[Paraview] CoProcessing with Fortran and ParaView 3.98
Andy Bauer
andy.bauer at kitware.com
Thu Mar 21 16:00:13 EDT 2013
How about trying:
psi01_.UpdatePipeline()
print psi01_.GetDataInformation().DataInformation.GetNumberOfPoints()
right about where the writer was created. This will give print out the
number of points in the data set that you have.
Andy
On Thu, Mar 21, 2013 at 3:47 PM, Pettey . Lucas <LPettey at drc.com> wrote:
> Sorry, Andy, that didn't seem to work either.
>
> Let me know what information would be useful to print.
>
> Thanks
> Lucas
>
> ________________________________
> From: Andy Bauer [andy.bauer at kitware.com]
> Sent: Thursday, March 21, 2013 2:36 PM
> To: Pettey . Lucas
> Cc: paraview [paraview at paraview.org]
> Subject: Re: [Paraview] CoProcessing with Fortran and ParaView 3.98
>
> Hmm, how about trying replacing those two lines with:
> ParallelImageDataWriter1 = CreateCPWriter( XMLPImageDataWriter,
> "fullgrid_%t.pvti", 1, cp_writers )
>
> Let me know how that goes.
>
> If not, I think we'll need to put some print statements in there.
>
> Andy
>
> On Thu, Mar 21, 2013 at 3:31 PM, Pettey . Lucas <LPettey at drc.com<mailto:
> LPettey at drc.com>> wrote:
> Yes I did. I have attached the latest script.
>
> Thank you for your valiant efforts in trying to solve this problem.
>
> Lucas
>
> ________________________________
> From: Andy Bauer [andy.bauer at kitware.com<mailto:andy.bauer at kitware.com>]
> Sent: Thursday, March 21, 2013 2:22 PM
> To: Pettey . Lucas
> Cc: paraview [paraview at paraview.org<mailto:paraview at paraview.org>]
> Subject: Re: [Paraview] CoProcessing with Fortran and ParaView 3.98
>
> Did you also include the w.UpdatePipeline() part after the writer was
> created? It won't create the file unless that's in there.
>
> Andy
>
> On Thu, Mar 21, 2013 at 3:17 PM, Pettey . Lucas <LPettey at drc.com<mailto:
> LPettey at drc.com><mailto:LPettey at drc.com<mailto:LPettey at drc.com>>> wrote:
> Hi Andy,
>
> Changing to Scalars=['POINTS','psi01'] did not change anything. I still
> get the same error and blank image.
>
> I tried adding the XMLPImageDataWriter command, but no file
> 'fullgrid.pvti' was produced so I can't tell what is being populated into
> the grid.
>
> I hardwired the C++ adaptor to 'psi01' rather than the character array
> name in case their was a problem with the way the string was passed. I had
> checked that name contained the correct characters, but I figured
> hardwiring would be safer at this stage.
>
> Anything else that you think I should try?
>
> Thanks,
> Lucas
>
> ________________________________
> From: paraview-bounces at paraview.org<mailto:paraview-bounces at paraview.org
> ><mailto:paraview-bounces at paraview.org<mailto:
> paraview-bounces at paraview.org>> [paraview-bounces at paraview.org<mailto:
> paraview-bounces at paraview.org><mailto:paraview-bounces at paraview.org
> <mailto:paraview-bounces at paraview.org>>] on behalf of Andy Bauer [
> andy.bauer at kitware.com<mailto:andy.bauer at kitware.com><mailto:
> andy.bauer at kitware.com<mailto:andy.bauer at kitware.com>>]
> Sent: Thursday, March 21, 2013 12:49 PM
> To: Pettey . Lucas
> Cc: paraview [paraview at paraview.org<mailto:paraview at paraview.org><mailto:
> paraview at paraview.org<mailto:paraview at paraview.org>>]
> Subject: Re: [Paraview] CoProcessing with Fortran and ParaView 3.98
>
> I think the problem is that:
> Clip1 = Clip( guiName="Clip1", InsideOut=0, Scalars=['POINTS', ''],
> Value=95.0, UseValueAsOffset=0, Crinkleclip=0, ClipType="Scalar" )
>
> Should probably have the name of the point data field set in it. Do this
> with (assuming psi01 is the name of the field you want to clip with respect
> to:
> Scalars=['POINTS', 'psi01']
>
>
> My guess is that the scalar field isn't getting set properly. Try adding
> in:
> w = XMLPImageDataWriter(Input=psi01_, FileName = 'fullgrid.pvti')
> w.UpdatePipeline()
>
> right after the CreateProducer() method to see what's in your grid.
