engineer
> 21 Corporate Drive
> Clifton Park, NY 12065-8662
> Phone: 518-881-4909
>
>
>
> On Mon, Sep 26, 2016 at 5:17 AM, Albina, Frank <frank.albina at sauber-
> motorsport.com> wrote:
>
> Dear all,
>
> after having downloaded last week the latest ParaView release (v5.1.2) for
> Linux, I have found out that the binary version has the following folder
> structure in lib/paraview-5.1:
>
> *mesa-llvm*
>
> |-- *libGL.so* -> libGL.so.1
>
> |-- *libGL.so.1 *-> libGL.so.1.5
>
> |-- libGL.so.1.5
>
> |-- *libOSMesa.so* -> libOSMesa.so.8
>
> |-- *libOSMesa.so.8* -> libOSMesa.so.8.0.0
>
> `-- libOSMesa.so.8.0.0
>
> *mesa-swr-avx*
>
> |-- *libGL.so* -> libGL.so.1
>
> |-- *libGL.so.1* -> libGL.so.1.5
>
> |-- libGL.so.1.5
>
> |-- *libOSMesa.so* -> libOSMesa.so.8
>
> |-- *libOSMesa.so.8* -> libOSMesa.so.8.0.0
>
> `-- libOSMesa.so.8.0.0
>
> *mesa-swr-avx2*
>
> |-- *libGL.so* -> libGL.so.1
>
> |-- *libGL.so.1 *-> libGL.so.1.5
>
> |-- libGL.so.1.5
>
> |-- *libOSMesa.so* -> libOSMesa.so.8
>
> |-- *libOSMesa.so.8* -> libOSMesa.so.8.0.0
>
> `-- libOSMesa.so.8.0.0
>
> Which is an elegant way of providing a binary package for GPU and non-GPU
> architectures at the same time.
>
> Hence my question: How do I build ParaView v5.1.2 from source to have the
> same folder structure so that I have one version for GPU and software
> rendering? I understand that swr-avx(2) should be also available from Mesa
> v12.x. Is there anything I?d need to consider / take care of before
> building the different OSMesa libraries with LLVM / OpenSWR?
>
> *Frank Albina*
>
>
>
>
> _______________________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at http://www.kitware.com/
> opensource/opensource.html
>
> Please keep messages on-topic and check the ParaView Wiki at:
> http://paraview.org/Wiki/ParaView
>
> Search the list archives at: http://markmail.org/search/?q=ParaView
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/paraview
>
>
>
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From frank.albina at sauber-motorsport.com  Mon Sep 26 09:49:12 2016
From: frank.albina at sauber-motorsport.com (Albina, Frank)
Date: Mon, 26 Sep 2016 15:49:12 +0200
Subject: [Paraview] Paraview v5.1.2: SurfaceLIC & software rendering
 issues
In-Reply-To: <608793f2-58b1-273c-1c97-664f5db4c5bf@yahoo.com>
References: <4373b551-40c8-44ca-8b27-9106bceac88c@srvcli01.spe-ch-md9.net>
 <4c88d331-ce16-b8d1-6fe4-269df9877947@yahoo.com>
 <a4c51f72-f684-4bbf-871d-ba4fb5002935@srvcli01.spe-ch-md9.net>
 <645f8026-6a09-d096-feeb-f8248f71f408@yahoo.com>
 <6ef5223d-6810-4e0a-a78a-180bec4cad14@srvcli01.spe-ch-md9.net>
 <608793f2-58b1-273c-1c97-664f5db4c5bf@yahoo.com>
Message-ID: <14d4d7ad-4dbc-4b45-8506-c9d1e8dc493a@srvcli01.spe-ch-md9.net>

Benson,
if you re-distribute, please state in the code where this file originates from.
Talking about "parallel computing packages are used in industry", I would really appreciate if this SurfaceLIC benchmark would become a standard benchmark to measure rendering times across a variety of platforms and ParaView versions. This would be also a good candidate benchmark to check new ParaView release candidates, I think.
Frank.
From: Benson Muite [mailto:benson_muite at yahoo.com]
Sent: Montag, 26. September 2016 15:16
To: Albina, Frank; paraview at paraview.org
Cc: Del Citto, Francesco
Subject: Re: [Paraview] Paraview v5.1.2: SurfaceLIC & software rendering issues

Frank,

Will see if can generate an example data set, in case am able to do so, can I redistribute the file (in particular would like to show several students how some of these parallel computing packages are used in industry)? Line 640 makes it difficult to re-distribute.

Benson
On 09/26/2016 03:23 PM, Albina, Frank wrote:
Benson,
I won't be able to provide you with the dataset you are requesting since the IP is protected. I might be able to provide it to Kitware for debugging purposes with the condition of not distributing it to any third parties. However, I can access your request to share the benchmarking code.
Please find attached the code I am using for my benchmark.
Hope you will find it useful.
Nonetheless, I would it useful if someone could point me towards a resolution of the issue I reported in my original email.
Regards,
Frank.
From: Benson Muite [mailto:benson_muite at yahoo.com]
Sent: Montag, 26. September 2016 11:30
To: Albina, Frank; paraview at paraview.org<mailto:paraview at paraview.org>
Cc: Del Citto, Francesco
Subject: Re: [Paraview] Paraview v5.1.2: SurfaceLIC & software rendering issues


Both would be great if possible.

On 09/26/2016 12:22 PM, Albina, Frank wrote:
Benson,

do you need the data and the example code, or only the example code?

Frank.

From: Benson Muite [mailto:benson_muite at yahoo.com]
Sent: Montag, 26. September 2016 11:17
To: Albina, Frank; paraview at paraview.org<mailto:paraview at paraview.org>
Cc: Del Citto, Francesco
Subject: Re: [Paraview] Paraview v5.1.2: SurfaceLIC & software rendering issues


Hi,

Is the benchmark available? Would be interested in looking at this if possible to get example code.

Regards,

Benson

On 09/26/2016 11:55 AM, Albina, Frank wrote:
Dear all,

I have downloaded from the paraview.org the latest binaries for Linux of ParaView v5.1.2. My main purpose is to make use of ParaView with software rendering in a clustered environment without GPU and, as such, I have been going through my small benchmark on a generic F1 car.

This what I have found so far when generating a SurfaceLIC representation on the whole car surface in batch mode.

Using pvbatch -mesa-llvm works fine. This is one of the produced images for reference:
[cid:image001.jpg at 01D2180D.86C9A890]
Using 4 cores to perform the same task (with the same script) with mpiexec -np 4 pvbatch --mesa-llvm shows a good speed-up but the background is black instead of white (although view.Backgound = [1,1,1] is set explicitely), as shown hereafter:

[cid:image002.jpg at 01D2180D.86C9A890]

On the same server (Intel Xeon ES-2650 v3), the CPU is AVX2 capable, so I tried also the same script with pvbatch --mesa-swr-avx2. The image background is corrupted with leftover frames apparently, as shown hereafter:

[cid:image003.jpg at 01D2180D.86C9A890]
Was this behavior to be expected?

Please let me know if there is any interest in providing with my benchmark.

Frank Albina











_______________________________________________

Powered by www.kitware.com<http://www.kitware.com>



Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html



Please keep messages on-topic and check the ParaView Wiki at: http://paraview.org/Wiki/ParaView



Search the list archives at: http://markmail.org/search/?q=ParaView



Follow this link to subscribe/unsubscribe:

http://public.kitware.com/mailman/listinfo/paraview



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From frank.albina at sauber-motorsport.com  Mon Sep 26 09:51:03 2016
From: frank.albina at sauber-motorsport.com (Albina, Frank)
Date: Mon, 26 Sep 2016 15:51:03 +0200
Subject: [Paraview] Building ParaView v5.1.2 on Linux from source with
 support for GPU and SWR.
In-Reply-To: <CANjZAi-RTCXFQqLnrw0izaX_OQwvR0iHqym7nTCiWuevyE9wvQ@mail.gmail.com>
References: <591d7e7c-08d5-4787-8703-d90fd2be1bdb@srvcli01.spe-ch-md9.net>
 <CANjZAi-m+7tU0U5piT-FszDTNbJdDkyZ6hs3Yue-rOwi2B8eog@mail.gmail.com>
 <98b353c4-1c35-47a8-808b-e37fa0385776@srvcli01.spe-ch-md9.net>
 <CANjZAi-RTCXFQqLnrw0izaX_OQwvR0iHqym7nTCiWuevyE9wvQ@mail.gmail.com>
Message-ID: <95e35867-31a7-449b-bc6a-eb67b54eb4f3@srvcli01.spe-ch-md9.net>

Perfect!

Thanks.

Frank.

From: David E DeMarle [mailto:dave.demarle at kitware.com]
Sent: Montag, 26. September 2016 15:49
To: Albina, Frank
Cc: paraview at paraview.org; Del Citto, Francesco
Subject: Re: [Paraview] Building ParaView v5.1.2 on Linux from source with support for GPU and SWR.

3.3

David E DeMarle
Kitware, Inc.
R&D Engineer
21 Corporate Drive
Clifton Park, NY 12065-8662
Phone: 518-881-4909

On Mon, Sep 26, 2016 at 9:42 AM, Albina, Frank <frank.albina at sauber-motorsport.com<mailto:frank.albina at sauber-motorsport.com>> wrote:
Hi David!

Thanks for the swift feedback. As I have been compiling ParaView from source for at least the last 6 years, it never came to my mind trying out the super-build. ?

I?ll try it out and report if I find myself stuck.

By the way, which CMake version do you recommend for building ParaView v5.1.2 from the git repository?

Best regards,

Frank.

From: David E DeMarle [mailto:dave.demarle at kitware.com<mailto:dave.demarle at kitware.com>]
Sent: Montag, 26. September 2016 15:37
To: Albina, Frank
Cc: paraview at paraview.org<mailto:paraview at paraview.org>; Del Citto, Francesco
Subject: Re: [Paraview] Building ParaView v5.1.2 on Linux from source with support for GPU and SWR.

I recommend the ParaView superbuild. All of the incantations that we use to setup and build paraview, mesa and the rest of our dependencies are written down and maintained there.

https://gitlab.kitware.com/paraview/paraview-superbuild
We've used it for our Desktop binaries for years, and more and more often we use it for our HPC installs as well.

David E DeMarle
Kitware, Inc.
R&D Engineer
21 Corporate Drive
Clifton Park, NY 12065-8662
Phone: 518-881-4909<tel:518-881-4909>

On Mon, Sep 26, 2016 at 5:17 AM, Albina, Frank <frank.albina at sauber-motorsport.com<mailto:frank.albina at sauber-motorsport.com>> wrote:
Dear all,
after having downloaded last week the latest ParaView release (v5.1.2) for Linux, I have found out that the binary version has the following folder structure in lib/paraview-5.1:
mesa-llvm
|-- libGL.so -> libGL.so.1
|-- libGL.so.1 -> libGL.so.1.5
|-- libGL.so.1.5
|-- libOSMesa.so -> libOSMesa.so.8
|-- libOSMesa.so.8 -> libOSMesa.so.8.0.0
`-- libOSMesa.so.8.0.0
mesa-swr-avx
|-- libGL.so -> libGL.so.1
|-- libGL.so.1 -> libGL.so.1.5
|-- libGL.so.1.5
|-- libOSMesa.so -> libOSMesa.so.8
|-- libOSMesa.so.8 -> libOSMesa.so.8.0.0
`-- libOSMesa.so.8.0.0
mesa-swr-avx2
|-- libGL.so -> libGL.so.1
|-- libGL.so.1 -> libGL.so.1.5
|-- libGL.so.1.5
|-- libOSMesa.so -> libOSMesa.so.8
|-- libOSMesa.so.8 -> libOSMesa.so.8.0.0
`-- libOSMesa.so.8.0.0
Which is an elegant way of providing a binary package for GPU and non-GPU architectures at the same time.
Hence my question: How do I build ParaView v5.1.2 from source to have the same folder structure so that I have one version for GPU and software rendering? I understand that swr-avx(2) should be also available from Mesa v12.x. Is there anything I?d need to consider / take care of before building the different OSMesa libraries with LLVM / OpenSWR?
Frank Albina


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From sebastien.jourdain at kitware.com  Mon Sep 26 10:39:59 2016
From: sebastien.jourdain at kitware.com (Sebastien Jourdain)
Date: Mon, 26 Sep 2016 08:39:59 -0600
Subject: [Paraview] x3d export issue : only transform nodes exists in x3d
In-Reply-To: <1743124c-f5c8-7738-7505-34271d3a0e65@gmail.com>
References: <1743124c-f5c8-7738-7505-34271d3a0e65@gmail.com>
Message-ID: <CABObKxdJD30BHCKxcyrLbVk0KP_Ef1w4yGg-k61Ys72_qdt2eQ@mail.gmail.com>

I think you need to adjust the "*Remote Render Threshold" *to "102400" so
the scene geometry (surface mesh) can be sent to the client (if the client
can handle it) and export again.
At that point the exporter should find some geometry to write.

On Mon, Sep 26, 2016 at 7:05 AM, SeongMo Yeon <seongmo.yeon at gmail.com>
wrote:

> Hi,
>
> I am trying to postprocess OpenFOAM results with paraview and export a
> scene into x3d format.
>
> OpenFOAM results are in remote server and I have to use paraview
> client/server to work with them.
>
> After reading the results with OpenFOAM reader and postprocessing them,
> the scene is exported into x3d format and I found that the file has only
> <Transform node ... /> without any vertices, faces, etc.. Am I doing
> something wrong?
>
> FYI, I am using ParaView 5.1.2.
>
>
> -- x3d file contents goes below
>
> <?xml version="1.0" encoding ="UTF-8"?>
>
> <X3D profile="Immersive" version="3.0">
>   <head>
>     <meta name="filename" content="/home/seongmo/Desktop/sece.x3d"/>
>     <meta name="generator" content="Visualization ToolKit X3D exporter
> v0.9.1"/>
>     <meta name="numberofelements" content="25"/>
>   </head>
>   <Scene>
>     <Background skyColor="0.32 0.34 0.43"/>
>     <Viewpoint fieldOfView="0.523599" position="-0.0179753 3.71721 1.2599"
> description="Default View" orientation="0.974067 0.214559 0.0718191
> -1.34581" centerOfRotation="0.5 0.5 0.5"/>
>     <NavigationInfo type='"EXAMINE" "FLY" "ANY"' speed="4"
> headlight="true"/>
>     <DirectionalLight ambientIntensity="1" intensity="0" color="1 1 1"/>
>     <Transform DEF="ROOT" translation="0 0 0">
>       <DirectionalLight direction="-0.111619 -0.766044 -0.633022" color="1
> 0.97232 0.90222" intensity="0.75" on="true"/>
>       <DirectionalLight direction="0.0449435 0.965926 -0.254887"
> color="0.90824 0.93314 1" intensity="0.25" on="true"/>
>       <DirectionalLight direction="-0.939693 0 0.34202" color="0.9998
> 0.9998 0.9998" intensity="0.214286" on="true"/>
>       <DirectionalLight direction="0.939693 0 0.34202" color="0.9998
> 0.9998 0.9998" intensity="0.214286" on="true"/>
>       <Transform translation="0 0 0" rotation="0 0 1 -0" scale="1 1 1"/>
>       <Transform translation="0 0 0" rotation="0 0 1 -0" scale="1 1 1"/>
>     </Transform>
>   </Scene>
> </X3D>
>
>
>
> --
> Seong Mo Yeon
> IIHR - Hydroscience & Engineering
> College of Engineering, University of Iowa
> Iowa City, IA 52242 USA
>
> E-mail : seongmo.yeon at gmail.com
> Tel :
> --------------------------------------------------------
> Fluctuat nec mergitur
>
> _______________________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at http://www.kitware.com/opensou
> rce/opensource.html
>
> Please keep messages on-topic and check the ParaView Wiki at:
> http://paraview.org/Wiki/ParaView
>
> Search the list archives at: http://markmail.org/search/?q=ParaView
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/paraview
>
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From Matthias.Zenker at erbe-med.com  Mon Sep 26 12:08:49 2016
From: Matthias.Zenker at erbe-med.com (Zenker, Dr. Matthias)
Date: Mon, 26 Sep 2016 16:08:49 +0000
Subject: [Paraview] WG:  save filter result
In-Reply-To: <F9562F3B302F29479A203FC5AF9E3E050F9E3BE9@SERBE4I1.intra.erbe-med.de>
References: <F9562F3B302F29479A203FC5AF9E3E050F9E3BDA@SERBE4I1.intra.erbe-med.de>
 <CAMaOp+F57qMAcK7FYOHjmoxjnBQPayon7uH3ULai0DLU6QbNxQ@mail.gmail.com>
 <F9562F3B302F29479A203FC5AF9E3E050F9E3BE9@SERBE4I1.intra.erbe-med.de>
Message-ID: <F9562F3B302F29479A203FC5AF9E3E050F9E3C0F@SERBE4I1.intra.erbe-med.de>


Hi Andy,

thank you for the quick reply!
When I highlight the slice filter, I can just save the slice indeed, so this solves a part of my problem.
But I would also like to save the calculated gradient for the whole 3D dataset, and cannot manage to do it the same way: If I highlight the calculator and do Save Data, ParaView saves everything, not just the calculator result. What can I do to just save the calculator result?

Thank you,

Matthias


Von: Andy Bauer [mailto:andy.bauer at kitware.com]
Gesendet: Montag, 26. September 2016 15:22
An: Zenker, Dr. Matthias
Cc: paraview at paraview.org<mailto:paraview at paraview.org>
Betreff: Re: [Paraview] save filter result

Do you have the Slice filter highlighted in the GUI when you save the data set? That's the proper way to just save out the results from that filter and not the others. Also, you can use the Pass Arrays filter to selectively choose which arrays you want to pass through the pipeline.

On Mon, Sep 26, 2016 at 9:11 AM, Zenker, Dr. Matthias <Matthias.Zenker at erbe-med.com<mailto:Matthias.Zenker at erbe-med.com>> wrote:
Hi,

I want to visualize the gradient of a potential, calculated in 3D, on a slice, with some coputours. My workflow is:


?         Open dataset (vtu),

?         apply ?gradient of unstructured dataset? filter,

?         apply calculator to compute the magnitude of the gradient,

?         apply slice filter,

?         apply contour filter.
Since it takes some time to calculate gradient, magnitude and extract the slice, I would like to save the result in a file so that I can open it instantaneously later. How do I do that? If I just use ?save data?, ParaView saves all the data, including the initial potential values, which gives a huge file. Is there a way to just save the result of the calculator, or better, of the slice filter?
I have tried with the extract selection filter, but I seem not to manage to extract the results I want. How can I do that?

Thanks for a hint,

Matthias
________________________________

Erbe Elektromedizin GmbH Firmensitz: 72072 Tuebingen Geschaeftsfuehrer: Christian O. Erbe, Reiner Thede Registergericht: Stuttgart HRB 380137

_______________________________________________
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________________________________

Erbe Elektromedizin GmbH Firmensitz: 72072 Tuebingen Geschaeftsfuehrer: Christian O. Erbe, Reiner Thede Registergericht: Stuttgart HRB 380137

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From andy.bauer at kitware.com  Mon Sep 26 13:09:11 2016
From: andy.bauer at kitware.com (Andy Bauer)
Date: Mon, 26 Sep 2016 13:09:11 -0400
Subject: [Paraview] WG: save filter result
In-Reply-To: <F9562F3B302F29479A203FC5AF9E3E050F9E3C0F@SERBE4I1.intra.erbe-med.de>
References: <F9562F3B302F29479A203FC5AF9E3E050F9E3BDA@SERBE4I1.intra.erbe-med.de>
 <CAMaOp+F57qMAcK7FYOHjmoxjnBQPayon7uH3ULai0DLU6QbNxQ@mail.gmail.com>
 <F9562F3B302F29479A203FC5AF9E3E050F9E3BE9@SERBE4I1.intra.erbe-med.de>
 <F9562F3B302F29479A203FC5AF9E3E050F9E3C0F@SERBE4I1.intra.erbe-med.de>
Message-ID: <CAMaOp+Ex0Jm52oC3tsKx1VKekWnE08+heCJ39-xFy641ygZv=Q@mail.gmail.com>

Use the Pass Arrays filter to get avoid passing unwanted arrays through the
pipeline (i.e. after the gradient filter) and then save the output from the
Pass Arrays filter.

On Mon, Sep 26, 2016 at 12:08 PM, Zenker, Dr. Matthias <
Matthias.Zenker at erbe-med.com> wrote:

>
>
> Hi Andy,
>
>
>
> thank you for the quick reply!
>
> When I highlight the slice filter, I can just save the slice indeed, so
> this solves a part of my problem.
>
> But I would also like to save the calculated gradient for the whole 3D
> dataset, and cannot manage to do it the same way: If I highlight the
> calculator and do Save Data, ParaView saves everything, not just the
> calculator result. What can I do to just save the calculator result?
>
>
>
> Thank you,
>
>
>
> Matthias
>
>
>
>
>
> *Von:* Andy Bauer [mailto:andy.bauer at kitware.com <andy.bauer at kitware.com>]
>
> *Gesendet:* Montag, 26. September 2016 15:22
> *An:* Zenker, Dr. Matthias
> *Cc:* paraview at paraview.org
> *Betreff:* Re: [Paraview] save filter result
>
>
>
> Do you have the Slice filter highlighted in the GUI when you save the data
> set? That's the proper way to just save out the results from that filter
> and not the others. Also, you can use the Pass Arrays filter to selectively
> choose which arrays you want to pass through the pipeline.
>
>
>
> On Mon, Sep 26, 2016 at 9:11 AM, Zenker, Dr. Matthias <
> Matthias.Zenker at erbe-med.com> wrote:
>
> Hi,
>
>
>
> I want to visualize the gradient of a potential, calculated in 3D, on a
> slice, with some coputours. My workflow is:
>
>
>
> ?         Open dataset (vtu),
>
> ?         apply ?gradient of unstructured dataset? filter,
>
> ?         apply calculator to compute the magnitude of the gradient,
>
> ?         apply slice filter,
>
> ?         apply contour filter.
>
> Since it takes some time to calculate gradient, magnitude and extract the
> slice, I would like to save the result in a file so that I can open it
> instantaneously later. How do I do that? If I just use ?save data?,
> ParaView saves all the data, including the initial potential values, which
> gives a huge file. Is there a way to just save the result of the
> calculator, or better, of the slice filter?
>
> I have tried with the extract selection filter, but I seem not to manage
> to extract the results I want. How can I do that?
>
>
>
> Thanks for a hint,
>
>
>
> Matthias
> ------------------------------
>
>
> Erbe Elektromedizin GmbH Firmensitz: 72072 Tuebingen Geschaeftsfuehrer:
> Christian O. Erbe, Reiner Thede Registergericht: Stuttgart HRB 380137
>
>
> _______________________________________________
> Powered by www.kitware.com
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.kitware.com&d=DQMFaQ&c=7vND7vRFB1FzfxRXc-X80O-MJSZd5Q-IVyyYW-Ff2gY&r=3enlI3TuQDmO9BnMCnxq2Mfm4tAO6Z3_Ae1Yc57DMr4&m=95cNBMH6n4JMFIzJi3VEx07aRAWMc7U6_imwzUWzMeA&s=6uc7K9VGCLO-G19IH040pK7osRfnQQ6I_Ofas_2JYRw&e=>
>
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>
> Please keep messages on-topic and check the ParaView Wiki at:
> http://paraview.org/Wiki/ParaView
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__paraview.org_Wiki_ParaView&d=DQMFaQ&c=7vND7vRFB1FzfxRXc-X80O-MJSZd5Q-IVyyYW-Ff2gY&r=3enlI3TuQDmO9BnMCnxq2Mfm4tAO6Z3_Ae1Yc57DMr4&m=95cNBMH6n4JMFIzJi3VEx07aRAWMc7U6_imwzUWzMeA&s=XlOPr-wlILTkdJ4qvwORsrRjbjQTf7uiQP8I4AaqWTs&e=>
>
> Search the list archives at: http://markmail.org/search/?q=ParaView
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>
> Follow this link to subscribe/unsubscribe:
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>
>
> ------------------------------
>
> Erbe Elektromedizin GmbH Firmensitz: 72072 Tuebingen Geschaeftsfuehrer:
> Christian O. Erbe, Reiner Thede Registergericht: Stuttgart HRB 380137
>
>
> _______________________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at http://www.kitware.com/
> opensource/opensource.html
>
> Please keep messages on-topic and check the ParaView Wiki at:
> http://paraview.org/Wiki/ParaView
>
> Search the list archives at: http://markmail.org/search/?q=ParaView
>
> Follow this link to subscribe/unsubscribe:
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>
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From chuck.atkins at kitware.com  Mon Sep 26 14:01:38 2016
From: chuck.atkins at kitware.com (Chuck Atkins)
Date: Mon, 26 Sep 2016 14:01:38 -0400
Subject: [Paraview] Which Compilers and Operating Systems to you require
 for VTK and / ParaView?
In-Reply-To: <CAOXZzG6zhq=vhNeP_2H_hgdiHQht2pvgC6JFnLXQ2nRjf-X_Xw@mail.gmail.com>
References: <CAOXZzG6zhq=vhNeP_2H_hgdiHQht2pvgC6JFnLXQ2nRjf-X_Xw@mail.gmail.com>
Message-ID: <CAOXZzG5JATvx0raB2ioEugME5K8mihmNgnJ7=kabze00fSYSNw@mail.gmail.com>

Just as a follow-up, I will be leaving this survey open all week and stop
accepting responses on Friday, October 30.

