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HDF5 errors with evaluate_model on NG #38

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Thomas-Ulrich opened this issue Oct 19, 2022 · 4 comments
Closed

HDF5 errors with evaluate_model on NG #38

Thomas-Ulrich opened this issue Oct 19, 2022 · 4 comments
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@sebwolf-de

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@Thomas-Ulrich
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Lots of An HDF5 error occurred when running and then when reading the output file

XDMF Error in /builds/gitlab-kitware-sciviz-ci/build/superbuild/paraview/src/VTK/ThirdParty/xdmf2/vtkxdmf2/libsrc/XdmfValuesHDF.cxx line 76 (Can't Open Dataset ./test.h5:/group)
XDMF Error in /builds/gitlab-kitware-sciviz-ci/build/superbuild/paraview/src/VTK/ThirdParty/xdmf2/vtkxdmf2/libsrc/XdmfDataItem.cxx line 534 (Reading Values Failed)
(   8.518s) [paraview        ]   vtkXdmfHeavyData.cxx:1212   ERR| vtkXdmfReader (0x17549fe0): Failed to read attribute data

di73yeq4@login01:/hppfs/work/pr45fi/di73yeq4/Meshing> module list
Currently Loaded Modulefiles:
 1) admin/1.0     3) lrz/1.0        5) intel-oneapi-compilers/2021.4.0   7) intel-mpi/2019-intel   9) cmake/3.21.4            11) numactl/2.0.14-intel21  13) yaml-cpp/0.7.0-intel21                
 2) tempdir/1.0   4) spack/22.2.1   6) intel-mkl/2020                    8) gcc/11.2.0            10) python/3.8.11-extended  12) libszip/2.1.1           14) seissol-env/develop-intel21-impi-x2b  
di73yeq4@login01:/hppfs/work/pr45fi/di73yeq4/Meshing> cd evaluate_material/
di73yeq4@login01:/hppfs/work/pr45fi/di73yeq4/Meshing/evaluate_material/build> cmake ..
-- The C compiler identification is Intel 2021.4.0.20210910
-- The CXX compiler identification is Intel 2021.4.0.20210910
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /dss/lrzsys/sys/spack/release/22.2.1/opt/x86_64/intel-mpi/2019.12.320-gcc-wx7cjlg/compilers_and_libraries_2020.4.320/linux/mpi/intel64/bin/mpiicc - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /dss/lrzsys/sys/spack/release/22.2.1/opt/x86_64/intel-mpi/2019.12.320-gcc-wx7cjlg/compilers_and_libraries_2020.4.320/linux/mpi/intel64/bin/mpiicpc - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Found MPI_C: /dss/lrzsys/sys/spack/release/22.2.1/opt/x86_64/intel-mpi/2019.12.320-gcc-wx7cjlg/compilers_and_libraries_2020.4.320/linux/mpi/intel64/bin/mpiicc (found version "3.1") 
-- Found MPI_CXX: /dss/lrzsys/sys/spack/release/22.2.1/opt/x86_64/intel-mpi/2019.12.320-gcc-wx7cjlg/compilers_and_libraries_2020.4.320/linux/mpi/intel64/bin/mpiicpc (found version "3.1") 
-- Found MPI: TRUE (found version "3.1")  
-- Found HDF5: hdf5-shared (found version "1.10.7") found components: C HL 
-- Found OpenMP_C: -qopenmp (found version "5.0") 
-- Found OpenMP_CXX: -qopenmp (found version "5.0") 
