slurm-example

This directory contains an example for running BoltzGen on SLURM.

The approach we use is to launch a job array that runs many single-GPU jobs. Each job calls "boltzgen run" to go through all pipeline steps (design generation, refolding, etc.) for a small number of designs. After all the jobs have completed, on a login node we use "boltzgen merge" to merge all individual task results together, then "boltzgen run --steps filtering" to apply filters to the combined set.

Note that other parallelization strategies could also work here. In particular, the individual BoltzGen pipeline steps (e.g. design generation, refolding) support parallelization across multiple GPUs within the step.

You will need to modify run.sh and probably also run_job_array.slurm for your site and analysis task.

After you've made your modifications, you can run:

$ bash run.sh submit

To submit the job array.

After that has finished, you can run:

$ bash run.sh process

to merge and filter the results.