----------
Chuck Atkins
Staff R&D Engineer, Scientific Computing
Kitware, Inc.


On Fri, Sep 23, 2016 at 3:05 PM, Chuck Atkins <chuck.atkins at kitware.com>
wrote:

> We're trying to identify where we may have gaps in our testing
> infrastructure for both VTK and ParaView and how to prioritize filling
> those gaps. Certain compilers like GCC and Intel on Linux or Visual Studio
> on Windows will essentially always be supported with issues addressed
> ASAP.  Others, however, sometimes come and go depending on available
> testing resources, licensing, customer demand, etc.
>
> Please take a brief moment to let us know which operating systems and
> compilers are important to howe you use VTK and ParaView from a testing and
> support standpoint.  The survey is very brief and should only take a minute
> or two.
>
> Note: If you are a current support customer with specific critical
> requirements, please feel free to email me off-list.
>
> https://docs.google.com/forms/d/e/1FAIpQLSczYSEWMr90ywhTg1jL
> g2u6JWVNRh6zUzCLeFPRnc_Qyc13dg/viewform
>
> Thank you.
>
> ----------
> Chuck Atkins
> Staff R&D Engineer, Scientific Computing
> Kitware, Inc.
>
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From ben.boeckel at kitware.com  Mon Sep 26 15:03:58 2016
From: ben.boeckel at kitware.com (Ben Boeckel)
Date: Mon, 26 Sep 2016 15:03:58 -0400
Subject: [Paraview] [vtk-developers] Which Compilers and Operating
 Systems to you require for VTK and / ParaView?
In-Reply-To: <CAOXZzG5JATvx0raB2ioEugME5K8mihmNgnJ7=kabze00fSYSNw@mail.gmail.com>
References: <CAOXZzG6zhq=vhNeP_2H_hgdiHQht2pvgC6JFnLXQ2nRjf-X_Xw@mail.gmail.com>
 <CAOXZzG5JATvx0raB2ioEugME5K8mihmNgnJ7=kabze00fSYSNw@mail.gmail.com>
Message-ID: <20160926190358.GA20771@megas.kitware.com>

On Mon, Sep 26, 2016 at 14:01:38 -0400, Chuck Atkins wrote:
> Just as a follow-up, I will be leaving this survey open all week and stop
> accepting responses on Friday, October 30.

I assume you mean September 30?

--Ben

From rdjamis at sandia.gov  Mon Sep 26 23:21:47 2016
From: rdjamis at sandia.gov (Jamison, Ryan Dale)
Date: Tue, 27 Sep 2016 03:21:47 +0000
Subject: [Paraview] Create animation and center geometry
Message-ID: <8e14f00bddce4898b92624fbe57680fb@ES08AMSNLNT.srn.sandia.gov>

Hello Everyone,

I'm trying to save an animation of a finite element model that has large deformation. The center of the deformed geometry changes quite a lot during the simulation.

When I save the animation, I'm actually saving it as png's and combining them afterwards in another tool. I can figure out a center for the model to use that will center on the final geometry but it doesn't look good at the beginning.

How can I change the center of the geometry as time progresses and then save the animations as png's?

Thanks, Ryan



Sent with Good (www.good.com)
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From rccm.kyoshimi at gmail.com  Tue Sep 27 00:40:47 2016
From: rccm.kyoshimi at gmail.com (kenichiro yoshimi)
Date: Tue, 27 Sep 2016 13:40:47 +0900
Subject: [Paraview] Create animation and center geometry
In-Reply-To: <8e14f00bddce4898b92624fbe57680fb@ES08AMSNLNT.srn.sandia.gov>
References: <8e14f00bddce4898b92624fbe57680fb@ES08AMSNLNT.srn.sandia.gov>
Message-ID: <CAHDyfPCLYie6i=7myuR4_DcdjSjbt4D=UL7QEgM+nBMiuR_hHA@mail.gmail.com>

Hi, Ryan

You try the script as follows from [Tools]-[Python Shell] after
reading datasets into ParaView.

---------save_screenshots.py---------
from paraview.simple import *

# Change 10 to the amount of timesteps
for num in range(0,10):
    print 'Save screenshot ' + str(num)

    renderView1 = GetActiveViewOrCreate('RenderView')
    renderView1.ResetCamera()

    # Save screenshot
    # Change to your folder
    name = 'G:/ParaViewData-v4.1/Data/singleSphereAnimation/singleSphere'
+ str(num).zfill(4) + '.png'
    print 'Save as ' + str(name)
    SaveScreenshot(name, magnification=1, quality=100, view=renderView1)

    animationScene1 = GetAnimationScene()

    animationScene1.GoToNext()
---------

Thanks,
yoshimi

2016-09-27 12:21 GMT+09:00 Jamison, Ryan Dale <rdjamis at sandia.gov>:
> Hello Everyone,
>
> I'm trying to save an animation of a finite element model that has large
> deformation. The center of the deformed geometry changes quite a lot during
> the simulation.
>
> When I save the animation, I'm actually saving it as png's and combining
> them afterwards in another tool. I can figure out a center for the model to
> use that will center on the final geometry but it doesn't look good at the
> beginning.
>
> How can I change the center of the geometry as time progresses and then save
> the animations as png's?
>
> Thanks, Ryan
>
>
>
> Sent with Good (www.good.com)
>
> _______________________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Please keep messages on-topic and check the ParaView Wiki at:
> http://paraview.org/Wiki/ParaView
>
> Search the list archives at: http://markmail.org/search/?q=ParaView
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/paraview
>

From Stefan.Melber at DLR.de  Tue Sep 27 00:42:40 2016
From: Stefan.Melber at DLR.de (Stefan Melber)
Date: Tue, 27 Sep 2016 06:42:40 +0200
Subject: [Paraview] Combination of polygonal-data and unstructured grid?
In-Reply-To: <9d42f4ef-1082-6004-85ef-0457cb649bef@gmail.com>
References: <e883554e-4476-f8c6-755c-549d1e5449a2@DLR.de>
 <9d42f4ef-1082-6004-85ef-0457cb649bef@gmail.com>
Message-ID: <55cbc6de-0eeb-3973-ae56-10a5225249fc@DLR.de>

Hi Armin,

sounds thats the thing i searched for! Will check it out today and see 
if it does the job. Is there a demo-xml file around with such polyhedral 
cells?

Best regards and thank you,

       Stefan


> Hi Stefan,
>
> If I understand your problem correctly, then you are looking for
> polyhedral cells (i.e. N face cells, where each face is a M edge
> polygon). Polyhedral cells are commonly used in Computational Fluid
> Dynamics codes, as e.g. OpenFOAM, and VTK/ParaView support them already
> for quite some time (i.e. since around 2010), see [1] for more details.
>
>> My problem is now i have a set of complex shaped volumes (dual-grid
>> data) which cannot be found in the list of cell types for
>> unstructured grid data. Therefore i use the polygonal data and color
>> each cell with one color. Of course for further analysis (e.g.
>> integration of the cell volumes, volume gradient and so on) i need a
>> way to give a set of (closed surface) poly-data elements a kind
>> connection to form a volume to handle them together.
> In which file format do you store your data?
>
> For example, the unstructured VTK XML format [2] has support for
> polyhedral cells. An alternative would be the XDMF file format [3] to
> which I recently added polyhedral cell support [4,5]. Please note that
> the latest release versions of VTK (7.0) or ParaView (5.1) don't support
> the polyhedral cells in XDMF yet, but the nightly builds and the
> upcoming releases (i.e. VTK 7.1 and ParaView 5.2) will have this feature.
>
> Cheers,
> Armin
>
>
> [1] http://www.vtk.org/Wiki/VTK/Polyhedron_Support
> [2] http://www.vtk.org/Wiki/VTK_XML_Formats
> [3] http://www.xdmf.org
> [4] 
> https://gitlab.kitware.com/xdmf/xdmf/commit/0a9fbd0590dff8a677c86754169cd2ccd72fe4b1
> [5] 
> https://gitlab.kitware.com/vtk/vtk/commit/802c9b61de28e560c2659d2af76660bbb49c68be
>
>


From Matthias.Zenker at erbe-med.com  Tue Sep 27 04:42:15 2016
From: Matthias.Zenker at erbe-med.com (Zenker, Dr. Matthias)
Date: Tue, 27 Sep 2016 08:42:15 +0000
Subject: [Paraview] WG: save filter result
In-Reply-To: <CAMaOp+Ex0Jm52oC3tsKx1VKekWnE08+heCJ39-xFy641ygZv=Q@mail.gmail.com>
References: <F9562F3B302F29479A203FC5AF9E3E050F9E3BDA@SERBE4I1.intra.erbe-med.de>
 <CAMaOp+F57qMAcK7FYOHjmoxjnBQPayon7uH3ULai0DLU6QbNxQ@mail.gmail.com>
 <F9562F3B302F29479A203FC5AF9E3E050F9E3BE9@SERBE4I1.intra.erbe-med.de>
 <F9562F3B302F29479A203FC5AF9E3E050F9E3C0F@SERBE4I1.intra.erbe-med.de>
 <CAMaOp+Ex0Jm52oC3tsKx1VKekWnE08+heCJ39-xFy641ygZv=Q@mail.gmail.com>
Message-ID: <F9562F3B302F29479A203FC5AF9E3E050F9E3C76@SERBE4I1.intra.erbe-med.de>

Works perfectly, thank you!


Von: Andy Bauer [mailto:andy.bauer at kitware.com]
Gesendet: Montag, 26. September 2016 19:09
An: Zenker, Dr. Matthias
Cc: paraview at paraview.org
Betreff: Re: [Paraview] WG: save filter result

Use the Pass Arrays filter to get avoid passing unwanted arrays through the pipeline (i.e. after the gradient filter) and then save the output from the Pass Arrays filter.

On Mon, Sep 26, 2016 at 12:08 PM, Zenker, Dr. Matthias <Matthias.Zenker at erbe-med.com<mailto:Matthias.Zenker at erbe-med.com>> wrote:

Hi Andy,

thank you for the quick reply!
When I highlight the slice filter, I can just save the slice indeed, so this solves a part of my problem.
But I would also like to save the calculated gradient for the whole 3D dataset, and cannot manage to do it the same way: If I highlight the calculator and do Save Data, ParaView saves everything, not just the calculator result. What can I do to just save the calculator result?

Thank you,

Matthias


Von: Andy Bauer [mailto:andy.bauer at kitware.com]
Gesendet: Montag, 26. September 2016 15:22
An: Zenker, Dr. Matthias
Cc: paraview at paraview.org<mailto:paraview at paraview.org>
Betreff: Re: [Paraview] save filter result

Do you have the Slice filter highlighted in the GUI when you save the data set? That's the proper way to just save out the results from that filter and not the others. Also, you can use the Pass Arrays filter to selectively choose which arrays you want to pass through the pipeline.

On Mon, Sep 26, 2016 at 9:11 AM, Zenker, Dr. Matthias <Matthias.Zenker at erbe-med.com<mailto:Matthias.Zenker at erbe-med.com>> wrote:
Hi,

I want to visualize the gradient of a potential, calculated in 3D, on a slice, with some coputours. My workflow is:


?         Open dataset (vtu),

?         apply ?gradient of unstructured dataset? filter,

?         apply calculator to compute the magnitude of the gradient,

?         apply slice filter,

?         apply contour filter.
Since it takes some time to calculate gradient, magnitude and extract the slice, I would like to save the result in a file so that I can open it instantaneously later. How do I do that? If I just use ?save data?, ParaView saves all the data, including the initial potential values, which gives a huge file. Is there a way to just save the result of the calculator, or better, of the slice filter?
I have tried with the extract selection filter, but I seem not to manage to extract the results I want. How can I do that?

Thanks for a hint,

Matthias
________________________________

Erbe Elektromedizin GmbH Firmensitz: 72072 Tuebingen Geschaeftsfuehrer: Christian O. Erbe, Reiner Thede Registergericht: Stuttgart HRB 380137

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________________________________

Erbe Elektromedizin GmbH Firmensitz: 72072 Tuebingen Geschaeftsfuehrer: Christian O. Erbe, Reiner Thede Registergericht: Stuttgart HRB 380137

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From Matthias.Zenker at erbe-med.com  Tue Sep 27 05:45:52 2016
From: Matthias.Zenker at erbe-med.com (Zenker, Dr. Matthias)
Date: Tue, 27 Sep 2016 09:45:52 +0000
Subject: [Paraview] Gradient filter: boundary effects
Message-ID: <F9562F3B302F29479A203FC5AF9E3E050F9E3C87@SERBE4I1.intra.erbe-med.de>

Hi,

when I use the gradient filter (unstructured dataset), I observe edge effects which are IMO unphysical. For the nodes on the outer boundary of my domain, the gradient magnitude is smaller than I would expect. The behavior is like the filter tries to use the adjacent nodes to calculate the gradient, and since there are none  outside the domain, it assumes zero and finds a lower result.
If so, I would consider this a bug - is there a fix or workaround?

Thanks,

Matthias
________________________________

Erbe Elektromedizin GmbH Firmensitz: 72072 Tuebingen Geschaeftsfuehrer: Christian O. Erbe, Reiner Thede Registergericht: Stuttgart HRB 380137

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From kmorel at sandia.gov  Tue Sep 27 08:14:06 2016
From: kmorel at sandia.gov (Moreland, Kenneth)
Date: Tue, 27 Sep 2016 12:14:06 +0000
Subject: [Paraview] Gradient filter: boundary effects
Message-ID: <235C908C-3435-4027-B312-6061BF992F1F@sandia.gov>

Matthias,

The gradient is estimated with finite differences. Thus, it is not wholly unexpected that there could be differences at the boundaries. However, the algorithm does not assume zero for adjacent cells at the boundaries.

The way the unstructured gradient filter works is that it computes the local gradient in each cell at each of the cell?s points. Then for every point it averages the gradient from all incident cells at that point. (If you have the Faster Approximation option on, then the filter only computes one gradient per cell in the center and averages those. Faster, but more artifacts, particularly at the edges.)

If this averaging is causing you an issue, you might try the Compute Derivatives filter. This does a wholly local operation within each cell, so you should not see any artifacts (unless the field itself has artifacts at the boundaries).

-Ken


From: ParaView <paraview-bounces at paraview.org> on behalf of "Zenker, Dr. Matthias" <Matthias.Zenker at erbe-med.com>
Date: Tuesday, September 27, 2016 at 5:45 AM
To: "paraview at paraview.org" <paraview at paraview.org>
Subject: [EXTERNAL] [Paraview] Gradient filter: boundary effects

Hi,

when I use the gradient filter (unstructured dataset), I observe edge effects which are IMO unphysical. For the nodes on the outer boundary of my domain, the gradient magnitude is smaller than I would expect. The behavior is like the filter tries to use the adjacent nodes to calculate the gradient, and since there are none  outside the domain, it assumes zero and finds a lower result.
If so, I would consider this a bug ? is there a fix or workaround?

Thanks,

Matthias
________________________________

Erbe Elektromedizin GmbH Firmensitz: 72072 Tuebingen Geschaeftsfuehrer: Christian O. Erbe, Reiner Thede Registergericht: Stuttgart HRB 380137
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From Matthias.Zenker at erbe-med.com  Tue Sep 27 08:28:52 2016
From: Matthias.Zenker at erbe-med.com (Zenker, Dr. Matthias)
Date: Tue, 27 Sep 2016 12:28:52 +0000
Subject: [Paraview] Gradient filter: boundary effects
In-Reply-To: <235C908C-3435-4027-B312-6061BF992F1F@sandia.gov>
References: <235C908C-3435-4027-B312-6061BF992F1F@sandia.gov>
Message-ID: <F9562F3B302F29479A203FC5AF9E3E050F9E3CBC@SERBE4I1.intra.erbe-med.de>

Hi Kenneth,

thank you for the quick answer!
So it seems not that trivial to calculate an electrical field between a rod and a plane given the potential?
The compute derivatives filter does not give me the problem at the boundary indeed. Instead it gives a value per cell, not per node, which does not look nice.
Is there a friendly filter or switch which would give me the smoothed surface representation back?

Thanks,

Matthias


Von: Moreland, Kenneth [mailto:kmorel at sandia.gov]
Gesendet: Dienstag, 27. September 2016 14:14
An: Zenker, Dr. Matthias; paraview at paraview.org
Betreff: Re: [Paraview] Gradient filter: boundary effects

Matthias,

The gradient is estimated with finite differences. Thus, it is not wholly unexpected that there could be differences at the boundaries. However, the algorithm does not assume zero for adjacent cells at the boundaries.

The way the unstructured gradient filter works is that it computes the local gradient in each cell at each of the cell?s points. Then for every point it averages the gradient from all incident cells at that point. (If you have the Faster Approximation option on, then the filter only computes one gradient per cell in the center and averages those. Faster, but more artifacts, particularly at the edges.)

If this averaging is causing you an issue, you might try the Compute Derivatives filter. This does a wholly local operation within each cell, so you should not see any artifacts (unless the field itself has artifacts at the boundaries).

-Ken


From: ParaView <paraview-bounces at paraview.org<mailto:paraview-bounces at paraview.org>> on behalf of "Zenker, Dr. Matthias" <Matthias.Zenker at erbe-med.com<mailto:Matthias.Zenker at erbe-med.com>>
Date: Tuesday, September 27, 2016 at 5:45 AM
To: "paraview at paraview.org<mailto:paraview at paraview.org>" <paraview at paraview.org<mailto:paraview at paraview.org>>
Subject: [EXTERNAL] [Paraview] Gradient filter: boundary effects

Hi,

when I use the gradient filter (unstructured dataset), I observe edge effects which are IMO unphysical. For the nodes on the outer boundary of my domain, the gradient magnitude is smaller than I would expect. The behavior is like the filter tries to use the adjacent nodes to calculate the gradient, and since there are none  outside the domain, it assumes zero and finds a lower result.
If so, I would consider this a bug ? is there a fix or workaround?

Thanks,

Matthias
________________________________

Erbe Elektromedizin GmbH Firmensitz: 72072 Tuebingen Geschaeftsfuehrer: Christian O. Erbe, Reiner Thede Registergericht: Stuttgart HRB 380137
________________________________

Erbe Elektromedizin GmbH Firmensitz: 72072 Tuebingen Geschaeftsfuehrer: Christian O. Erbe, Reiner Thede Registergericht: Stuttgart HRB 380137

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From kmorel at sandia.gov  Tue Sep 27 08:36:09 2016
From: kmorel at sandia.gov (Moreland, Kenneth)
Date: Tue, 27 Sep 2016 12:36:09 +0000
Subject: [Paraview] Gradient filter: boundary effects
Message-ID: <BC6EAFA9-E86C-44C9-9A09-7C221FEE09DB@sandia.gov>

You could run the results through the point to cell filter, but that would give you the same answer as the gradient of unstructured dataset filter with the faster approximation option on.

-Ken

From: "Zenker, Dr. Matthias" <Matthias.Zenker at erbe-med.com>
Date: Tuesday, September 27, 2016 at 8:28 AM
To: "Moreland, Kenneth" <kmorel at sandia.gov>, "paraview at paraview.org" <paraview at paraview.org>
Subject: [EXTERNAL] AW: [Paraview] Gradient filter: boundary effects

Hi Kenneth,

thank you for the quick answer!
So it seems not that trivial to calculate an electrical field between a rod and a plane given the potential?
The compute derivatives filter does not give me the problem at the boundary indeed. Instead it gives a value per cell, not per node, which does not look nice.
Is there a friendly filter or switch which would give me the smoothed surface representation back?

Thanks,

Matthias


Von: Moreland, Kenneth [mailto:kmorel at sandia.gov]
Gesendet: Dienstag, 27. September 2016 14:14
An: Zenker, Dr. Matthias; paraview at paraview.org
Betreff: Re: [Paraview] Gradient filter: boundary effects

Matthias,

The gradient is estimated with finite differences. Thus, it is not wholly unexpected that there could be differences at the boundaries. However, the algorithm does not assume zero for adjacent cells at the boundaries.

The way the unstructured gradient filter works is that it computes the local gradient in each cell at each of the cell?s points. Then for every point it averages the gradient from all incident cells at that point. (If you have the Faster Approximation option on, then the filter only computes one gradient per cell in the center and averages those. Faster, but more artifacts, particularly at the edges.)

If this averaging is causing you an issue, you might try the Compute Derivatives filter. This does a wholly local operation within each cell, so you should not see any artifacts (unless the field itself has artifacts at the boundaries).

-Ken


From: ParaView <paraview-bounces at paraview.org<mailto:paraview-bounces at paraview.org>> on behalf of "Zenker, Dr. Matthias" <Matthias.Zenker at erbe-med.com<mailto:Matthias.Zenker at erbe-med.com>>
Date: Tuesday, September 27, 2016 at 5:45 AM
To: "paraview at paraview.org<mailto:paraview at paraview.org>" <paraview at paraview.org<mailto:paraview at paraview.org>>
Subject: [EXTERNAL] [Paraview] Gradient filter: boundary effects

Hi,

when I use the gradient filter (unstructured dataset), I observe edge effects which are IMO unphysical. For the nodes on the outer boundary of my domain, the gradient magnitude is smaller than I would expect. The behavior is like the filter tries to use the adjacent nodes to calculate the gradient, and since there are none  outside the domain, it assumes zero and finds a lower result.
If so, I would consider this a bug ? is there a fix or workaround?

Thanks,

Matthias
________________________________

Erbe Elektromedizin GmbH Firmensitz: 72072 Tuebingen Geschaeftsfuehrer: Christian O. Erbe, Reiner Thede Registergericht: Stuttgart HRB 380137
________________________________

Erbe Elektromedizin GmbH Firmensitz: 72072 Tuebingen Geschaeftsfuehrer: Christian O. Erbe, Reiner Thede Registergericht: Stuttgart HRB 380137
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From chuck.atkins at kitware.com  Tue Sep 27 08:40:39 2016
From: chuck.atkins at kitware.com (Chuck Atkins)
Date: Tue, 27 Sep 2016 08:40:39 -0400
Subject: [Paraview] [vtk-developers] Which Compilers and Operating
 Systems to you require for VTK and / ParaView?
In-Reply-To: <20160926190358.GA20771@megas.kitware.com>
References: <CAOXZzG6zhq=vhNeP_2H_hgdiHQht2pvgC6JFnLXQ2nRjf-X_Xw@mail.gmail.com>
 <CAOXZzG5JATvx0raB2ioEugME5K8mihmNgnJ7=kabze00fSYSNw@mail.gmail.com>
 <20160926190358.GA20771@megas.kitware.com>
Message-ID: <CAOXZzG5x7wDcgPAJLnQVQxZF61C_7vVPS_EixtnbifADEn+5CQ@mail.gmail.com>

Yes.  Off by a month, my mistake.  The intent is to let the survey run for
a week.

----------
Chuck Atkins
Staff R&D Engineer, Scientific Computing
Kitware, Inc.


On Mon, Sep 26, 2016 at 3:03 PM, Ben Boeckel <ben.boeckel at kitware.com>
wrote:

> On Mon, Sep 26, 2016 at 14:01:38 -0400, Chuck Atkins wrote:
> > Just as a follow-up, I will be leaving this survey open all week and stop
> > accepting responses on Friday, October 30.
>
> I assume you mean September 30?
>
> --Ben
>
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From dkxls23 at gmail.com  Tue Sep 27 09:03:00 2016
From: dkxls23 at gmail.com (Armin Wehrfritz)
Date: Tue, 27 Sep 2016 16:03:00 +0300
Subject: [Paraview] Combination of polygonal-data and unstructured grid?
In-Reply-To: <55cbc6de-0eeb-3973-ae56-10a5225249fc@DLR.de>
References: <e883554e-4476-f8c6-755c-549d1e5449a2@DLR.de>
 <9d42f4ef-1082-6004-85ef-0457cb649bef@gmail.com>
 <55cbc6de-0eeb-3973-ae56-10a5225249fc@DLR.de>
Message-ID: <d5e0904d-ebdc-b830-43ab-33dad3eddc53@gmail.com>

Hi Stefan,

IIRC there is a .vtu file containing polyhderal cells in the VTK DATA
repository.

Otherwise, I attached a .xmf and a .vtu file containing each containing
identical data, i.e. 2 hexahedral and 2 polyhderal cell.
Please note that the white-space in these files has no meaning, and that
for the .xmf file you need a recent ParaView nightly build.

Best regards,
Armin





On 09/27/2016 07:42 AM, Stefan Melber wrote:
> Hi Armin,
>
> sounds thats the thing i searched for! Will check it out today and see
> if it does the job. Is there a demo-xml file around with such polyhedral
> cells?
>
> Best regards and thank you,
>
>       Stefan
>
>
>> Hi Stefan,
>>
>> If I understand your problem correctly, then you are looking for
>> polyhedral cells (i.e. N face cells, where each face is a M edge
>> polygon). Polyhedral cells are commonly used in Computational Fluid
>> Dynamics codes, as e.g. OpenFOAM, and VTK/ParaView support them already
>> for quite some time (i.e. since around 2010), see [1] for more details.
>>
>>> My problem is now i have a set of complex shaped volumes (dual-grid
>>> data) which cannot be found in the list of cell types for
>>> unstructured grid data. Therefore i use the polygonal data and color
>>> each cell with one color. Of course for further analysis (e.g.
>>> integration of the cell volumes, volume gradient and so on) i need a
>>> way to give a set of (closed surface) poly-data elements a kind
>>> connection to form a volume to handle them together.
>> In which file format do you store your data?
>>
>> For example, the unstructured VTK XML format [2] has support for
>> polyhedral cells. An alternative would be the XDMF file format [3] to
>> which I recently added polyhedral cell support [4,5]. Please note that
>> the latest release versions of VTK (7.0) or ParaView (5.1) don't support
>> the polyhedral cells in XDMF yet, but the nightly builds and the
>> upcoming releases (i.e. VTK 7.1 and ParaView 5.2) will have this feature.
>>
>> Cheers,
>> Armin
>>
>>
>> [1] http://www.vtk.org/Wiki/VTK/Polyhedron_Support
>> [2] http://www.vtk.org/Wiki/VTK_XML_Formats
>> [3] http://www.xdmf.org
>> [4]
>> https://gitlab.kitware.com/xdmf/xdmf/commit/0a9fbd0590dff8a677c86754169cd2ccd72fe4b1
>>
>> [5]
>> https://gitlab.kitware.com/vtk/vtk/commit/802c9b61de28e560c2659d2af76660bbb49c68be
>>
>>
>>
>
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From Matthias.Zenker at erbe-med.com  Tue Sep 27 09:06:56 2016
From: Matthias.Zenker at erbe-med.com (Zenker, Dr. Matthias)
Date: Tue, 27 Sep 2016 13:06:56 +0000
Subject: [Paraview] Gradient filter: boundary effects
In-Reply-To: <BC6EAFA9-E86C-44C9-9A09-7C221FEE09DB@sandia.gov>
References: <BC6EAFA9-E86C-44C9-9A09-7C221FEE09DB@sandia.gov>
Message-ID: <F9562F3B302F29479A203FC5AF9E3E050F9E3CE1@SERBE4I1.intra.erbe-med.de>

Hi Ken,

what I don?t understand is that the cell gradients are correct, but their average at the border is not. (Example: All cell gradients adjacent to one node at the border have approx. 7900 units in y direction, the node has approx. 5300)
So it seems I cannot determine the gradient in the postprocessing step, but have to calculate it in the FEM solver (where I do get correct results now ? I didn?t initially, which was the reason why I tried it with ParaView).

Thank you anyway, I have learned new bits of ParaView again (which is great software BTW)!

Have a nice holiday (if I interpret your autoreply correctly)!

Matthias

Von: Moreland, Kenneth [mailto:kmorel at sandia.gov]
Gesendet: Dienstag, 27. September 2016 14:36
An: Zenker, Dr. Matthias; paraview at paraview.org
Betreff: Re: [Paraview] Gradient filter: boundary effects

You could run the results through the point to cell filter, but that would give you the same answer as the gradient of unstructured dataset filter with the faster approximation option on.

-Ken

From: "Zenker, Dr. Matthias" <Matthias.Zenker at erbe-med.com<mailto:Matthias.Zenker at erbe-med.com>>
Date: Tuesday, September 27, 2016 at 8:28 AM
To: "Moreland, Kenneth" <kmorel at sandia.gov<mailto:kmorel at sandia.gov>>, "paraview at paraview.org<mailto:paraview at paraview.org>" <paraview at paraview.org<mailto:paraview at paraview.org>>
Subject: [EXTERNAL] AW: [Paraview] Gradient filter: boundary effects

Hi Kenneth,

thank you for the quick answer!
So it seems not that trivial to calculate an electrical field between a rod and a plane given the potential?
The compute derivatives filter does not give me the problem at the boundary indeed. Instead it gives a value per cell, not per node, which does not look nice.
Is there a friendly filter or switch which would give me the smoothed surface representation back?

Thanks,

Matthias


Von: Moreland, Kenneth [mailto:kmorel at sandia.gov]
Gesendet: Dienstag, 27. September 2016 14:14
An: Zenker, Dr. Matthias; paraview at paraview.org<mailto:paraview at paraview.org>
Betreff: Re: [Paraview] Gradient filter: boundary effects

Matthias,

The gradient is estimated with finite differences. Thus, it is not wholly unexpected that there could be differences at the boundaries. However, the algorithm does not assume zero for adjacent cells at the boundaries.

The way the unstructured gradient filter works is that it computes the local gradient in each cell at each of the cell?s points. Then for every point it averages the gradient from all incident cells at that point. (If you have the Faster Approximation option on, then the filter only computes one gradient per cell in the center and averages those. Faster, but more artifacts, particularly at the edges.)

If this averaging is causing you an issue, you might try the Compute Derivatives filter. This does a wholly local operation within each cell, so you should not see any artifacts (unless the field itself has artifacts at the boundaries).

-Ken


From: ParaView <paraview-bounces at paraview.org<mailto:paraview-bounces at paraview.org>> on behalf of "Zenker, Dr. Matthias" <Matthias.Zenker at erbe-med.com<mailto:Matthias.Zenker at erbe-med.com>>
Date: Tuesday, September 27, 2016 at 5:45 AM
To: "paraview at paraview.org<mailto:paraview at paraview.org>" <paraview at paraview.org<mailto:paraview at paraview.org>>
Subject: [EXTERNAL] [Paraview] Gradient filter: boundary effects

Hi,

when I use the gradient filter (unstructured dataset), I observe edge effects which are IMO unphysical. For the nodes on the outer boundary of my domain, the gradient magnitude is smaller than I would expect. The behavior is like the filter tries to use the adjacent nodes to calculate the gradient, and since there are none  outside the domain, it assumes zero and finds a lower result.
If so, I would consider this a bug ? is there a fix or workaround?

Thanks,

Matthias
________________________________

Erbe Elektromedizin GmbH Firmensitz: 72072 Tuebingen Geschaeftsfuehrer: Christian O. Erbe, Reiner Thede Registergericht: Stuttgart HRB 380137
________________________________

Erbe Elektromedizin GmbH Firmensitz: 72072 Tuebingen Geschaeftsfuehrer: Christian O. Erbe, Reiner Thede Registergericht: Stuttgart HRB 380137
________________________________

Erbe Elektromedizin GmbH Firmensitz: 72072 Tuebingen Geschaeftsfuehrer: Christian O. Erbe, Reiner Thede Registergericht: Stuttgart HRB 380137

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From Stefan.Melber at DLR.de  Tue Sep 27 09:18:13 2016
From: Stefan.Melber at DLR.de (Stefan Melber)
Date: Tue, 27 Sep 2016 15:18:13 +0200
Subject: [Paraview] Combination of polygonal-data and unstructured grid?
In-Reply-To: <d5e0904d-ebdc-b830-43ab-33dad3eddc53@gmail.com>
References: <e883554e-4476-f8c6-755c-549d1e5449a2@DLR.de>
 <9d42f4ef-1082-6004-85ef-0457cb649bef@gmail.com>
 <55cbc6de-0eeb-3973-ae56-10a5225249fc@DLR.de>
 <d5e0904d-ebdc-b830-43ab-33dad3eddc53@gmail.com>
Message-ID: <5dea9604-87d7-95d8-3cc2-baa089a04fa2@DLR.de>

Hi Armin,

thank you  - thats what i searched for ...

      Stefan
> Hi Stefan,
>
> IIRC there is a .vtu file containing polyhderal cells in the VTK DATA
> repository.
>
> Otherwise, I attached a .xmf and a .vtu file containing each containing
> identical data, i.e. 2 hexahedral and 2 polyhderal cell.
> Please note that the white-space in these files has no meaning, and that
> for the .xmf file you need a recent ParaView nightly build.
>
> Best regards,
> Armin
>
>
>
>
>
> On 09/27/2016 07:42 AM, Stefan Melber wrote:
>> Hi Armin,
>>
>> sounds thats the thing i searched for! Will check it out today and see
>> if it does the job. Is there a demo-xml file around with such polyhedral
>> cells?
>>
>> Best regards and thank you,
>>
>>       Stefan
>>
>>
>>> Hi Stefan,
>>>
>>> If I understand your problem correctly, then you are looking for
>>> polyhedral cells (i.e. N face cells, where each face is a M edge
>>> polygon). Polyhedral cells are commonly used in Computational Fluid
>>> Dynamics codes, as e.g. OpenFOAM, and VTK/ParaView support them already
>>> for quite some time (i.e. since around 2010), see [1] for more details.
>>>
>>>> My problem is now i have a set of complex shaped volumes (dual-grid
>>>> data) which cannot be found in the list of cell types for
>>>> unstructured grid data. Therefore i use the polygonal data and color
>>>> each cell with one color. Of course for further analysis (e.g.
>>>> integration of the cell volumes, volume gradient and so on) i need a
>>>> way to give a set of (closed surface) poly-data elements a kind
>>>> connection to form a volume to handle them together.
>>> In which file format do you store your data?
>>>
>>> For example, the unstructured VTK XML format [2] has support for
>>> polyhedral cells. An alternative would be the XDMF file format [3] to
>>> which I recently added polyhedral cell support [4,5]. Please note that
>>> the latest release versions of VTK (7.0) or ParaView (5.1) don't 
>>> support
>>> the polyhedral cells in XDMF yet, but the nightly builds and the
>>> upcoming releases (i.e. VTK 7.1 and ParaView 5.2) will have this 
>>> feature.
>>>
>>> Cheers,
>>> Armin
>>>
>>>
>>> [1] http://www.vtk.org/Wiki/VTK/Polyhedron_Support
>>> [2] http://www.vtk.org/Wiki/VTK_XML_Formats
>>> [3] http://www.xdmf.org
>>> [4]
>>> https://gitlab.kitware.com/xdmf/xdmf/commit/0a9fbd0590dff8a677c86754169cd2ccd72fe4b1 
>>>
>>>
>>> [5]
>>> https://gitlab.kitware.com/vtk/vtk/commit/802c9b61de28e560c2659d2af76660bbb49c68be 
>>>
>>>
>>>
>>>
>>


From kmorel at sandia.gov  Tue Sep 27 09:40:28 2016
From: kmorel at sandia.gov (Moreland, Kenneth)
Date: Tue, 27 Sep 2016 13:40:28 +0000
Subject: [Paraview] Gradient filter: boundary effects
Message-ID: <3E5E6925-A0B2-4344-AA98-07F55039FF4B@sandia.gov>

Matthias,

If values are being pulled from 7900 units down to 5300 units, there must be some neighbor with lower values. Why that is happening for you I cannot say without looking at your data. Perhaps on the boundary there are some malformed or 2D cells with invalid gradients.

-Ken


From: "Zenker, Dr. Matthias" <Matthias.Zenker at erbe-med.com>
Date: Tuesday, September 27, 2016 at 9:06 AM
To: "Moreland, Kenneth" <kmorel at sandia.gov>
Cc: "paraview at paraview.org" <paraview at paraview.org>
Subject: [EXTERNAL] AW: [Paraview] Gradient filter: boundary effects

Hi Ken,

what I don?t understand is that the cell gradients are correct, but their average at the border is not. (Example: All cell gradients adjacent to one node at the border have approx. 7900 units in y direction, the node has approx. 5300)
So it seems I cannot determine the gradient in the postprocessing step, but have to calculate it in the FEM solver (where I do get correct results now ? I didn?t initially, which was the reason why I tried it with ParaView).

Thank you anyway, I have learned new bits of ParaView again (which is great software BTW)!

Have a nice holiday (if I interpret your autoreply correctly)!

Matthias

Von: Moreland, Kenneth [mailto:kmorel at sandia.gov]
Gesendet: Dienstag, 27. September 2016 14:36
An: Zenker, Dr. Matthias; paraview at paraview.org
Betreff: Re: [Paraview] Gradient filter: boundary effects

You could run the results through the point to cell filter, but that would give you the same answer as the gradient of unstructured dataset filter with the faster approximation option on.

-Ken

From: "Zenker, Dr. Matthias" <Matthias.Zenker at erbe-med.com<mailto:Matthias.Zenker at erbe-med.com>>
Date: Tuesday, September 27, 2016 at 8:28 AM
To: "Moreland, Kenneth" <kmorel at sandia.gov<mailto:kmorel at sandia.gov>>, "paraview at paraview.org<mailto:paraview at paraview.org>" <paraview at paraview.org<mailto:paraview at paraview.org>>
Subject: [EXTERNAL] AW: [Paraview] Gradient filter: boundary effects

Hi Kenneth,

thank you for the quick answer!
So it seems not that trivial to calculate an electrical field between a rod and a plane given the potential?
The compute derivatives filter does not give me the problem at the boundary indeed. Instead it gives a value per cell, not per node, which does not look nice.
Is there a friendly filter or switch which would give me the smoothed surface representation back?

Thanks,

Matthias


Von: Moreland, Kenneth [mailto:kmorel at sandia.gov]
Gesendet: Dienstag, 27. September 2016 14:14
An: Zenker, Dr. Matthias; paraview at paraview.org<mailto:paraview at paraview.org>
Betreff: Re: [Paraview] Gradient filter: boundary effects

Matthias,

The gradient is estimated with finite differences. Thus, it is not wholly unexpected that there could be differences at the boundaries. However, the algorithm does not assume zero for adjacent cells at the boundaries.

The way the unstructured gradient filter works is that it computes the local gradient in each cell at each of the cell?s points. Then for every point it averages the gradient from all incident cells at that point. (If you have the Faster Approximation option on, then the filter only computes one gradient per cell in the center and averages those. Faster, but more artifacts, particularly at the edges.)

If this averaging is causing you an issue, you might try the Compute Derivatives filter. This does a wholly local operation within each cell, so you should not see any artifacts (unless the field itself has artifacts at the boundaries).

-Ken


From: ParaView <paraview-bounces at paraview.org<mailto:paraview-bounces at paraview.org>> on behalf of "Zenker, Dr. Matthias" <Matthias.Zenker at erbe-med.com<mailto:Matthias.Zenker at erbe-med.com>>
Date: Tuesday, September 27, 2016 at 5:45 AM
To: "paraview at paraview.org<mailto:paraview at paraview.org>" <paraview at paraview.org<mailto:paraview at paraview.org>>
Subject: [EXTERNAL] [Paraview] Gradient filter: boundary effects

Hi,

when I use the gradient filter (unstructured dataset), I observe edge effects which are IMO unphysical. For the nodes on the outer boundary of my domain, the gradient magnitude is smaller than I would expect. The behavior is like the filter tries to use the adjacent nodes to calculate the gradient, and since there are none  outside the domain, it assumes zero and finds a lower result.
If so, I would consider this a bug ? is there a fix or workaround?

Thanks,

Matthias
________________________________

Erbe Elektromedizin GmbH Firmensitz: 72072 Tuebingen Geschaeftsfuehrer: Christian O. Erbe, Reiner Thede Registergericht: Stuttgart HRB 380137
________________________________

Erbe Elektromedizin GmbH Firmensitz: 72072 Tuebingen Geschaeftsfuehrer: Christian O. Erbe, Reiner Thede Registergericht: Stuttgart HRB 380137
________________________________

Erbe Elektromedizin GmbH Firmensitz: 72072 Tuebingen Geschaeftsfuehrer: Christian O. Erbe, Reiner Thede Registergericht: Stuttgart HRB 380137
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From Matthias.Zenker at erbe-med.com  Tue Sep 27 09:51:29 2016
From: Matthias.Zenker at erbe-med.com (Zenker, Dr. Matthias)
Date: Tue, 27 Sep 2016 13:51:29 +0000
Subject: [Paraview] Gradient filter: boundary effects
In-Reply-To: <3E5E6925-A0B2-4344-AA98-07F55039FF4B@sandia.gov>
References: <3E5E6925-A0B2-4344-AA98-07F55039FF4B@sandia.gov>
Message-ID: <F9562F3B302F29479A203FC5AF9E3E050F9E3D06@SERBE4I1.intra.erbe-med.de>

Hi Ken,

if you want to have a look ? here is a simple test file. At  the bottom side, there are 4 adjacent cells having grad(y)~7900 from computederivatives, but all 3 nodes on the bottom side have grad(y) ~ 5300 from celldatatopointdata.

Thanks,

Matthias

Von: Moreland, Kenneth [mailto:kmorel at sandia.gov]
Gesendet: Dienstag, 27. September 2016 15:40
An: Zenker, Dr. Matthias
Cc: paraview at paraview.org
Betreff: Re: [Paraview] Gradient filter: boundary effects

Matthias,

If values are being pulled from 7900 units down to 5300 units, there must be some neighbor with lower values. Why that is happening for you I cannot say without looking at your data. Perhaps on the boundary there are some malformed or 2D cells with invalid gradients.

-Ken


From: "Zenker, Dr. Matthias" <Matthias.Zenker at erbe-med.com<mailto:Matthias.Zenker at erbe-med.com>>
Date: Tuesday, September 27, 2016 at 9:06 AM
To: "Moreland, Kenneth" <kmorel at sandia.gov<mailto:kmorel at sandia.gov>>
Cc: "paraview at paraview.org<mailto:paraview at paraview.org>" <paraview at paraview.org<mailto:paraview at paraview.org>>
Subject: [EXTERNAL] AW: [Paraview] Gradient filter: boundary effects

Hi Ken,

what I don?t understand is that the cell gradients are correct, but their average at the border is not. (Example: All cell gradients adjacent to one node at the border have approx. 7900 units in y direction, the node has approx. 5300)
So it seems I cannot determine the gradient in the postprocessing step, but have to calculate it in the FEM solver (where I do get correct results now ? I didn?t initially, which was the reason why I tried it with ParaView).

Thank you anyway, I have learned new bits of ParaView again (which is great software BTW)!

Have a nice holiday (if I interpret your autoreply correctly)!

Matthias

Von: Moreland, Kenneth [mailto:kmorel at sandia.gov]
Gesendet: Dienstag, 27. September 2016 14:36
An: Zenker, Dr. Matthias; paraview at paraview.org<mailto:paraview at paraview.org>
Betreff: Re: [Paraview] Gradient filter: boundary effects

You could run the results through the point to cell filter, but that would give you the same answer as the gradient of unstructured dataset filter with the faster approximation option on.

-Ken

From: "Zenker, Dr. Matthias" <Matthias.Zenker at erbe-med.com<mailto:Matthias.Zenker at erbe-med.com>>
Date: Tuesday, September 27, 2016 at 8:28 AM
To: "Moreland, Kenneth" <kmorel at sandia.gov<mailto:kmorel at sandia.gov>>, "paraview at paraview.org<mailto:paraview at paraview.org>" <paraview at paraview.org<mailto:paraview at paraview.org>>
Subject: [EXTERNAL] AW: [Paraview] Gradient filter: boundary effects

Hi Kenneth,

thank you for the quick answer!
So it seems not that trivial to calculate an electrical field between a rod and a plane given the potential?
The compute derivatives filter does not give me the problem at the boundary indeed. Instead it gives a value per cell, not per node, which does not look nice.
Is there a friendly filter or switch which would give me the smoothed surface representation back?

Thanks,

Matthias


Von: Moreland, Kenneth [mailto:kmorel at sandia.gov]
Gesendet: Dienstag, 27. September 2016 14:14
An: Zenker, Dr. Matthias; paraview at paraview.org<mailto:paraview at paraview.org>
Betreff: Re: [Paraview] Gradient filter: boundary effects

Matthias,

The gradient is estimated with finite differences. Thus, it is not wholly unexpected that there could be differences at the boundaries. However, the algorithm does not assume zero for adjacent cells at the boundaries.