-- Found OpenMP: TRUE (found version "5.0")  
-- Found PkgConfig: /usr/bin/pkg-config (found version "0.29.2") 
-- Checking for module 'asagi'
--   Found asagi, version 1.0
-- Checking for module 'netcdf'
--   Found netcdf, version 4.7.4
-- Configuring done
-- Generating done
-- Build files have been written to: /hppfs/work/pr45fi/di73yeq4/Meshing/evaluate_material/build
di73yeq4@login01:/hppfs/work/pr45fi/di73yeq4/Meshing/evaluate_material/build> make -j 
[ 20%] Building CXX object CMakeFiles/evaluate_easi.dir/src/mesh.cpp.o
[ 40%] Building CXX object CMakeFiles/evaluate_easi.dir/src/main.cpp.o
[ 60%] Building CXX object CMakeFiles/evaluate_easi.dir/src/parameterDB.cpp.o
[ 80%] Building CXX object CMakeFiles/evaluate_easi.dir/src/writer.cpp.o
[100%] Linking CXX executable evaluate_easi
[100%] Built target evaluate_easi
di73yeq4@login01:/hppfs/work/pr45fi/di73yeq4/Meshing/evaluate_material/build> cd /hppfs/work/pr45fi/di73yeq4/Training/sulawesi
di73yeq4@login01:/hppfs/work/pr45fi/di73yeq4/Training/sulawesi> /hppfs/work/pr45fi/di73yeq4/Meshing/evaluate_material/build/evaluate_easi -m Sulawesi_65dip_straightBay_ShortNorth_micro -e Sulawesi_material3dLSW.yaml -o ./test
Wed Oct 19 13:54:54, Info:  Read "Sulawesi_65dip_straightBay_ShortNorth_micro" . 
Wed Oct 19 13:54:54, Info:  Found 214690 cells 
Wed Oct 19 13:54:54, Info:  Found 47841 vertices 
Wed Oct 19 13:54:54, Info:  Done 
Wed Oct 19 13:54:54, Info:  Evaluate material from "Sulawesi_material3dLSW.yaml" on the mesh. 
Wed Oct 19 13:54:54, Info:  Done 
Wed Oct 19 13:54:54, Info:  Write result to  "./test" . 
An HDF5 error occurred (/hppfs/work/pr45fi/di73yeq4/Meshing/evaluate_material/src/writer.cpp: 6)
An HDF5 error occurred (/hppfs/work/pr45fi/di73yeq4/Meshing/evaluate_material/src/writer.cpp: 20)
An HDF5 error occurred (/hppfs/work/pr45fi/di73yeq4/Meshing/evaluate_material/src/writer.cpp: 23)
An HDF5 error occurred (/hppfs/work/pr45fi/di73yeq4/Meshing/evaluate_material/src/writer.cpp: 26)
An HDF5 error occurred (/hppfs/work/pr45fi/di73yeq4/Meshing/evaluate_material/src/writer.cpp: 37)
An HDF5 error occurred (/hppfs/work/pr45fi/di73yeq4/Meshing/evaluate_material/src/writer.cpp: 6)
An HDF5 error occurred (/hppfs/work/pr45fi/di73yeq4/Meshing/evaluate_material/src/writer.cpp: 20)
An HDF5 error occurred (/hppfs/work/pr45fi/di73yeq4/Meshing/evaluate_material/src/writer.cpp: 23)
An HDF5 error occurred (/hppfs/work/pr45fi/di73yeq4/Meshing/evaluate_material/src/writer.cpp: 26)
An HDF5 error occurred (/hppfs/work/pr45fi/di73yeq4/Meshing/evaluate_material/src/writer.cpp: 40)
An HDF5 error occurred (/hppfs/work/pr45fi/di73yeq4/Meshing/evaluate_material/src/writer.cpp: 6)
An HDF5 error occurred (/hppfs/work/pr45fi/di73yeq4/Meshing/evaluate_material/src/writer.cpp: 20)
An HDF5 error occurred (/hppfs/work/pr45fi/di73yeq4/Meshing/evaluate_material/src/writer.cpp: 23)
