A comprehensive library attending Gromacs simulations on HPC clusters.
Features:
- Works with slurm, moab, gridengine and can also attend local simulations.
- Track simulations and files using easy to understand databases.
- One place to get status updates on all your runnung gromacs simulations.
- Undo-feature: Did an oopsie? Undo the last command using
python simulation_attender.py undo
simulation_attender.py is a monolithic script you just need two files:
- First install the requirements via:
$ pip install -r https://raw.githubusercontent.com/kevinsawade/simulation_attender/main/requirements.txt- Then get the main file:
$ wget https://raw.githubusercontent.com/kevinsawade/simulation_attender/main/simulation_attender/simulation_attender.py# collect simulations
python simulation_attender.py collect /work
# template the simulations
python ../simulation_attender/simulation_attender.py template --module_loads "module load gromacs/2023.1" --command "gmx mdrun -deffnm {{ stem }}"
# list simulations
python ../simulation_attender/simulation_attender.py list
# submit
python ../simulation_attender/simulation_attender.py submit
# run and check
python ../simulation_attender/simulation_attender.py runVisit: https://kevinsawade.github.io/simulation_attender/ to get to the full documentation./
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