The way the unstructured gradient filter works is that it computes the local gradient in each cell at each of the cell?s points. Then for every point it averages the gradient from all incident cells at that point. (If you have the Faster Approximation option on, then the filter only computes one gradient per cell in the center and averages those. Faster, but more artifacts, particularly at the edges.)

If this averaging is causing you an issue, you might try the Compute Derivatives filter. This does a wholly local operation within each cell, so you should not see any artifacts (unless the field itself has artifacts at the boundaries).

-Ken


From: ParaView <paraview-bounces at paraview.org<mailto:paraview-bounces at paraview.org>> on behalf of "Zenker, Dr. Matthias" <Matthias.Zenker at erbe-med.com<mailto:Matthias.Zenker at erbe-med.com>>
Date: Tuesday, September 27, 2016 at 5:45 AM
To: "paraview at paraview.org<mailto:paraview at paraview.org>" <paraview at paraview.org<mailto:paraview at paraview.org>>
Subject: [EXTERNAL] [Paraview] Gradient filter: boundary effects

Hi,

when I use the gradient filter (unstructured dataset), I observe edge effects which are IMO unphysical. For the nodes on the outer boundary of my domain, the gradient magnitude is smaller than I would expect. The behavior is like the filter tries to use the adjacent nodes to calculate the gradient, and since there are none  outside the domain, it assumes zero and finds a lower result.
If so, I would consider this a bug ? is there a fix or workaround?

Thanks,

Matthias
________________________________

Erbe Elektromedizin GmbH Firmensitz: 72072 Tuebingen Geschaeftsfuehrer: Christian O. Erbe, Reiner Thede Registergericht: Stuttgart HRB 380137
________________________________

Erbe Elektromedizin GmbH Firmensitz: 72072 Tuebingen Geschaeftsfuehrer: Christian O. Erbe, Reiner Thede Registergericht: Stuttgart HRB 380137
________________________________

Erbe Elektromedizin GmbH Firmensitz: 72072 Tuebingen Geschaeftsfuehrer: Christian O. Erbe, Reiner Thede Registergericht: Stuttgart HRB 380137
________________________________

Erbe Elektromedizin GmbH Firmensitz: 72072 Tuebingen Geschaeftsfuehrer: Christian O. Erbe, Reiner Thede Registergericht: Stuttgart HRB 380137

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From rdjamis at sandia.gov  Tue Sep 27 10:10:02 2016
From: rdjamis at sandia.gov (Jamison, Ryan Dale)
Date: Tue, 27 Sep 2016 14:10:02 +0000
Subject: [Paraview] [EXTERNAL] Re: Create animation and center geometry
In-Reply-To: <CAHDyfPCLYie6i=7myuR4_DcdjSjbt4D=UL7QEgM+nBMiuR_hHA@mail.gmail.com>
References: <8e14f00bddce4898b92624fbe57680fb@ES08AMSNLNT.srn.sandia.gov>
 <CAHDyfPCLYie6i=7myuR4_DcdjSjbt4D=UL7QEgM+nBMiuR_hHA@mail.gmail.com>
Message-ID: <D0ABD0B9-B26B-4C91-881D-DAEEAFA4F3E4@sandia.gov>

Yoshimi,

Thanks for the script! This does exactly what I was wanting to do.

One further question, where in the script can I define the size of the images to save?

Best, Ryan 

> On Sep 26, 2016, at 10:40 PM, kenichiro yoshimi <rccm.kyoshimi at gmail.com> wrote:
> 
> Hi, Ryan
> 
> You try the script as follows from [Tools]-[Python Shell] after
> reading datasets into ParaView.
> 
> ---------save_screenshots.py---------
> from paraview.simple import *
> 
> # Change 10 to the amount of timesteps
> for num in range(0,10):
>    print 'Save screenshot ' + str(num)
> 
>    renderView1 = GetActiveViewOrCreate('RenderView')
>    renderView1.ResetCamera()
> 
>    # Save screenshot
>    # Change to your folder
>    name = 'G:/ParaViewData-v4.1/Data/singleSphereAnimation/singleSphere'
> + str(num).zfill(4) + '.png'
>    print 'Save as ' + str(name)
>    SaveScreenshot(name, magnification=1, quality=100, view=renderView1)
> 
>    animationScene1 = GetAnimationScene()
> 
>    animationScene1.GoToNext()
> ---------
> 
> Thanks,
> yoshimi


From kmorel at sandia.gov  Tue Sep 27 10:41:14 2016
From: kmorel at sandia.gov (Moreland, Kenneth)
Date: Tue, 27 Sep 2016 14:41:14 +0000
Subject: [Paraview] Gradient filter: boundary effects
Message-ID: <4692C574-20C5-405F-8433-C5ED4F3D97E4@sandia.gov>

Matthias,

As I suspected, your data has some boundary elements that are throwing off the gradient calculation. The data you sent me has line cells around the boarder of the data. The easiest way to see these line cells is to go to the Properties panel and change the ?Line Width? parameter to something large. (Attached is an image that shows the boundary cells by setting the line width to 20.)

So in the example you gave, the gradient is computed correctly in the triangles, but the finite differences computation for the line cells can only compute the gradient in the direction of the line. Thus, there is no y component for the gradient in these line cells. Because the line cells share the points of the triangles along the bottom, the gradient average becomes incorrect.

-Ken


From: "Zenker, Dr. Matthias" <Matthias.Zenker at erbe-med.com>
Date: Tuesday, September 27, 2016 at 9:51 AM
To: "Moreland, Kenneth" <kmorel at sandia.gov>
Cc: "paraview at paraview.org" <paraview at paraview.org>
Subject: [EXTERNAL] AW: [Paraview] Gradient filter: boundary effects

Hi Ken,

if you want to have a look ? here is a simple test file. At  the bottom side, there are 4 adjacent cells having grad(y)~7900 from computederivatives, but all 3 nodes on the bottom side have grad(y) ~ 5300 from celldatatopointdata.

Thanks,

Matthias

Von: Moreland, Kenneth [mailto:kmorel at sandia.gov]
Gesendet: Dienstag, 27. September 2016 15:40
An: Zenker, Dr. Matthias
Cc: paraview at paraview.org
Betreff: Re: [Paraview] Gradient filter: boundary effects

Matthias,

If values are being pulled from 7900 units down to 5300 units, there must be some neighbor with lower values. Why that is happening for you I cannot say without looking at your data. Perhaps on the boundary there are some malformed or 2D cells with invalid gradients.

-Ken


From: "Zenker, Dr. Matthias" <Matthias.Zenker at erbe-med.com<mailto:Matthias.Zenker at erbe-med.com>>
Date: Tuesday, September 27, 2016 at 9:06 AM
To: "Moreland, Kenneth" <kmorel at sandia.gov<mailto:kmorel at sandia.gov>>
Cc: "paraview at paraview.org<mailto:paraview at paraview.org>" <paraview at paraview.org<mailto:paraview at paraview.org>>
Subject: [EXTERNAL] AW: [Paraview] Gradient filter: boundary effects

Hi Ken,

what I don?t understand is that the cell gradients are correct, but their average at the border is not. (Example: All cell gradients adjacent to one node at the border have approx. 7900 units in y direction, the node has approx. 5300)
So it seems I cannot determine the gradient in the postprocessing step, but have to calculate it in the FEM solver (where I do get correct results now ? I didn?t initially, which was the reason why I tried it with ParaView).

Thank you anyway, I have learned new bits of ParaView again (which is great software BTW)!

Have a nice holiday (if I interpret your autoreply correctly)!

Matthias

Von: Moreland, Kenneth [mailto:kmorel at sandia.gov]
Gesendet: Dienstag, 27. September 2016 14:36
An: Zenker, Dr. Matthias; paraview at paraview.org<mailto:paraview at paraview.org>
Betreff: Re: [Paraview] Gradient filter: boundary effects

You could run the results through the point to cell filter, but that would give you the same answer as the gradient of unstructured dataset filter with the faster approximation option on.

-Ken

From: "Zenker, Dr. Matthias" <Matthias.Zenker at erbe-med.com<mailto:Matthias.Zenker at erbe-med.com>>
Date: Tuesday, September 27, 2016 at 8:28 AM
To: "Moreland, Kenneth" <kmorel at sandia.gov<mailto:kmorel at sandia.gov>>, "paraview at paraview.org<mailto:paraview at paraview.org>" <paraview at paraview.org<mailto:paraview at paraview.org>>
Subject: [EXTERNAL] AW: [Paraview] Gradient filter: boundary effects

Hi Kenneth,

thank you for the quick answer!
So it seems not that trivial to calculate an electrical field between a rod and a plane given the potential?
The compute derivatives filter does not give me the problem at the boundary indeed. Instead it gives a value per cell, not per node, which does not look nice.
Is there a friendly filter or switch which would give me the smoothed surface representation back?

Thanks,

Matthias


Von: Moreland, Kenneth [mailto:kmorel at sandia.gov]
Gesendet: Dienstag, 27. September 2016 14:14
An: Zenker, Dr. Matthias; paraview at paraview.org<mailto:paraview at paraview.org>
Betreff: Re: [Paraview] Gradient filter: boundary effects

Matthias,

The gradient is estimated with finite differences. Thus, it is not wholly unexpected that there could be differences at the boundaries. However, the algorithm does not assume zero for adjacent cells at the boundaries.

The way the unstructured gradient filter works is that it computes the local gradient in each cell at each of the cell?s points. Then for every point it averages the gradient from all incident cells at that point. (If you have the Faster Approximation option on, then the filter only computes one gradient per cell in the center and averages those. Faster, but more artifacts, particularly at the edges.)

If this averaging is causing you an issue, you might try the Compute Derivatives filter. This does a wholly local operation within each cell, so you should not see any artifacts (unless the field itself has artifacts at the boundaries).

-Ken


From: ParaView <paraview-bounces at paraview.org<mailto:paraview-bounces at paraview.org>> on behalf of "Zenker, Dr. Matthias" <Matthias.Zenker at erbe-med.com<mailto:Matthias.Zenker at erbe-med.com>>
Date: Tuesday, September 27, 2016 at 5:45 AM
To: "paraview at paraview.org<mailto:paraview at paraview.org>" <paraview at paraview.org<mailto:paraview at paraview.org>>
Subject: [EXTERNAL] [Paraview] Gradient filter: boundary effects

Hi,

when I use the gradient filter (unstructured dataset), I observe edge effects which are IMO unphysical. For the nodes on the outer boundary of my domain, the gradient magnitude is smaller than I would expect. The behavior is like the filter tries to use the adjacent nodes to calculate the gradient, and since there are none  outside the domain, it assumes zero and finds a lower result.
If so, I would consider this a bug ? is there a fix or workaround?

Thanks,

Matthias
________________________________

Erbe Elektromedizin GmbH Firmensitz: 72072 Tuebingen Geschaeftsfuehrer: Christian O. Erbe, Reiner Thede Registergericht: Stuttgart HRB 380137
________________________________

Erbe Elektromedizin GmbH Firmensitz: 72072 Tuebingen Geschaeftsfuehrer: Christian O. Erbe, Reiner Thede Registergericht: Stuttgart HRB 380137
________________________________

Erbe Elektromedizin GmbH Firmensitz: 72072 Tuebingen Geschaeftsfuehrer: Christian O. Erbe, Reiner Thede Registergericht: Stuttgart HRB 380137
________________________________

Erbe Elektromedizin GmbH Firmensitz: 72072 Tuebingen Geschaeftsfuehrer: Christian O. Erbe, Reiner Thede Registergericht: Stuttgart HRB 380137
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From Matthias.Zenker at erbe-med.com  Tue Sep 27 10:59:55 2016
From: Matthias.Zenker at erbe-med.com (Zenker, Dr. Matthias)
Date: Tue, 27 Sep 2016 14:59:55 +0000
Subject: [Paraview] Gradient filter: boundary effects
In-Reply-To: <4692C574-20C5-405F-8433-C5ED4F3D97E4@sandia.gov>
References: <4692C574-20C5-405F-8433-C5ED4F3D97E4@sandia.gov>
Message-ID: <F9562F3B302F29479A203FC5AF9E3E050F9E3D26@SERBE4I1.intra.erbe-med.de>

Hi Ken,

thank you for pointing this out! I was not aware that boundary lines are also inifinitely flat cells. This seems true for all boundaries, also the internal boundaries between the two faces.
The question for me is now: Is this normal, or does that mean that the whole FEM simulation is corrupt? Should I have a mesh that does not have those line cells? The mesh has been calculated by the Salome mesher, which uses netgen. The boundaries were declared as groups. The mesh has then been exported as unv, imported by Elmer which has done the FEM calculations, and saved the results as vtu. If those line cells represent a problem, where in this chain do I have to look for the mistake?

Matthias

Von: Moreland, Kenneth [mailto:kmorel at sandia.gov]
Gesendet: Dienstag, 27. September 2016 16:41
An: Zenker, Dr. Matthias
Cc: paraview at paraview.org
Betreff: Re: [Paraview] Gradient filter: boundary effects

Matthias,

As I suspected, your data has some boundary elements that are throwing off the gradient calculation. The data you sent me has line cells around the boarder of the data. The easiest way to see these line cells is to go to the Properties panel and change the ?Line Width? parameter to something large. (Attached is an image that shows the boundary cells by setting the line width to 20.)

So in the example you gave, the gradient is computed correctly in the triangles, but the finite differences computation for the line cells can only compute the gradient in the direction of the line. Thus, there is no y component for the gradient in these line cells. Because the line cells share the points of the triangles along the bottom, the gradient average becomes incorrect.

-Ken


From: "Zenker, Dr. Matthias" <Matthias.Zenker at erbe-med.com<mailto:Matthias.Zenker at erbe-med.com>>
Date: Tuesday, September 27, 2016 at 9:51 AM
To: "Moreland, Kenneth" <kmorel at sandia.gov<mailto:kmorel at sandia.gov>>
Cc: "paraview at paraview.org<mailto:paraview at paraview.org>" <paraview at paraview.org<mailto:paraview at paraview.org>>
Subject: [EXTERNAL] AW: [Paraview] Gradient filter: boundary effects

Hi Ken,

if you want to have a look ? here is a simple test file. At  the bottom side, there are 4 adjacent cells having grad(y)~7900 from computederivatives, but all 3 nodes on the bottom side have grad(y) ~ 5300 from celldatatopointdata.

Thanks,

Matthias

Von: Moreland, Kenneth [mailto:kmorel at sandia.gov]
Gesendet: Dienstag, 27. September 2016 15:40
An: Zenker, Dr. Matthias
Cc: paraview at paraview.org<mailto:paraview at paraview.org>
Betreff: Re: [Paraview] Gradient filter: boundary effects

Matthias,

If values are being pulled from 7900 units down to 5300 units, there must be some neighbor with lower values. Why that is happening for you I cannot say without looking at your data. Perhaps on the boundary there are some malformed or 2D cells with invalid gradients.

-Ken


From: "Zenker, Dr. Matthias" <Matthias.Zenker at erbe-med.com<mailto:Matthias.Zenker at erbe-med.com>>
Date: Tuesday, September 27, 2016 at 9:06 AM
To: "Moreland, Kenneth" <kmorel at sandia.gov<mailto:kmorel at sandia.gov>>
Cc: "paraview at paraview.org<mailto:paraview at paraview.org>" <paraview at paraview.org<mailto:paraview at paraview.org>>
Subject: [EXTERNAL] AW: [Paraview] Gradient filter: boundary effects

Hi Ken,

what I don?t understand is that the cell gradients are correct, but their average at the border is not. (Example: All cell gradients adjacent to one node at the border have approx. 7900 units in y direction, the node has approx. 5300)
So it seems I cannot determine the gradient in the postprocessing step, but have to calculate it in the FEM solver (where I do get correct results now ? I didn?t initially, which was the reason why I tried it with ParaView).

Thank you anyway, I have learned new bits of ParaView again (which is great software BTW)!

Have a nice holiday (if I interpret your autoreply correctly)!

Matthias

Von: Moreland, Kenneth [mailto:kmorel at sandia.gov]
Gesendet: Dienstag, 27. September 2016 14:36
An: Zenker, Dr. Matthias; paraview at paraview.org<mailto:paraview at paraview.org>
Betreff: Re: [Paraview] Gradient filter: boundary effects

You could run the results through the point to cell filter, but that would give you the same answer as the gradient of unstructured dataset filter with the faster approximation option on.

-Ken

From: "Zenker, Dr. Matthias" <Matthias.Zenker at erbe-med.com<mailto:Matthias.Zenker at erbe-med.com>>
Date: Tuesday, September 27, 2016 at 8:28 AM
To: "Moreland, Kenneth" <kmorel at sandia.gov<mailto:kmorel at sandia.gov>>, "paraview at paraview.org<mailto:paraview at paraview.org>" <paraview at paraview.org<mailto:paraview at paraview.org>>
Subject: [EXTERNAL] AW: [Paraview] Gradient filter: boundary effects

Hi Kenneth,

thank you for the quick answer!
So it seems not that trivial to calculate an electrical field between a rod and a plane given the potential?
The compute derivatives filter does not give me the problem at the boundary indeed. Instead it gives a value per cell, not per node, which does not look nice.
Is there a friendly filter or switch which would give me the smoothed surface representation back?

Thanks,

Matthias


Von: Moreland, Kenneth [mailto:kmorel at sandia.gov]
Gesendet: Dienstag, 27. September 2016 14:14
An: Zenker, Dr. Matthias; paraview at paraview.org<mailto:paraview at paraview.org>
Betreff: Re: [Paraview] Gradient filter: boundary effects

Matthias,

The gradient is estimated with finite differences. Thus, it is not wholly unexpected that there could be differences at the boundaries. However, the algorithm does not assume zero for adjacent cells at the boundaries.

The way the unstructured gradient filter works is that it computes the local gradient in each cell at each of the cell?s points. Then for every point it averages the gradient from all incident cells at that point. (If you have the Faster Approximation option on, then the filter only computes one gradient per cell in the center and averages those. Faster, but more artifacts, particularly at the edges.)

If this averaging is causing you an issue, you might try the Compute Derivatives filter. This does a wholly local operation within each cell, so you should not see any artifacts (unless the field itself has artifacts at the boundaries).

-Ken


From: ParaView <paraview-bounces at paraview.org<mailto:paraview-bounces at paraview.org>> on behalf of "Zenker, Dr. Matthias" <Matthias.Zenker at erbe-med.com<mailto:Matthias.Zenker at erbe-med.com>>
Date: Tuesday, September 27, 2016 at 5:45 AM
To: "paraview at paraview.org<mailto:paraview at paraview.org>" <paraview at paraview.org<mailto:paraview at paraview.org>>
Subject: [EXTERNAL] [Paraview] Gradient filter: boundary effects

Hi,

when I use the gradient filter (unstructured dataset), I observe edge effects which are IMO unphysical. For the nodes on the outer boundary of my domain, the gradient magnitude is smaller than I would expect. The behavior is like the filter tries to use the adjacent nodes to calculate the gradient, and since there are none  outside the domain, it assumes zero and finds a lower result.
If so, I would consider this a bug ? is there a fix or workaround?

Thanks,

Matthias
________________________________

Erbe Elektromedizin GmbH Firmensitz: 72072 Tuebingen Geschaeftsfuehrer: Christian O. Erbe, Reiner Thede Registergericht: Stuttgart HRB 380137
________________________________

Erbe Elektromedizin GmbH Firmensitz: 72072 Tuebingen Geschaeftsfuehrer: Christian O. Erbe, Reiner Thede Registergericht: Stuttgart HRB 380137
________________________________

Erbe Elektromedizin GmbH Firmensitz: 72072 Tuebingen Geschaeftsfuehrer: Christian O. Erbe, Reiner Thede Registergericht: Stuttgart HRB 380137
________________________________

Erbe Elektromedizin GmbH Firmensitz: 72072 Tuebingen Geschaeftsfuehrer: Christian O. Erbe, Reiner Thede Registergericht: Stuttgart HRB 380137
________________________________

Erbe Elektromedizin GmbH Firmensitz: 72072 Tuebingen Geschaeftsfuehrer: Christian O. Erbe, Reiner Thede Registergericht: Stuttgart HRB 380137

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From Matthias.Zenker at erbe-med.com  Tue Sep 27 11:43:44 2016
From: Matthias.Zenker at erbe-med.com (Zenker, Dr. Matthias)
Date: Tue, 27 Sep 2016 15:43:44 +0000
Subject: [Paraview] Gradient filter: boundary effects
In-Reply-To: <F9562F3B302F29479A203FC5AF9E3E050F9E3D26@SERBE4I1.intra.erbe-med.de>
References: <4692C574-20C5-405F-8433-C5ED4F3D97E4@sandia.gov>
 <F9562F3B302F29479A203FC5AF9E3E050F9E3D26@SERBE4I1.intra.erbe-med.de>
Message-ID: <F9562F3B302F29479A203FC5AF9E3E050F9E3D40@SERBE4I1.intra.erbe-med.de>

Hi again,

I have examined my mesh (which you can find in the attachment) with Salome and gmsh ? there are no flat faces at the boundaries. But there are line elements! So I am relieved as far as my worried questions in the last mail are concerned ? mesher and the FEM solver are doing their work as they should.
But IMO it makes no sense to compute the derivatives over the line elements and average it with the derivatives over the face elements. Is it possible that this is exactly what happens in the gradient filter (and in the computederivative + celldatatopointdata filters)? If so, why? And can that be switched off, as IMO it should?
Or, to put it differently: Apparently ParaView does not make a difference between a line and a face. Why is this so? Shouldn?t it do that?

Thanks for a clarification,

Matthias


Von: Zenker, Dr. Matthias
Gesendet: Dienstag, 27. September 2016 17:00
An: 'Moreland, Kenneth'
Cc: paraview at paraview.org
Betreff: AW: [Paraview] Gradient filter: boundary effects

Hi Ken,

thank you for pointing this out! I was not aware that boundary lines are also inifinitely flat cells. This seems true for all boundaries, also the internal boundaries between the two faces.
The question for me is now: Is this normal, or does that mean that the whole FEM simulation is corrupt? Should I have a mesh that does not have those line cells? The mesh has been calculated by the Salome mesher, which uses netgen. The boundaries were declared as groups. The mesh has then been exported as unv, imported by Elmer which has done the FEM calculations, and saved the results as vtu. If those line cells represent a problem, where in this chain do I have to look for the mistake?

Matthias

Von: Moreland, Kenneth [mailto:kmorel at sandia.gov]
Gesendet: Dienstag, 27. September 2016 16:41
An: Zenker, Dr. Matthias
Cc: paraview at paraview.org<mailto:paraview at paraview.org>
Betreff: Re: [Paraview] Gradient filter: boundary effects

Matthias,

As I suspected, your data has some boundary elements that are throwing off the gradient calculation. The data you sent me has line cells around the boarder of the data. The easiest way to see these line cells is to go to the Properties panel and change the ?Line Width? parameter to something large. (Attached is an image that shows the boundary cells by setting the line width to 20.)

So in the example you gave, the gradient is computed correctly in the triangles, but the finite differences computation for the line cells can only compute the gradient in the direction of the line. Thus, there is no y component for the gradient in these line cells. Because the line cells share the points of the triangles along the bottom, the gradient average becomes incorrect.

