Troubleshooting

Common problems, and how to handle them.

HDF5 Import Errors

A common import error is:

ImportError: libhdf5.so.10: cannot open shared object file: No such file or directory

To solve this ensure you have the right HDF5 library loaded. For example in the case of Python3 on Stampede 2 you probably need module load phdf5 instead of module load hdf5.

Firefly Fails to Install

If Firefly fails to install (as part of the visualization step), there’s a good chance it’s because you haven’t set up an automatic connection to GitHub using ssh. Follow GitHub’s tutorial to do so. Alternatively you can turn the Firefly install off (install_firefly=False as one of the visualization_kwargs) and clone it yourself. Afterwards change firefly_dir in export_to_firefly_kwargs to the location of the Firefly repository you clone.