When I used the hdf5 format in a 3DH1D simulation using our school’s hpc hanhai22, the triangle elements was not output. This issue only occurs on that hpc. Does any one encountered similar issue?
FieldConvert failed.
$ FieldConvert ring.xml ringc.xml ring.fld ring.plt
HDF5-DIAG: Error detected in HDF5 (1.12.3) MPI-process 0:
#000: /home/agao/testcode/nektar/ThirdParty/hdf5-1.12.3/src/H5G.c line 509 in H5Gopen2(): unable to open group
major: Symbol table
minor: Can’t open object
#001: /home/agao/testcode/nektar/ThirdParty/hdf5-1.12.3/src/H5VLcallback.c line 4187 in H5VL_group_open(): group open failed
major: Virtual Object Layer
minor: Can’t open object
#002: /home/agao/testcode/nektar/ThirdParty/hdf5-1.12.3/src/H5VLcallback.c line 4154 in H5VL__group_open(): group open failed
major: Virtual Object Layer
minor: Can’t open object
#003: /home/agao/testcode/nektar/ThirdParty/hdf5-1.12.3/src/H5VLnative_group.c line 123 in H5VL__native_group_open(): unable to open group
major: Symbol table
minor: Can’t open object
#004: /home/agao/testcode/nektar/ThirdParty/hdf5-1.12.3/src/H5Gint.c line 269 in H5G__open_name(): group not found
major: Symbol table
minor: Object not found
#005: /home/agao/testcode/nektar/ThirdParty/hdf5-1.12.3/src/H5Gloc.c line 441 in H5G_loc_find(): can’t find object
major: Symbol table
minor: Object not found
#006: /home/agao/testcode/nektar/ThirdParty/hdf5-1.12.3/src/H5Gtraverse.c line 836 in H5G_traverse(): internal path traversal failed
major: Symbol table
minor: Object not found
#007: /home/agao/testcode/nektar/ThirdParty/hdf5-1.12.3/src/H5Gtraverse.c line 612 in H5G__traverse_real(): traversal operator failed
major: Symbol table
minor: Callback failed
#008: /home/agao/testcode/nektar/ThirdParty/hdf5-1.12.3/src/H5Gloc.c line 398 in H5G__loc_find_cb(): object ‘11331225666440264896’ doesn’t exist
major: Symbol table
minor: Object not found
Fatal : Level 0 assertion violation
HDF5 error in API function H5Gopen2
terminate called after throwing an instance of ‘Nektar::ErrorUtil::NekError’
what(): Level 0 assertion violation
HDF5 error in API function H5Gopen2
[ubuntu22:2216912] *** Process received signal ***
[ubuntu22:2216912] Signal: Aborted (6)
[ubuntu22:2216912] Signal code: (-6)
[ubuntu22:2216912] [ 0] /lib/x86_64-linux-gnu/libc.so.6(+0x42520)[0x7af2ba442520]
[ubuntu22:2216912] [ 1] /lib/x86_64-linux-gnu/libc.so.6(pthread_kill+0x12c)[0x7af2ba4969bc]
[ubuntu22:2216912] [ 2] /lib/x86_64-linux-gnu/libc.so.6(raise+0x16)[0x7af2ba442476]
[ubuntu22:2216912] [ 3] /lib/x86_64-linux-gnu/libc.so.6(abort+0xd3)[0x7af2ba4287f3]
[ubuntu22:2216912] [ 4] /lib/x86_64-linux-gnu/libstdc++.so.6(+0xa2b9e)[0x7af2ba8a2b9e]
[ubuntu22:2216912] [ 5] /lib/x86_64-linux-gnu/libstdc++.so.6(+0xae20c)[0x7af2ba8ae20c]
[ubuntu22:2216912] [ 6] /lib/x86_64-linux-gnu/libstdc++.so.6(+0xae277)[0x7af2ba8ae277]
[ubuntu22:2216912] [ 7] /lib/x86_64-linux-gnu/libstdc++.so.6(+0xae4d8)[0x7af2ba8ae4d8]
[ubuntu22:2216912] [ 8] FieldConvert(_ZN6Nektar9ErrorUtil5ErrorENS0_7ErrTypeEPKciS3_jb+0x508)[0x610214c225f8]
[ubuntu22:2216912] [ 9] /apps/nektar++/latest/lib64/libLibUtilities.so.5.10.0(_ZNK6Nektar12LibUtilities2H521CanHaveGroupsDataSets9OpenGroupERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt10shared_ptrINS1_5PListEE+0x148)[0x7af2bae611e8]
[ubuntu22:2216912] [10] /apps/nektar++/latest/lib64/libLibUtilities.so.5.10.0(_ZN6Nektar12LibUtilities11FieldIOHdf514ImportFieldDefESt10shared_ptrINS0_2H55PListEES2_INS3_5GroupEERSt6vectorImSaImEEmNS1_12OffsetHelperENSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES2_INS0_16FieldDefinitionsEE+0xce)[0x7af2bae6acde]
[ubuntu22:2216912] [11] /apps/nektar++/latest/lib64/libLibUtilities.so.5.10.0(_ZN6Nektar12LibUtilities11FieldIOHdf58v_ImportERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERSt6vectorISt10shared_ptrINS0_16FieldDefinitionsEESaISD_EERSA_ISA_IdSaIdEESaISI_EERSt3mapIS7_S7_St4lessIS7_ESaISt4pairIS8_S7_EEERKNS_5ArrayINS_4OneDEiEE+0x15ee)[0x7af2bae6e1de]
[ubuntu22:2216912] [12] /apps/nektar++/latest/lib64/libFieldUtils.so.5.10.0(_ZN6Nektar10FieldUtils8InputFld9v_ProcessERN5boost15program_options13variables_mapE+0xb96)[0x7af2bbb8a166]
[ubuntu22:2216912] [13] FieldConvert(+0x2008d)[0x610214c1d08d]
[ubuntu22:2216912] [14] FieldConvert(+0x1bc08)[0x610214c18c08]
[ubuntu22:2216912] [15] /lib/x86_64-linux-gnu/libc.so.6(+0x29d90)[0x7af2ba429d90]
[ubuntu22:2216912] [16] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0x80)[0x7af2ba429e40]
[ubuntu22:2216912] [17] FieldConvert(+0x1e665)[0x610214c1b665]
[ubuntu22:2216912] *** End of error message ***
Aborted (core dumped)