[Paraview] FW: FW: Coloured isosurfaces when running MPI
Biddiscombe, John A.
biddisco at cscs.ch
Sat Oct 1 15:11:08 EDT 2011
Philip,
Great bug report. I also had trouble with replicated colours when using rectilinear grid but due to time constraints didn't have time to track down the problem. In my case I was able to switch to ImageData since my grids were regular at the time and the problem went away. However with your detailed post I'll have another crack at locating the problem. My own suspicion was that the contouring and everything works fine, the scalars are actually correct, but somewhere in the mpi collection of the results, something gets gathered up wrongly. It seemed to me that the extent handling / piece requests for rectilinear grids was somehow broken -
[pause for 5 minutes]
Loading the rect2.vtk dataset and following your example I see the problem, but I also see that if you add a process ID filter and then open a spreadsheet view, you can see the original elevation values are correctly computed (as we'd expect), but then looking at the contour filter and seeing the values of elevation matched to processId and they're clearly wrong (in the spreadsheet you can select the points with zero elevation and they're visibly in the wrong place).
I'll pursue this further .....
JB
-----Original Message-----
From: paraview-bounces at paraview.org [mailto:paraview-bounces at paraview.org] On Behalf Of Philipp Schlatter
Sent: 01 October 2011 15:32
To: paraview at paraview.org
Subject: Re: [Paraview] FW: FW: Coloured isosurfaces when running MPI
Dear all,
sorry for warming up this older bug report; but I just tried out version 3.12 RC2, and I found that the bug (at least I believe it is one) is still present. As the problem is really being very important for my work, but presumably also for many others, I am taking the opportunity to bring it up once more.
The issue is as follows:
If I load a rectilinear grid, and then plot isosurfaces of the data with a certain "color by" turned on, I am experiencing that the colouring is not done correctly depending on the number of MPI processes paraview/pvserver is running on. Let me illustrate that with a simple example:
The pipeline is simply reading data (for instance RectGrid2.vtk from the examples), then applying the Elevation filter to get a second scalar to do the colouring; in the example we just use elevation along the x axis. Then, we plot a bunch of isosurfaces to illustrate the problem:
1) one isosurface for the actual data (scalars), coloured by elevation. This gives a repeated colour pattern as shown in the screenshot:
http://dl.dropbox.com/u/39264314/paraview/Screenshot.png and http://dl.dropbox.com/u/39264314/paraview/mpi_2.png
The correct colour of course would be one single sequence starting from blue to red as the elevation gradually changes without jumping. This is shown in another screenshot, obtained with one single MPI processor:
http://dl.dropbox.com/u/39264314/paraview/mpi_1.png: All is ok.
For instance running on 10 processors, we get an even more strange picture: http://dl.dropbox.com/u/39264314/paraview/mpi_10.png
It appears to me that the data structure that is use to colour the isosurfaces is not properly recomputed on each processor, but rather computed on one, and then used on all the others, although their own data would require different data.
There are a few workarounds, see below, however they are not practical as both the memory footprint is increased considerably, but also the quality of the rendering is very poor when going to unstructured grids.
The background of the issue is that I am intending to visualise large data sets and plot isosurfaces of say vorticity which is then coloured by a velocity component. Due to the size of the dataset I would like to use parallel visualisation, instead of just running serially on very fat nodes. I believe that such a visualisation technique is quite common in our area, which makes me think that the present bug is quite important.
Of course I would be happy to provide more information (e.g. the state file: http://dl.dropbox.com/u/39264314/paraview/mpitest.pvsm), or also fill in an official bug report if this helps.
Best regards,
Philipp Schlatter
KTH Mechanics, Stockholm, Sweden.
-----Original Message-----
From: Philipp Schlatter [mailto:pschlatt at mech.kth.se]
Sent: den 1 juli 2011 16:40
To: pat marion
Cc: paraview at paraview.org
Subject: Re: [Paraview] FW: FW: Coloured isosurfaces when running MPI
Thanks!
The "Compute Normals" is checked in the contour filter after the CleanToGrid filter, however the Gouraud shading does not work. But using an additional "Generate Surface Normals" then does the trick, at least partially. The contours look nicer than without Gouraud shading, obviously, but the best result (and also the cheapest one, I will use it on large data sets) would still be obtained when directly doing a contour on the original rectilinear data without transforming it to unstructured.