-Ken


From: "Zenker, Dr. Matthias" <Matthias.Zenker at erbe-med.com<mailto:Matthias.Zenker at erbe-med.com>>
Date: Tuesday, September 27, 2016 at 9:51 AM
To: "Moreland, Kenneth" <kmorel at sandia.gov<mailto:kmorel at sandia.gov>>
Cc: "paraview at paraview.org<mailto:paraview at paraview.org>" <paraview at paraview.org<mailto:paraview at paraview.org>>
Subject: [EXTERNAL] AW: [Paraview] Gradient filter: boundary effects

Hi Ken,

if you want to have a look ? here is a simple test file. At  the bottom side, there are 4 adjacent cells having grad(y)~7900 from computederivatives, but all 3 nodes on the bottom side have grad(y) ~ 5300 from celldatatopointdata.

Thanks,

Matthias

Von: Moreland, Kenneth [mailto:kmorel at sandia.gov]
Gesendet: Dienstag, 27. September 2016 15:40
An: Zenker, Dr. Matthias
Cc: paraview at paraview.org<mailto:paraview at paraview.org>
Betreff: Re: [Paraview] Gradient filter: boundary effects

Matthias,

If values are being pulled from 7900 units down to 5300 units, there must be some neighbor with lower values. Why that is happening for you I cannot say without looking at your data. Perhaps on the boundary there are some malformed or 2D cells with invalid gradients.

-Ken


From: "Zenker, Dr. Matthias" <Matthias.Zenker at erbe-med.com<mailto:Matthias.Zenker at erbe-med.com>>
Date: Tuesday, September 27, 2016 at 9:06 AM
To: "Moreland, Kenneth" <kmorel at sandia.gov<mailto:kmorel at sandia.gov>>
Cc: "paraview at paraview.org<mailto:paraview at paraview.org>" <paraview at paraview.org<mailto:paraview at paraview.org>>
Subject: [EXTERNAL] AW: [Paraview] Gradient filter: boundary effects

Hi Ken,

what I don?t understand is that the cell gradients are correct, but their average at the border is not. (Example: All cell gradients adjacent to one node at the border have approx. 7900 units in y direction, the node has approx. 5300)
So it seems I cannot determine the gradient in the postprocessing step, but have to calculate it in the FEM solver (where I do get correct results now ? I didn?t initially, which was the reason why I tried it with ParaView).

Thank you anyway, I have learned new bits of ParaView again (which is great software BTW)!

Have a nice holiday (if I interpret your autoreply correctly)!

Matthias

Von: Moreland, Kenneth [mailto:kmorel at sandia.gov]
Gesendet: Dienstag, 27. September 2016 14:36
An: Zenker, Dr. Matthias; paraview at paraview.org<mailto:paraview at paraview.org>
Betreff: Re: [Paraview] Gradient filter: boundary effects

You could run the results through the point to cell filter, but that would give you the same answer as the gradient of unstructured dataset filter with the faster approximation option on.

-Ken

From: "Zenker, Dr. Matthias" <Matthias.Zenker at erbe-med.com<mailto:Matthias.Zenker at erbe-med.com>>
Date: Tuesday, September 27, 2016 at 8:28 AM
To: "Moreland, Kenneth" <kmorel at sandia.gov<mailto:kmorel at sandia.gov>>, "paraview at paraview.org<mailto:paraview at paraview.org>" <paraview at paraview.org<mailto:paraview at paraview.org>>
Subject: [EXTERNAL] AW: [Paraview] Gradient filter: boundary effects

Hi Kenneth,

thank you for the quick answer!
So it seems not that trivial to calculate an electrical field between a rod and a plane given the potential?
The compute derivatives filter does not give me the problem at the boundary indeed. Instead it gives a value per cell, not per node, which does not look nice.
Is there a friendly filter or switch which would give me the smoothed surface representation back?

Thanks,

Matthias


Von: Moreland, Kenneth [mailto:kmorel at sandia.gov]
Gesendet: Dienstag, 27. September 2016 14:14
An: Zenker, Dr. Matthias; paraview at paraview.org<mailto:paraview at paraview.org>
Betreff: Re: [Paraview] Gradient filter: boundary effects

Matthias,

The gradient is estimated with finite differences. Thus, it is not wholly unexpected that there could be differences at the boundaries. However, the algorithm does not assume zero for adjacent cells at the boundaries.

The way the unstructured gradient filter works is that it computes the local gradient in each cell at each of the cell?s points. Then for every point it averages the gradient from all incident cells at that point. (If you have the Faster Approximation option on, then the filter only computes one gradient per cell in the center and averages those. Faster, but more artifacts, particularly at the edges.)

If this averaging is causing you an issue, you might try the Compute Derivatives filter. This does a wholly local operation within each cell, so you should not see any artifacts (unless the field itself has artifacts at the boundaries).

-Ken


From: ParaView <paraview-bounces at paraview.org<mailto:paraview-bounces at paraview.org>> on behalf of "Zenker, Dr. Matthias" <Matthias.Zenker at erbe-med.com<mailto:Matthias.Zenker at erbe-med.com>>
Date: Tuesday, September 27, 2016 at 5:45 AM
To: "paraview at paraview.org<mailto:paraview at paraview.org>" <paraview at paraview.org<mailto:paraview at paraview.org>>
Subject: [EXTERNAL] [Paraview] Gradient filter: boundary effects

Hi,

when I use the gradient filter (unstructured dataset), I observe edge effects which are IMO unphysical. For the nodes on the outer boundary of my domain, the gradient magnitude is smaller than I would expect. The behavior is like the filter tries to use the adjacent nodes to calculate the gradient, and since there are none  outside the domain, it assumes zero and finds a lower result.
If so, I would consider this a bug ? is there a fix or workaround?

Thanks,

Matthias
________________________________

Erbe Elektromedizin GmbH Firmensitz: 72072 Tuebingen Geschaeftsfuehrer: Christian O. Erbe, Reiner Thede Registergericht: Stuttgart HRB 380137
________________________________

Erbe Elektromedizin GmbH Firmensitz: 72072 Tuebingen Geschaeftsfuehrer: Christian O. Erbe, Reiner Thede Registergericht: Stuttgart HRB 380137
________________________________

Erbe Elektromedizin GmbH Firmensitz: 72072 Tuebingen Geschaeftsfuehrer: Christian O. Erbe, Reiner Thede Registergericht: Stuttgart HRB 380137
________________________________

Erbe Elektromedizin GmbH Firmensitz: 72072 Tuebingen Geschaeftsfuehrer: Christian O. Erbe, Reiner Thede Registergericht: Stuttgart HRB 380137
________________________________

Erbe Elektromedizin GmbH Firmensitz: 72072 Tuebingen Geschaeftsfuehrer: Christian O. Erbe, Reiner Thede Registergericht: Stuttgart HRB 380137

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From samuelkey at bresnan.net  Tue Sep 27 12:12:46 2016
From: samuelkey at bresnan.net (Samuel Key)
Date: Tue, 27 Sep 2016 10:12:46 -0600
Subject: [Paraview] Gradient filter: boundary effects
In-Reply-To: <F9562F3B302F29479A203FC5AF9E3E050F9E3D40@SERBE4I1.intra.erbe-med.de>
References: <4692C574-20C5-405F-8433-C5ED4F3D97E4@sandia.gov>
 <F9562F3B302F29479A203FC5AF9E3E050F9E3D26@SERBE4I1.intra.erbe-med.de>
 <F9562F3B302F29479A203FC5AF9E3E050F9E3D40@SERBE4I1.intra.erbe-med.de>
Message-ID: <5d9629a5-4320-cf96-7e58-45df4cf451f6@bresnan.net>

An HTML attachment was scrubbed...
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From gao at pztop.com  Tue Sep 27 12:09:27 2016
From: gao at pztop.com (Gao)
Date: Tue, 27 Sep 2016 09:09:27 -0700
Subject: [Paraview] 3D system
Message-ID: <c094b89b-ad98-412b-eb77-6dc66b431ad5@pztop.com>

Hi, everyone,

I am new to this list. I like to ask few questions about how to setup a 
3D system. Please give me some suggestions if you have experiences.

My goal is to let people able to watch the VTK files through Paraview 
with a 3D glasses on the monitor or TV. So here are the questions:

1. Computer system: Which video card is supported? Do I have to use 
Nvidia card? If yes then which model?

2. OS: If I use the Nvidia card for example, will it supported on Ubuntu 
16.04 and Paraview?

3. Monitor or ??. Is 120Hz the only requirement?

4. 3D glasses: Which one do you recommend for multiple person use?

5. Touchpad: Any recommendation for a touchpad to do the control through 
multi-touch, like pan, zoom.,etc?

Thanks for help.

Gao



From kmorel at sandia.gov  Tue Sep 27 17:41:50 2016
From: kmorel at sandia.gov (Moreland, Kenneth)
Date: Tue, 27 Sep 2016 21:41:50 +0000
Subject: [Paraview] Gradient filter: boundary effects
Message-ID: <C2095BD1-8E66-4D6A-8F56-309DBC4F3336@sandia.gov>

As far as VTK/ParaView are concerned, lines and triangles are just different types of cells. The filters treat each cell uniformly. That is, the gradient filter is treating triangles and lines the same and mixing the results together in the same way as if the data contained triangles and quadrilaterals.

In many ways, the problem is that the mesh and boundary cells are not properly distinguished in the data. The lines in the data are really a ?face set? or ?edge set? that has different properties that the interior triangle cells (in addition to the difference in dimentionality). Although this is not specifically supported in VTK?s data structures, we typically manage it by creating a multiblock data set with the interior and boundary cells in different blocks.

However, although I don?t think the gradient filter?s treatment of the data is fundamentally wrong, I cannot think of a viable use case for computing gradients over cells of different dimensionality. So it would probably be a reasonable feature request to ask that the gradient filter only average gradients from cells of the highest dimension. That said, I don?t think it would be correct to change the behavior of cell data to point data as that is used for plenty of use cases other than gradients.

-Ken

From: "Zenker, Dr. Matthias" <Matthias.Zenker at erbe-med.com>
Date: Tuesday, September 27, 2016 at 11:43 AM
To: "Moreland, Kenneth" <kmorel at sandia.gov>
Cc: "'paraview at paraview.org'" <paraview at paraview.org>
Subject: [EXTERNAL] AW: [Paraview] Gradient filter: boundary effects

Hi again,

I have examined my mesh (which you can find in the attachment) with Salome and gmsh ? there are no flat faces at the boundaries. But there are line elements! So I am relieved as far as my worried questions in the last mail are concerned ? mesher and the FEM solver are doing their work as they should.
But IMO it makes no sense to compute the derivatives over the line elements and average it with the derivatives over the face elements. Is it possible that this is exactly what happens in the gradient filter (and in the computederivative + celldatatopointdata filters)? If so, why? And can that be switched off, as IMO it should?
Or, to put it differently: Apparently ParaView does not make a difference between a line and a face. Why is this so? Shouldn?t it do that?

Thanks for a clarification,

Matthias


Von: Zenker, Dr. Matthias
Gesendet: Dienstag, 27. September 2016 17:00
An: 'Moreland, Kenneth'
Cc: paraview at paraview.org
Betreff: AW: [Paraview] Gradient filter: boundary effects

Hi Ken,

thank you for pointing this out! I was not aware that boundary lines are also inifinitely flat cells. This seems true for all boundaries, also the internal boundaries between the two faces.
The question for me is now: Is this normal, or does that mean that the whole FEM simulation is corrupt? Should I have a mesh that does not have those line cells? The mesh has been calculated by the Salome mesher, which uses netgen. The boundaries were declared as groups. The mesh has then been exported as unv, imported by Elmer which has done the FEM calculations, and saved the results as vtu. If those line cells represent a problem, where in this chain do I have to look for the mistake?

Matthias

Von: Moreland, Kenneth [mailto:kmorel at sandia.gov]
Gesendet: Dienstag, 27. September 2016 16:41
An: Zenker, Dr. Matthias
Cc: paraview at paraview.org<mailto:paraview at paraview.org>
Betreff: Re: [Paraview] Gradient filter: boundary effects

Matthias,

As I suspected, your data has some boundary elements that are throwing off the gradient calculation. The data you sent me has line cells around the boarder of the data. The easiest way to see these line cells is to go to the Properties panel and change the ?Line Width? parameter to something large. (Attached is an image that shows the boundary cells by setting the line width to 20.)

So in the example you gave, the gradient is computed correctly in the triangles, but the finite differences computation for the line cells can only compute the gradient in the direction of the line. Thus, there is no y component for the gradient in these line cells. Because the line cells share the points of the triangles along the bottom, the gradient average becomes incorrect.

-Ken


From: "Zenker, Dr. Matthias" <Matthias.Zenker at erbe-med.com<mailto:Matthias.Zenker at erbe-med.com>>
Date: Tuesday, September 27, 2016 at 9:51 AM
To: "Moreland, Kenneth" <kmorel at sandia.gov<mailto:kmorel at sandia.gov>>
Cc: "paraview at paraview.org<mailto:paraview at paraview.org>" <paraview at paraview.org<mailto:paraview at paraview.org>>
Subject: [EXTERNAL] AW: [Paraview] Gradient filter: boundary effects

Hi Ken,

if you want to have a look ? here is a simple test file. At  the bottom side, there are 4 adjacent cells having grad(y)~7900 from computederivatives, but all 3 nodes on the bottom side have grad(y) ~ 5300 from celldatatopointdata.

Thanks,

Matthias

Von: Moreland, Kenneth [mailto:kmorel at sandia.gov]
Gesendet: Dienstag, 27. September 2016 15:40
An: Zenker, Dr. Matthias
Cc: paraview at paraview.org<mailto:paraview at paraview.org>
Betreff: Re: [Paraview] Gradient filter: boundary effects

Matthias,

If values are being pulled from 7900 units down to 5300 units, there must be some neighbor with lower values. Why that is happening for you I cannot say without looking at your data. Perhaps on the boundary there are some malformed or 2D cells with invalid gradients.

-Ken


From: "Zenker, Dr. Matthias" <Matthias.Zenker at erbe-med.com<mailto:Matthias.Zenker at erbe-med.com>>
Date: Tuesday, September 27, 2016 at 9:06 AM
To: "Moreland, Kenneth" <kmorel at sandia.gov<mailto:kmorel at sandia.gov>>
Cc: "paraview at paraview.org<mailto:paraview at paraview.org>" <paraview at paraview.org<mailto:paraview at paraview.org>>
Subject: [EXTERNAL] AW: [Paraview] Gradient filter: boundary effects

Hi Ken,

what I don?t understand is that the cell gradients are correct, but their average at the border is not. (Example: All cell gradients adjacent to one node at the border have approx. 7900 units in y direction, the node has approx. 5300)
So it seems I cannot determine the gradient in the postprocessing step, but have to calculate it in the FEM solver (where I do get correct results now ? I didn?t initially, which was the reason why I tried it with ParaView).

Thank you anyway, I have learned new bits of ParaView again (which is great software BTW)!

Have a nice holiday (if I interpret your autoreply correctly)!

Matthias

Von: Moreland, Kenneth [mailto:kmorel at sandia.gov]
Gesendet: Dienstag, 27. September 2016 14:36
An: Zenker, Dr. Matthias; paraview at paraview.org<mailto:paraview at paraview.org>
Betreff: Re: [Paraview] Gradient filter: boundary effects

You could run the results through the point to cell filter, but that would give you the same answer as the gradient of unstructured dataset filter with the faster approximation option on.

-Ken

From: "Zenker, Dr. Matthias" <Matthias.Zenker at erbe-med.com<mailto:Matthias.Zenker at erbe-med.com>>
Date: Tuesday, September 27, 2016 at 8:28 AM
To: "Moreland, Kenneth" <kmorel at sandia.gov<mailto:kmorel at sandia.gov>>, "paraview at paraview.org<mailto:paraview at paraview.org>" <paraview at paraview.org<mailto:paraview at paraview.org>>
Subject: [EXTERNAL] AW: [Paraview] Gradient filter: boundary effects

Hi Kenneth,

thank you for the quick answer!
So it seems not that trivial to calculate an electrical field between a rod and a plane given the potential?
The compute derivatives filter does not give me the problem at the boundary indeed. Instead it gives a value per cell, not per node, which does not look nice.
Is there a friendly filter or switch which would give me the smoothed surface representation back?

Thanks,

Matthias


Von: Moreland, Kenneth [mailto:kmorel at sandia.gov]
Gesendet: Dienstag, 27. September 2016 14:14
An: Zenker, Dr. Matthias; paraview at paraview.org<mailto:paraview at paraview.org>
Betreff: Re: [Paraview] Gradient filter: boundary effects

Matthias,

The gradient is estimated with finite differences. Thus, it is not wholly unexpected that there could be differences at the boundaries. However, the algorithm does not assume zero for adjacent cells at the boundaries.

The way the unstructured gradient filter works is that it computes the local gradient in each cell at each of the cell?s points. Then for every point it averages the gradient from all incident cells at that point. (If you have the Faster Approximation option on, then the filter only computes one gradient per cell in the center and averages those. Faster, but more artifacts, particularly at the edges.)

If this averaging is causing you an issue, you might try the Compute Derivatives filter. This does a wholly local operation within each cell, so you should not see any artifacts (unless the field itself has artifacts at the boundaries).

-Ken


From: ParaView <paraview-bounces at paraview.org<mailto:paraview-bounces at paraview.org>> on behalf of "Zenker, Dr. Matthias" <Matthias.Zenker at erbe-med.com<mailto:Matthias.Zenker at erbe-med.com>>
Date: Tuesday, September 27, 2016 at 5:45 AM
To: "paraview at paraview.org<mailto:paraview at paraview.org>" <paraview at paraview.org<mailto:paraview at paraview.org>>
Subject: [EXTERNAL] [Paraview] Gradient filter: boundary effects

Hi,

when I use the gradient filter (unstructured dataset), I observe edge effects which are IMO unphysical. For the nodes on the outer boundary of my domain, the gradient magnitude is smaller than I would expect. The behavior is like the filter tries to use the adjacent nodes to calculate the gradient, and since there are none  outside the domain, it assumes zero and finds a lower result.
If so, I would consider this a bug ? is there a fix or workaround?

Thanks,

Matthias
________________________________

Erbe Elektromedizin GmbH Firmensitz: 72072 Tuebingen Geschaeftsfuehrer: Christian O. Erbe, Reiner Thede Registergericht: Stuttgart HRB 380137
________________________________

Erbe Elektromedizin GmbH Firmensitz: 72072 Tuebingen Geschaeftsfuehrer: Christian O. Erbe, Reiner Thede Registergericht: Stuttgart HRB 380137
________________________________

Erbe Elektromedizin GmbH Firmensitz: 72072 Tuebingen Geschaeftsfuehrer: Christian O. Erbe, Reiner Thede Registergericht: Stuttgart HRB 380137
________________________________

Erbe Elektromedizin GmbH Firmensitz: 72072 Tuebingen Geschaeftsfuehrer: Christian O. Erbe, Reiner Thede Registergericht: Stuttgart HRB 380137
________________________________

Erbe Elektromedizin GmbH Firmensitz: 72072 Tuebingen Geschaeftsfuehrer: Christian O. Erbe, Reiner Thede Registergericht: Stuttgart HRB 380137
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From rccm.kyoshimi at gmail.com  Tue Sep 27 19:43:02 2016
From: rccm.kyoshimi at gmail.com (kenichiro yoshimi)
Date: Wed, 28 Sep 2016 08:43:02 +0900
Subject: [Paraview] [EXTERNAL] Re: Create animation and center geometry
In-Reply-To: <D0ABD0B9-B26B-4C91-881D-DAEEAFA4F3E4@sandia.gov>
References: <8e14f00bddce4898b92624fbe57680fb@ES08AMSNLNT.srn.sandia.gov>
 <CAHDyfPCLYie6i=7myuR4_DcdjSjbt4D=UL7QEgM+nBMiuR_hHA@mail.gmail.com>
 <D0ABD0B9-B26B-4C91-881D-DAEEAFA4F3E4@sandia.gov>
Message-ID: <CAHDyfPBkRxi6VP4X6sLkG65LiLfpyyQyy31CmCEBCR+d5B2aCw@mail.gmail.com>

Hi, Ryan

You can specify the size of the images by assigning the render view
properties: view size.

---------
    renderView1 = GetActiveViewOrCreate('RenderView')
    renderView1.ViewSize = [600, 557]
    renderView1.ResetCamera()
---------

Thanks,
Yoshimi

2016-09-27 23:10 GMT+09:00 Jamison, Ryan Dale <rdjamis at sandia.gov>:
> Yoshimi,
>
> Thanks for the script! This does exactly what I was wanting to do.
>
> One further question, where in the script can I define the size of the images to save?
>
> Best, Ryan
>
>> On Sep 26, 2016, at 10:40 PM, kenichiro yoshimi <rccm.kyoshimi at gmail.com> wrote:
>>
>> Hi, Ryan
>>
>> You try the script as follows from [Tools]-[Python Shell] after
>> reading datasets into ParaView.
>>
>> ---------save_screenshots.py---------
>> from paraview.simple import *
>>
>> # Change 10 to the amount of timesteps
>> for num in range(0,10):
>>    print 'Save screenshot ' + str(num)
>>
>>    renderView1 = GetActiveViewOrCreate('RenderView')
>>    renderView1.ResetCamera()
>>
>>    # Save screenshot
>>    # Change to your folder
>>    name = 'G:/ParaViewData-v4.1/Data/singleSphereAnimation/singleSphere'
>> + str(num).zfill(4) + '.png'
>>    print 'Save as ' + str(name)
>>    SaveScreenshot(name, magnification=1, quality=100, view=renderView1)
>>
>>    animationScene1 = GetAnimationScene()
>>
>>    animationScene1.GoToNext()
>> ---------
>>
>> Thanks,
>> yoshimi
>

From frank.albina at sauber-motorsport.com  Wed Sep 28 04:06:15 2016
From: frank.albina at sauber-motorsport.com (Albina, Frank)
Date: Wed, 28 Sep 2016 10:06:15 +0200
Subject: [Paraview] Building ParaView v5.1.2 on Linux from source with
 support for GPU and SWR.
References: <591d7e7c-08d5-4787-8703-d90fd2be1bdb@srvcli01.spe-ch-md9.net>
 <CANjZAi-m+7tU0U5piT-FszDTNbJdDkyZ6hs3Yue-rOwi2B8eog@mail.gmail.com>
 <98b353c4-1c35-47a8-808b-e37fa0385776@srvcli01.spe-ch-md9.net>
 <CANjZAi-RTCXFQqLnrw0izaX_OQwvR0iHqym7nTCiWuevyE9wvQ@mail.gmail.com> 
Message-ID: <89ac1f3a-7f7b-4d55-9ed6-09eda5e9a572@srvcli01.spe-ch-md9.net>

David,

I could manage to get Paraview 5.1.2 compiled using the ParaView superbuild on my Linux desktop running OpenSuSE 12.3.

In this regard, I would like to point out a few things I have found while performing the build process on the aforementioned Linux distribution. Note that my incentive is to help improve the ParaView software suite as well as helping others to be able to build and use the software.


1.     I found it this page quite useful for having at least a starting point for building ParaView v5.1.2 on Linux: https://cmake.org/Wiki/ParaView/Binaries

2.     You definitely need cmake at least cmake v3.5 (and not v3.3) to compile ParaView from SuperBuild.

3.     You need a GNU compiler v4.8.0 or above to build. My Linux distribution comes with gcc v4.7.2. Fortunately, I had gcc v4.9.2 installed with which I could perform a successful build.