>
> By the way, does adding in the "//char(0)" work for converting Fortran
> strings to C/C++ strings (e.g. in "call addfield(psi,"psi01"//char(0))") ?
> If it does, will it also work for Fortran77? That's a neat little trick!
>
> Andy
>
>
> On Wed, Mar 20, 2013 at 5:29 PM, Pettey . Lucas <LPettey at drc.com<mailto:
> LPettey at drc.com><mailto:LPettey at drc.com<mailto:LPettey at drc.com>><mailto:
> LPettey at drc.com<mailto:LPettey at drc.com><mailto:LPettey at drc.com<mailto:
> LPettey at drc.com>>>> wrote:
> I have solved the C++ to Fortran array issues, but I am still not getting
> a meaningful visualization. I have attached the latest files, including a
> screenshot of the exported state and the resulting image that is produced
> by the coprocessor.
>
> The coprocessor is generating an error:
>
> ERROR: In
> /Users/lucaspettey/ParaView-git/ParaView/VTK/Filters/General/vtkTableBasedClipDataSet.cxx,
> line 1956
> vtkPVClipDataSet (0x7feaa4998550): no input scalars.
>
> This error is not appearing at the time=0 co-process, but it is appearing
> each time step the co-processor is being asked to write an image. All of
> the images are the same blank axes as in the attached image0.png.
>
> I'm not sure what to try next so any help is appreciated.
>
> Thanks,
> Lucas
>
> ________________________________________
> From: paraview-bounces at paraview.org<mailto:paraview-bounces at paraview.org
> ><mailto:paraview-bounces at paraview.org<mailto:
> paraview-bounces at paraview.org>><mailto:paraview-bounces at paraview.org
> <mailto:paraview-bounces at paraview.org><mailto:
> paraview-bounces at paraview.org<mailto:paraview-bounces at paraview.org>>> [
> paraview-bounces at paraview.org<mailto:paraview-bounces at paraview.org
> ><mailto:paraview-bounces at paraview.org<mailto:
> paraview-bounces at paraview.org>><mailto:paraview-bounces at paraview.org
> <mailto:paraview-bounces at paraview.org><mailto:
> paraview-bounces at paraview.org<mailto:paraview-bounces at paraview.org>>>] on
> behalf of Pettey . Lucas [LPettey at drc.com<mailto:LPettey at drc.com><mailto:
> LPettey at drc.com<mailto:LPettey at drc.com>><mailto:LPettey at drc.com<mailto:
> LPettey at drc.com><mailto:LPettey at drc.com<mailto:LPettey at drc.com>>>]
> Sent: Wednesday, March 20, 2013 11:45 AM
> To: Andy Bauer
> Cc: paraview [paraview at paraview.org<mailto:paraview at paraview.org><mailto:
> paraview at paraview.org<mailto:paraview at paraview.org>><mailto:
> paraview at paraview.org<mailto:paraview at paraview.org><mailto:
> paraview at paraview.org<mailto:paraview at paraview.org>>>]
> Subject: Re: [Paraview] CoProcessing with Fortran and ParaView 3.98
>
> So after some troubleshooting it seems that C++ doesn't like the complex
> data type the way Fortran is sending it.
>
> The code runs when I just send a real value. Images appear, but of course
> they are meaningless since it isn't the correct data. I may try passing the
> real and imaginary separate. I may also look into row/column order issues
> although this grid is 100x100x100 so it shouldn't affect anything.