An HDF5 error occurred (/hppfs/work/pr45fi/di73yeq4/Meshing/evaluate_material/src/writer.cpp: 26)
An HDF5 error occurred (/hppfs/work/pr45fi/di73yeq4/Meshing/evaluate_material/src/writer.cpp: 40)
An HDF5 error occurred (/hppfs/work/pr45fi/di73yeq4/Meshing/evaluate_material/src/writer.cpp: 6)
An HDF5 error occurred (/hppfs/work/pr45fi/di73yeq4/Meshing/evaluate_material/src/writer.cpp: 20)
An HDF5 error occurred (/hppfs/work/pr45fi/di73yeq4/Meshing/evaluate_material/src/writer.cpp: 23)
An HDF5 error occurred (/hppfs/work/pr45fi/di73yeq4/Meshing/evaluate_material/src/writer.cpp: 26)
An HDF5 error occurred (/hppfs/work/pr45fi/di73yeq4/Meshing/evaluate_material/src/writer.cpp: 40)
An HDF5 error occurred (/hppfs/work/pr45fi/di73yeq4/Meshing/evaluate_material/src/writer.cpp: 6)
An HDF5 error occurred (/hppfs/work/pr45fi/di73yeq4/Meshing/evaluate_material/src/writer.cpp: 20)
An HDF5 error occurred (/hppfs/work/pr45fi/di73yeq4/Meshing/evaluate_material/src/writer.cpp: 23)
An HDF5 error occurred (/hppfs/work/pr45fi/di73yeq4/Meshing/evaluate_material/src/writer.cpp: 26)
An HDF5 error occurred (/hppfs/work/pr45fi/di73yeq4/Meshing/evaluate_material/src/writer.cpp: 40)
An HDF5 error occurred (/hppfs/work/pr45fi/di73yeq4/Meshing/evaluate_material/src/writer.cpp: 6)
An HDF5 error occurred (/hppfs/work/pr45fi/di73yeq4/Meshing/evaluate_material/src/writer.cpp: 20)
An HDF5 error occurred (/hppfs/work/pr45fi/di73yeq4/Meshing/evaluate_material/src/writer.cpp: 23)
An HDF5 error occurred (/hppfs/work/pr45fi/di73yeq4/Meshing/evaluate_material/src/writer.cpp: 26)
An HDF5 error occurred (/hppfs/work/pr45fi/di73yeq4/Meshing/evaluate_material/src/writer.cpp: 40)
An HDF5 error occurred (/hppfs/work/pr45fi/di73yeq4/Meshing/evaluate_material/src/writer.cpp: 6)
An HDF5 error occurred (/hppfs/work/pr45fi/di73yeq4/Meshing/evaluate_material/src/writer.cpp: 20)
An HDF5 error occurred (/hppfs/work/pr45fi/di73yeq4/Meshing/evaluate_material/src/writer.cpp: 23)
An HDF5 error occurred (/hppfs/work/pr45fi/di73yeq4/Meshing/evaluate_material/src/writer.cpp: 26)
An HDF5 error occurred (/hppfs/work/pr45fi/di73yeq4/Meshing/evaluate_material/src/writer.cpp: 40)
An HDF5 error occurred (/hppfs/work/pr45fi/di73yeq4/Meshing/evaluate_material/src/writer.cpp: 6)
An HDF5 error occurred (/hppfs/work/pr45fi/di73yeq4/Meshing/evaluate_material/src/writer.cpp: 20)
An HDF5 error occurred (/hppfs/work/pr45fi/di73yeq4/Meshing/evaluate_material/src/writer.cpp: 23)
An HDF5 error occurred (/hppfs/work/pr45fi/di73yeq4/Meshing/evaluate_material/src/writer.cpp: 26)
An HDF5 error occurred (/hppfs/work/pr45fi/di73yeq4/Meshing/evaluate_material/src/writer.cpp: 40)
An HDF5 error occurred (/hppfs/work/pr45fi/di73yeq4/Meshing/evaluate_material/src/writer.cpp: 6)
An HDF5 error occurred (/hppfs/work/pr45fi/di73yeq4/Meshing/evaluate_material/src/writer.cpp: 20)
An HDF5 error occurred (/hppfs/work/pr45fi/di73yeq4/Meshing/evaluate_material/src/writer.cpp: 23)
