It is critical that jobscripts are self contained, and do not utilise environment variables inherited from external sources such as ~/.profile, or the environment from which the job was launched. The reasons for this are that:
- Pawsey staff are able to reproduce your job if you require assistance,
- you can share jobscripts with colleagues and they will get the same results, and
- you can move your workflow to another system and expect it to work the same.
The below code in a jobscript will ensure that a SLURM job starts with a clean environment, and no environment variables are inherited from your interactive shell.
Do not put "module use" or "module load" in Shell Initialisation Scripts (~/.login, ~/.profile, ~/.cshrc, ~/.bashrc etc). Altering a job's environment in this manner is difficult and slow to debug, and you cannot grant access to colleagues without reducing the security of your login account.