4.     Dependencies such libsz, libxml, libbzip2 are built and stored in the <build>/install/lib64 directory on my platform. This creates linking issues which I could partly resolve by pushing the missing libraries into the <build>/install/lib directory. This is not ideal but could be solved by forcing the lib directory to <build>/install/lib using the --libdir option.

5.     The vistrails plugin cannot be built. After 3 attempts, the git clone from https://kwgitlab.kitware.com/paraview/vistrails.git fails. Either the link is wrong or the server is unreachable.

6.     The mesa libraries are pre-compiled and downloaded to <buils>/mesa-downloads. They are unpacked and moved into the ParaView installation directory when performing ?make install?. These libraries are dating from May 3rd, hence prior to the release of Mesa 12.0 which embeds OpenSWR as a build option. Is there a way to build new libGL.so and libOSMesa.so libraries based on Mesa3D v12.0 and replace the currently pre-compiled binaries? If so,what are the typical configuration options used in this case?



Any feedback/comments are most welcome.



Regards,

Frank.

From: Albina, Frank
Sent: Montag, 26. September 2016 15:51
To: 'David E DeMarle'
Cc: paraview at paraview.org; Del Citto, Francesco
Subject: RE: [Paraview] Building ParaView v5.1.2 on Linux from source with support for GPU and SWR.

Perfect!

Thanks.

Frank.

From: David E DeMarle [mailto:dave.demarle at kitware.com]
Sent: Montag, 26. September 2016 15:49
To: Albina, Frank
Cc: paraview at paraview.org<mailto:paraview at paraview.org>; Del Citto, Francesco
Subject: Re: [Paraview] Building ParaView v5.1.2 on Linux from source with support for GPU and SWR.

3.3

David E DeMarle
Kitware, Inc.
R&D Engineer
21 Corporate Drive
Clifton Park, NY 12065-8662
Phone: 518-881-4909

On Mon, Sep 26, 2016 at 9:42 AM, Albina, Frank <frank.albina at sauber-motorsport.com<mailto:frank.albina at sauber-motorsport.com>> wrote:
Hi David!

Thanks for the swift feedback. As I have been compiling ParaView from source for at least the last 6 years, it never came to my mind trying out the super-build. ?

I?ll try it out and report if I find myself stuck.

By the way, which CMake version do you recommend for building ParaView v5.1.2 from the git repository?

Best regards,

Frank.

From: David E DeMarle [mailto:dave.demarle at kitware.com<mailto:dave.demarle at kitware.com>]
Sent: Montag, 26. September 2016 15:37
To: Albina, Frank
Cc: paraview at paraview.org<mailto:paraview at paraview.org>; Del Citto, Francesco
Subject: Re: [Paraview] Building ParaView v5.1.2 on Linux from source with support for GPU and SWR.

I recommend the ParaView superbuild. All of the incantations that we use to setup and build paraview, mesa and the rest of our dependencies are written down and maintained there.

https://gitlab.kitware.com/paraview/paraview-superbuild
We've used it for our Desktop binaries for years, and more and more often we use it for our HPC installs as well.

David E DeMarle
Kitware, Inc.
R&D Engineer
21 Corporate Drive
Clifton Park, NY 12065-8662
Phone: 518-881-4909<tel:518-881-4909>

On Mon, Sep 26, 2016 at 5:17 AM, Albina, Frank <frank.albina at sauber-motorsport.com<mailto:frank.albina at sauber-motorsport.com>> wrote:
Dear all,
after having downloaded last week the latest ParaView release (v5.1.2) for Linux, I have found out that the binary version has the following folder structure in lib/paraview-5.1:
mesa-llvm
|-- libGL.so -> libGL.so.1
|-- libGL.so.1 -> libGL.so.1.5
|-- libGL.so.1.5
|-- libOSMesa.so -> libOSMesa.so.8
|-- libOSMesa.so.8 -> libOSMesa.so.8.0.0
`-- libOSMesa.so.8.0.0
mesa-swr-avx
|-- libGL.so -> libGL.so.1
|-- libGL.so.1 -> libGL.so.1.5
|-- libGL.so.1.5
|-- libOSMesa.so -> libOSMesa.so.8
|-- libOSMesa.so.8 -> libOSMesa.so.8.0.0
`-- libOSMesa.so.8.0.0
mesa-swr-avx2
|-- libGL.so -> libGL.so.1
|-- libGL.so.1 -> libGL.so.1.5
|-- libGL.so.1.5
|-- libOSMesa.so -> libOSMesa.so.8
|-- libOSMesa.so.8 -> libOSMesa.so.8.0.0
`-- libOSMesa.so.8.0.0
Which is an elegant way of providing a binary package for GPU and non-GPU architectures at the same time.
Hence my question: How do I build ParaView v5.1.2 from source to have the same folder structure so that I have one version for GPU and software rendering? I understand that swr-avx(2) should be also available from Mesa v12.x. Is there anything I?d need to consider / take care of before building the different OSMesa libraries with LLVM / OpenSWR?
Frank Albina


_______________________________________________
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From dave.demarle at kitware.com  Wed Sep 28 06:50:19 2016
From: dave.demarle at kitware.com (David E DeMarle)
Date: Wed, 28 Sep 2016 06:50:19 -0400
Subject: [Paraview] Building ParaView v5.1.2 on Linux from source with
 support for GPU and SWR.
In-Reply-To: <89ac1f3a-7f7b-4d55-9ed6-09eda5e9a572@srvcli01.spe-ch-md9.net>
References: <591d7e7c-08d5-4787-8703-d90fd2be1bdb@srvcli01.spe-ch-md9.net>
 <CANjZAi-m+7tU0U5piT-FszDTNbJdDkyZ6hs3Yue-rOwi2B8eog@mail.gmail.com>
 <98b353c4-1c35-47a8-808b-e37fa0385776@srvcli01.spe-ch-md9.net>
 <CANjZAi-RTCXFQqLnrw0izaX_OQwvR0iHqym7nTCiWuevyE9wvQ@mail.gmail.com>
 <89ac1f3a-7f7b-4d55-9ed6-09eda5e9a572@srvcli01.spe-ch-md9.net>
Message-ID: <CANjZAi80hHjeGM04zd1mgudD_VXDspEXjxvdqock1qWhOYgKSw@mail.gmail.com>

On Wed, Sep 28, 2016 at 4:06 AM, Albina, Frank <
frank.albina at sauber-motorsport.com> wrote:

> David,
>
>
>
> I could manage to get Paraview 5.1.2 compiled using the ParaView
> superbuild on my Linux desktop running OpenSuSE 12.3.
>
>
>
> In this regard, I would like to point out a few things I have found while
> performing the build process on the aforementioned Linux distribution. Note
> that my incentive is to help improve the ParaView software suite as well as
> helping others to be able to build and use the software.
>
>
Thanks, we appreciate it!


>
> 1.     I found it this page quite useful for having at least a starting
> point for building ParaView v5.1.2 on Linux: https://cmake.org/Wiki/
> ParaView/Binaries
>
> 2.     You definitely need cmake at least *cmake v3.5* (and not v3.3) to
> compile ParaView from SuperBuild.
>

 Ah yes, sorry for the misinformation on my part.

> 3.     You need a *GNU compiler v4.8.0 or above* to build. My Linux
> distribution comes with gcc v4.7.2. Fortunately, I had gcc v4.9.2 installed
> with which I could perform a successful build.
>
> 4.     Dependencies such libsz, libxml, libbzip2 are built and stored in
> the <build>/install/lib64 directory on my platform. This creates linking
> issues which I could partly resolve by pushing the missing libraries into
> the <build>/install/lib directory. This is not ideal but could be solved by
> forcing the lib directory to <build>/install/lib using the --libdir option.
>
> 5.     The vistrails plugin cannot be built. After 3 attempts, the git
> clone from https://kwgitlab.kitware.com/paraview/vistrails.git fails.
> Either the link is wrong or the server is unreachable.
>
> 6.     The mesa libraries are pre-compiled and downloaded to
> <buils>/mesa-downloads. They are unpacked and moved into the ParaView
> installation directory when performing ?make install?. These libraries are
> dating from May 3rd, hence prior to the release of Mesa 12.0 which embeds
> OpenSWR as a build option. Is there a way to build new libGL.so and
> libOSMesa.so libraries based on Mesa3D v12.0 and replace the currently
> pre-compiled binaries? If so,what are the typical configuration options
> used in this case?
>
>
I believe the plan is to update to 12 before 5.2. Is that right @chuck and
@ben?


> Any feedback/comments are most welcome.
>
>
>
> Regards,
>
>
> Frank.
>
>
>
> *From:* Albina, Frank
> *Sent:* Montag, 26. September 2016 15:51
> *To:* 'David E DeMarle'
> *Cc:* paraview at paraview.org; Del Citto, Francesco
> *Subject:* RE: [Paraview] Building ParaView v5.1.2 on Linux from source
> with support for GPU and SWR.
>
>
>
> Perfect!
>
>
>
> Thanks.
>
>
>
> Frank.
>
>
>
> *From:* David E DeMarle [mailto:dave.demarle at kitware.com
> <dave.demarle at kitware.com>]
> *Sent:* Montag, 26. September 2016 15:49
>
> *To:* Albina, Frank
> *Cc:* paraview at paraview.org; Del Citto, Francesco
> *Subject:* Re: [Paraview] Building ParaView v5.1.2 on Linux from source
> with support for GPU and SWR.
>
>
>
> 3.3
>
>
> David E DeMarle
> Kitware, Inc.
> R&D Engineer
> 21 Corporate Drive
> Clifton Park, NY 12065-8662
> Phone: 518-881-4909
>
>
>
> On Mon, Sep 26, 2016 at 9:42 AM, Albina, Frank <frank.albina at sauber-
> motorsport.com> wrote:
>
> Hi David!
>
>
>
> Thanks for the swift feedback. As I have been compiling ParaView from
> source for at least the last 6 years, it never came to my mind trying out
> the super-build. ?
>
>
>
> I?ll try it out and report if I find myself stuck.
>
>
>
> By the way, which CMake version do you recommend for building ParaView
> v5.1.2 from the git repository?
>
>
>
> Best regards,
>
>
> Frank.
>
>
>
> *From:* David E DeMarle [mailto:dave.demarle at kitware.com]
> *Sent:* Montag, 26. September 2016 15:37
> *To:* Albina, Frank
> *Cc:* paraview at paraview.org; Del Citto, Francesco
> *Subject:* Re: [Paraview] Building ParaView v5.1.2 on Linux from source
> with support for GPU and SWR.
>
>
>
> I recommend the ParaView superbuild. All of the incantations that we use
> to setup and build paraview, mesa and the rest of our dependencies are
> written down and maintained there.
>
> https://gitlab.kitware.com/paraview/paraview-superbuild
>
> We've used it for our Desktop binaries for years, and more and more often
> we use it for our HPC installs as well.
>
>
> David E DeMarle
> Kitware, Inc.
> R&D Engineer
> 21 Corporate Drive
> Clifton Park, NY 12065-8662
> Phone: 518-881-4909
>
>
>
> On Mon, Sep 26, 2016 at 5:17 AM, Albina, Frank <frank.albina at sauber-
> motorsport.com> wrote:
>
> Dear all,
>
> after having downloaded last week the latest ParaView release (v5.1.2) for
> Linux, I have found out that the binary version has the following folder
> structure in lib/paraview-5.1:
>
> *mesa-llvm*
>
> |-- *libGL.so* -> libGL.so.1
>
> |-- *libGL.so.1 *-> libGL.so.1.5
>
> |-- libGL.so.1.5
>
> |-- *libOSMesa.so* -> libOSMesa.so.8
>
> |-- *libOSMesa.so.8* -> libOSMesa.so.8.0.0
>
> `-- libOSMesa.so.8.0.0
>
> *mesa-swr-avx*
>
> |-- *libGL.so* -> libGL.so.1
>
> |-- *libGL.so.1* -> libGL.so.1.5
>
> |-- libGL.so.1.5
>
> |-- *libOSMesa.so* -> libOSMesa.so.8
>
> |-- *libOSMesa.so.8* -> libOSMesa.so.8.0.0
>
> `-- libOSMesa.so.8.0.0
>
> *mesa-swr-avx2*
>
> |-- *libGL.so* -> libGL.so.1
>
> |-- *libGL.so.1 *-> libGL.so.1.5
>
> |-- libGL.so.1.5
>
> |-- *libOSMesa.so* -> libOSMesa.so.8
>
> |-- *libOSMesa.so.8* -> libOSMesa.so.8.0.0
>
> `-- libOSMesa.so.8.0.0
>
> Which is an elegant way of providing a binary package for GPU and non-GPU
> architectures at the same time.
>
> Hence my question: How do I build ParaView v5.1.2 from source to have the
> same folder structure so that I have one version for GPU and software
> rendering? I understand that swr-avx(2) should be also available from Mesa
> v12.x. Is there anything I?d need to consider / take care of before
> building the different OSMesa libraries with LLVM / OpenSWR?
>
> *Frank Albina*
>
>
>
>
> _______________________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at http://www.kitware.com/
> opensource/opensource.html
>
> Please keep messages on-topic and check the ParaView Wiki at:
> http://paraview.org/Wiki/ParaView
>
> Search the list archives at: http://markmail.org/search/?q=ParaView
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/paraview
>
>
>
>
>
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From ben.boeckel at kitware.com  Wed Sep 28 08:45:16 2016
From: ben.boeckel at kitware.com (Ben Boeckel)
Date: Wed, 28 Sep 2016 08:45:16 -0400
Subject: [Paraview] Building ParaView v5.1.2 on Linux from source with
 support for GPU and SWR.
In-Reply-To: <89ac1f3a-7f7b-4d55-9ed6-09eda5e9a572@srvcli01.spe-ch-md9.net>
References: <591d7e7c-08d5-4787-8703-d90fd2be1bdb@srvcli01.spe-ch-md9.net>
 <CANjZAi-m+7tU0U5piT-FszDTNbJdDkyZ6hs3Yue-rOwi2B8eog@mail.gmail.com>
 <98b353c4-1c35-47a8-808b-e37fa0385776@srvcli01.spe-ch-md9.net>
 <CANjZAi-RTCXFQqLnrw0izaX_OQwvR0iHqym7nTCiWuevyE9wvQ@mail.gmail.com>
 <89ac1f3a-7f7b-4d55-9ed6-09eda5e9a572@srvcli01.spe-ch-md9.net>
Message-ID: <20160928124516.GB4078@megas.kitware.com>

On Wed, Sep 28, 2016 at 10:06:15 +0200, Albina, Frank wrote:
> In this regard, I would like to point out a few things I have found
> while performing the build process on the aforementioned Linux
> distribution. Note that my incentive is to help improve the ParaView
> software suite as well as helping others to be able to build and use
> the software.

Thanks for the feedback. Responses inline.

> 2.     You definitely need cmake at least cmake v3.5 (and not v3.3) to
> compile ParaView from SuperBuild.

Ah, ParaView is 3.3, but the superbuild is 3.5. As a heads up, the new
superbuild which will be used for ParaView 5.2 will require at least
3.6.1.

> 3.     You need a GNU compiler v4.8.0 or above to build. My Linux
> distribution comes with gcc v4.7.2. Fortunately, I had gcc v4.9.2
> installed with which I could perform a successful build.

What subproject required this?

> 4.     Dependencies such libsz, libxml, libbzip2 are built and stored
> in the <build>/install/lib64 directory on my platform. This creates
> linking issues which I could partly resolve by pushing the missing
> libraries into the <build>/install/lib directory. This is not ideal
> but could be solved by forcing the lib directory to
> <build>/install/lib using the --libdir option.

Hrm. I'm on Fedora (which also uses lib64) and though I had gotten all
the lib64-isms out of the superbuild. Maybe I had missed some before
5.1.2 (the superbuild now uses common infrastructure shared between
other similar superbuilds).

> 5.     The vistrails plugin cannot be built. After 3 attempts, the git
> clone from https://kwgitlab.kitware.com/paraview/vistrails.git fails.
> Either the link is wrong or the server is unreachable.

vistrails should be hidden behind a "USE_NONFREE_COMPONENTS" flag.
vistrails (and acusolve) are not FOSS, so their git repos are on our
internal server.

> 6.     The mesa libraries are pre-compiled and downloaded to
> <buils>/mesa-downloads. They are unpacked and moved into the ParaView
> installation directory when performing ?make install?. These libraries
> are dating from May 3rd, hence prior to the release of Mesa 12.0 which
> embeds OpenSWR as a build option. Is there a way to build new libGL.so
> and libOSMesa.so libraries based on Mesa3D v12.0 and replace the
> currently pre-compiled binaries? If so,what are the typical
> configuration options used in this case?

The new superbuild has support for building mesa 12.0.3 as part of the
build. We used prebuilt binaries before because our build machine was
Debian 6 which was not easily capable of compiling the LLVM -> Mesa
chain without a self-compiled compiler and such, so it was built once
and that was it. I think it did contain SWR since it was a git snapshot.
Utkarsh?

--Ben

From frank.albina at sauber-motorsport.com  Wed Sep 28 11:36:24 2016
From: frank.albina at sauber-motorsport.com (Albina, Frank)
Date: Wed, 28 Sep 2016 17:36:24 +0200
Subject: [Paraview] Paraview v5.1.2: SurfaceLIC & software rendering
 issues
In-Reply-To: <CANXz0SbBvoFwp-abt2g77bXkUfq+FW=NA-pTeUJOBtZJ5w9ttA@mail.gmail.com>
References: <4373b551-40c8-44ca-8b27-9106bceac88c@srvcli01.spe-ch-md9.net>
 <CANXz0SbBvoFwp-abt2g77bXkUfq+FW=NA-pTeUJOBtZJ5w9ttA@mail.gmail.com>
Message-ID: <543a0559-2b3c-4284-9b27-92b35cf3b65a@srvcli01.spe-ch-md9.net>

Hi Ken!

Sure will do. I?ll come back to you asap with a self-contained test loop using your shuttle data.

Regards,

Frank.

From: Ken Martin [mailto:ken.martin at kitware.com]
Sent: Mittwoch, 28. September 2016 17:20
To: Albina, Frank
Cc: paraview at paraview.org; Del Citto, Francesco
Subject: Re: [Paraview] Paraview v5.1.2: SurfaceLIC & software rendering issues

Running from the GUI with mpi and 2 nodes seems to maintain the background on my quick tests. Could you update your script to use the shuttle dataset? I included a copy of that data on this email. That would make it easier to debug.

Thanks
Ken



On Mon, Sep 26, 2016 at 4:55 AM, Albina, Frank <frank.albina at sauber-motorsport.com<mailto:frank.albina at sauber-motorsport.com>> wrote:
Dear all,

I have downloaded from the paraview.org<http://paraview.org> the latest binaries for Linux of ParaView v5.1.2. My main purpose is to make use of ParaView with software rendering in a clustered environment without GPU and, as such, I have been going through my small benchmark on a generic F1 car.

This what I have found so far when generating a SurfaceLIC representation on the whole car surface in batch mode.

Using pvbatch ?mesa-llvm works fine. This is one of the produced images for reference:
[cid:image001.jpg at 01D219AE.D5764EB0]
Using 4 cores to perform the same task (with the same script) with mpiexec ?np 4 pvbatch --mesa-llvm shows a good speed-up but the background is black instead of white (although view.Backgound = [1,1,1] is set explicitely), as shown hereafter:

[cid:image002.jpg at 01D219AE.D5764EB0]

On the same server (Intel Xeon ES-2650 v3), the CPU is AVX2 capable, so I tried also the same script with pvbatch --mesa-swr-avx2. The image background is corrupted with leftover frames apparently, as shown hereafter:

[cid:image003.jpg at 01D219AE.D5764EB0]
Was this behavior to be expected?

Please let me know if there is any interest in providing with my benchmark.

Frank Albina


_______________________________________________
Powered by www.kitware.com<http://www.kitware.com>

Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html

Please keep messages on-topic and check the ParaView Wiki at: http://paraview.org/Wiki/ParaView

Search the list archives at: http://markmail.org/search/?q=ParaView

Follow this link to subscribe/unsubscribe:
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--
Ken Martin PhD
Chairman & CFO
Kitware Inc.
28 Corporate Drive
Clifton Park NY 12065
518 371 3971

This communication, including all attachments, contains confidential and legally privileged information, and it is intended only for the use of the addressee.  Access to this email by anyone else is unauthorized. If you are not the intended recipient, any disclosure, copying, distribution or any action taken in reliance on it is prohibited and may be unlawful. If you received this communication in error please notify us immediately and destroy the original message.  Thank you.
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From utkarsh.ayachit at kitware.com  Wed Sep 28 11:43:00 2016
From: utkarsh.ayachit at kitware.com (Utkarsh Ayachit)
Date: Wed, 28 Sep 2016 11:43:00 -0400
Subject: [Paraview] [vtkusers] Please nominate ParaView for for the 2016
 HPCwire Readers' Choice Awards
In-Reply-To: <CANjZAi9GPQ9uuUruMwDb5xKGuoOuvYwXYgbooBSXL8=BrWyvpw@mail.gmail.com>
References: <CANjZAi_sm9363V3sUDijivg3pQLPXoOY3spgTWDDsp=tgr=ajQ@mail.gmail.com>
 <CANjZAi9GPQ9uuUruMwDb5xKGuoOuvYwXYgbooBSXL8=BrWyvpw@mail.gmail.com>
Message-ID: <CADHSJjB-ajGtr5bhkcccV1c0Va+OHefs8zDiTYUD=3J0mBKDKg@mail.gmail.com>

A quick reminder: today is the last day to cast your vote.

https://www.hpcwire.com/2016-hpcwire-readers-choice-awards/

Thank you!

On Wed, Sep 7, 2016 at 5:15 PM, David E DeMarle
<dave.demarle at kitware.com> wrote:
> Thank you to everyone who nominated ParaView for the HPCwire Readers? Choice
> Awards.
>
> The survey is now open for voting, and ParaView is included in the ?Best HPC
> Visualization Product or Technology? category.? To vote for ParaView, please
> visit https://www.hpcwire.com/2016-hpcwire-readers-choice-awards/.
>
> Thank you for your continued support!
>
> David E DeMarle
> Kitware, Inc.
> R&D Engineer
> 21 Corporate Drive
> Clifton Park, NY 12065-8662
> Phone: 518-881-4909
>
> On Tue, Aug 2, 2016 at 11:54 AM, David E DeMarle <dave.demarle at kitware.com>
> wrote:
>>
>> We would like to thank everyone who contributed to version 5.1.2 of
>> ParaView. To acknowledge the growth of ParaView, please join us in
>> nominating the fruit of our combined efforts for a 2016 HPCwire Readers?
>> Award in the ?Best HPC Visualization Product or Technology? category.
>>
>> Nominations can be made at
>> http://www.hpcwire.com/2015-hpcwire-readers-choice-awards. Thank you for
>> your support!
>>
>> For reference, here are some recent updates made to ParaView:
>>
>> Enabled ray tracing through OSPRay
>> Added ?Point Interpolation? filters
>> Introduced the capability to render picture-in-picture visualizations
>> Launched a welcome screen with a link to ?ParaView Getting Started Guide?
>> Improved ParaView Catalyst and Cinema for In-Situ processing at extreme
>> scales
>>
>> David E DeMarle
>> Kitware, Inc.
>> R&D Engineer
>> 21 Corporate Drive
>> Clifton Park, NY 12065-8662
>> Phone: 518-881-4909
>
>
>
> _______________________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Please keep messages on-topic and check the VTK FAQ at:
> http://www.vtk.org/Wiki/VTK_FAQ
>
> Search the list archives at: http://markmail.org/search/?q=vtkusers
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/vtkusers
>

From frank.albina at sauber-motorsport.com  Wed Sep 28 11:54:53 2016
From: frank.albina at sauber-motorsport.com (Albina, Frank)
Date: Wed, 28 Sep 2016 17:54:53 +0200
Subject: [Paraview] Building ParaView v5.1.2 on Linux from source with
 support for GPU and SWR.
In-Reply-To: <20160928124516.GB4078@megas.kitware.com>
References: <591d7e7c-08d5-4787-8703-d90fd2be1bdb@srvcli01.spe-ch-md9.net>
 <CANjZAi-m+7tU0U5piT-FszDTNbJdDkyZ6hs3Yue-rOwi2B8eog@mail.gmail.com>
 <98b353c4-1c35-47a8-808b-e37fa0385776@srvcli01.spe-ch-md9.net>
 <CANjZAi-RTCXFQqLnrw0izaX_OQwvR0iHqym7nTCiWuevyE9wvQ@mail.gmail.com>
 <89ac1f3a-7f7b-4d55-9ed6-09eda5e9a572@srvcli01.spe-ch-md9.net>
 <20160928124516.GB4078@megas.kitware.com>
Message-ID: <203a14d3-f703-45b0-85c6-95c3a830d518@srvcli01.spe-ch-md9.net>

Ben,

Thank you very much for the information in your email. 

