[Paraview] FW: FW: Coloured isosurfaces when running MPI

Wed Jun 29 11:24:58 EDT 2011

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
>> is the intended result, obtained using a single core (no Auto-MPI etc.)
>>
>> http://www.mech.kth.se/~pschlatt/files/Screenshot2.png
>> is the result obtained with Auto-MPI, running on my two cores.
>>
>> http://www.mech.kth.se/~pschlatt/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)? 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; 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.
>>>>
>>>> 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 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). 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