[Paraview] CoProcessing
Andy Bauer
andy.bauer at kitware.com
Mon Aug 9 10:58:26 EDT 2010
Hi Jacques,
I put an example on the wiki based on Pat's example for running a
coprocessing. It's at:
http://paraview.org/Wiki/Coprocessing_example#Python_Scripts
Let me know if you have any problems with it so that I can fix any errors
that I have.
Also, I just made changes so that the coprocessing library gets installed
properly.
Thanks,
Andy
On Wed, Aug 4, 2010 at 7:21 PM, Jacques Papper <jacques.papper at gmail.com>wrote:
> Thanks Pat,
>
> I am trying to compile my first attempt.
> Although I do find the headers I need, I am having some trouble identifying
> which libraries I need to link to.
> For example, I assume that I should be linking to libvtkCoProcessor.so ...
> Although I find this library in the compilation folder (under bin), I do not
> find it in the make installed version under lib...
> Is this normal ?
>
> Best,
> Jacques
>
> 2010/8/4 pat marion <pat.marion at kitware.com>
>
> Below is a simple cxx program I have used for testing. It creates one
>> sphere per process, positions the sphere as a function of the process id,
>> and the spheres grow/shrink over time.
>>
>> Pat
>>
>> #include "vtkCPProcessor.h"
>> #include "vtkCPPythonScriptPipeline.h"
>> #include "vtkMultiProcessController.h"
>> #include "vtkXMLUnstructuredGridReader.h"
>> #include "vtkUnstructuredGrid.h"
>> #include "vtkCPDataDescription.h"
>> #include "vtkCPInputDataDescription.h"
>> #include "vtkSmartPointer.h"
>> #include "vtkPolyData.h"
>> #include "vtkSphereSource.h"
>>
>> #include <stdio.h>
>> #include <string>
>> #include <sstream>
>>
>> static unsigned int procId;
>>
>> void myprint(const std::string& str)
>> {
>> printf("driver (%u): %s\n", procId, str.c_str());
>> }
>>
>> class DataGenerator {
>> public:
>>
>> DataGenerator()
>> {
>> this->Sphere = vtkSmartPointer<vtkSphereSource>::New();
>> this->Sphere->SetThetaResolution(30);
>> this->Sphere->SetPhiResolution(30);
>> this->Sphere->SetCenter(procId*4.0, 0, 0);
>> this->Index = 0;
>> }
>>
>> vtkSmartPointer<vtkPolyData> GetNext()
>> {
>> double radius = fabs(sin(0.1 * this->Index));
>> this->Index++;
>> this->Sphere->SetRadius(1.0 + radius);
>> this->Sphere->Update();
>> vtkSmartPointer<vtkPolyData> ret =
>> vtkSmartPointer<vtkPolyData>::New();
>> ret->DeepCopy(this->Sphere->GetOutput());
>> return ret;
>> }
>>
>> protected:
>>
>> int Index;
>> vtkSmartPointer<vtkSphereSource> Sphere;
>>
>>
>> };
>>
>> int main(int argc, char* argv[])
>> {
>> if (argc < 3)
>> {
>> printf("Usage: %s <cp python file> <number of steps>\n", argv[0]);
>> return 1;
>> }
>>
>> std::string cpPythonFile = argv[1];
>> int nSteps = atoi(argv[2]);
>>
>> myprint("starting coprocessor");
>>
>> vtkCPProcessor* processor = vtkCPProcessor::New();
>> processor->Initialize();
>> vtkCPPythonScriptPipeline* pipeline = vtkCPPythonScriptPipeline::New();
>>
>> // mpi was initialized when we called vtkCPPythonScriptPipeline::New()
>> procId =
>> vtkMultiProcessController::GetGlobalController()->GetLocalProcessId();
>>
>>
>> // read the coprocessing python file
>> myprint("loading pipeline python file: " + cpPythonFile);
>> int success = pipeline->Initialize(cpPythonFile.c_str());
>> if (!success)
>> {
>> myprint("aborting");
>> return 1;
>> }
>>
>> processor->AddPipeline(pipeline);
>> pipeline->Delete();
>>
>> if (nSteps == 0)
>> {
>> return 0;
>> }
>>
>> // create a data source
>> DataGenerator generator;
>>
>> // do coprocessing
>> double tStart = 0.0;
>> double tEnd = 1.0;
>> double stepSize = (tEnd - tStart)/nSteps;
>>
>> vtkCPDataDescription* dataDesc = vtkCPDataDescription::New();
>> dataDesc->AddInput("input");
>>
>> for (int i = 0; i < nSteps; ++i)
>> {
>>
>> double currentTime = tStart + stepSize*i;
>> std::stringstream timeStr;
>> timeStr << "time(" << i << ", " << currentTime << ")";
>>
>>
>> dataDesc->SetTimeData(currentTime, i);
>>
>> myprint("call RequestDataDescription, " + timeStr.str());
>> int do_coprocessing = processor->RequestDataDescription(dataDesc);
>>
>> if (do_coprocessing)
>> {
>> myprint("calling CoProcess, " + timeStr.str());
>>
>> vtkSmartPointer<vtkDataObject> dataObject =
>> generator.GetNext();
>>
>> dataDesc->GetInputDescriptionByName("input")->SetGrid(dataObject);
>> processor->CoProcess(dataDesc);
>> }
>> }
>>
>>
>> myprint("finalizing");
>> dataDesc->Delete();
>> processor->Finalize();
>> processor->Delete();
>>
>> return 0;
>>
>> }
>>
>>
>>
>> On Wed, Aug 4, 2010 at 12:14 PM, Andy Bauer <andy.bauer at kitware.com>wrote:
>>
>>> Hi Jacques,
>>>
>>> There is a polyhedra cell type in VTK now --
>>> http://www.vtk.org/doc/nightly/html/classvtkPolyhedron.html
>>> As far as I know it works with all of the proper filters but since I
>>> haven't tried it yet I won't promise that. The good news is that Will
>>> Schroeder had a high interest in it and probably worked on some of it so I'd
>>> assume that it's working quite well right now.