>> 3.     You need a GNU compiler v4.8.0 or above to build. My Linux
>> distribution comes with gcc v4.7.2. Fortunately, I had gcc v4.9.2 
>> installed with which I could perform a successful build.

> What subproject required this?

I had to recompile from scractch, which took a bit of time. Actually, the GNU compiler requirement is coming from building the OSPRAY project, as shown hereafter:

[...]
CMake Error at cmake/gcc.cmake:48 (MESSAGE):
  GCC version 4.8.0 or greater is required to build OSPRay.
Call Stack (most recent call first):
  cmake/ospray.cmake:97 (INCLUDE)
  common/CMakeLists.txt:17 (CONFIGURE_OSPRAY)


-- Configuring incomplete, errors occurred!
[...]

> The new superbuild has support for building mesa 12.0.3 as part of the build. We used prebuilt binaries before because our build machine was Debian 6 which was not easily capable of compiling the LLVM -> Mesa chain > without a self-compiled compiler and such, so it was built once and that was it. I think it did contain SWR since it was a git snapshot.
> Utkarsh?

As additional information, I have cloned the git repository and did:
git checkout origin/release

which I then used to build Paraview V5.1.2 along with all dependencies.

If the new superbuild has support for building mesa 12.0.3, I would be interested in trying this out. Are there any instructions I can follow to do that?

My intention is to compile paraview without GUI to run it in batch on our cluster. This is the main reason why I am using a specific test suite to check the performance of mesa-llvm vs. mesa-swr vs. GPU. At the moment, on CPUs supporting AVX2 instruction set, mesa-swr shows a very decent performance. Hence, my interest also to try out the latest mesa 12.0.3 version, which I have downloaded today and started compiling. In this regard, do you have any configuration options you can share for use in offscreen mode? If this is handled already by the latest superbuild version, then please disregard the questions above.

Thanks a lot in advance.

Regards,

Frank.

-----Original Message-----
From: Ben Boeckel [mailto:ben.boeckel at kitware.com] 
Sent: Mittwoch, 28. September 2016 14:45
To: Albina, Frank
Cc: David E DeMarle; Del Citto, Francesco; paraview at paraview.org
Subject: Re: [Paraview] Building ParaView v5.1.2 on Linux from source with support for GPU and SWR.

On Wed, Sep 28, 2016 at 10:06:15 +0200, Albina, Frank wrote:
> In this regard, I would like to point out a few things I have found 
> while performing the build process on the aforementioned Linux 
> distribution. Note that my incentive is to help improve the ParaView 
> software suite as well as helping others to be able to build and use 
> the software.

Thanks for the feedback. Responses inline.

> 2.     You definitely need cmake at least cmake v3.5 (and not v3.3) to
> compile ParaView from SuperBuild.

Ah, ParaView is 3.3, but the superbuild is 3.5. As a heads up, the new superbuild which will be used for ParaView 5.2 will require at least 3.6.1.

> 3.     You need a GNU compiler v4.8.0 or above to build. My Linux
> distribution comes with gcc v4.7.2. Fortunately, I had gcc v4.9.2 
> installed with which I could perform a successful build.

What subproject required this?

> 4.     Dependencies such libsz, libxml, libbzip2 are built and stored
> in the <build>/install/lib64 directory on my platform. This creates 
> linking issues which I could partly resolve by pushing the missing 
> libraries into the <build>/install/lib directory. This is not ideal 
> but could be solved by forcing the lib directory to 
> <build>/install/lib using the --libdir option.

Hrm. I'm on Fedora (which also uses lib64) and though I had gotten all the lib64-isms out of the superbuild. Maybe I had missed some before
5.1.2 (the superbuild now uses common infrastructure shared between other similar superbuilds).

> 5.     The vistrails plugin cannot be built. After 3 attempts, the git
> clone from https://kwgitlab.kitware.com/paraview/vistrails.git fails.
> Either the link is wrong or the server is unreachable.

vistrails should be hidden behind a "USE_NONFREE_COMPONENTS" flag.
vistrails (and acusolve) are not FOSS, so their git repos are on our internal server.

> 6.     The mesa libraries are pre-compiled and downloaded to
> <buils>/mesa-downloads. They are unpacked and moved into the ParaView 
> installation directory when performing ?make install?. These libraries 
> are dating from May 3rd, hence prior to the release of Mesa 12.0 which 
> embeds OpenSWR as a build option. Is there a way to build new libGL.so 
> and libOSMesa.so libraries based on Mesa3D v12.0 and replace the 
> currently pre-compiled binaries? If so,what are the typical 
> configuration options used in this case?

The new superbuild has support for building mesa 12.0.3 as part of the build. We used prebuilt binaries before because our build machine was Debian 6 which was not easily capable of compiling the LLVM -> Mesa chain without a self-compiled compiler and such, so it was built once and that was it. I think it did contain SWR since it was a git snapshot.
Utkarsh?

--Ben

From Matthias.Zenker at erbe-med.com  Wed Sep 28 12:10:44 2016
From: Matthias.Zenker at erbe-med.com (Zenker, Dr. Matthias)
Date: Wed, 28 Sep 2016 16:10:44 +0000
Subject: [Paraview] ParaView Digest, Vol 149, Issue 33
In-Reply-To: <mailman.5511.1475078108.17623.paraview@paraview.org>
References: <mailman.5511.1475078108.17623.paraview@paraview.org>
Message-ID: <F9562F3B302F29479A203FC5AF9E3E050F9E3EBE@SERBE4I1.intra.erbe-med.de>

Thanks for the hint, I will try that out.

Matthias

---------------------------------------------------------------------------
Samuel Key wrote:

In the off-chance that the various mesh components (node
         sets, line-sets, surface facet sets, ...) have been written to
         the simulation results output as distinct displayable graphics
         objects, you might be able to use the PV Extract Block filter to
         get the 3-D volume "separated" from the other mesh objects, and,
         then use PV's Gradient filter?
     (I routinely do this via EnSight's PART-construct for my simulation
         results output.)
Sam Key
________________________________

Erbe Elektromedizin GmbH Firmensitz: 72072 Tuebingen Geschaeftsfuehrer: Christian O. Erbe, Reiner Thede Registergericht: Stuttgart HRB 380137


From ben.boeckel at kitware.com  Wed Sep 28 13:31:20 2016
From: ben.boeckel at kitware.com (Ben Boeckel)
Date: Wed, 28 Sep 2016 13:31:20 -0400
Subject: [Paraview] Building ParaView v5.1.2 on Linux from source with
 support for GPU and SWR.
In-Reply-To: <203a14d3-f703-45b0-85c6-95c3a830d518@srvcli01.spe-ch-md9.net>
References: <591d7e7c-08d5-4787-8703-d90fd2be1bdb@srvcli01.spe-ch-md9.net>
 <CANjZAi-m+7tU0U5piT-FszDTNbJdDkyZ6hs3Yue-rOwi2B8eog@mail.gmail.com>
 <98b353c4-1c35-47a8-808b-e37fa0385776@srvcli01.spe-ch-md9.net>
 <CANjZAi-RTCXFQqLnrw0izaX_OQwvR0iHqym7nTCiWuevyE9wvQ@mail.gmail.com>
 <89ac1f3a-7f7b-4d55-9ed6-09eda5e9a572@srvcli01.spe-ch-md9.net>
 <20160928124516.GB4078@megas.kitware.com>
 <203a14d3-f703-45b0-85c6-95c3a830d518@srvcli01.spe-ch-md9.net>
Message-ID: <20160928173120.GA31590@megas.kitware.com>

On Wed, Sep 28, 2016 at 17:54:53 +0200, Albina, Frank wrote:
> I had to recompile from scractch, which took a bit of time. Actually,
> the GNU compiler requirement is coming from building the OSPRAY
> project, as shown hereafter:
> 
> [...]
> CMake Error at cmake/gcc.cmake:48 (MESSAGE):
>   GCC version 4.8.0 or greater is required to build OSPRay.
> Call Stack (most recent call first):
>   cmake/ospray.cmake:97 (INCLUDE)
>   common/CMakeLists.txt:17 (CONFIGURE_OSPRAY)

This makes sense; ospray requires C++11 support for which GCC 4.8 was
the first release with viable support (4.7.x had some, but not enough).

> If the new superbuild has support for building mesa 12.0.3, I would be
> interested in trying this out. Are there any instructions I can follow
> to do that?

It's on my list to improve docs here. I'd welcome feedback where the
existing docs are deficient (they're in README.md on the master branch)
so I can improve those parts.

> My intention is to compile paraview without GUI to run it in batch on
> our cluster. This is the main reason why I am using a specific test
> suite to check the performance of mesa-llvm vs. mesa-swr vs. GPU. At
> the moment, on CPUs supporting AVX2 instruction set, mesa-swr shows a
> very decent performance. Hence, my interest also to try out the latest
> mesa 12.0.3 version, which I have downloaded today and started
> compiling. In this regard, do you have any configuration options you
> can share for use in offscreen mode? If this is handled already by the
> latest superbuild version, then please disregard the questions above.

Chuck (Cc'd) does this quite a bit. There are scripts he has committed
which are used to build for specific platforms which you may be able to
start using, but he's the best source of instructions for those.

--Ben

From chuck.atkins at kitware.com  Wed Sep 28 15:17:49 2016
From: chuck.atkins at kitware.com (Chuck Atkins)
Date: Wed, 28 Sep 2016 15:17:49 -0400
Subject: [Paraview] Building ParaView v5.1.2 on Linux from source with
 support for GPU and SWR.
In-Reply-To: <20160928173120.GA31590@megas.kitware.com>
References: <591d7e7c-08d5-4787-8703-d90fd2be1bdb@srvcli01.spe-ch-md9.net>
 <CANjZAi-m+7tU0U5piT-FszDTNbJdDkyZ6hs3Yue-rOwi2B8eog@mail.gmail.com>
 <98b353c4-1c35-47a8-808b-e37fa0385776@srvcli01.spe-ch-md9.net>
 <CANjZAi-RTCXFQqLnrw0izaX_OQwvR0iHqym7nTCiWuevyE9wvQ@mail.gmail.com>
 <89ac1f3a-7f7b-4d55-9ed6-09eda5e9a572@srvcli01.spe-ch-md9.net>
 <20160928124516.GB4078@megas.kitware.com>
 <203a14d3-f703-45b0-85c6-95c3a830d518@srvcli01.spe-ch-md9.net>
 <20160928173120.GA31590@megas.kitware.com>
Message-ID: <CAOXZzG5ph0CpP7gwcOF4AWkgiFGU_hsUX7zkPmbqnVqWijVuzw@mail.gmail.com>

>
> > My intention is to compile paraview without GUI to run it in batch on
> > our cluster. This is the main reason why I am using a specific test
> > suite to check the performance of mesa-llvm vs. mesa-swr vs. GPU. At
> > the moment, on CPUs supporting AVX2 instruction set, mesa-swr shows a
> > very decent performance. Hence, my interest also to try out the latest
> > mesa 12.0.3 version, which I have downloaded today and started
> > compiling. In this regard, do you have any configuration options you
> > can share for use in offscreen mode? If this is handled already by the
> > latest superbuild version, then please disregard the questions above.
>
> Chuck (Cc'd) does this quite a bit. There are scripts he has committed
> which are used to build for specific platforms which you may be able to
> start using, but he's the best source of instructions for those.
>

Hi Frank,

The updated superbuild uses a common shared set of packages that we use for
several different projects and then the top level project which is ParaView
specific. To use this, you'll want to check out the current master branch
in the paraview-superbuild, run "git submodule init", and then "git
submodule update".  This will put you at the current state of things.

You can browse the build script I have committed in Scripts/sites for linux
clusters and Cray systems at Los Alamos National Labs and the DoD HPC
network.  They but they're a bit complicated though as I use them in a very
generic fashion with lots of options for a lot of different build
configurations.  The gist of it though is to encode all of the options you
would need to turn on in a pre-configured CMake cache script. Note that
this is actually a CMake script that sets the initial cache values and not
and not just a list of variables like in CMakeCache.txt .  See cmake/sites
for a few examples.  Doing this simplifies your build to just:

cd /path/to/build/location
cmake -C /path/to/MySystem-Cache.cmake /path/to/superbuild/source

# no -j here but don't worry, the subprojects will build in parallel
make

# Make the resulting ParaView package
ctest -R cpack-paraview-TGZ


The end result is ParaView-5.1.2-OpenGL2-MPI-Linux-64bit.tar.gz that you
can extract anywhere to install.  Using ctest to drive the packaging is a
bit weird, I know, but trust me that there were various reasons for that
which could warrant it's own separate thread.

This allows you to keep MySystem-Cache.cmake under source control to
maintain a consistent build.  For your configuration, the specific options
of interest to run on are ENABLE_osmesa and ENABLE_ospray.  Our default
configuration of osmesa will enable SWR.  What you'll end up with is a
pvserver / pvbatch that uses OSMesa for off-screen CPU based rendering
without X but with both llvmpipe and swr drivers built.  You can switch
between the by setting the GALLIUM_DRIVER env var to either llvmpipe or
swr.

Hope that gives you a good place to get started.
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From s_ringe at gmx.de  Wed Sep 28 18:13:57 2016
From: s_ringe at gmx.de (Stefan Ringe)
Date: Thu, 29 Sep 2016 00:13:57 +0200
Subject: [Paraview] Crash among plotting cml files
Message-ID: <trinity-044df7c4-353b-41cf-840f-74f2687bb829-1475100837777@3capp-gmx-bs34>

An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/paraview/attachments/20160929/b9ef59fe/attachment.html>

From utkarsh.ayachit at kitware.com  Wed Sep 28 19:04:14 2016
From: utkarsh.ayachit at kitware.com (Utkarsh Ayachit)
Date: Wed, 28 Sep 2016 19:04:14 -0400
Subject: [Paraview] Crash among plotting cml files
In-Reply-To: <trinity-044df7c4-353b-41cf-840f-74f2687bb829-1475100837777@3capp-gmx-bs34>
References: <trinity-044df7c4-353b-41cf-840f-74f2687bb829-1475100837777@3capp-gmx-bs34>
Message-ID: <CADHSJjAkzydd81oeasE+iVUEc6_bQEkSqmhxETUtsFq+hOWpQg@mail.gmail.com>

Stefan,

A lot of fixes have gone into ParaView "master" that fixes and
improves CML support. If you're not keen on building, let me know
which OS you're on and I can point you to the nightly binaries for the
same. BTW, ParaView 5.2 release candidates should come out around Oct
7, if that helps.

Utkarsh

On Wed, Sep 28, 2016 at 6:13 PM, Stefan Ringe <s_ringe at gmx.de> wrote:
> Hi!
>
> I love working with paraview but there are continuous problems with showing
> cml files. I used to have these problems before on Debian Jessie, so after
> opening cml geometry files (e.g. as produced by avogadro), and hitting the
> "apply" button, paraview crashes. I circumvented this problem by compiling
> paraview from source with the at that time most current version. But now I
> updated on Debian Skretch and got the brand new version of Paraview but
> still it is crashing with CML files. Why is that and is that going to be
> fixed soon? And which versions may work out, I would not like to do the
> whole compiling stuff again, it was a lot of work,
>
> best,
>
> Stefan
>
> _______________________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Please keep messages on-topic and check the ParaView Wiki at:
> http://paraview.org/Wiki/ParaView
>
> Search the list archives at: http://markmail.org/search/?q=ParaView
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/paraview
>

From s_ringe at gmx.de  Thu Sep 29 02:55:56 2016
From: s_ringe at gmx.de (Stefan Ringe)
Date: Thu, 29 Sep 2016 08:55:56 +0200
Subject: [Paraview] Crash among plotting cml files
Message-ID: <trinity-d02e777d-8caf-4def-b930-353598b0d265-1475132156605@3capp-gmx-bs80>

An HTML attachment was scrubbed...
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From frank.albina at sauber-motorsport.com  Thu Sep 29 07:54:53 2016
From: frank.albina at sauber-motorsport.com (Albina, Frank)
Date: Thu, 29 Sep 2016 13:54:53 +0200
Subject: [Paraview] Building ParaView v5.1.2 on Linux from source with
 support for GPU and SWR.
In-Reply-To: <CAOXZzG5ph0CpP7gwcOF4AWkgiFGU_hsUX7zkPmbqnVqWijVuzw@mail.gmail.com>
References: <591d7e7c-08d5-4787-8703-d90fd2be1bdb@srvcli01.spe-ch-md9.net>
 <CANjZAi-m+7tU0U5piT-FszDTNbJdDkyZ6hs3Yue-rOwi2B8eog@mail.gmail.com>
 <98b353c4-1c35-47a8-808b-e37fa0385776@srvcli01.spe-ch-md9.net>
 <CANjZAi-RTCXFQqLnrw0izaX_OQwvR0iHqym7nTCiWuevyE9wvQ@mail.gmail.com>
 <89ac1f3a-7f7b-4d55-9ed6-09eda5e9a572@srvcli01.spe-ch-md9.net>
 <20160928124516.GB4078@megas.kitware.com>
 <203a14d3-f703-45b0-85c6-95c3a830d518@srvcli01.spe-ch-md9.net>
 <20160928173120.GA31590@megas.kitware.com>
 <CAOXZzG5ph0CpP7gwcOF4AWkgiFGU_hsUX7zkPmbqnVqWijVuzw@mail.gmail.com>
Message-ID: <c62dbcf8-22ab-4104-b193-19073b27d5bb@srvcli01.spe-ch-md9.net>

Hi Chuck,
Thank you very much for your reply. It is very interesting and I will try my best to get ParaView compiled following your recommendations.
Unfortunately, others duties are holding me off this week from concentrating on this but I will share my test results comparing ParaView on GPU, with mesa-llvm and mesa-swr-avx2.
Talk to you soon.
Best regards,
Frank.
From: Chuck Atkins [mailto:chuck.atkins at kitware.com]
Sent: Mittwoch, 28. September 2016 21:18
To: Ben Boeckel
Cc: Albina, Frank; David E DeMarle; Del Citto, Francesco; paraview at paraview.org
Subject: Re: [Paraview] Building ParaView v5.1.2 on Linux from source with support for GPU and SWR.

> My intention is to compile paraview without GUI to run it in batch on
> our cluster. This is the main reason why I am using a specific test
> suite to check the performance of mesa-llvm vs. mesa-swr vs. GPU. At
> the moment, on CPUs supporting AVX2 instruction set, mesa-swr shows a
> very decent performance. Hence, my interest also to try out the latest
> mesa 12.0.3 version, which I have downloaded today and started
> compiling. In this regard, do you have any configuration options you
> can share for use in offscreen mode? If this is handled already by the
> latest superbuild version, then please disregard the questions above.

Chuck (Cc'd) does this quite a bit. There are scripts he has committed
which are used to build for specific platforms which you may be able to
start using, but he's the best source of instructions for those.

Hi Frank,

The updated superbuild uses a common shared set of packages that we use for several different projects and then the top level project which is ParaView specific. To use this, you'll want to check out the current master branch in the paraview-superbuild, run "git submodule init", and then "git submodule update".  This will put you at the current state of things.

You can browse the build script I have committed in Scripts/sites for linux clusters and Cray systems at Los Alamos National Labs and the DoD HPC network.  They but they're a bit complicated though as I use them in a very generic fashion with lots of options for a lot of different build configurations.  The gist of it though is to encode all of the options you would need to turn on in a pre-configured CMake cache script. Note that this is actually a CMake script that sets the initial cache values and not and not just a list of variables like in CMakeCache.txt .  See cmake/sites for a few examples.  Doing this simplifies your build to just:
cd /path/to/build/location
cmake -C /path/to/MySystem-Cache.cmake /path/to/superbuild/source

# no -j here but don't worry, the subprojects will build in parallel
make

# Make the resulting ParaView package
ctest -R cpack-paraview-TGZ

The end result is ParaView-5.1.2-OpenGL2-MPI-Linux-64bit.tar.gz that you can extract anywhere to install.  Using ctest to drive the packaging is a bit weird, I know, but trust me that there were various reasons for that which could warrant it's own separate thread.

This allows you to keep MySystem-Cache.cmake under source control to maintain a consistent build.  For your configuration, the specific options of interest to run on are ENABLE_osmesa and ENABLE_ospray.  Our default configuration of osmesa will enable SWR.  What you'll end up with is a pvserver / pvbatch that uses OSMesa for off-screen CPU based rendering without X but with both llvmpipe and swr drivers built.  You can switch between the by setting the GALLIUM_DRIVER env var to either llvmpipe or swr.
Hope that gives you a good place to get started.
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From s_ringe at gmx.de  Thu Sep 29 08:38:12 2016
From: s_ringe at gmx.de (Stefan Ringe)
Date: Thu, 29 Sep 2016 14:38:12 +0200
Subject: [Paraview] Crash among plotting cml files
In-Reply-To: <CADHSJjAkzydd81oeasE+iVUEc6_bQEkSqmhxETUtsFq+hOWpQg@mail.gmail.com>
References: <trinity-044df7c4-353b-41cf-840f-74f2687bb829-1475100837777@3capp-gmx-bs34>, 
 <CADHSJjAkzydd81oeasE+iVUEc6_bQEkSqmhxETUtsFq+hOWpQg@mail.gmail.com>
Message-ID: <trinity-bc003d7f-8f83-4c5e-a647-ec2c1f546b14-1475152692633@3capp-gmx-bs10>

An HTML attachment was scrubbed...
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From utkarsh.ayachit at kitware.com  Thu Sep 29 09:42:36 2016
From: utkarsh.ayachit at kitware.com (Utkarsh Ayachit)
Date: Thu, 29 Sep 2016 09:42:36 -0400
Subject: [Paraview] Crash among plotting cml files
In-Reply-To: <trinity-bc003d7f-8f83-4c5e-a647-ec2c1f546b14-1475152692633@3capp-gmx-bs10>
References: <trinity-044df7c4-353b-41cf-840f-74f2687bb829-1475100837777@3capp-gmx-bs34>
 <CADHSJjAkzydd81oeasE+iVUEc6_bQEkSqmhxETUtsFq+hOWpQg@mail.gmail.com>
 <trinity-bc003d7f-8f83-4c5e-a647-ec2c1f546b14-1475152692633@3capp-gmx-bs10>
Message-ID: <CADHSJjDZ-ga8vMPgNO5M-a4g+tC2vM6xp45G1juxjpLW+JO95A@mail.gmail.com>

Great! Yup that's the one. Glad it's working better.