An HDF5 error occurred (/hppfs/work/pr45fi/di73yeq4/Meshing/evaluate_material/src/writer.cpp: 26)
An HDF5 error occurred (/hppfs/work/pr45fi/di73yeq4/Meshing/evaluate_material/src/writer.cpp: 40)
An HDF5 error occurred (/hppfs/work/pr45fi/di73yeq4/Meshing/evaluate_material/src/writer.cpp: 6)
An HDF5 error occurred (/hppfs/work/pr45fi/di73yeq4/Meshing/evaluate_material/src/writer.cpp: 20)
An HDF5 error occurred (/hppfs/work/pr45fi/di73yeq4/Meshing/evaluate_material/src/writer.cpp: 23)
An HDF5 error occurred (/hppfs/work/pr45fi/di73yeq4/Meshing/evaluate_material/src/writer.cpp: 26)
An HDF5 error occurred (/hppfs/work/pr45fi/di73yeq4/Meshing/evaluate_material/src/writer.cpp: 40)
An HDF5 error occurred (/hppfs/work/pr45fi/di73yeq4/Meshing/evaluate_material/src/writer.cpp: 6)
An HDF5 error occurred (/hppfs/work/pr45fi/di73yeq4/Meshing/evaluate_material/src/writer.cpp: 20)
An HDF5 error occurred (/hppfs/work/pr45fi/di73yeq4/Meshing/evaluate_material/src/writer.cpp: 23)
An HDF5 error occurred (/hppfs/work/pr45fi/di73yeq4/Meshing/evaluate_material/src/writer.cpp: 26)
An HDF5 error occurred (/hppfs/work/pr45fi/di73yeq4/Meshing/evaluate_material/src/writer.cpp: 40)
An HDF5 error occurred (/hppfs/work/pr45fi/di73yeq4/Meshing/evaluate_material/src/writer.cpp: 6)
An HDF5 error occurred (/hppfs/work/pr45fi/di73yeq4/Meshing/evaluate_material/src/writer.cpp: 20)
An HDF5 error occurred (/hppfs/work/pr45fi/di73yeq4/Meshing/evaluate_material/src/writer.cpp: 23)
An HDF5 error occurred (/hppfs/work/pr45fi/di73yeq4/Meshing/evaluate_material/src/writer.cpp: 26)
An HDF5 error occurred (/hppfs/work/pr45fi/di73yeq4/Meshing/evaluate_material/src/writer.cpp: 40)
An HDF5 error occurred (/hppfs/work/pr45fi/di73yeq4/Meshing/evaluate_material/src/writer.cpp: 6)
An HDF5 error occurred (/hppfs/work/pr45fi/di73yeq4/Meshing/evaluate_material/src/writer.cpp: 20)
An HDF5 error occurred (/hppfs/work/pr45fi/di73yeq4/Meshing/evaluate_material/src/writer.cpp: 23)
An HDF5 error occurred (/hppfs/work/pr45fi/di73yeq4/Meshing/evaluate_material/src/writer.cpp: 26)
An HDF5 error occurred (/hppfs/work/pr45fi/di73yeq4/Meshing/evaluate_material/src/writer.cpp: 40)
An HDF5 error occurred (/hppfs/work/pr45fi/di73yeq4/Meshing/evaluate_material/src/writer.cpp: 6)
An HDF5 error occurred (/hppfs/work/pr45fi/di73yeq4/Meshing/evaluate_material/src/writer.cpp: 20)
An HDF5 error occurred (/hppfs/work/pr45fi/di73yeq4/Meshing/evaluate_material/src/writer.cpp: 23)
An HDF5 error occurred (/hppfs/work/pr45fi/di73yeq4/Meshing/evaluate_material/src/writer.cpp: 26)
An HDF5 error occurred (/hppfs/work/pr45fi/di73yeq4/Meshing/evaluate_material/src/writer.cpp: 40)
Wed Oct 19 13:54:54, Info:  Done 
Attempting to use an MPI routine after finalizing MPICH
@Thomas-Ulrich
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Thomas-Ulrich commented Oct 19, 2022 •
edited
Loading

