Troubleshooting

Here are some errors users might encounter and their solutions:

In EMD/workspaceXXX/lammps_files/slurm*.out users might get the following error:

from numpy import (exp, inf, pi, sqrt, floor, sin, cos, around, int,

ImportError: cannot import name 'int' from 'numpy' (/home/shaleek/.local/lib/python3.8/site-packages/numpy/__init__.py)

This error occurs because of a version mismatch on scipy and numpy. FSL recently updated the python/3.8 module this software uses which is causing this issue to occur (numpy recently deprecated the "from numpy import int" functionality).

Updating scipy fixes this issue, as it no longer calls "from numpy import int"

This can be done via:

module load python/3.8

pip3 install --upgrade --user scipy

This loads the python/3.8 FSL module and then upgrades scipy (only for the user! We don't have permissions to fix things over at FSL and can only fix it for our own user account!)