On Thu, Sep 29, 2016 at 8:38 AM, Stefan Ringe <s_ringe at gmx.de> wrote:
> I downloaded the binary
>
> ParaView-5.1.2-522-g96621b3-Qt4-OpenGL2-MPI-Linux-64bit
>
> and with that it does not crash,
>
> thanks again,
>
> best
>
> Stefan
>
> Gesendet: Donnerstag, 29. September 2016 um 01:04 Uhr
> Von: "Utkarsh Ayachit" <utkarsh.ayachit at kitware.com>
> An: "Stefan Ringe" <s_ringe at gmx.de>
> Cc: ParaView <paraview at paraview.org>
> Betreff: Re: [Paraview] Crash among plotting cml files
> Stefan,
>
> A lot of fixes have gone into ParaView "master" that fixes and
> improves CML support. If you're not keen on building, let me know
> which OS you're on and I can point you to the nightly binaries for the
> same. BTW, ParaView 5.2 release candidates should come out around Oct
> 7, if that helps.
>
> Utkarsh
>
> On Wed, Sep 28, 2016 at 6:13 PM, Stefan Ringe <s_ringe at gmx.de> wrote:
>> Hi!
>>
>> I love working with paraview but there are continuous problems with
>> showing
>> cml files. I used to have these problems before on Debian Jessie, so after
>> opening cml geometry files (e.g. as produced by avogadro), and hitting the
>> "apply" button, paraview crashes. I circumvented this problem by compiling
>> paraview from source with the at that time most current version. But now I
>> updated on Debian Skretch and got the brand new version of Paraview but
>> still it is crashing with CML files. Why is that and is that going to be
>> fixed soon? And which versions may work out, I would not like to do the
>> whole compiling stuff again, it was a lot of work,
>>
>> best,
>>
>> Stefan
>>
>> _______________________________________________
>> Powered by www.kitware.com
>>
>> Visit other Kitware open-source projects at
>> http://www.kitware.com/opensource/opensource.html
>>
>> Please keep messages on-topic and check the ParaView Wiki at:
>> http://paraview.org/Wiki/ParaView
>>
>> Search the list archives at: http://markmail.org/search/?q=ParaView
>>
>> Follow this link to subscribe/unsubscribe:
>> http://public.kitware.com/mailman/listinfo/paraview
>>

From david.lonie at kitware.com  Thu Sep 29 13:44:59 2016
From: david.lonie at kitware.com (David Lonie)
Date: Thu, 29 Sep 2016 13:44:59 -0400
Subject: [Paraview] At last -- Anti-aliasing in ParaView!
Message-ID: <CA+=e1osBhfKf1KQmKHV8Dy0rQBFrAG3JUFNuh1Zn8rrDXMBnyA@mail.gmail.com>

I'm happy to announce that ParaView now includes an option for FXAA
anti-aliasing, which works quite nicely for both serial and parallel
rendering. It is available in the current master branch on gitlab/github,
but is disabled by default so you'll need to check some boxes in the
Settings to use it.

You can read more about it on the Kitware blog:

https://blog.kitware.com/new-fxaa-anti-aliasing-option-in-paraviewvtk/

Big thanks to Sandia National Labs for supporting this work.

Cheers,
Dave
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From P.Crepier at marin.nl  Fri Sep 30 02:57:37 2016
From: P.Crepier at marin.nl (Crepier, Pierre)
Date: Fri, 30 Sep 2016 06:57:37 +0000
Subject: [Paraview] CGNSSeriesReader - python - cell arrays
Message-ID: <5641ed971bf44425812b6178f823e152@MAR190n2.marin.local>

Hi everybody,

This is my first e-mail to this mailing list after looking around a lot in the wiki/manual/google.
I am busy trying to automate CGNS data loading using a python script but I am now stuck at listing the variables contained in the CGNS file

The CGNS data is 3D data and contains some variables. I want to specify which data to load.

When loading a cgns file manually, it gives list of the variables available in the file. See this picture:
http://www.pixhoster.info/f/2016-09/9b456f7a80da44827835ecddb0073ee6.jpg

I am wondering how I can get access to this list via the python scripting API.
I searched in the CompositeDataInformation object, but all I succeed to obtain is the list of selected arrays once those are selected.

Is it possible to achieve that from python ?

Thanks in advance,

P. Crepier

ir. Pierre Crepier | Project Manager Ships | CFD
MARIN | T +31 317 49 34 75 | P.Crepier at marin.nl<mailto:P.Crepier at marin.nl> | www.marin.nl<http://www.marin.nl>

[LinkedIn]<https://www.linkedin.com/company/marin> [YouTube] <http://www.youtube.com/marinmultimedia>  [Twitter] <https://twitter.com/MARIN_nieuws>  [Facebook] <https://www.facebook.com/marin.wageningen>
MARIN news: MARIN at Monaco Yacht Show, September 28-October 1<http://www.marin.nl/web/News/News-items/MARIN-at-Monaco-Yacht-Show-September-28October-1.htm>


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From agsmith424 at gmail.com  Fri Sep 30 11:03:59 2016
From: agsmith424 at gmail.com (Andy Smith)
Date: Fri, 30 Sep 2016 11:03:59 -0400
Subject: [Paraview] CGNSSeriesReader - python - cell arrays
In-Reply-To: <5641ed971bf44425812b6178f823e152@MAR190n2.marin.local>
References: <5641ed971bf44425812b6178f823e152@MAR190n2.marin.local>
Message-ID: <CA+yV-vC79mP-MZ=Qmn0ZMB1bXiTY6Fwp9P+vd6TvgcOwZEuOjQ@mail.gmail.com>

Would something like this work for you?

from __future__ import print_function
from paraview.simple import *

cgns = CGNSSeriesReader(FileNames=['SC10_steady.cgns'])
availableCellArrays = cgns.GetPropertyValue('CellArrayInfo')[::2]

print(availableCellArrays)


On Fri, Sep 30, 2016 at 2:57 AM, Crepier, Pierre <P.Crepier at marin.nl> wrote:

> Hi everybody,
>
>
>
> This is my first e-mail to this mailing list after looking around a lot in
> the wiki/manual/google.
>
> I am busy trying to automate CGNS data loading using a python script but I
> am now stuck at listing the variables contained in the CGNS file
>
>
>
> The CGNS data is 3D data and contains some variables. I want to specify
> which data to load.
>
>
>
> When loading a cgns file manually, it gives list of the variables
> available in the file. See this picture:
>
> http://www.pixhoster.info/f/2016-09/9b456f7a80da44827835ecddb0073ee6.jpg
>
>
>
> I am wondering how I can get access to this list via the python scripting
> API.
>
> I searched in the CompositeDataInformation object, but all I succeed to
> obtain is the list of selected arrays once those are selected.
>
>
>
> Is it possible to achieve that from python ?
>
>
>
> Thanks in advance,
>
>
>
> P. Crepier
>
> ir. Pierre Crepier | Project Manager Ships | CFD
> MARIN | T +31 317 49 34 75 | P.Crepier at marin.nl | www.marin.nl
>
> [image: LinkedIn] <https://www.linkedin.com/company/marin> [image:
> YouTube] <http://www.youtube.com/marinmultimedia> [image: Twitter]
> <https://twitter.com/MARIN_nieuws> [image: Facebook]
> <https://www.facebook.com/marin.wageningen>
> MARIN news: MARIN at Monaco Yacht Show, September 28-October 1
> <http://www.marin.nl/web/News/News-items/MARIN-at-Monaco-Yacht-Show-September-28October-1.htm>
>
>
> _______________________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at http://www.kitware.com/
> opensource/opensource.html
>
> Please keep messages on-topic and check the ParaView Wiki at:
> http://paraview.org/Wiki/ParaView
>
> Search the list archives at: http://markmail.org/search/?q=ParaView
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/paraview
>
>
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From P.Crepier at marin.nl  Fri Sep 30 11:37:29 2016
From: P.Crepier at marin.nl (Crepier, Pierre)
Date: Fri, 30 Sep 2016 15:37:29 +0000
Subject: [Paraview] CGNSSeriesReader - python - cell arrays
In-Reply-To: <CA+yV-vC79mP-MZ=Qmn0ZMB1bXiTY6Fwp9P+vd6TvgcOwZEuOjQ@mail.gmail.com>
References: <5641ed971bf44425812b6178f823e152@MAR190n2.marin.local>
 <CA+yV-vC79mP-MZ=Qmn0ZMB1bXiTY6Fwp9P+vd6TvgcOwZEuOjQ@mail.gmail.com>
Message-ID: <9b5700c02df945cca59c9b3dee88d6d2@MAR190n2.marin.local>

That works perfectly!

For some reason I could not see the GetPropertyValue and ListProperties functions in the dir output of the object.

Thanks a lot for the solution.


ir. Pierre Crepier | Project Manager Ships | CFD
MARIN | T +31 317 49 34 75 | P.Crepier at marin.nl<mailto:P.Crepier at marin.nl> | www.marin.nl<http://www.marin.nl>

[LinkedIn]<https://www.linkedin.com/company/marin> [YouTube] <http://www.youtube.com/marinmultimedia>  [Twitter] <https://twitter.com/MARIN_nieuws>  [Facebook] <https://www.facebook.com/marin.wageningen>
MARIN news: On the design of anti-roll tanks<http://www.marin.nl/web/News/News-items/On-the-design-of-antiroll-tanks-1.htm>
From: Andy Smith [mailto:agsmith424 at gmail.com]
Sent: Friday, September 30, 2016 5:04 PM
To: Crepier, Pierre
Cc: paraview at paraview.org
Subject: Re: [Paraview] CGNSSeriesReader - python - cell arrays

Would something like this work for you?

from __future__ import print_function
from paraview.simple import *

cgns = CGNSSeriesReader(FileNames=['SC10_steady.cgns'])
availableCellArrays = cgns.GetPropertyValue('CellArrayInfo')[::2]

print(availableCellArrays)

On Fri, Sep 30, 2016 at 2:57 AM, Crepier, Pierre <P.Crepier at marin.nl<mailto:P.Crepier at marin.nl>> wrote:
Hi everybody,

This is my first e-mail to this mailing list after looking around a lot in the wiki/manual/google.
I am busy trying to automate CGNS data loading using a python script but I am now stuck at listing the variables contained in the CGNS file

The CGNS data is 3D data and contains some variables. I want to specify which data to load.

When loading a cgns file manually, it gives list of the variables available in the file. See this picture:
http://www.pixhoster.info/f/2016-09/9b456f7a80da44827835ecddb0073ee6.jpg

I am wondering how I can get access to this list via the python scripting API.
I searched in the CompositeDataInformation object, but all I succeed to obtain is the list of selected arrays once those are selected.

Is it possible to achieve that from python ?

Thanks in advance,

P. Crepier

ir. Pierre Crepier | Project Manager Ships | CFD
MARIN | T +31 317 49 34 75<tel:%2B31%20317%2049%2034%2075> | P.Crepier at marin.nl<mailto:P.Crepier at marin.nl> | www.marin.nl<http://www.marin.nl>

[LinkedIn]<https://www.linkedin.com/company/marin> [YouTube] <http://www.youtube.com/marinmultimedia>  [Twitter] <https://twitter.com/MARIN_nieuws>  [Facebook] <https://www.facebook.com/marin.wageningen>
MARIN news: MARIN at Monaco Yacht Show, September 28-October 1<http://www.marin.nl/web/News/News-items/MARIN-at-Monaco-Yacht-Show-September-28October-1.htm>

_______________________________________________
Powered by www.kitware.com<http://www.kitware.com>

Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html

Please keep messages on-topic and check the ParaView Wiki at: http://paraview.org/Wiki/ParaView

Search the list archives at: http://markmail.org/search/?q=ParaView

Follow this link to subscribe/unsubscribe:
http://public.kitware.com/mailman/listinfo/paraview



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From taylorbrennen731 at gmail.com  Sun Sep 18 16:32:06 2016
From: taylorbrennen731 at gmail.com (Brennen Taylor)
Date: Sun, 18 Sep 2016 20:32:06 -0000
Subject: [Paraview] How to merge .vtk files to visualize the result in
	Paraview
Message-ID: <CABxKrco8e5wo+Rc5u3Krjv-7vEBhnb+OSR58gGfTzk7NbGZ+Lw@mail.gmail.com>

Dear All,

I am using Paraview in order to visualize the result produced by parallel
program.
Each processor currently outputs its own .vtk files , which corresponsd to
the value of the fields in the domain.

I would like to know if there is a way of merging these .vtk files into one
.vtk file so that I can visualize using Paraview.

Attaching the required .vtk files for the reference.


Thanks in advance !!

Best ,

Brennen
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From ken.martin at kitware.com  Wed Sep 28 11:19:39 2016
From: ken.martin at kitware.com (Ken Martin)
Date: Wed, 28 Sep 2016 15:19:39 -0000
Subject: [Paraview] Paraview v5.1.2: SurfaceLIC & software rendering
	issues
In-Reply-To: <4373b551-40c8-44ca-8b27-9106bceac88c@srvcli01.spe-ch-md9.net>
References: <4373b551-40c8-44ca-8b27-9106bceac88c@srvcli01.spe-ch-md9.net>
Message-ID: <CANXz0SbBvoFwp-abt2g77bXkUfq+FW=NA-pTeUJOBtZJ5w9ttA@mail.gmail.com>

Running from the GUI with mpi and 2 nodes seems to maintain the background
on my quick tests. Could you update your script to use the shuttle dataset?
I included a copy of that data on this email. That would make it easier to
debug.

Thanks
Ken



On Mon, Sep 26, 2016 at 4:55 AM, Albina, Frank <
frank.albina at sauber-motorsport.com> wrote:

> Dear all,
>
>
>
> I have downloaded from the paraview.org the latest binaries for Linux of
> ParaView v5.1.2. My main purpose is to make use of ParaView with software
> rendering in a clustered environment without GPU and, as such, I have been
> going through my small benchmark on a generic F1 car.
>
>
>
> This what I have found so far when generating a SurfaceLIC representation
> on the whole car surface in batch mode.
>
>
>
> Using pvbatch ?mesa-llvm works fine. This is one of the produced images
> for reference:
>
> Using 4 cores to perform the same task (with the same script) with mpiexec
> ?np 4 pvbatch --mesa-llvm shows a good speed-up but the background is black
> instead of white (although view.Backgound = [1,1,1] is set explicitely), as
> shown hereafter:
>
>
>
>
>
> On the same server (Intel Xeon ES-2650 v3), the CPU is AVX2 capable, so I
> tried also the same script with pvbatch --mesa-swr-avx2. The image
> background is corrupted with leftover frames apparently, as shown hereafter:
>
>
>
> Was this behavior to be expected?
>
>
>
> Please let me know if there is any interest in providing with my benchmark.
>
>
>
> *Frank Albina*
>
>
>
> _______________________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at http://www.kitware.com/
> opensource/opensource.html
>
> Please keep messages on-topic and check the ParaView Wiki at:
> http://paraview.org/Wiki/ParaView
>
> Search the list archives at: http://markmail.org/search/?q=ParaView
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/paraview
>
>


-- 
Ken Martin PhD
Chairman & CFO
Kitware Inc.
28 Corporate Drive
Clifton Park NY 12065
518 371 3971

This communication, including all attachments, contains confidential and
legally privileged information, and it is intended only for the use of the
addressee.  Access to this email by anyone else is unauthorized. If you are
not the intended recipient, any disclosure, copying, distribution or any
action taken in reliance on it is prohibited and may be unlawful. If you
received this communication in error please notify us immediately and
destroy the original message.  Thank you.
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From frank.albina at sauber-motorsport.com  Thu Sep 29 12:25:25 2016
From: frank.albina at sauber-motorsport.com (Albina, Frank)
Date: Thu, 29 Sep 2016 16:25:25 -0000
Subject: [Paraview] Paraview v5.1.2: SurfaceLIC & software rendering
 issues
In-Reply-To: <543a0559-2b3c-4284-9b27-92b35cf3b65a@srvcli01.spe-ch-md9.net>
References: <4373b551-40c8-44ca-8b27-9106bceac88c@srvcli01.spe-ch-md9.net>
 <CANXz0SbBvoFwp-abt2g77bXkUfq+FW=NA-pTeUJOBtZJ5w9ttA@mail.gmail.com>
 <543a0559-2b3c-4284-9b27-92b35cf3b65a@srvcli01.spe-ch-md9.net>
Message-ID: <81dea72d-a45b-4780-85dc-b8f2f5f8148a@srvcli01.spe-ch-md9.net>

Ken,

I have included as attachment to this email the script I modified to reproduce the issue reported earlier with our generic F1 car. You will find the following structure once you have unpacked the zip archive:

Benchmark/
|-- Binaries
|   `-- ParaView-5.1.2
|-- Data
|   `-- shuttle-surf
|       |-- shuttle-surf_0_0.vtp
|       |-- shuttle-surf_0_0.vtp.md5-stamp
|       |-- shuttle-surf_1_0.vtp
|       |-- shuttle-surf_1_0.vtp.md5-stamp
|       |-- shuttle-surf_2_0.vtp
|       |-- shuttle-surf_2_0.vtp.md5-stamp
|       |-- shuttle-surf_3_0.vtp
|       |-- shuttle-surf_3_0.vtp.md5-stamp
|       |-- shuttle-surf_4_0.vtp
|       |-- shuttle-surf_4_0.vtp.md5-stamp
|       |-- shuttle-surf_5_0.vtp
|       |-- shuttle-surf_5_0.vtp.md5-stamp
|       |-- shuttle-surf_6_0.vtp
|       |-- shuttle-surf_6_0.vtp.md5-stamp
|       |-- shuttle-surf_7_0.vtp
|       `-- shuttle-surf_7_0.vtp.md5-stamp
`-- ParaView-5.1.2
    |-- LoResImages
    |-- runShuttle.sh
    `-- shuttleBenchmarkSurfaceLIC.py

The Data directory contains all surface files used for performing rendering. Binaries/ParaView-5.1.2 contains the installation of ParaView. This is where I have extracted the ParaView binaries I downloaded last week from the paraview.org site (ParaView-5.1.2-Qt4-OpenGL2-MPI-Linux-64bit.tar.gz).

The benchmark is started using script ?runShuttle.sh?. It will use pvbatch to run the python script shuttleBenchmarkSurfaceLIC.py using OSMesa with llvm-pipe and swr-avx2. Both options are run using 1 core, 2 cores and 3 cores. Generated images are stored respectively in folder LoResImages.

With this script, I got the same issues as reported earlier, i.e. the --mesa-llvm on 1 core works well, on 2 cores the background is black instead of white, the --mesa-swr-avx2 option delivers a corrupted image:

mesa-llvm 1 core:
[cid:image001.jpg at 01D21A7E.C927DCC0]
mesa-llvm 2 cores:
[cid:image002.jpg at 01D21A7E.C927DCC0]

mesa-swr-avx2 1 core:
[cid:image003.jpg at 01D21A7E.C927DCC0]
The plaftorm I used to generate these images is:

OpenSuSE 12.3
Linux 3.7.10-1.45-desktop #1 SMP PREEMPT x86_64 GNU/Linux
2 x 10 core Intel Xeon ES-2650 @ 2.30GHz

Thank you very much in advance for your help.

Best regards,

Frank.

From: ParaView [mailto:paraview-bounces at paraview.org] On Behalf Of Albina, Frank
Sent: Mittwoch, 28. September 2016 17:36
To: Ken Martin
Cc: Del Citto, Francesco; paraview at paraview.org
Subject: Re: [Paraview] Paraview v5.1.2: SurfaceLIC & software rendering issues

Hi Ken!

Sure will do. I?ll come back to you asap with a self-contained test loop using your shuttle data.

Regards,

Frank.

From: Ken Martin [mailto:ken.martin at kitware.com]
Sent: Mittwoch, 28. September 2016 17:20
To: Albina, Frank
Cc: paraview at paraview.org<mailto:paraview at paraview.org>; Del Citto, Francesco
Subject: Re: [Paraview] Paraview v5.1.2: SurfaceLIC & software rendering issues

Running from the GUI with mpi and 2 nodes seems to maintain the background on my quick tests. Could you update your script to use the shuttle dataset? I included a copy of that data on this email. That would make it easier to debug.

Thanks
Ken



On Mon, Sep 26, 2016 at 4:55 AM, Albina, Frank <frank.albina at sauber-motorsport.com<mailto:frank.albina at sauber-motorsport.com>> wrote:
Dear all,

I have downloaded from the paraview.org<http://paraview.org> the latest binaries for Linux of ParaView v5.1.2. My main purpose is to make use of ParaView with software rendering in a clustered environment without GPU and, as such, I have been going through my small benchmark on a generic F1 car.

This what I have found so far when generating a SurfaceLIC representation on the whole car surface in batch mode.

Using pvbatch ?mesa-llvm works fine. This is one of the produced images for reference:
[cid:image022.jpg at 01D21A7C.A741F430]
Using 4 cores to perform the same task (with the same script) with mpiexec ?np 4 pvbatch --mesa-llvm shows a good speed-up but the background is black instead of white (although view.Backgound = [1,1,1] is set explicitely), as shown hereafter:

[cid:image023.jpg at 01D21A7C.A741F430]

On the same server (Intel Xeon ES-2650 v3), the CPU is AVX2 capable, so I tried also the same script with pvbatch --mesa-swr-avx2. The image background is corrupted with leftover frames apparently, as shown hereafter:

[cid:image024.jpg at 01D21A7C.A741F430]
Was this behavior to be expected?

Please let me know if there is any interest in providing with my benchmark.

Frank Albina


_______________________________________________
Powered by www.kitware.com<http://www.kitware.com>

Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html

Please keep messages on-topic and check the ParaView Wiki at: http://paraview.org/Wiki/ParaView

Search the list archives at: http://markmail.org/search/?q=ParaView

Follow this link to subscribe/unsubscribe:
http://public.kitware.com/mailman/listinfo/paraview



--
Ken Martin PhD
Chairman & CFO
Kitware Inc.
28 Corporate Drive
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518 371 3971

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From stephane at fujielectric.com  Fri Sep  2 04:36:41 2016
From: stephane at fujielectric.com (=?UTF-8?B?c3RlcGhhbmXjg7Pjg4njg7PjgrAg44Oh44OV44Kh44ON?=)
Date: Fri, 02 Sep 2016 08:36:41 -0000
Subject: [Paraview] Nastran file
Message-ID: <CADLMsL5jRa6ydg+hArZSpcco_GQ+UttL3jYCx8hBK=Pr7m5poQ@mail.gmail.com>

Hello,

I am using the Paraview 5.1.2 binary on windows 7.
I made a simple nastran file but I cannot load it.
Paraview crashes immediately.

I am sending the file so that you can try it yourself

Ndong-Mefane Stephane, Dr.Eng
Basic Design Sec.
Steam Turbine Dept.
Kawasaki Factory

Fuji Electric Co., Ltd
1-1, Tanabeshinden, Kawasaki-ku,
Kawasaki-city 210-9530, Japan
Phone: +81-44-329-2155
Fax: +81-44-329-2394
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