[Paraview] ParaView Digest, Vol 120, Issue 35

Tue Apr 22 13:05:24 EDT 2014

I'm trying to build Paraview 4.1 with mvapich2, gcc, cuda55, and qt 4.8.1.
 I've done the iterative configure process and I generate a make file but
make -j 8 gives me this error:

/usr/bin/ld: /cm/shared/apps/mvapich2/gcc/64/1.9/lib/libmpich.a(setbotf.o):
relocation R_X86_64_32 against `mpifcmb2_' can not be used when making a
shared object; recompile with -fPIC

/cm/shared/apps/mvapich2/gcc/64/1.9/lib/libmpich.a: could not read symbols:
Bad value

collect2: ld returned 1 exit status

make[2]: *** [lib/libvtkVPIC-pv4.1.so.1] Error 1

make[1]: *** [VTK/ThirdParty/VPIC/CMakeFiles/VPIC.dir/all] Error 2

make[1]: *** Waiting for unfinished jobs....

The make ends with

[  4%] Building CXX object
ThirdParty/protobuf/vtkprotobuf/src/CMakeFiles/protoc_compiler.dir/google/protobuf/compiler/parser.cc.o

[  4%] Building C object
VTK/ThirdParty/libxml2/vtklibxml2/CMakeFiles/vtklibxml2.dir/xpath.c.o

[  4%] Building C object
VTK/ThirdParty/libxml2/vtklibxml2/CMakeFiles/vtklibxml2.dir/xpointer.c.o

Linking CXX executable ../../../../bin/protoc

[  4%] Built target protoc_compiler

Linking C shared library ../../../../lib/libvtklibxml2-pv4.1.so

[  4%] Built target vtklibxml2

make: *** [all] Error 2
Can someone translate for me?  Can I buy a vowel?  The google has run out
of gas.

On Tue, Apr 22, 2014 at 10:00 AM, <paraview-request at paraview.org> wrote:

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> Today's Topics:
>
>    1. Re: Fwd: Stream Tracer Scaling (Amir A)
>    2. Re: [vtkusers] vtkStripper/TriangleStrips not working on this
>       particular data, why? (Dr. Roman Grothausmann)
>    3. Re: Fwd: Stream Tracer Scaling (Berk Geveci)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Mon, 21 Apr 2014 17:20:24 -0500
> From: Amir A <amiramir12345 at outlook.com>
> To: Berk Geveci <berk.geveci at kitware.com>, "paraview at paraview.org"
>         <paraview at paraview.org>
> Subject: Re: [Paraview] Fwd: Stream Tracer Scaling
> Message-ID: <SNT151-W25522E46C192AC769D4DDFED5E0 at phx.gbl>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hi Berk:
> Thank you for your reply. I am doing the visualization on a distributed
> cluster. And the StreamTracer filter is used with a point source of radius
> 0.1 and 100 seeds.
> It is surprising that the streamtracer in parallel takes orders of
> magnitude more time than when applied in serial. I tried to first apply D3
> filter and then the streamtracer. That helps a little bit but still the
> time is prohibitively long (about an hour compared to ~5min when done in
> serial). I do not know if I am missing something or this is usual.
> Here is the visualization that I want to create in parallel (I had to do
> it in serial because of this problem):
> https://www.dropbox.com/s/r3kkon3khjdpqs6/foam_3.png
> The original dataset is about 4GB.  Here is a smaller one (~1GB) with the
> state files: https://www.dropbox.com/s/r6lh3sx2wojfva2/sample.tar.gz
> I would highly appreciate any suggestions.-Amir
> From: berk.geveci at kitware.com
> Date: Mon, 21 Apr 2014 11:34:25 -0400
> To: andy.bauer at kitware.com
> CC: paraview at paraview.org
> Subject: Re: [Paraview] Fwd: Stream Tracer Scaling
>
> Actually, if the integration is fairly load balanced across partitions,
> the streamline integration can scale OK. It is highly dependent on how the
> seeds are distributed and if the integration ends up clustering on a few
> processes. Amir:
>
>
> - How big is your seed source? Does it span multiple partitions? How many
> seed points?- Do the streamlines stay together or do the move around the
> domain more independently?
>
>
> Are you running on a single machine by the way? I have been thinking about
> parallelizing the streamline filter over threads, which should scale better
> on a single machine.
> Best,-berk
>
>
>
>
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> ------------------------------
>
> Message: 2
> Date: Tue, 22 Apr 2014 11:33:46 +0200
> From: "Dr. Roman Grothausmann" <grothausmann.roman at mh-hannover.de>
> Cc: VTK Mailing List <vtkusers at vtk.org>, "paraview at paraview.org"
>         <paraview at paraview.org>
> Subject: Re: [Paraview] [vtkusers] vtkStripper/TriangleStrips not
>         working on this particular data, why?
> Message-ID: <5356377A.1020809 at mh-hannover.de>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> Thanks Bill, Goodwin and Des for Your answers.
> I see, perhaps this should be given as a hint in the docs. The patch seems
> to be
> doing something similar to my new approach. However, since my polylines
> originate from a vtkGraph, I decided to reorder the nodes/vertices with
> BFS.
>
> Many thanks again for Your help
> Roman
>
> On 11/04/14 17:13, Bill Lorensen wrote:
> > If this were a closed contour, I believe you would get one polyline.
> > But for a open contour you are not guaranteed to get a single
> > polyline. The algorithm starts with a point (looks like it is the
> > first point in the first line segment) and collects as many points as
> > it can for the first polyline. This completes the first polyline. If
> > the first point of the first line is not one of the end points of your
> > original data, then it will generate two polylines. At least that is
> > what I recall.
> >
> > Bill
> >
> >
> > On Fri, Apr 11, 2014 at 10:43 AM, Dr. Roman Grothausmann
> > <grothausmann.roman at mh-hannover.de> wrote:
> >> Dear mailing list members,
> >>
> >>
> >> Attached is a very simple test.vtp (see *_01.png) which for some reason
> >> cannot be converted into a single vtkPolyLine with vtkStripper. Even if
> I
> >> use paraview with Clean+Triangulate+TriangleStrip the result still
> consists
> >> of two vtkPolyLine (see extracted cell 0 (thicker line) and green cell
> >> labels in *_03.png).
> >> Why does vtkStripper not yield a single vtkPolyLine from this particular
> >> dataset? Is it the odd order of the points and lines?
> >> Is this a bug?
> >> If not, how can I achieve what I need, i.e. getting a single
> vtkPolyLine?
> >>
> >> Any help or hints are very much appreciated
> >> 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. +49 511 532-9574
> >>
> >> _______________________________________________
> >> 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
> >>
> >> Follow this link to subscribe/unsubscribe:
> >> http://www.vtk.org/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. +49 511 532-9574
>
>
> ------------------------------
>
> Message: 3
> Date: Tue, 22 Apr 2014 09:07:18 -0400
> From: Berk Geveci <berk.geveci at kitware.com>
> To: Amir A <amiramir12345 at outlook.com>
> Cc: "paraview at paraview.org" <paraview at paraview.org>
> Subject: Re: [Paraview] Fwd: Stream Tracer Scaling
> Message-ID:
>         <CAE32kpWSP-cvM=Y-crFx4PxaicJaGnxSki3nYa8aTQ=
> USH+gbg at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Hmmm. It certainly should not be much slower. Even in the worst load
> balancing case, it should be at most slightly slower. I will take a look.
>
> -berk
>
>
> On Mon, Apr 21, 2014 at 6:20 PM, Amir A <amiramir12345 at outlook.com> wrote:
>
> > Hi Berk:
> >
> > Thank you for your reply. I am doing the visualization on a distributed
> > cluster. And the StreamTracer filter is used with a point source of
> radius
> > 0.1 and 100 seeds.
> >
> > It is surprising that the streamtracer in parallel takes orders of
> > magnitude more time than when applied in serial. I tried to first apply
> D3
> > filter and then the streamtracer. That helps a little bit but still the
> > time is prohibitively long (about an hour compared to ~5min when done in
> > serial). I do not know if I am missing something or this is usual.
> >
> > Here is the visualization that I want to create in parallel (I had to do
> > it in serial because of this problem):
> > https://www.dropbox.com/s/r3kkon3khjdpqs6/foam_3.png
> >
> > The original dataset is about 4GB.  Here is a smaller one (~1GB) with the
> > state files:
> > https://www.dropbox.com/s/r6lh3sx2wojfva2/sample.tar.gz
> >
> > I would highly appreciate any suggestions.
> > -Amir
> >
> > ------------------------------
> > From: berk.geveci at kitware.com
> > Date: Mon, 21 Apr 2014 11:34:25 -0400
> > To: andy.bauer at kitware.com
> > CC: paraview at paraview.org
> > Subject: Re: [Paraview] Fwd: Stream Tracer Scaling
> >
> >
> > Actually, if the integration is fairly load balanced across partitions,
> > the streamline integration can scale OK. It is highly dependent on how
> the
> > seeds are distributed and if the integration ends up clustering on a few
> > processes. Amir:
> >
> > - How big is your seed source? Does it span multiple partitions? How many
> > seed points?
> > - Do the streamlines stay together or do the move around the domain more
> > independently?
> >
> >  Are you running on a single machine by the way? I have been thinking
> > about parallelizing the streamline filter over threads, which should
> scale
> > better on a single machine.
> >
> > Best,
> > -berk
> >
> >
> > _______________________________________________ Powered by
> www.kitware.comVisit other Kitware open-source projects at
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> > on-topic and check the ParaView Wiki at:
> http://paraview.org/Wiki/ParaViewFollow this link to
> subscribe/unsubscribe:
> > http://www.paraview.org/mailman/listinfo/paraview
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> End of ParaView Digest, Vol 120, Issue 35
> *****************************************
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-- 
Jack Vant
System Engineer - HPC
Office of Information Technology
Boise State University
208-426-4446
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