[Paraview] CoProcessing
Jacques Papper
jacques.papper at gmail.com
Thu Aug 12 14:38:01 EDT 2010
Hi All,
I am making some more progress on this. Everything was working until I tried
adding field data... I now get an explosion :
#2 ?? in "/lib64/libc.so.6"
#3 vtkDataArrayTemplate<double>::ComputeScalarRange(int) in
"/users/boreas01/jacques/PARAVIEW/ParaView-bin/bin/libvtkCommon.so.pv3.9"
#4 vtkDataArray::ComputeRange(int) in
"/users/boreas01/jacques/PARAVIEW/ParaView-bin/bin/libvtkCommon.so.pv3.9"
#5 vtkPVArrayInformation::CopyFromObject(vtkObject*) in
"/users/boreas01/jacques/PARAVIEW/ParaView-bin/bin/libvtkPVServerCommon.so"
#6
vtkPVDataSetAttributesInformation::CopyFromDataSetAttributes(vtkDataSetAttributes*)
in
"/users/boreas01/jacques/PARAVIEW/ParaView-bin/bin/libvtkPVServerCommon.so"
#7 vtkPVDataInformation::CopyFromDataSet(vtkDataSet*) in
"/users/boreas01/jacques/PARAVIEW/ParaView-bin/bin/libvtkPVServerCommon.so"
#8 vtkPVDataInformation::CopyFromObject(vtkObject*) in
"/users/boreas01/jacques/PARAVIEW/ParaView-bin/bin/libvtkPVServerCommon.so"
#9 vtkPVCompositeDataInformation::CopyFromObject(vtkObject*) in
"/users/boreas01/jacques/PARAVIEW/ParaView-bin/bin/libvtkPVServerCommon.so"
#10 vtkPVDataInformation::CopyFromCompositeDataSet(vtkCompositeDataSet*) in
"/users/boreas01/jacques/PARAVIEW/ParaView-bin/bin/libvtkPVServerCommon.so"
#11 vtkPVDataInformation::CopyFromObject(vtkObject*) in
"/users/boreas01/jacques/PARAVIEW/ParaView-bin/bin/libvtkPVServerCommon.so"
#12 vtkSelfConnection::GatherInformation(unsigned int, vtkPVInformation*,
vtkClientServerID) in
"/users/boreas01/jacques/PARAVIEW/ParaView-bin/bin/libvtkPVServerCommon.so"
#13 vtkSynchronousMPISelfConnection::GatherInformation(unsigned int,
vtkPVInformation*, vtkClientServerID) in
"/users/boreas01/jacques/PARAVIEW/ParaView-bin/bin/libvtkPVServerCommon.so"
#14 vtkSMOutputPort::GatherDataInformation() in
"/users/boreas01/jacques/PARAVIEW/ParaView-bin/bin/libvtkPVServerManager.so"
#15 vtkSMOutputPort::GetDataInformation() in
"/users/boreas01/jacques/PARAVIEW/ParaView-bin/bin/libvtkPVServerManager.so"
#16 vtkSMDataTypeDomain::IsInDomain(vtkSMSourceProxy*, int) in
"/users/boreas01/jacques/PARAVIEW/ParaView-bin/bin/libvtkPVServerManager.so"
#17 vtkSMDataTypeDomain::IsInDomain(vtkSMProperty*) in
"/users/boreas01/jacques/PARAVIEW/ParaView-bin/bin/libvtkPVServerManager.so"
#18 vtkSMProperty::IsInDomains() in
"/users/boreas01/jacques/PARAVIEW/ParaView-bin/bin/libvtkPVServerManager.so"
#19 vtkSMRenderViewProxy::CreateDefaultRepresentation(vtkSMProxy*, int) in
"/users/boreas01/jacques/PARAVIEW/ParaView-bin/bin/libvtkPVServerManager.so"
#20 ?? at vtkSMRenderViewProxyPython.cxx:0
#21 PyEval_EvalFrameEx in "/usr/lib64/libpython2.6.so.1.0"
#22 PyEval_EvalCodeEx in "/usr/lib64/libpython2.6.so.1.0"
#23 PyEval_EvalFrameEx in "/usr/lib64/libpython2.6.so.1.0"
#24 PyEval_EvalCodeEx in "/usr/lib64/libpython2.6.so.1.0"
#25 PyEval_EvalFrameEx in "/usr/lib64/libpython2.6.so.1.0"
#26 PyEval_EvalCodeEx in "/usr/lib64/libpython2.6.so.1.0"
#27 PyEval_EvalFrameEx in "/usr/lib64/libpython2.6.so.1.0"
#28 PyEval_EvalCodeEx in "/usr/lib64/libpython2.6.so.1.0"
#29 PyEval_EvalFrameEx in "/usr/lib64/libpython2.6.so.1.0"
#30 PyEval_EvalFrameEx in "/usr/lib64/libpython2.6.so.1.0"
#31 PyEval_EvalCodeEx in "/usr/lib64/libpython2.6.so.1.0"
#32 PyEval_EvalCode in "/usr/lib64/libpython2.6.so.1.0"
#33 ?? in "/usr/lib64/libpython2.6.so.1.0"
#34 PyRun_StringFlags in "/usr/lib64/libpython2.6.so.1.0"
#35 PyRun_SimpleStringFlags in "/usr/lib64/libpython2.6.so.1.0"
#36 vtkPVPythonInterpretor::RunSimpleString(char const*) in
"/users/boreas01/jacques/PARAVIEW/ParaView-bin/bin/libvtkPVPythonInterpretor.so"
#37 vtkCPPythonScriptPipeline::CoProcess(vtkCPDataDescription*) in
"/users/boreas01/jacques/PARAVIEW/ParaView-bin/bin/libvtkCoProcessor.so"
#38 vtkCPProcessor::CoProcess(vtkCPDataDescription*) in
"/users/boreas01/jacques/PARAVIEW/ParaView-bin/bin/libvtkCoProcessor.so"
Any ideas where this can be coming from ?
When I do not add the field data it just complains about missing fields so I
know that the code is not completely wrong...
I am adding the data to the first block of my multiblockdataset... Is that a
problem ?
Thanks !
Jacques
2010/8/12 Jacques Papper <jacques.papper at gmail.com>
> 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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>>>>
>>>
>>
>
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