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rinikerlab / reeds

This pipeline is executing a RE-EDS run for relative free energy calculations. It can be used for example for calculation of hydration free energies or ligand binding free energies.
https://rinikerlab.github.io/reeds/
MIT License
30 stars 8 forks source link

Slurm compatibility #79

Closed candidechamp closed 2 years ago

candidechamp commented 2 years ago

Description

This PR contains the slight modifications to the RE-EDS code that allow submission of simulations using the Slurm submission system. The changes are essentially just import statements, and changes to the default options. I suggest keeping this PR open until euler has completely migrated to Slurm.

I tested submission of all steps of the pipeline successfully.

The only real change I made was that the "overall analysis" of each optimization iteration also creates a bash file to submit the analysis, instead of submitting it as a command, as I couldn't fix the bug I had otherwise.

Please let me know if you encounter any bugs and I'll fix them.

Also be careful that slurm reads 24:00 as 24 minutes and not 24 hours, (24:00:00 is the correct slurm syntax).

lgtm-com[bot] commented 2 years ago

This pull request introduces 8 alerts when merging 50c9faf7a8e28f1ad72edbda2b75ca7d7f220505 into bda4e81fcc99bcaa3755ea2a2eb34f2f3866635d - view on LGTM.com

new alerts:

lgtm-com[bot] commented 2 years ago

This pull request introduces 8 alerts when merging 13f2d1b02d6c4a2be97e87c1c6a956fff7592a12 into bda4e81fcc99bcaa3755ea2a2eb34f2f3866635d - view on LGTM.com

new alerts: