[Paraview] ParaView5.1.0 fails to read XDMF 3DCoRectMesh
David E DeMarle
dave.demarle at kitware.com
Tue Jul 12 10:11:21 EDT 2016
Can replicate the problem, thanks.
I don't see any suspicious changes in the ThirdParty/xdmf2 or vtkIOXdmf2
directories that might cause this.
Trying with the newer Xdmf3 path now.
Mind filing a bug report?
David E DeMarle
Kitware, Inc.
R&D Engineer
21 Corporate Drive
Clifton Park, NY 12065-8662
Phone: 518-881-4909
On Tue, Jul 12, 2016 at 9:07 AM, Sonja Habbinga <s.habbinga at fz-juelich.de>
wrote:
> Hello,
>
> since Version 5, I have several problems using the xdmf reader.
> Unlike ParaView4.4.0, which is able to read it withou any problems,
> ParaView 5.1.0 and 5.0.1 fail to read the following xdmf file:
> (Please find the complete xdmf file here:
> https://fz-juelich.sciebo.de/index.php/s/f6VicXjvJz64q3l
> and the binary file here:
> https://fz-juelich.sciebo.de/index.php/s/XKcfR9kDKW9Nmct )
>
> Can anyone reproduce the error? Has the xdmf reader changed sice 4.4.0?
>
> thanks for your help,
> Sonja
>
>
> #############################################################################################
> <?xml version="1.0" ?>
> <!DOCTYPE Xdmf SYSTEM "Xdmf.dtd" []>
> <Xdmf xmlns:xi="http://www.w3.org/2001/XInclude" Version="2.0">
> <Domain>
> <Grid Name="timeslice 784" GridType="Uniform">
> <Topology name="T00000" TopologyType="3DCoRectMesh"
> Dimensions=" 1000 400 1">
> </Topology>
> <Geometry name="G00000" Type="ORIGIN_DXDYDZ">
> <!-- Origin [um] -->
> <DataItem Format="XML" Dimensions="3">
> 0.00000000E+00 0.00000000E+00 0.19949875E+02
> </DataItem>
> <!-- DzDyDx [um] -->
> <DataItem Format="XML" Dimensions="3">
> 0.50050050E-01 0.10025063E+00 0.10025063E+00
> </DataItem>
> </Geometry>
> <!-- Time of timeslice [fs] -->
> <Time TimeType="Single" Value=" 0.93397947E+02"/>
>
> <!-- Particle densities per particle species [units] -->
> <Attribute Name="Charge density - electrons" Center="Node">
> <DataItem Format="Binary" Seek=" 0" DataType="Float"
> Precision="4" Endian="Little"
> Dimensions=" 1000 400 1">
> pfield00784
> </DataItem>
> </Attribute>
> <Attribute Name="Charge density - protons" Center="Node">
> <DataItem Format="Binary" Seek=" 1600000" DataType="Float"
> Precision="4" Endian="Little"
> Dimensions=" 1000 400 1">
> pfield00784
> </DataItem>
> </Attribute>
>
> ...
>
> #############################################################################################
> the error message looks like this:
>
> Alloc :: Resource temporarily unavailable
> ERROR: In
>
> /dev/shm/domini/ParaView/5.1.0/ipsmpi-2016a/ParaView-v5.1.0/VTK/IO/Xdmf2/vtkXdmfHeavyData.cxx,
> line 1208
> vtkXdmfReader (0x3c794c0): Failed to read attribute data
>
>
> Alloc :: Resource temporarily unavailable
> ERROR: In
>
> /dev/shm/domini/ParaView/5.1.0/ipsmpi-2016a/ParaView-v5.1.0/VTK/IO/Xdmf2/vtkXdmfHeavyData.cxx,
> line 1208
> vtkXdmfReader (0x3c794c0): Failed to read attribute data
>
>
> Alloc :: Resource temporarily unavailable
> ERROR: In
>
> /dev/shm/domini/ParaView/5.1.0/ipsmpi-2016a/ParaView-v5.1.0/VTK/IO/Xdmf2/vtkXdmfHeavyData.cxx,
> line 1208
> vtkXdmfReader (0x3c794c0): Failed to read attribute data
>
> ....