>
> Lucas
> ________________________________________
> From: paraview-bounces at paraview.org<mailto:paraview-bounces at paraview.org
> ><mailto:paraview-bounces at paraview.org<mailto:
> paraview-bounces at paraview.org>><mailto:paraview-bounces at paraview.org
> <mailto:paraview-bounces at paraview.org><mailto:
> paraview-bounces at paraview.org<mailto:paraview-bounces at paraview.org>>> [
> paraview-bounces at paraview.org<mailto:paraview-bounces at paraview.org
> ><mailto:paraview-bounces at paraview.org<mailto:
> paraview-bounces at paraview.org>><mailto:paraview-bounces at paraview.org
> <mailto:paraview-bounces at paraview.org><mailto:
> paraview-bounces at paraview.org<mailto:paraview-bounces at paraview.org>>>] on
> behalf of Pettey . Lucas [LPettey at drc.com<mailto:LPettey at drc.com><mailto:
> LPettey at drc.com<mailto:LPettey at drc.com>><mailto:LPettey at drc.com<mailto:
> LPettey at drc.com><mailto:LPettey at drc.com<mailto:LPettey at drc.com>>>]
> Sent: Wednesday, March 20, 2013 11:12 AM
> To: Andy Bauer
> Cc: paraview [paraview at paraview.org<mailto:paraview at paraview.org><mailto:
> paraview at paraview.org<mailto:paraview at paraview.org>><mailto:
> paraview at paraview.org<mailto:paraview at paraview.org><mailto:
> paraview at paraview.org<mailto:paraview at paraview.org>>>]
> Subject: Re: [Paraview] CoProcessing with Fortran and ParaView 3.98
>
> Hi Andy and Berk,
>
> Here is the error that I am receiving.
>
> I know that it is initializing ok and failing at the first call to the
> co-processor. I have attached my python script output as well as my test
> code and adaptors.
>
> CoProcessingExample(19247,0x7fff77470180) malloc: ***
> mmap(size=3739605888335872) failed (error code=12)
> *** error: can't allocate region
> *** set a breakpoint in malloc_error_break to debug
> Operating system error: Cannot allocate memory
> Memory allocation failed
>
> Thanks for the help,
> Lucas
>
> From: Andy Bauer [andy.bauer at kitware.com<mailto:andy.bauer at kitware.com
> ><mailto:andy.bauer at kitware.com<mailto:andy.bauer at kitware.com>><mailto:
> andy.bauer at kitware.com<mailto:andy.bauer at kitware.com><mailto:
> andy.bauer at kitware.com<mailto:andy.bauer at kitware.com>>>]
> Sent: Wednesday, March 20, 2013 9:08 AM
> To: Pettey . Lucas
> Cc: Berk Geveci; paraview [paraview at paraview.org<mailto:
> paraview at paraview.org><mailto:paraview at paraview.org<mailto:
> paraview at paraview.org>><mailto:paraview at paraview.org<mailto:
> paraview at paraview.org><mailto:paraview at paraview.org<mailto:
> paraview at paraview.org>>>]
> Subject: Re: [Paraview] CoProcessing with Fortran and ParaView 3.98
>
> Hi Lucas,
>
> Can you share your co-processing script and any run output? There may be
> warnings in the output or info in the script that will help figure that out.
>
> Thanks,
> Andy
>
> On Wed, Mar 20, 2013 at 10:04 AM, Pettey . Lucas <LPettey at drc.com<mailto:
> LPettey at drc.com><mailto:LPettey at drc.com<mailto:LPettey at drc.com>><mailto:
> LPettey at drc.com<mailto:LPettey at drc.com><mailto:LPettey at drc.com<mailto:
> LPettey at drc.com>>><mailto:LPettey at drc.com<mailto:LPettey at drc.com><mailto:
> LPettey at drc.com<mailto:LPettey at drc.com>><mailto:LPettey at drc.com<mailto:
> LPettey at drc.com><mailto:LPettey at drc.com<mailto:LPettey at drc.com>>>>> wrote:
> Hi Berk,
>
> Thanks for the help.
>
> I found that this example is written based on an earlier version of VTK so
> some of the function calls have changed. Based on your advice and some of
> the examples contained in the ParaView wiki, I have gotten it to compile
> and run.
