I’m having issues reading an XDMF structured grid in parallel. This issues seems similar to LINK1 and LINK2. Here I’m uploading the .xmf header and .h5 dataset.
singlerotorfdom.396.h5 (3.6 MB)
singlerotorfdom.396.xmf (814 Bytes)
Launching the server (headless machine) with only two threads:
PVPATH=/path/to/ParaView-5.10.0-RC1-egl-MPI-Linux-Python3.9-x86_64/bin/
$PVPATH/mpiexec -np 2 $PVPATH/pvserver --server-port=11111
Connecting the client:
PVPATH=/path/to/ParaView-5.10.0-RC1-MPI-Linux-Python3.9-x86_64/bin/
$PVPATH/paraview --server-url=cs://m9g-2-16.rc.byu.edu:11111
Opening the .xmf file and selecting XDMF Reader I get the following error in Output Messages:
ERROR: In /builds/gitlab-kitware-sciviz-ci/build/superbuild/paraview/src/VTK/IO/Xdmf2/vtkXdmfHeavyData.cxx, line 1212
vtkXdmfReader (0x1818a8e0): Failed to read attribute data
ERROR: In /builds/gitlab-kitware-sciviz-ci/build/superbuild/paraview/src/VTK/IO/Xdmf2/vtkXdmfHeavyData.cxx, line 1212
vtkXdmfReader (0x1818a8e0): Failed to read attribute data
And the following error is printed in the terminal running pvserver:
XDMF Error in /builds/gitlab-kitware-sciviz-ci/build/superbuild/paraview/src/VTK/ThirdParty/xdmf2/vtkxdmf2/libsrc/XdmfHDF.cxx line 558 (Source and Target Spaces specify different sizes)
XDMF Error in /builds/gitlab-kitware-sciviz-ci/build/superbuild/paraview/src/VTK/ThirdParty/xdmf2/vtkxdmf2/libsrc/XdmfHDF.cxx line 559 (Source = 729 items)
XDMF Error in /builds/gitlab-kitware-sciviz-ci/build/superbuild/paraview/src/VTK/ThirdParty/xdmf2/vtkxdmf2/libsrc/XdmfHDF.cxx line 560 (Target = 124659 items)
XDMF Error in /builds/gitlab-kitware-sciviz-ci/build/superbuild/paraview/src/VTK/ThirdParty/xdmf2/vtkxdmf2/libsrc/XdmfValuesHDF.cxx line 112 (Can’t Read Dataset singlerotorfdom.395.h5:U)
XDMF Error in /builds/gitlab-kitware-sciviz-ci/build/superbuild/paraview/src/VTK/ThirdParty/xdmf2/vtkxdmf2/libsrc/XdmfDataItem.cxx line 534 (Reading Values Failed)
( 123.036s) [pvserver.0 ] vtkXdmfHeavyData.cxx:1212 ERR| vtkXdmfReader (0x1818a8e0): Failed to read attribute data
XDMF Error in /builds/gitlab-kitware-sciviz-ci/build/superbuild/paraview/src/VTK/ThirdParty/xdmf2/vtkxdmf2/libsrc/XdmfHDF.cxx line 558 (Source and Target Spaces specify different sizes)
XDMF Error in /builds/gitlab-kitware-sciviz-ci/build/superbuild/paraview/src/VTK/ThirdParty/xdmf2/vtkxdmf2/libsrc/XdmfHDF.cxx line 559 (Source = 729 items)
XDMF Error in /builds/gitlab-kitware-sciviz-ci/build/superbuild/paraview/src/VTK/ThirdParty/xdmf2/vtkxdmf2/libsrc/XdmfHDF.cxx line 560 (Target = 124659 items)
XDMF Error in /builds/gitlab-kitware-sciviz-ci/build/superbuild/paraview/src/VTK/ThirdParty/xdmf2/vtkxdmf2/libsrc/XdmfValuesHDF.cxx line 112 (Can’t Read Dataset singlerotorfdom.395.h5:W)
