FYI, we use HDF5 version 1.10.2 released on 2018-03-29. This works fine with the netCDF bundled with libMesh for us.
David On Thu, Jul 4, 2019 at 10:02 AM Alexander Lindsay <alexlindsay...@gmail.com> wrote: > 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 <alexlindsay...@gmail.com > > > 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... > > > > _______________________________________________ > Libmesh-users mailing list > Libmesh-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/libmesh-users > _______________________________________________ Libmesh-users mailing list Libmesh-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/libmesh-users
