Re: [Libmesh-users] HDF5 compatibility

[Alexander L. <ale...@gm...>]

I was able to successfully run using HDF5 version 1.8.20. Based on the
issue I referenced, I wonder whether 1.10.1 and 1.10.2 may also work.

On Wed, Jul 3, 2019 at 5:57 PM Alexander Lindsay <ale...@gm...>
wrote:

> Do we know what version of HDF5 is compatabile with our current netCDF
> release (4.6.2)? There is some discussion on compatability here:
> https://github.com/Unidata/netcdf-c/issues/951. I've configured libmesh
> with the options: --enable-hdf5 and --with-hdf5 where I point to a 1.10.5
> hdf5 version. However, when I try to run MOOSE's simple_diffusion test, I
> get this error:
>
> Exodus Library Error: [ex_create]
> Error: file create failed for simple_diffusion_out.e in NETCDF4 and
> CLOBBER mode.
> This library probably does not support netcdf-4 files.
>     exerrval = 13
> Error creating ExodusII mesh file.
> Stack frames: 18
> 0: 0   libmesh_dbg.0.dylib                 0x0000000106c691ba
> libMesh::print_trace(std::__1::basic_ostream<char,
> std::__1::char_traits<char> >&) + 458
> 1: 1   libmesh_dbg.0.dylib                 0x0000000106c5fe6e
> libMesh::MacroFunctions::report_error(char const*, int, char const*, char
> const*) + 222
> 2: 2   libmesh_dbg.0.dylib                 0x0000000107223d9c
> libMesh::ExodusII_IO_Helper::create(std::__1::basic_string<char,
> std::__1::char_traits<char>, std::__1::allocator<char> >) + 444
> 3: 3   libmesh_dbg.0.dylib                 0x000000010720eeab
> libMesh::ExodusII_IO::write_nodal_data_common(std::__1::basic_string<char,
> std::__1::char_traits<char>, std::__1::allocator<char> >,
> std::__1::vector<std::__1::basic_string<char, std::__1::char_traits<char>,
> std::__1::allocator<char> >,
> std::__1::allocator<std::__1::basic_string<char,
> std::__1::char_traits<char>, std::__1::allocator<char> > > > const&, bool)
> + 315
> 4: 4   libmesh_dbg.0.dylib                 0x000000010720e8c4
> libMesh::ExodusII_IO::write_nodal_data(std::__1::basic_string<char,
> std::__1::char_traits<char>, std::__1::allocator<char> > const&,
> std::__1::vector<double, std::__1::allocator<double> > const&,
> std::__1::vector<std::__1::basic_string<char, std::__1::char_traits<char>,
> std::__1::allocator<char> >,
> std::__1::allocator<std::__1::basic_string<char,
> std::__1::char_traits<char>, std::__1::allocator<char> > > > const&) + 276
> 5: 5   libmesh_dbg.0.dylib                 0x00000001073e525f
> libMesh::MeshOutput<libMesh::MeshBase>::write_equation_systems(std::__1::basic_string<char,
> std::__1::char_traits<char>, std::__1::allocator<char> > const&,
> libMesh::EquationSystems const&, std::__1::set<std::__1::basic_string<char,
> std::__1::char_traits<char>, std::__1::allocator<char> >,
> std::__1::less<std::__1::basic_string<char, std::__1::char_traits<char>,
> std::__1::allocator<char> > >,
> std::__1::allocator<std::__1::basic_string<char,
> std::__1::char_traits<char>, std::__1::allocator<char> > > > const*) + 1551
> 6: 6   libmesh_dbg.0.dylib                 0x000000010720f8b6
> libMesh::ExodusII_IO::write_timestep(std::__1::basic_string<char,
> std::__1::char_traits<char>, std::__1::allocator<char> > const&,
> libMesh::EquationSystems const&, int, double,
> std::__1::set<std::__1::basic_string<char, std::__1::char_traits<char>,
> std::__1::allocator<char> >, std::__1::less<std::__1::basic_string<char,
> std::__1::char_traits<char>, std::__1::allocator<char> > >,
> std::__1::allocator<std::__1::basic_string<char,
> std::__1::char_traits<char>, std::__1::allocator<char> > > > const*) + 86
> 7: 7   libmoose-dbg.0.dylib                0x00000001021df9a0
> Exodus::outputNodalVariables() + 576
> 8: 8   libmoose-dbg.0.dylib                0x00000001021c2b4d
> AdvancedOutput::output(MooseEnumItem const&) + 157
> 9: 9   libmoose-dbg.0.dylib                0x00000001021e0747
> Exodus::output(MooseEnumItem const&) + 391
> 10: 10  libmoose-dbg.0.dylib                0x00000001021eacd8
> OversampleOutput::outputStep(MooseEnumItem const&) + 520
> 11: 11  libmoose-dbg.0.dylib                0x00000001021e9387
> OutputWarehouse::outputStep(MooseEnumItem) + 183
> 12: 12  libmoose-dbg.0.dylib                0x0000000101ace8e7
> FEProblemBase::outputStep(MooseEnumItem) + 279
>
> I'm wondering what's going on...
>