XDMF Error in /builds/gitlab-kitware-sciviz-ci/build/superbuild/paraview/src/VTK/ThirdParty/xdmf2/vtkxdmf2/libsrc/XdmfDataItem.cxx line 534 (Reading Values Failed)
( 123.037s) [pvserver.0 ] vtkXdmfHeavyData.cxx:1212 ERR| vtkXdmfReader (0x1818a8e0): Failed to read attribute data
XDMF Error in /builds/gitlab-kitware-sciviz-ci/build/superbuild/paraview/src/VTK/ThirdParty/xdmf2/vtkxdmf2/libsrc/XdmfHDF.cxx line 558 (Source and Target Spaces specify different sizes)
XDMF Error in /builds/gitlab-kitware-sciviz-ci/build/superbuild/paraview/src/VTK/ThirdParty/xdmf2/vtkxdmf2/libsrc/XdmfHDF.cxx line 559 (Source = 729 items)
XDMF Error in /builds/gitlab-kitware-sciviz-ci/build/superbuild/paraview/src/VTK/ThirdParty/xdmf2/vtkxdmf2/libsrc/XdmfHDF.cxx line 560 (Target = 126846 items)
XDMF Error in /builds/gitlab-kitware-sciviz-ci/build/superbuild/paraview/src/VTK/ThirdParty/xdmf2/vtkxdmf2/libsrc/XdmfValuesHDF.cxx line 112 (Can’t Read Dataset singlerotorfdom.395.h5:U)
XDMF Error in /builds/gitlab-kitware-sciviz-ci/build/superbuild/paraview/src/VTK/ThirdParty/xdmf2/vtkxdmf2/libsrc/XdmfDataItem.cxx line 534 (Reading Values Failed)
( 123.041s) [pvserver.1 ] vtkXdmfHeavyData.cxx:1212 ERR| vtkXdmfReader (0x14b4eff0): Failed to read attribute data
XDMF Error in /builds/gitlab-kitware-sciviz-ci/build/superbuild/paraview/src/VTK/ThirdParty/xdmf2/vtkxdmf2/libsrc/XdmfHDF.cxx line 558 (Source and Target Spaces specify different sizes)
XDMF Error in /builds/gitlab-kitware-sciviz-ci/build/superbuild/paraview/src/VTK/ThirdParty/xdmf2/vtkxdmf2/libsrc/XdmfHDF.cxx line 559 (Source = 729 items)
XDMF Error in /builds/gitlab-kitware-sciviz-ci/build/superbuild/paraview/src/VTK/ThirdParty/xdmf2/vtkxdmf2/libsrc/XdmfHDF.cxx line 560 (Target = 126846 items)
XDMF Error in /builds/gitlab-kitware-sciviz-ci/build/superbuild/paraview/src/VTK/ThirdParty/xdmf2/vtkxdmf2/libsrc/XdmfValuesHDF.cxx line 112 (Can’t Read Dataset singlerotorfdom.395.h5:W)
XDMF Error in /builds/gitlab-kitware-sciviz-ci/build/superbuild/paraview/src/VTK/ThirdParty/xdmf2/vtkxdmf2/libsrc/XdmfDataItem.cxx line 534 (Reading Values Failed)
( 123.042s) [pvserver.1 ] vtkXdmfHeavyData.cxx:1212 ERR| vtkXdmfReader (0x14b4eff0): Failed to read attribute data
Since the error indicates a different size between target and source, it seems to me that the error stems from the parallelization splitting the geometry into two chunks but then trying to read the entire field for each process. Running the same workflow with mpiexec -np 1 (meaning, not parallelized) reads the XDMF without any issues.
ENVIRONMENT
- Hardware: The same error was reproduced in both the BYU FSL supercomputer (Red Hat 7.9) and my laptop (Ubuntu 16.04.6 LTS).
- Paraview version: 5.10.0 binaries downloaded from paraview.org/download