>
> Now I just have to figure out why it isn't generating any VTK objects....
>
> Probably something wrong with my python co-processing script.
>
> Thanks
> Lucas
> ________________________________
> From: Berk Geveci [berk.geveci at kitware.com<mailto:berk.geveci at kitware.com
> ><mailto:berk.geveci at kitware.com<mailto:berk.geveci at kitware.com>><mailto:
> berk.geveci at kitware.com<mailto:berk.geveci at kitware.com><mailto:
> berk.geveci at kitware.com<mailto:berk.geveci at kitware.com>>><mailto:
> berk.geveci at kitware.com<mailto:berk.geveci at kitware.com><mailto:
> berk.geveci at kitware.com<mailto:berk.geveci at kitware.com>><mailto:
> berk.geveci at kitware.com<mailto:berk.geveci at kitware.com><mailto:
> berk.geveci at kitware.com<mailto:berk.geveci at kitware.com>>>>]
> Sent: Tuesday, March 19, 2013 6:48 PM
> To: Pettey . Lucas
> Cc: paraview [paraview at paraview.org<mailto:paraview at paraview.org><mailto:
> paraview at paraview.org<mailto:paraview at paraview.org>><mailto:
> paraview at paraview.org<mailto:paraview at paraview.org><mailto:
> paraview at paraview.org<mailto:paraview at paraview.org>>><mailto:
> paraview at paraview.org<mailto:paraview at paraview.org><mailto:
> paraview at paraview.org<mailto:paraview at paraview.org>><mailto:
> paraview at paraview.org<mailto:paraview at paraview.org><mailto:
> paraview at paraview.org<mailto:paraview at paraview.org>>>>]
> Subject: Re: [Paraview] CoProcessing with Fortran and ParaView 3.98
>
> You can simply delete this line:
>
> Grid->SetNumberOfScalarComponents(2);
>
> It is redundant given the following later:
>
> field->SetNumberOfComponents(2);
>
> You also need to #include <vtkSmartPointer.h>.
>
> Best,
> -berk
>
>
>
> On Tue, Mar 19, 2013 at 2:31 PM, Pettey . Lucas <LPettey at drc.com<mailto:
> LPettey at drc.com><mailto:LPettey at drc.com<mailto:LPettey at drc.com>><mailto:
> LPettey at drc.com<mailto:LPettey at drc.com><mailto:LPettey at drc.com<mailto:
> LPettey at drc.com>>><mailto:LPettey at drc.com<mailto:LPettey at drc.com><mailto:
> LPettey at drc.com<mailto:LPettey at drc.com>><mailto:LPettey at drc.com<mailto:
> LPettey at drc.com><mailto:LPettey at drc.com<mailto:LPettey at drc.com>>>><mailto:
> LPettey at drc.com<mailto:LPettey at drc.com><mailto:LPettey at drc.com<mailto:
> LPettey at drc.com>><mailto:LPettey at drc.com<mailto:LPettey at drc.com><mailto:
> LPettey at drc.com<mailto:LPettey at drc.com>>><mailto:LPettey at drc.com<mailto:
> LPettey at drc.com><mailto:LPettey at drc.com<mailto:LPettey at drc.com>><mailto:
> LPettey at drc.com<mailto:LPettey at drc.com><mailto:LPettey at drc.com<mailto:
> LPettey at drc.com>>>>>> wrote:
> Hello everyone,
>
> I am trying to run a simple Fortran coprocessing example with a complex
> data type. I am following the example here:
>
>
> http://en.wikibooks.org/wiki/Parallel_Spectral_Numerical_Methods/Visualization_with_ParaView_CoProcessing#ParaView_CoProcessing_Resources
>
> I have written a basic Fortran code that outputs the data in binary,
> opened that in ParaView, output the coprocessing script and then written
> the adaptor following the example in the above link. My adaptor looks like:
>
> extern "C" void createcpimagedata_(int* nx, int* ny, int* nz)
> {
> if (!ParaViewCoProcessing::GetCoProcessorData()) {
> vtkGenericWarningMacro("Unable to access CoProcessorData.");
> return;
> }
>
> // The simulation grid is a 2-dimensional topologically and geometrically
> // regular grid. In VTK/ParaView, this is considered an image data set.
