I was running a simulation in parallel and saving results to an xdmf file. The process was terminated and I cannot open my results files in paraview. I know this is because the file filename.close() command was never called before exiting. Is there a way to close the xdmf/h5 files after the process has exited? I’d like to be able to use the results.
Thank you. When I try that, it looks like there’s a problem with the h5 file. I get the following error:
HDF5-DIAG: Error detected in HDF5 (1.12.2) MPI-process 0:
#000: H5F.c line 620 in H5Fopen(): unable to open file
major: File accessibility
minor: Unable to open file
#001: H5VLcallback.c line 3502 in H5VL_file_open(): failed to iterate over available VOL connector plugins
major: Virtual Object Layer
minor: Iteration failed
#002: H5PLpath.c line 579 in H5PL__path_table_iterate(): can't iterate over plugins in plugin path '(null)'
major: Plugin for dynamically loaded library
minor: Iteration failed
#003: H5PLpath.c line 620 in H5PL__path_table_iterate_process_path(): can't open directory: /usr/local/anaconda3/envs/fenicsx-env/lib/hdf5/plugin
major: Plugin for dynamically loaded library
minor: Can't open directory or file
#004: H5VLcallback.c line 3351 in H5VL__file_open(): open failed
major: Virtual Object Layer
minor: Can't open object
#005: H5VLnative_file.c line 97 in H5VL__native_file_open(): unable to open file
major: File accessibility
minor: Unable to open file
#006: H5Fint.c line 1990 in H5F_open(): unable to read superblock
major: File accessibility
minor: Read failed
#007: H5Fsuper.c line 405 in H5F__super_read(): file signature not found
major: File accessibility
minor: Not an HDF5 file
I can’t seem to make a simple reproducible example and the file itself is too large. It must be that something is messed up in the h5 file from the process terminating possibly mid-write.