[petsc-users] Error in creating compressed data using HDF5

[Danyang Su]

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

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