<div dir="ltr"><div dir="ltr">On Tue, Sep 3, 2019 at 1:57 AM Danyang Su via petsc-users <<a href="mailto:petsc-users@mcs.anl.gov">petsc-users@mcs.anl.gov</a>> wrote:<br></div><div class="gmail_quote"><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">Unfortunately, the master branch with hdf-1.10.5 returns similar error.<br></blockquote><div><br></div><div>It looks like its complaining about the group_id. Are you sure its correct?</div><div><br></div><div> Matt</div><div> </div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
Danyang<br>
<br>
On 2019-09-02 5:31 p.m., Danyang Su wrote:<br>
> Hi Barry,<br>
><br>
> Yes, I have already included zlib and szlib during the configuration. <br>
> I will try the dev version to see if it works.<br>
><br>
> Thanks,<br>
><br>
> Danyang<br>
><br>
> On 2019-09-02 12:45 p.m., Smith, Barry F. wrote:<br>
>> You could try the master branch of PETSc that uses a much more <br>
>> recent branch of hdf5<br>
>><br>
>> When you did the --download-hdf5 did you also do --download-zlib <br>
>> and --download-szlib (though I would hope hdf5 would give you a very <br>
>> useful error message that they need to be installed instead of the <br>
>> vague error message they do provide.)<br>
>><br>
>> Barry<br>
>><br>
>><br>
>>> On Sep 2, 2019, at 2:24 PM, Danyang Su via petsc-users <br>
>>> <<a href="mailto:petsc-users@mcs.anl.gov" target="_blank">petsc-users@mcs.anl.gov</a>> wrote:<br>
>>><br>
>>> Dear All,<br>
>>><br>
>>> Not sure if this is the right place to ask hdf5 question. I <br>
>>> installed hdf5 through PETSc configuration --download-hdf5=yes. The <br>
>>> code runs without problem except the function to create compressed <br>
>>> data (red part shown below).<br>
>>><br>
>>> !c create local memory space and hyperslab<br>
>>> call h5screate_simple_f(hdf5_ndim, hdf5_dsize, <br>
>>> memspace, &<br>
>>> hdf5_ierr)<br>
>>> call h5sselect_hyperslab_f(memspace, <br>
>>> H5S_SELECT_SET_F, &<br>
>>> hdf5_offset, hdf5_count, <br>
>>> 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, <br>
>>> H5S_SELECT_SET_F, &<br>
>>> hdf5_goffset, hdf5_count, <br>
>>> 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>
>>> !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<br>
>>><br>
>>> ! 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)<br>
>>><br>
>>> ! 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, <br>
>>> szip_options_mask, &<br>
>>> ! szip_pixels_per_block, hdf5_ierr)<br>
>>><br>
>>> !c create the dataset id<br>
>>> call h5dcreate_f(group_id, dataname, <br>
>>> H5T_NATIVE_INTEGER, &<br>
>>> filespace, dset_id, <br>
>>> 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, <br>
>>> H5FD_MPIO_COLLECTIVE_F, &<br>
>>> hdf5_ierr)<br>
>>><br>
>>> !c write the dataset collectively<br>
>>> call h5dwrite_f(dset_id, H5T_NATIVE_INTEGER, dataset, <br>
>>> hdf5_dsize, &<br>
>>> hdf5_ierr, <br>
>>> 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)<br>
>>><br>
>>><br>
>>><br>
>>> Both h5pset_deflate_f and H5Pset_szip_f crashes the code with error <br>
>>> information as shown below. If I comment out h5pset_deflate_f and <br>
>>> H5Pset_szip_f, then everything works fine.<br>
>>><br>
>>> 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 <br>
>>> 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 <br>
>>> 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 <br>
>>> traversal failed<br>
>>> major: Symbol table<br>
>>> minor: Object not found<br>
>>><br>
>>> Does anyone encounter this kind of error before?<br>
>>><br>
>>> Kind regards,<br>
>>><br>
>>> Danyang<br>
>>><br>
</blockquote></div><br clear="all"><div><br></div>-- <br><div dir="ltr" class="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div>What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead.<br>-- Norbert Wiener</div><div><br></div><div><a href="http://www.cse.buffalo.edu/~knepley/" target="_blank">https://www.cse.buffalo.edu/~knepley/</a><br></div></div></div></div></div></div></div></div>