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

Fri Jul 1 09:53:18 EDT 2011

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://www.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://www.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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