[Paraview] Linking to Catalyst

Tue May 10 00:35:19 EDT 2016

Ah hah, the errors were being sent somewhere else and not caught properly by my submission script.

I found the error and now it works, I get my images and my VTK files. The only warnings now are:

24vtkCPTensorArrayTemplateIdE (0x23b4320): GetVoidPointer called. This is very expensive for vtkMappedDataArray subclasses, since the scalar array must be generated for each call. Consider using a vtkTypedDataArrayIterator instead.

which is something I can deal with later. I have to figure out what the vtkCPTensorArrayTemplate does exactly -- I believe that was something you had added when you took a look at our code awhile back. But it doesn't seem to matter for what we're doing now.

It feels good to close the ticket in our tracker about getting coprocessing on Crays -- it's been open since 2012.

Thanks again for all your help.

Tim

________________________________
From: Andy Bauer <andy.bauer at kitware.com>
Sent: Monday, May 9, 2016 10:41 PM
To: Gallagher, Timothy P
Cc: paraview at paraview.org
Subject: Re: [Paraview] Linking to Catalyst

Hi Tim,

I assume that writing out a data set works on other machines, correct? Can you try the gridwriter.py script at https://gitlab.kitware.com/paraview/paraview/blob/master/Examples/Catalyst/SampleScripts/gridwriter.py to output the full data set? It should work with PV 4.4. Note that outputs a full data set every time step. I'm not sure about Python warnings or errors but the C++ warnings and errors will be sent to std::cerr instead of std::cout.
[https://gitlab.kitware.com/uploads/project/avatar/14/pvIcon-512x512.png]<https://gitlab.kitware.com/paraview/paraview/blob/master/Examples/Catalyst/SampleScripts/gridwriter.py>

Examples/Catalyst/SampleScripts/gridwriter.py · master · ParaView / ParaView<https://gitlab.kitware.com/paraview/paraview/blob/master/Examples/Catalyst/SampleScripts/gridwriter.py>
gitlab.kitware.com
Parallel Data Analysis and Visualization Application based on VTK.

Did you make the script with PV 4.4? The PV Python API has some changes (especially for rendering) between revisions. I think the best option is to just comment out the parts that are causing trouble.

If you're still having issues, maybe send your full script along with std::cout and std::cerr outputs so I can get a little deeper into the issues.

Good luck,
Andy

On Mon, May 9, 2016 at 6:14 PM, Gallagher, Timothy P <tim.gallagher at gatech.edu<mailto:tim.gallagher at gatech.edu>> wrote:

Okay, really close to finally crossing this off my list -- it's been on it for years.

I can get the code to generate images but it won't save data files. I don't get any errors and I get my images, just no VTK files. I have tried the default that the catalyst generator creates:

parallelMultiBlockDataSetWriter1 = servermanager.writers.XMLMultiBlockDataWriter(Input=slice1)

coprocessor.RegisterWriter(parallelMultiBlockDataSetWriter1, filename='slices_%t.vtm', freq=freq_file)

and I tried another form that the grid writer you've send me in the past used:

writer = coprocessor.CreateWriter(XMLMultiBlockDataWriter, filename='slices_%t.vtm', freq=freq_file)

in all cases, freq_file = 1000.

Neither one will output any vtk files.

Any thoughts?

Also, minor note but it is kind of annoying -- both the catalyst generator and the trace generator seem to do this, but they add commands that set attributes that are not part of the classes when run through the python script. For example, I had to comment out:

#      slice1Display.SelectInputVectors = ['CELLS', 'Velocity [m/s]']
#      slice1Display.WriteLog = ''

Any ideas why it does that? Or is there a way (and downfall) to just let it add attributes without manually calling add_attribute() each time?

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, May 9, 2016 5:13 PM
To: Andy Bauer

Cc: paraview at paraview.org<mailto:paraview at paraview.org>
Subject: Re: [Paraview] Linking to Catalyst

Yeah -- okay, pointing it to the build directory instead of the install made sure everything was found.

One step closer to getting this working on Cray.

Thanks,

Tim

________________________________
From: Andy Bauer <andy.bauer at kitware.com<mailto:andy.bauer at kitware.com>>
Sent: Monday, May 9, 2016 4:54 PM
To: Gallagher, Timothy P
Cc: paraview at paraview.org<mailto:paraview at paraview.org>
Subject: Re: [Paraview] Linking to Catalyst

Hmm, that could be a bug in the superbuild. The superbuild arguments aren't all passed to the ParaView build itself and it could be that this option was missing for the PV specific build part. Instead of doing the whole build from scratch, I'd suggest you just search for the ParaViewConfig.cmake file to find where PV was actually built and just point to that.

On Mon, May 9, 2016 at 4:50 PM, Gallagher, Timothy P <tim.gallagher at gatech.edu<mailto:tim.gallagher at gatech.edu>> wrote:

Well shoot, it looks like I didn't build with the install development files on, even though I set it when I configured the superbuild. I must have done that part wrong

My configure line is:

cmake \
-DCMAKE_INSTALL_PREFIX:PATH=${HOME}/pv-test/${version}_osmesa \
-DCMAKE_BUILD_TYPE=Release \
...

