You could try the master branch of PETSc that uses a much more recent branch
of hdf5
When you did the --download-hdf5 did you also do --download-zlib and
--download-szlib (though I would hope hdf5 would give you a very useful error
message that they need to be installed instead of the vague error message they
do provide.)
Barry
> On Sep 2, 2019, at 2:24 PM, Danyang Su via petsc-users
> wrote:
>
> 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
>
