Error in read hdf5 1.10


(Duo Li) #1

Hi,

I run into the following error when loading hdf5 1.10:

HDF5-DIAG: Error detected in HDF5 (1.8.13) thread 0:
#000: /Users/kitware/dashboards/buildbot-slave/8275bd07/build/superbuild/hdf5/src/src/H5F.c line 1594 in H5Fopen(): unable to open file
major: File accessibilty
minor: Unable to open file
#001: /Users/kitware/dashboards/buildbot-slave/8275bd07/build/superbuild/hdf5/src/src/H5F.c line 1385 in H5F_open(): unable to read superblock
major: File accessibilty
minor: Read failed
#002: /Users/kitware/dashboards/buildbot-slave/8275bd07/build/superbuild/hdf5/src/src/H5Fsuper.c line 353 in H5F_super_read(): unable to load superblock
major: Object cache
minor: Unable to protect metadata
#003: /Users/kitware/dashboards/buildbot-slave/8275bd07/build/superbuild/hdf5/src/src/H5AC.c line 1323 in H5AC_protect(): H5C_protect() failed.
major: Object cache
minor: Unable to protect metadata
#004: /Users/kitware/dashboards/buildbot-slave/8275bd07/build/superbuild/hdf5/src/src/H5C.c line 3574 in H5C_protect(): can’t load entry
major: Object cache
minor: Unable to load metadata into cache
#005: /Users/kitware/dashboards/buildbot-slave/8275bd07/build/superbuild/hdf5/src/src/H5C.c line 7954 in H5C_load_entry(): unable to load entry
major: Object cache
minor: Unable to load metadata into cache
#006: /Users/kitware/dashboards/buildbot-slave/8275bd07/build/superbuild/hdf5/src/src/H5Fsuper_cache.c line 169 in H5F_sblock_load(): bad superblock version number
major: File accessibilty
minor: Bad value
XDMF Error in /Users/kitware/dashboards/buildbot-slave/8275bd07/build/superbuild/paraview/src/VTK/ThirdParty/xdmf2/vtkxdmf2/libsrc/XdmfHDF.cxx line 817 (Cannot open data-surface_cell.h5 / /Users/duoli/Documents/SeisSol/Cascadia/UMich1//data-surface_cell.h5)
XDMF Error in /Users/kitware/dashboards/buildbot-slave/8275bd07/build/superbuild/paraview/src/VTK/ThirdParty/xdmf2/vtkxdmf2/libsrc/XdmfValuesHDF.cxx line 76 (Can’t Open Dataset data-surface_cell.h5:/mesh0/connect)
XDMF Error in /Users/kitware/dashboards/buildbot-slave/8275bd07/build/superbuild/paraview/src/VTK/ThirdParty/xdmf2/vtkxdmf2/libsrc/XdmfDataItem.cxx line 534 (Reading Values Failed)
XDMF Error in /Users/kitware/dashboards/buildbot-slave/8275bd07/build/superbuild/paraview/src/VTK/ThirdParty/xdmf2/vtkxdmf2/libsrc/XdmfGrid.cxx line 755 (Error in Update() of Topology)
ERROR: In /Users/kitware/dashboards/buildbot-slave/8275bd07/build/superbuild/paraview/src/VTK/IO/Xdmf2/vtkXdmfReader.cxx, line 421
vtkXdmfReader (0x7f93a36abea0): Failed to read data.

ERROR: In /Users/kitware/dashboards/buildbot-slave/8275bd07/build/superbuild/paraview/src/VTK/Common/ExecutionModel/vtkExecutive.cxx, line 782
vtkPVCompositeDataPipeline (0x7f93a26be440): Algorithm vtkFileSeriesReader(0x7f93a36ae670) returned failure for request: vtkInformation (0x7f93a3544fc0)
Debug: Off
Modified Time: 618690
Reference Count: 1
Registered Events: (none)
Request: REQUEST_DATA
FROM_OUTPUT_PORT: 0
ALGORITHM_AFTER_FORWARD: 1
FORWARD_DIRECTION: 0

I reall appreciate for a solution, Thanks!

Best,
Eliza


(Ben Boeckel) #2

Where are you getting HDF 1.10? How is it being loaded? The output you’ve pasted mentions 1.8.13.


(Duo Li) #3

The hdf5 is written by 1.10. When I open it in Paraview 5.6, it gave me this error.


(Ben Boeckel) #4

Cc: @Dave_DeMarle since it looks like an xdmf2 bug.