Thus, I was wondering whether I should submit the present case also as a bug report, as I guess also other people might need coloured isosurfaces when running MPI?
Best regards,
Philipp
On Fri, 01 Jul 2011 15:53:18 +0200, pat marion <pat.marion at kitware.com>
wrote:
> Hi Philipp,
>
> You need to check the "Compute Normals" box on the properties panel of
> the contour filter. Alternatively, you can apply the "Generate
> Surface Normals"
> to any polydata dataset to enable correct Gouraud shading.
>
> Pat
>
> On Wed, Jun 29, 2011 at 11:24 AM, Philipp Schlatter
> <pschlatt at mech.kth.se>wrote:
>
>> Thanks a lot for the help!
>> Concerning the suggested workaround, I have a follow-up question: How
>> would one get the Gouraud shading of the isocontours working? In my
>> case I will get properly coloured isocontours, but they seem to have
>> uniform shade for each triangle as opposed to an interpolated shade.
>>
>> Thanks,
>> philipp
>>
>>
>> On Wed, 29 Jun 2011 14:34:34 +0200, Karl König <kkoenig11 at web.de> wrote:
>>
>> Hi Philipp,
>>>
>>> It seems you have hit a bug in the Contour filter occurring with > 1
>>> pvserver process and rectilinear grid input. I can reproduce the
>>> issue you reported as such:
>>>
>>> Load ParaView, connect to > 1 pvserver processes Open
>>> Data/RectGrid2.vtk (e.g. from git://vtk.org/VTKData.git) Calculator
>>> filter, operation: "coordsX",
>>> Result Array Name: "Result", Apply Contour filter, Contour by
>>> "scalars", Compute Normals,
>>> Isosurface Value 0.5, Apply
>>> Representation "Surface", Color by "Result"
>>>
>>> With 1 pvserver process the surface coloring is indeed a single
>>> smooth gradient while with more than 1 pvserver process the gradient
>>> starts anew at half the X range. If applying an additional "Process
>>> ID Scalars"
>>> filter, one can confirm that the "reset" happens at a process boundary.
>>>
>>> Converting the rectilinear grid to an unstructured grid prior to
>>> applying the contour filter may serve as as a workaround. The
>>> filters "Clean to Grid", "Tetrahedralize" and "Tesselate" all do
>>> that trick (they are listed with increasing memory footprint). So, I
>>> recommend using "Clean to Grid" somewhere before applying the
>>> contour filter in the parallel case.
>>>
>>> Karl
>>>
>>>
>>>
>>> Philipp Schlatter wrote, On 29.06.2011 11:50:
>>>
>>>> Hi!
>>>> Thanks for the answer. Let me give some comments to your questions:
>>>> - I am using the distributed 3.10.1 binaries (32 bit), and I tried
>>>> it on a Ubuntu 11.04 system (older dualcore T60p)
>>>> - I used now the sample dataset Data/RectGrid2.vtk. Using the
>>>> calculator operation "CoordsX", I can reproduce the behaviour I was
>>>> originally describing. I simply use the Contour filter ("Compute
>>>> Scalars" did not change the behaviour). I have uploaded 3 more
>>>> screenshots:
>>>>
>>>>
>>>> http://www.mech.kth.se/~**pschlatt/files/Screenshot3.png<http://www
>>>> .mech.kth.se/%7Epschlatt/files/Screenshot3.png>
>>>> is the intended result, obtained using a single core (no Auto-MPI
>>>> etc.)
>>>>
>>>> http://www.mech.kth.se/~**pschlatt/files/Screenshot2.png<http://www
>>>> .mech.kth.se/%7Epschlatt/files/Screenshot2.png>
>>>> is the result obtained with Auto-MPI, running on my two cores.
>>>>
>>>> http://www.mech.kth.se/~**pschlatt/files/Screenshot1.png<http://www
>>>> .mech.kth.se/%7Epschlatt/files/Screenshot1.png>
>>>> is the result obtained with explicitly initiating paraview and
>>>> pvserver using a total of 16 MPI ranks.
>>>>
>>>> I tried all/most of the rendering options (LOD etc.), however it
>>>> did not help. Also, I have run on 64 bit version at the computer
>>>> centre (with older versions though), and the same problem appears
>>>> there too.
