Problem creating h5m file from pymoab Core object

LukeLabrie · July 21, 2022, 9:12am

We’ve been working on a cad to openmc toolchain without using cubit, which ultimately makes use of the pymoab Core object to build the h5m structure for an openmc simulation.

Currently getting the the following MOAB error on a test run:

--------------------- Error Message ------------------------------------ 
MOAB ERROR: 
Failed to setup problem indices! 
MOAB ERROR: 
init_OBBTree() line 652 in DagMC.cpp 
MOAB ERROR: init_dagmc() line 135 in dagmc.cpp  
WARNING: 
/home/luke/git/are/h5m_files/ARE.h5m is not an hdf5 file but a datapath was prodided!

We’re using the pymoab Core.write_file() method to write the h5m file. Anyone familiar with moab know what could be causing this?

Thanks,
Luke

Shimwell · July 21, 2022, 3:25pm

Looking at the source code for Pyne, it appears that this error message is suggesting the file is not in HDF5 format.

github.com

pyne/pyne/blob/800c75a6099f81ac73460166aea936dea4835f00/src/material_library.cpp#L28


      
          
          
  // Check that the file is there
            if (!pyne::file_exists(filename)) throw pyne::FileNotFound(filename);
          
          
  // Check to see if the file is in HDF5 format.
            bool ish5 = H5Fis_hdf5(filename.c_str());
            if (ish5)
              from_hdf5(filename, datapath);
            else if (datapath != "") {
              std::string wrng =
                  filename + " is not an hdf5 file but a datapath was prodided!";
              pyne::warning(wrng);
            }
            from_json(filename);
          };
          
          
// Append Material to the library from hdf5 file
          void pyne::MaterialLibrary::from_hdf5(const std::string& filename,
                                                const std::string& datapath) {
            if (!pyne::file_exists(filename)) {
              throw std::runtime_error("File " + filename +

Also I shall try to fix that typo in the error message

LukeLabrie · July 22, 2022, 2:38pm

Thanks Jonathan, that was indeed the issue. Moab was writing a .vtk file instead of an .h5m file. I didn’t notice at first because the extension was still .h5m. Fixed by including the ENABLE_HDF5 flag and recompiling moab.

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Problem creating h5m file from pymoab Core object

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