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

[Danyang Su]

Hi Barry,

Yes, I have already included zlib and szlib during the configuration. I 
will try the dev version to see if it works.

Thanks,

Danyang

On 2019-09-02 12:45 p.m., Smith, Barry F. wrote:
>    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 <petsc-users at mcs.anl.gov> 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
>>