> vtkImageData* Grid = vtkImageData::New();
>
> // assuming dimZ == 1 for now
> Grid->SetDimensions(*nx, *ny, *nz);
> Grid->SetNumberOfScalarComponents(2);
>
> // Setting the Origin and Spacing are also options.
>
> // Name should be consistent between here, Fortran and Python client
> script.
>
> ParaViewCoProcessing::GetCoProcessorData()->GetInputDescriptionByName("input")->SetGrid(Grid);
> }
>
> // Add field(s) to the data container.
> // Separate from above because this will be dynamic, grid is static.
> // Might be an issue, VTK probably assumes row major, but
> // omeg probably passed column major...
> // by hand name mangling for fortran
> extern "C" void addfield_(double* scalars, char* name)
> {
> vtkCPInputDataDescription *idd =
> ParaViewCoProcessing::GetCoProcessorData()->GetInputDescriptionByName("input");
>
> vtkImageData* Image = vtkImageData::SafeDownCast(idd->GetGrid());
>
> if (!Image) {
> vtkGenericWarningMacro("No adaptor grid to attach field data to.");
> return;
> }
>
>
> // field name must match that in the fortran code.
> if (idd->IsFieldNeeded(name)) {
> vtkSmartPointer<vtkDoubleArray> field =
> vtkSmartPointer<vtkDoubleArray>::New();
> field->SetNumberOfComponents(2);
> field->SetName(name);
> field->SetArray(scalars, 2* Image->GetNumberOfPoints(), 1);
> Image->GetPointData()->AddArray(field);
>
> }
> }
>
> I am getting some errors from the Makefile generated by Cmake:
>
> /Users/lucaspettey/codes/BEC/coprocVTK.cxx:40:38: error: too few arguments
> to function call, expected 2, have 1
> Grid->SetNumberOfScalarComponents(2);
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^
> /Users/lucaspettey/ParaView-git/ParaView/VTK/Common/DataModel/vtkImageData.h:298:3:
> note: 'SetNumberOfScalarComponents' declared here
> static void SetNumberOfScalarComponents( int n, vtkInformation*
> meta_data);
> ^
> /Users/lucaspettey/codes/BEC/coprocVTK.cxx:67:5: error: unknown type name
> 'vtkSmartPointer'; did you mean 'vtkSmartPointerBase'?
> vtkSmartPointer<vtkDoubleArray> field =
> vtkSmartPointer<vtkDoubleArray>::New();
> ^~~~~~~~~~~~~~~
> vtkSmartPointerBase
> /Users/lucaspettey/ParaView-git/ParaView/VTK/Common/Core/vtkOStreamWrapper.h:36:7:
> note: 'vtkSmartPointerBase' declared here
> class vtkSmartPointerBase;
> ^
> /Users/lucaspettey/codes/BEC/coprocVTK.cxx:67:20: error: expected
> unqualified-id
> vtkSmartPointer<vtkDoubleArray> field =
> vtkSmartPointer<vtkDoubleArray>::New();
> ^
> /Users/lucaspettey/codes/BEC/coprocVTK.cxx:68:5: error: use of undeclared
> identifier 'field'
> field->SetNumberOfComponents(2);
> ^
> /Users/lucaspettey/codes/BEC/coprocVTK.cxx:69:5: error: use of undeclared
> identifier 'field'
> field->SetName(name);
> ^
> /Users/lucaspettey/codes/BEC/coprocVTK.cxx:70:5: error: use of undeclared
> identifier 'field'
> field->SetArray(scalars, 2* Image->GetNumberOfPoints(), 1);
> ^
> /Users/lucaspettey/codes/BEC/coprocVTK.cxx:71:37: error: use of undeclared
> identifier 'field'
> Image->GetPointData()->AddArray(field);
> ^
>
> Any help is appreciated.
>
> Thanks,
> Lucas
>
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