>>>>
>>>> I am really puzzled by the fact that you could not reproduce the
>>>> problem. Could there be some setting that is for some reason wrong
>>>> in my setup?
>>>>
>>>> Best regards,
>>>> Philipp
>>>>
>>>>
>>>> On Tue, 28 Jun 2011 18:36:25 +0200, Karl König <kkoenig11 at web.de>
>>>> wrote:
>>>>
>>>> Hi Philipp,
>>>>>
>>>>> A couple of questions:
>>>>> * Are you using the distributed 3.10.1 binaries or did you compile
>>>>> PV
>>>>> 3.10.1 from source yourself?
>>>>> * Can you reproduce the behavior with the sample dataset
>>>>> Data/RectGrid2.vtk (part of both git://vtk.org/VTKData.git and
>>>>> http://www.paraview.org/files/**v3.10/ParaViewData-3.10.1.zip<http
>>>>> ://www.paraview.org/files/v3.10/ParaViewData-3.10.1.zip>
>>>>> )**? That's
>>>>> also a "Rectilinear Grid". Using the Calculator operation "1 +
>>>>> coordsX*coordsY" followed by a Contour filter with "Compute Scalars"
>>>>> checked and 10 auto-chosen values, I got identical results with 1
>>>>> and 16 cores (using PV 3.10.1 Linux 64-bit binaries and Windows
>>>>> 64-bit binaries, relying on Auto-MPI ("Settings" - "Use
>>>>> Multi-Core") for the 16 core case)
>>>>>
>>>>> Karl
>>>>>
>>>>>
>>>>> Philipp Schlatter wrote, On 28.06.2011 17:50:
>>>>>
>>>>>> Dear all,
>>>>>> Unfortunately, I am still struggling with running MPI and
>>>>>> producing coloured isosurfaces. A screenshot exemplifying the
>>>>>> problem can be found at
>>>>>> http://www.mech.kth.se/~**pschlatt/files/Screenshot.png<http://ww
>>>>>> w.mech.kth.se/%7Epschlatt/files/Screenshot.png>;
>>>>>> note that the
>>>>>> colour
>>>>>> scheme based on the x-coordinate is just to show the problem, but
>>>>>> in reality I am using some scalar data coming from file.
>>>>>>
>>>>>> Anyway, I wanted to ask you whether any of you has had similar
>>>>>> problems, i.e. colouring isosurfaces when running MPI. It seems
>>>>>> to me that the data field used to colour the surfaces is only
>>>>>> created on one MPI rank and then used by all other ranks, instead
>>>>>> of computed for each rank independently based on the local data.
>>>>>> Can anyone confirm that behaviour?
>>>>>>
>>>>>> This problem makes it at the moment impossible for me to
>>>>>> visualise a certain very large data set as I need to use MPI to
>>>>>> distribute the data due to memory limitation.
>>>>>>
>>>>>> Thanks a lot for any help!
>>>>>>
>>>>>> Philipp
>>>>>>
>>>>>> -----Original Message-----
>>>>>> From: Philipp Schlatter [mailto:pschlatt at mech.kth.se]
>>>>>> Sent: den 20 juni 2011 22:55
>>>>>> To: 'Utkarsh Ayachit'
>>>>>> Cc: paraview at paraview.org
>>>>>> Subject: RE: [Paraview] FW: Coloured isosurfaces when running MPI
>>>>>>
>>>>>> Dear Utkarsh,
>>>>>> Thanks a lot for your answer. The type of my data is "Rectilinear
>>>>>> Grid"
>>>>>> (turbulence data on a regular grid). The test case that I use to
>>>>>> reproduce the data leads to a size of the contours (from the
>>>>>> statistics
>>>>>> inspector)
>>>>>> 230316 cells, and a memory of 15 MB. I have turned off all the
>>>>>> remote render thresholds etc. and the problem persists. Thus it
>>>>>> is likely that it is the contour filter that causes the
>>>>>> miscolouring.
>>>>>>
>>>>>> I have just reroduced the problem using the latest version 3.10.1
>>>>>> (Linux 32-bit); and I generated a screenshot on
>>>>>> http://www.mech.kth.se/~**pschlatt/files/Screenshot.png<http://ww
>>>>>> w.mech.kth.se/%7Epschlatt/files/Screenshot.png>
>>>>>> .
