Control the number of OpenMM threads

[aozalevsky]

Since a non-docker setup doesn't have the cgroups limiting capabilities, it would be nice to have finer control over the relaxation step performed with OpenMM.

The default AF script uses OpenMM with a CPU platform which by default consumes all CPUs. The behavior can be tuned with the OPENMM_CPU_THREADS environment variable which can be setup similar to the GPU selection process.

For our local version I added following lines:

        c)
                openmm_threads=$OPTARG
        ;;
        <...>

if [[ "$openmm_threads" ]] ; then
    export OPENMM_CPU_THREADS=${openmm_threads}
fi

[sanjaysrikakulam]

Hi @aozalevsky

I have added OpenMM threads support to the script. Thank you for your suggestion.