Dear All,
Not sure if this is the right place to ask hdf5 question. I installed
hdf5 through PETSc configuration --download-hdf5=yes. The code runs
without problem except the function to create compressed data (red part
shown below).
!c create local memory space and hyperslab
call h5screate_simple_f(hdf5_ndim, hdf5_dsize, memspace, &
hdf5_ierr)
call h5sselect_hyperslab_f(memspace, H5S_SELECT_SET_F, &
hdf5_offset, hdf5_count, hdf5_ierr, &
hdf5_stride, hdf5_block)
!c create the global file space and hyperslab
call h5screate_simple_f(hdf5_ndim,hdf5_gdsize,filespace, &
hdf5_ierr)
call h5sselect_hyperslab_f(filespace, H5S_SELECT_SET_F, &
hdf5_goffset, hdf5_count, hdf5_ierr, &
hdf5_stride, hdf5_block)
!c create a data chunking property
call h5pcreate_f(H5P_DATASET_CREATE_F, chunk_id, hdf5_ierr)
call h5pset_chunk_f(chunk_id, hdf5_ndim, hdf5_csize, hdf5_ierr)
!c create compressed data, dataset must be chunked for compression
!c the following cause crash in hdf5 library, check when new
!c hdf5 version is available
! Set ZLIB / DEFLATE Compression using compression level 6.
! To use SZIP Compression comment out these lines.
!call h5pset_deflate_f(chunk_id, 6, hdf5_ierr)
! Uncomment these lines to set SZIP Compression
!szip_options_mask = H5_SZIP_NN_OM_F
!szip_pixels_per_block = 16
!call H5Pset_szip_f(chunk_id, szip_options_mask, &
! szip_pixels_per_block, hdf5_ierr)
!c create the dataset id
call h5dcreate_f(group_id, dataname, H5T_NATIVE_INTEGER, &
filespace, dset_id, hdf5_ierr, &
dcpl_id=chunk_id)
!c create a data transfer property
call h5pcreate_f(H5P_DATASET_XFER_F, xlist_id, hdf5_ierr)
call h5pset_dxpl_mpio_f(xlist_id, H5FD_MPIO_COLLECTIVE_F, &
hdf5_ierr)
!c write the dataset collectively
call h5dwrite_f(dset_id, H5T_NATIVE_INTEGER, dataset, hdf5_dsize, &
hdf5_ierr, file_space_id=filespace, &
mem_space_id=memspace, xfer_prp = xlist_id)
call h5dclose_f(dset_id, hdf5_ierr)
!c close resources
call h5sclose_f(filespace, hdf5_ierr)
call h5sclose_f(memspace, hdf5_ierr)
call h5pclose_f(chunk_id, hdf5_ierr)
call h5pclose_f(xlist_id, hdf5_ierr)
Both h5pset_deflate_f and H5Pset_szip_f crashes the code with error
information as shown below. If I comment out h5pset_deflate_f and
H5Pset_szip_f, then everything works fine.
HDF5-DIAG: Error detected in HDF5 (1.8.18) MPI-process 0:
#000: H5D.c line 194 in H5Dcreate2(): unable to create dataset
major: Dataset
minor: Unable to initialize object
#001: H5Dint.c line 455 in H5D__create_named(): unable to create and
link to dataset
major: Dataset
minor: Unable to initialize object
#002: H5L.c line 1638 in H5L_link_object(): unable to create new link
to object
major: Links
minor: Unable to initialize object
#003: H5L.c line 1882 in H5L_create_real(): can't insert link
major: Symbol table
minor: Unable to insert object
#004: H5Gtraverse.c line 861 in H5G_traverse(): internal path
traversal failed
major: Symbol table
minor: Object not found
Does anyone encounter this kind of error before?
Kind regards,
Danyang
