Here is how I call my data_out object to write HDF5,
DataOutBase::DataOutFilter
data_filter(DataOutBase::DataOutFilterFlags(true,true));
data_out.write_filtered_data(data_filter);
data_out.write_hdf5_parallel(data_filter,
write_mesh_file,
mesh_filename,
solution_filename,
mpi_comm);
Here are the lines pulled from data_out_base.cc (9.7.0 documentation)
833 node_dataset_id = H5Pcreate(H5P_DATASET_CREATE);
# ifdef DEAL_II_WITH_ZLIB
H5Pset_deflate(node_dataset_id,
get_zlib_compression_level(flags.compression_level));
H5Pset_chunk(node_dataset_id, 2, cell_ds_dim); //<------- Here it
sets some chunk size?
# endif
cell_dataset = H5Dcreate(h5_mesh_file_id,
"cells",
H5T_NATIVE_UINT,
cell_dataspace,
H5P_DEFAULT,
node_dataset_id,
H5P_DEFAULT);
H5Pclose(node_dataset_id);
# endif
840 AssertThrow(cell_dataset >= 0, ExcIO()); // <--- line 8330 in my error
On Tue, Sep 16, 2025 at 11:29 PM 'Wolfgang Bangerth' via deal.II User Group
<[email protected]> wrote:
>
> On 9/16/25 05:04, Jalil Khan wrote:
> >
> > From inspecting the source in data_out_base.cc, HDF5 uses chunked
> > layout, with chunk dimensions set internally in deal.II. At 512³, the
> > computed chunk size exceeds the HDF5 hard limit of 4 GB per chunk, which
> > leads to the failure.
> >
> > Is there a recommended way for users to avoid this error when writing
> > large output files?
>
> Jalil:
> that likely falls in the category of "the person who wrote these HDF5
> calls didn't think of this scenario, and nobody has run into it since
> then". Can you identify which line in data_out_base.cc specifically
> triggers the issue, and can you show how you call deal.II functions to
> run into this issue?
>
> In the end, this ought to be fixed of course. Any help is obviously
> always welcome!
>
> Best
> Wolfgang
>
>
> --
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--
Regards
J.R.Khan
8803985667
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