And another issue of Mathilde with a larger mesh:

./dss/dsshome1/0C/ra35zih2/Meshing/evaluate_material/build/evaluate_easi  -m ../mesh/mesh_norcia_allsegs_smoothed_test2 -e Norcia_material.yaml -o norcia_eva_mat
Wed Oct 19 13:16:17, Info:  Read "../mesh/mesh_norcia_allsegs_smoothed_test2" .
Wed Oct 19 13:16:17, Info:  Found 7474736 cells
Wed Oct 19 13:16:18, Info:  Found 1365778 vertices
Wed Oct 19 13:16:18, Info:  Done
Wed Oct 19 13:16:18, Info:  Evaluate material from "Norcia_material.yaml" on the mesh.
Wed Oct 19 13:16:20, Info:  Done
Wed Oct 19 13:16:20, Info:  Write result to  "norcia_eva_mat" .
HDF5-DIAG: Error detected in HDF5 (1.10.7) MPI-process 0:
  #000: /hppfs/scratch/07/ru76tuj2/tmp/x86_avx512/spack-stage-hdf5-1.10.7-nz33ctkzggdbh5oifr74jnlfgbrqihc7/spack-src/src/H5S.c line 1431 in H5Screate_simple(): dimensionality is too large
    major: Invalid arguments to routine
    minor: Bad value
An HDF5 error occurred (/dss/dsshome1/0C/ra35zih2/Meshing/evaluate_material/src/writer.cpp: 6)
HDF5-DIAG: Error detected in HDF5 (1.10.7) MPI-process 0:
  #000: /hppfs/scratch/07/ru76tuj2/tmp/x86_avx512/spack-stage-hdf5-1.10.7-nz33ctkzggdbh5oifr74jnlfgbrqihc7/spack-src/src/H5D.c line 124 in H5Dcreate2(): not a dataspace ID
    major: Invalid arguments to routine
    minor: Inappropriate type
An HDF5 error occurred (/dss/dsshome1/0C/ra35zih2/Meshing/evaluate_material/src/writer.cpp: 20)
HDF5-DIAG: Error detected in HDF5 (1.10.7) MPI-process 0:
  #000: /hppfs/scratch/07/ru76tuj2/tmp/x86_avx512/spack-stage-hdf5-1.10.7-nz33ctkzggdbh5oifr74jnlfgbrqihc7/spack-src/src/H5Shyper.c line 9997 in H5Sselect_hyperslab(): not a dataspace
    major: Invalid arguments to routine
    minor: Inappropriate type
An HDF5 error occurred (/dss/dsshome1/0C/ra35zih2/Meshing/evaluate_material/src/writer.cpp: 23)
HDF5-DIAG: Error detected in HDF5 (1.10.7) MPI-process 0:
  #000: /hppfs/scratch/07/ru76tuj2/tmp/x86_avx512/spack-stage-hdf5-1.10.7-nz33ctkzggdbh5oifr74jnlfgbrqihc7/spack-src/src/H5S.c line 1431 in H5Screate_simple(): dimensionality is too large
    major: Invalid arguments to routine
    minor: Bad value
An HDF5 error occurred (/dss/dsshome1/0C/ra35zih2/Meshing/evaluate_material/src/writer.cpp: 26)
HDF5-DIAG: Error detected in HDF5 (1.10.7) MPI-process 0:
  #000: /hppfs/scratch/07/ru76tuj2/tmp/x86_avx512/spack-stage-hdf5-1.10.7-nz33ctkzggdbh5oifr74jnlfgbrqihc7/spack-src/src/H5Dio.c line 313 in H5Dwrite(): dset_id is not a dataset ID
    major: Invalid arguments to routine
    minor: Inappropriate type
An HDF5 error occurred (/dss/dsshome1/0C/ra35zih2/Meshing/evaluate_material/src/writer.cpp: 37)
HDF5-DIAG: Error detected in HDF5 (1.10.7) MPI-process 0:
  #000: /hppfs/scratch/07/ru76tuj2/tmp/x86_avx512/spack-stage-hdf5-1.10.7-nz33ctkzggdbh5oifr74jnlfgbrqihc7/spack-src/src/H5S.c line 1431 in H5Screate_simple(): dimensionality is too large
    major: Invalid arguments to routine
    minor: Bad value

@sebwolf-de
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Can you try the fix? Should at least fix the first part

@Thomas-Ulrich
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Thx!
Yes, it fixes the first part.
@marcmath can test the second part

@marcmath
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It fixes the second part too. Thank you!

Thomas-Ulrich added a commit that referenced this issue Oct 19, 2022
@Thomas-Ulrich
Merge pull request #39 from SeisSol/fix-38
9c1ff84 
Fix #38
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@Thomas-Ulrich @sebwolf-de @marcmath