[Paraview] CoProcessing
Jacques Papper
jacques.papper at gmail.com
Thu Aug 12 06:19:27 EDT 2010
Hi Andy, Pat,
I have the skeleton of the coprocessing working (for the moment I just tried
by populating the point field - no cells, no data).
I am trying to figure out the most efficient way of transferring my data
structure to VTK with minimal copying and looping...
I would like to use the vtkUnstructuredGrid::SetCells() method, which means
I probably need to use the vtkCellArray::SetCells() method, and therefore
the vtkIdType::SetArray() method...
The problem is I am not sure what the format of the array should be ?
I am dealing with unstructured polyhedra cells (most of which are known
types like hex prism etc..).
Of course, I could also use the InsertNextCell() methods, but I was
wondering if there wasn't a more efficient way...
Best,
Jacques
2010/8/9 Andy Bauer <andy.bauer at kitware.com>
> 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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>>>> Visit other Kitware open-source projects at
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>>>
>>
>
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