>>>>>>
>>>>>> The test is simple; I read in a rectilinear grid with a few
>>>>>> velocity components. Then I compute a new scalar field,
>>>>>> essentially being the x-corrdinate. Then I plot an isocontour,
>>>>>> and colour it with the result of the calculator. I would expect a
>>>>>> continuous colour going from blue to red spread over the whole x
>>>>>> extent, however - according to the number of processors used (in
>>>>>> that case 16) - I get a repetitive pattern. By some more
>>>>>> experimenting it becomes clear that for some reason the colouring
>>>>>> is done based on the scalar value on the first processor only.
>>>>>>
>>>>>> Running on 1 processor everything is fine.
>>>>>>
>>>>>> I am of course happy to provide the respective data files, if
>>>>>> this could help.
>>>>>>
>>>>>> Thanks for any help!
>>>>>> Best regards,
>>>>>> Philipp
>>>>>>
>>>>>>
>>>>>> -----Original Message-----
>>>>>> From: Utkarsh Ayachit
>>>>>> [mailto:utkarsh.ayachit@**kitware.com<utkarsh.ayachit at kitware.com
>>>>>> >
>>>>>> ]
>>>>>> Sent: den 20 juni 2011 16:59
>>>>>> To: Philipp Schlatter
>>>>>> Cc: paraview at paraview.org
>>>>>> Subject: Re: [Paraview] FW: Coloured isosurfaces when running MPI
>>>>>>
>>>>>> That's very peculiar. What datatype are you contouring? (With the
>>>>>> reader selected in the pipeline browser, go to the information
>>>>>> tab, what does the "Type" field say?) Also after generating the
>>>>>> iso-surface, open the statistics inspector (View | Statistics
>>>>>> Inspector). What is the size of the geometry generated from the
>>>>>> contour filter. If that's not too large, you try doing
>>>>>> local-rendering (go to Edit | Settings, on the Server page,
>>>>>> uncheck Remote Render Threshold). Does that help? This will help
>>>>>> diagnose if the issue is with rendering or with the data
>>>>>> generated by the contour filter itself.
>>>>>>
>>>>>> Utkarsh
>>>>>>
>>>>>> On Sun, Jun 19, 2011 at 11:25 AM, Philipp Schlatter
>>>>>> <pschlatt at mech.kth.se>
>>>>>> wrote:
>>>>>>
>>>>>>> Dear forum,
>>>>>>>
>>>>>>> I am using Paraview to visualise a large dataset coming from a
>>>>>>> direct simulation of turbulence (size of the original data of
>>>>>>> order 10-100GB).
>>>>>>> Naturally, I am running in parallel on a cluster (using the
>>>>>>> mesa), which also works very well.
>>>>>>>
>>>>>>> However, there is one issue: I want to visualise isosurfaces of
>>>>>>> a quantity, and colour them using another scalar quantity. When
>>>>>>> running serial, everything is fine. When using multiple
>>>>>>> processors with MPI leading to the data being distributed, the
>>>>>>> rendering of the isosurfaces is
>>>>>>>
>>>>>> still ok.
>>>>>>
>>>>>>> However, the colouring seems to be based on the scalar field of
>>>>>>> the first data segment (i.e. the first processor) only. This
>>>>>>> then leads to very visible boundaries between the processors as
>>>>>>> the colours are clearly not correct (see example on
>>>>>>> http://www.mech.kth.se/~**pschlatt/files/resampled.jpg<http://www.mech.kth.se/%7Epschlatt/files/resampled.jpg>).
>>>>>>> Again, running
>>>>>>> on a single processor everything is correct, and running on
>>>>>>> different numbers of processors will shift the edges.
>>>>>>>
>>>>>>> This issue could be confirmed in all version up to 3.10.
>>>>>>>
>>>>>>> Due to this, I am required to run in serial, which is very
>>>>>>> painful both due to memory requirements and very long rendering
>>>>>>> times (up to
>>>>>>> 15 minutes for a single frame). Thus, if there would be a simple
>>>>>>> fix, I'd
>>>>>>>
>>>>>> be very interested.
>>>>>>
>>>>>>>
>>>>>>> Thanks a lot in advance for any hint.
>>>>>>> Best regards,
>>>>>>> Philipp Schlatter
>>>>>>> KTH Mechanics, Stockholm, Sweden
>>>>>>>
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