>>>
>>> As for Phasta, it does run in parallel (as props to their developers it
>>> was a finalist for the 2009 Gordon Bell prize). The grid is already
>>> partitioned and each process runs the adaptor and creates an unstructured
>>> grid from its portion of the partitioned mesh. Thus, there isn't any need
>>> for mpi calls in the adaptor code. If you had ghost cell information in
>>> your partitioned mesh and wanted to get fancy you should be able to add that
>>> to your partitioned grid to make some of the filters faster but I haven't
>>> tried that.
>>>
>>> Andy
>>>
>>>
>>> On Wed, Aug 4, 2010 at 11:58 AM, Jacques Papper <
>>> jacques.papper at gmail.com> wrote:
>>>
>>>> Thanks a lot Andy, Takuya,
>>>>
>>>> I'm using the PhastaAdaptor, and the FortranAdaptorAPI as a guide for
>>>> the moment.
>>>> I know there were talks of getting POLYHEDRAL cell support in VTK. Do
>>>> you know if this is there yet?
>>>> My dataset is multiregion unstructured polyhedral mesh domain decomposed
>>>> amongst each processor.
>>>>
>>>> Is the Phasta code parallelized ? If so, I do not see any MPI statements
>>>> in the adaptor code ?
>>>>
>>>> Jacques
>>>>
>>>> 2010/8/4 Andy Bauer <andy.bauer at kitware.com>
>>>>
>>>> Hi Jacques,
>>>>>
>>>>> What type of data set do you have? Even though the PHASTA adaptor (
>>>>> ParaView/CoProcessing/Adaptors/FortranAdaptors/PhastaAdaptor) is for fortran
>>>>> code it may give you an idea. Also stepping through the example in
>>>>> ParaView/CoProcessing/CoProcessor/Testing/Cxx/PythonScriptCoProcessingExample.cxx
>>>>> may help as well.
>>>>>
>>>>> I'll spend some time this week putting up a skeleton of a simulation
>>>>> code on the coprocessing wiki that should hopefully be easier to follow.
>>>>> I'll let you know when it's done.
>>>>>
>>>>> Andy
>>>>>
>>>>> On Wed, Aug 4, 2010 at 8:02 AM, Jacques Papper <
>>>>> jacques.papper at gmail.com> wrote:
>>>>>
>>>>>> Hi All,
>>>>>>
>>>>>> Sorry for my last post, I figured out that I had wrongly set my
>>>>>> PYTHONPATH..
>>>>>> All the tests work ok now. Still interested in CoProcessing adaptors
>>>>>> examples though :)
>>>>>>
>>>>>> Thanks
>>>>>> Jacques
>>>>>>
>>>>>> 2010/8/4 Jacques Papper <jacques.papper at gmail.com>
>>>>>>
>>>>>>
>>>>>>> Hi All,
>>>>>>>
>>>>>>> I'm starting to look into the ParaView CoProcessing libraries.
>>>>>>> I just pulled from git today, and compiled it all up following the
>>>>>>> guidelines in :
>>>>>>> http://www.paraview.org/Wiki/CoProcessing
>>>>>>> I didn't find :
>>>>>>> *BUILD_PYTHON_COPROCESSING_ADAPTOR
>>>>>>> *but instead :
>>>>>>> PARAVIEW_BUILD_PLUGIN_CoProcessingScriptGenerator
>>>>>>> anyway the compilation went through without any issues.
>>>>>>> I then tried :
>>>>>>>
>>>>>>> ctest -R CoProcessing
>>>>>>> Test project /users/boreas01/jacques/PARAVIEW/ParaView-bin
>>>>>>> Start 491: CoProcessingTestPythonScript
>>>>>>> 1/3 Test #491: CoProcessingTestPythonScript ........... Passed
>>>>>>> 0.45 sec
>>>>>>> Start 492: CoProcessingPythonScriptGridPlot
>>>>>>> 2/3 Test #492: CoProcessingPythonScriptGridPlot .......***Failed
>>>>>>> 0.09 sec
>>>>>>> Start 493: CoProcessingPythonScriptPressurePlot
>>>>>>> 3/3 Test #493: CoProcessingPythonScriptPressurePlot ...***Failed
>>>>>>> 0.09 sec
>>>>>>>
>>>>>>> 33% tests passed, 2 tests failed out of 3
>>>>>>>
>>>>>>> Total Test time (real) = 0.68 sec
>>>>>>>
>>>>>>> The following tests FAILED:
>>>>>>> 492 - CoProcessingPythonScriptGridPlot (Failed)
>>>>>>> 493 - CoProcessingPythonScriptPressurePlot (Failed)
>>>>>>> Errors while running CTest
>>>>>>>
>>>>>>> Is this a problem in my current installation or on the master branch
>>>>>>> ?
>>>>>>>
>>>>>>> Finally, I would like to start writing an adaptor to a C++
>>>>>>> parallelised code. Can you tell me what is the closest code I can inspire
>>>>>>> myself from ?
>>>>>>>
>>>>>>>
>>>>>>> Thank you,
>>>>>>> Jacques
>>>>>>>
>>>>>>>
>>>>>>> PS sorry mixed up the subjects..
>>>>>>>
>>>>>>
>>>>>>
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>>>>>>
>>>>>
>>>>
>>>
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>
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