-DPARAVIEW_ENABLE_CATALYST=ON \
-DPARAVIEW_ENABLE_PYTHON=ON \
-DPARAVIEW_INSTALL_DEVELOPMENT_FILES=ON \
-DPARAVIEW_BUILD_QT_GUI=OFF \
-DBUILD_TESTING=OFF \
-DVTK_USE_X=OFF \
...

-DVTK_OPENGL_HAS_OSMESA=ON \
-DOSMESA_INCLUDE_DIR:STRING="${INSTALLPATH}/osmesa/include" \
-DOSMESA_LIBRARY:STRING="${INSTALLPATH}/osmesa/lib/libOSMesa.so" \
./ParaViewSuperbuild

and all of the other PARAVIEW* options seemed to pass through properly when the superbuild made paraview. Any ideas why that option didn't pass through?

Thanks -- I knew it had to be something really obvious!

Tim

________________________________
From: Andy Bauer <andy.bauer at kitware.com<mailto:andy.bauer at kitware.com>>
Sent: Monday, May 9, 2016 4:43 PM
To: Gallagher, Timothy P
Cc: paraview at paraview.org<mailto:paraview at paraview.org>
Subject: Re: [Paraview] Linking to Catalyst

Hi Tim,

Is the PV directory you're pointing to a build directory or an install directory? If it's an install directory you'll need to enable PARAVIEW_INSTALL_DEVELOPMENT_FILES. Other than that, my suggestion would be to try linking one of the Catalyst examples from https://github.com/Kitware/ParaViewCatalystExampleCode and see how that works for you. Another thing you could try is using a newer version of CMake from https://cmake.org/download/. For the Linux x86_64 tarball, you can just untar the executables from that and use directly.
[https://avatars3.githubusercontent.com/u/87549?v=3&s=400]<https://github.com/Kitware/ParaViewCatalystExampleCode>

GitHub - Kitware/ParaViewCatalystExampleCode: Example ...<https://github.com/Kitware/ParaViewCatalystExampleCode>
github.com<http://github.com>
ParaViewCatalystExampleCode - Example problems and snippets of code to demonstrate ParaView's Catalyst.

Let us know if none of those ideas don't work for you.

Best,
Andy

On Mon, May 9, 2016 at 3:58 PM, Gallagher, Timothy P <tim.gallagher at gatech.edu<mailto:tim.gallagher at gatech.edu>> wrote:

Hello again,

I'm (finally) trying to get Catalyst to successfully link to our application code on Excalibur (Cray, ARL HPC). I was able to build paraview and all of the dependencies thanks to help I've gotten on the list here in the past. However, when I try to link my code to it (and this is a code that works fine with Catalyst on other platforms), I get:

 CMake Error at /p/home/tgallagh/pv-test/4.4.0_osmesa/lib/cmake/paraview-4.4/vtkModuleAPI.cmake:120 (message):
   Requested modules not available:

     vtkPVPythonCatalyst
 Call Stack (most recent call first):
   /p/home/tgallagh/pv-test/4.4.0_osmesa/lib/cmake/paraview-4.4/VTKConfig.cmake:80 (vtk_module_config)
   /p/home/tgallagh/pv-test/4.4.0_osmesa/lib/cmake/paraview-4.4/ParaViewConfig.cmake:49 (include)
   CMakeLists.txt:218 (find_package)

The section in my CMakeLists that looks for paraview is:

option(LESLIE_USE_COPROCESSING "Turn on CoProcessing with Paraview" OFF)
if(LESLIE_USE_COPROCESSING)
  find_package(ParaView REQUIRED vtkPVPythonCatalyst
               HINTS $ENV{PARAVIEW_CP_ROOT})
  include(${PARAVIEW_USE_FILE})
  include_directories(${PROJECT_SOURCE_DIR}/utils)
  add_definitions(-DPARAVIEW_COPROCESSING)
endif()
mark_as_advanced(LESLIE_USE_COPROCESSING)

and it doesn't seem to work. On other machines, I never needed to set the PARAVIEW_CP_ROOT variable, it always just found it. When I build my code, I point the paraview directory (where it finds the paraviewConfig.cmake file) to:

/p/home/tgallagh/pv-test/4.4.0_osmesa/lib/cmake/paraview-4.4

and it seems to find it okay.

Lastly, the vtkPVPythonCatalyst.so library is in the lib/paraview-4.4/site-packages/vtk directory and there is libvtkPVPythonCatalyst-pv4.4.so<http://libvtkPVPythonCatalyst-pv4.4.so>* and libvtkPVPythonCatalystPython27D-pv4.4.so<http://libvtkPVPythonCatalystPython27D-pv4.4.so>* in lib/paraview-4.4/

I'm at a loss to understand why it is reporting the module is missing -- did I miss something somewhere?

Thanks as always,

Tim

_______________________________________________
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

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/paraview/attachments/20160510/0fbf0065/attachment.html>