I have to set up parallel HDF5 for using it with h5py. I found that the default libraries available from Ubuntu apt-get does not support Parallel HDF5. So I compiled and installed mpich; and then ran CC=/usr/local/bin/mpicc ./…/configure --enable-shared --enable-parallel make && make check, after checking the location of installed mpicc.
The OS I am using is Ubuntu 18.04 with mpich 3.3.
Version that I’m trying to install : HDF5 v1.10.4
It passes t_mpi, testphdf5 and the previous tests.
I found that it fails to run parallel filters check as shown below.
============================ Testing t_filters_parallel ============================ t_filters_parallel Test Log ============================ ==========================Parallel Filters tests ========================== *** Hint *** You can use environment variable HDF5_PARAPREFIX to run parallel test files in a different directory or to add file type prefix. E.g., HDF5_PARAPREFIX=pfs:/PFS/user/me export HDF5_PARAPREFIX *** End of Hint *** Testing write to one-chunk filtered dataset HDF5-DIAG: Error detected in HDF5 (1.10.4) MPI-process 0: #000: .././../src/H5Dio.c line 336 in H5Dwrite(): can't write data major: Dataset minor: Write failed #001: .././../src/H5Dio.c line 828 in H5D__write(): can't write data major: Dataset minor: Write failed #002: .././../src/H5Dmpio.c line 893 in H5D__chunk_collective_write(): write error major: Dataspace minor: Write failed #003: .././../src/H5Dmpio.c line 811 in H5D__chunk_collective_io(): couldn't finish filtered linked chunk MPI-IO major: Low-level I/O minor: Can't get value #004: .././../src/H5Dmpio.c line 1317 in H5D__link_chunk_filtered_collective_io(): couldn't process chunk entry major: Dataset minor: Write failed #005: .././../src/H5Dmpio.c line 3099 in H5D__filtered_collective_chunk_entry_io(): couldn't unfilter chunk for modifying major: Dataset minor: Filter operation failed #006: .././../src/H5Z.c line 1303 in H5Z_pipeline(): required filter (name unavailable) is not registered major: Data filters minor: Read failed #007: .././../src/H5PLint.c line 270 in H5PL_load(): search in path table failed major: Plugin for dynamically loaded library minor: Can't get value #008: .././../src/H5PLpath.c line 604 in H5PL__find_plugin_in_path_table(): search in path /usr/local/hdf5/lib/plugin encountered an error major: Plugin for dynamically loaded library minor: Can't get value #009: .././../src/H5PLpath.c line 656 in H5PL__find_plugin_in_path(): can't open directory: /usr/local/hdf5/lib/plugin major: Plugin for dynamically loaded library Proc 0: *** Parallel ERROR *** VRFY (Dataset write succeeded) failed at line 279 in .././../testpar/t_filters_parallel.c aborting MPI processes minor: Can't open directory or file application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0 Command exited with non-zero status 1 0.00user 0.00system 0:00.16elapsed 1%CPU (0avgtext+0avgdata 3672maxresident)k 0inputs+0outputs (0major+420minor)pagefaults 0swaps Makefile:1436: recipe for target 't_filters_parallel.chkexe_' failed make: *** [t_filters_parallel.chkexe_] Error 1 make: Leaving directory '/home/ubuntu/Downloads/hdf5-1.10.4/build/testpar' Makefile:1545: recipe for target 'build-check-p' failed make: *** [build-check-p] Error 1 make: Leaving directory '/home/ubuntu/Downloads/hdf5-1.10.4/build/testpar' Makefile:1416: recipe for target 'test' failed make: *** [test] Error 2 make: Leaving directory '/home/ubuntu/Downloads/hdf5-1.10.4/build/testpar' Makefile:1217: recipe for target 'check-am' failed make: *** [check-am] Error 2 make: Leaving directory '/home/ubuntu/Downloads/hdf5-1.10.4/build/testpar' Makefile:654: recipe for target 'check-recursive' failed make: *** [check-recursive] Error 1
I read online that parallel filters were not implemented in HDF5 v1.10.0. Is it still the case in the current version?
Can I run make install and ignore this error?