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<p>Dear All,</p>
<p>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 (<font color="#ff0000">red part shown below</font>).
<br>
</p>
<p> !c create local memory space and hyperslab<br>
call h5screate_simple_f(hdf5_ndim, hdf5_dsize,
memspace, &<br>
hdf5_ierr)<br>
call h5sselect_hyperslab_f(memspace,
H5S_SELECT_SET_F, &<br>
hdf5_offset, hdf5_count,
hdf5_ierr, &<br>
hdf5_stride, hdf5_block)<br>
<br>
!c create the global file space and hyperslab<br>
call
h5screate_simple_f(hdf5_ndim,hdf5_gdsize,filespace,
&<br>
hdf5_ierr)<br>
call h5sselect_hyperslab_f(filespace,
H5S_SELECT_SET_F, &<br>
hdf5_goffset, hdf5_count,
hdf5_ierr, &<br>
hdf5_stride, hdf5_block)<br>
<br>
!c create a data chunking property<br>
call h5pcreate_f(H5P_DATASET_CREATE_F, chunk_id, hdf5_ierr)<br>
call h5pset_chunk_f(chunk_id, hdf5_ndim, hdf5_csize,
hdf5_ierr)<br>
<br>
<font color="#ff0000"> !c create compressed data, dataset must
be chunked for compression<br>
!c the following cause crash in hdf5 library, check when new<br>
!c hdf5 version is available</font><br>
<br>
<font color="#ff0000"> ! Set ZLIB / DEFLATE Compression using
compression level 6.<br>
! To use SZIP Compression comment out these lines.<br>
!call h5pset_deflate_f(chunk_id, 6, hdf5_ierr)</font><br>
<br>
<font color="#ff0000"> ! Uncomment these lines to set SZIP
Compression<br>
!szip_options_mask = H5_SZIP_NN_OM_F<br>
!szip_pixels_per_block = 16<br>
!call H5Pset_szip_f(chunk_id,
szip_options_mask, &<br>
! szip_pixels_per_block, hdf5_ierr)</font><br>
<br>
!c create the dataset id<br>
call h5dcreate_f(group_id, dataname,
H5T_NATIVE_INTEGER, &<br>
filespace, dset_id,
hdf5_ierr, &<br>
dcpl_id=chunk_id)<br>
<br>
!c create a data transfer property<br>
call h5pcreate_f(H5P_DATASET_XFER_F, xlist_id, hdf5_ierr)<br>
call h5pset_dxpl_mpio_f(xlist_id,
H5FD_MPIO_COLLECTIVE_F, &<br>
hdf5_ierr)<br>
<br>
!c write the dataset collectively<br>
call h5dwrite_f(dset_id, H5T_NATIVE_INTEGER, dataset,
hdf5_dsize, &<br>
hdf5_ierr,
file_space_id=filespace, &<br>
mem_space_id=memspace, xfer_prp = xlist_id)<br>
<br>
call h5dclose_f(dset_id, hdf5_ierr)<br>
<br>
!c close resources<br>
call h5sclose_f(filespace, hdf5_ierr)<br>
call h5sclose_f(memspace, hdf5_ierr)<br>
call h5pclose_f(chunk_id, hdf5_ierr)<br>
call h5pclose_f(xlist_id, hdf5_ierr)</p>
<p><br>
</p>
<p>Both h5pset_deflate_f and H5Pset_szip_f crashes the code with
error information as shown below. If I comment out <font
color="#ff0000">h5pset_deflate_f </font>and <font
color="#ff0000">H5Pset_szip_f</font>, then everything works
fine. <br>
</p>
<p><font color="#ff0000"><font color="#ff0000"><font color="#000000">HDF5-DIAG:
Error detected in HDF5 (1.8.18) MPI-process 0:<br>
#000: H5D.c line 194 in H5Dcreate2(): unable to create
dataset<br>
major: Dataset<br>
minor: Unable to initialize object<br>
#001: H5Dint.c line 455 in H5D__create_named(): unable to
create and link to dataset<br>
major: Dataset<br>
minor: Unable to initialize object<br>
#002: H5L.c line 1638 in H5L_link_object(): unable to
create new link to object<br>
major: Links<br>
minor: Unable to initialize object<br>
#003: H5L.c line 1882 in H5L_create_real(): can't insert
link<br>
major: Symbol table<br>
minor: Unable to insert object<br>
#004: H5Gtraverse.c line 861 in H5G_traverse(): internal
path traversal failed<br>
major: Symbol table<br>
minor: Object not found</font></font></font></p>
<p><font color="#ff0000"><font color="#ff0000"><font color="#000000">Does
anyone encounter this kind of error before? <br>
</font></font></font></p>
<p><font color="#ff0000"><font color="#ff0000"><font color="#000000">Kind
regards,</font></font></font></p>
<p><font color="#ff0000"><font color="#ff0000"><font color="#000000">Danyang<br>
</font></font></font></p>
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