>
> Alloc :: No such file or directory
> XDMF Error in
>
> /dev/shm/domini/ParaView/5.1.0/ipsmpi-2016a/ParaView-v5.1.0/VTK/ThirdParty/xdmf2/vtkxdmf2/libsrc/XdmfHDF.cxx
> line 551 (Memory Object Array has no data storage)
> XDMF Error in
>
> /dev/shm/domini/ParaView/5.1.0/ipsmpi-2016a/ParaView-v5.1.0/VTK/ThirdParty/xdmf2/vtkxdmf2/libsrc/XdmfHDF.cxx
> line 905 (Can't Read Temp Dataset)
> Alloc :: No such file or directory
> XDMF Error in
>
> /dev/shm/domini/ParaView/5.1.0/ipsmpi-2016a/ParaView-v5.1.0/VTK/ThirdParty/xdmf2/vtkxdmf2/libsrc/XdmfHDF.cxx
> line 551 (Memory Object Array has no data storage)
> XDMF Error in
>
> /dev/shm/domini/ParaView/5.1.0/ipsmpi-2016a/ParaView-v5.1.0/VTK/ThirdParty/xdmf2/vtkxdmf2/libsrc/XdmfHDF.cxx
> line 905 (Can't Read Temp Dataset)
> Alloc :: No such file or directory
> XDMF Error in
>
> /dev/shm/domini/ParaView/5.1.0/ipsmpi-2016a/ParaView-v5.1.0/VTK/ThirdParty/xdmf2/vtkxdmf2/libsrc/XdmfHDF.cxx
> line 551 (Memory Object Array has no data storage)
> XDMF Error in
>
> /dev/shm/domini/ParaView/5.1.0/ipsmpi-2016a/ParaView-v5.1.0/VTK/ThirdParty/xdmf2/vtkxdmf2/libsrc/XdmfHDF.cxx
> line 905 (Can't Read Temp Dataset)
> Alloc :: Success
> XDMF Error in
>
> /dev/shm/domini/ParaView/5.1.0/ipsmpi-2016a/ParaView-v5.1.0/VTK/ThirdParty/xdmf2/vtkxdmf2/libsrc/XdmfHDF.cxx
> line 551 (Memory Object Array has no data storage)
> XDMF Error in
>
> /dev/shm/domini/ParaView/5.1.0/ipsmpi-2016a/ParaView-v5.1.0/VTK/ThirdParty/xdmf2/vtkxdmf2/libsrc/XdmfHDF.cxx
> line 905 (Can't Read Temp Dataset)
> Alloc :: Success
>
> ...
>
> Generic Warning: In
>
> /dev/shm/domini/ParaView/5.1.0/ipsmpi-2016a/ParaView-v5.1.0/VTK/Rendering/Volume/vtkVolumeTextureMapper3D.cxx,
> line 682
> vtkVolumeTextureMapper3D::vtkVolumeTextureMapper3D was deprecated for
> VTK 7.0 and will be removed in a future version.
>
>
> Generic Warning: In
>
> /dev/shm/domini/ParaView/5.1.0/ipsmpi-2016a/ParaView-v5.1.0/VTK/Rendering/VolumeOpenGL/vtkOpenGLVolumeTextureMapper3D.cxx,
> line 57
> vtkOpenGLVolumeTextureMapper3D::vtkOpenGLVolumeTextureMapper3D was
> deprecated for VTK 7.0 and will be removed in a future version.
>
>
> ERROR: In
>
> /dev/shm/domini/ParaView/5.1.0/ipsmpi-2016a/ParaView-v5.1.0/VTK/Common/Core/vtkAOSDataArrayTemplate.txx,
> line 153
> vtkFloatArray (0x5490c60): Source array too small, requested tuple at
> index 0, but there are only 0 tuples in the array.
>
>
> ERROR: In
>
> /dev/shm/domini/ParaView/5.1.0/ipsmpi-2016a/ParaView-v5.1.0/VTK/Common/Core/vtkAOSDataArrayTemplate.txx,
> line 153
> vtkFloatArray (0x5490e60): Source array too small, requested tuple at
> index 0, but there are only 0 tuples in the array.
>
>
> ERROR: In
>
> /dev/shm/domini/ParaView/5.1.0/ipsmpi-2016a/ParaView-v5.1.0/VTK/Common/Core/vtkAOSDataArrayTemplate.txx,
> line 153
> vtkFloatArray (0x5491200): Source array too small, requested tuple at
> index 0, but there are only 0 tuples in the array.
>
>
> ERROR: In
>
> /dev/shm/domini/ParaView/5.1.0/ipsmpi-2016a/ParaView-v5.1.0/VTK/Common/Core/vtkAOSDataArrayTemplate.txx,
> line 153
> vtkFloatArray (0x54915a0): Source array too small, requested tuple at
> index 0, but there are only 0 tuples in the array.
>
>
> ...
>
>
>
>
>
>
>
>
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