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One way to regulate the number of jobs running simultaneously is to add dependencies to the jobs with the #SBATCH --dependency=previous_job_id command.Another way to regulate the number of jobs running simultaneously is to use job arrays and adding a percentage at the end to set the limit of jobs running at the same time, for example using #SBATCH --array=0-39%10 to run 40 jobs, but only 10 at the same time.
Another way to regulate the number of jobs running simultaneously is to add dependencies to the jobs with the #SBATCH --dependency=previous_job_id command. A sample script to submit multiple jobs with dependencies can be found here.
Important note: set up ssh communication keys between nodes, as explained in the pdf at the end of this page (ARIES_Quick_Start_wl52_20220406.pdf).
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For submitting OpenMM jobs, a singularity container containers with OpenMM pre-installed is are available .in:
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container=/home/pcw2/bin/openmm-ctbp.sif |
This container does not have OpenSMOG, or other CTBP-specific tools, and they will need to be installed with pip3. For example, to install OpenSMOG:
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If you can not find a container with suitable options available, you may contact Prof. Whitford, or you may be able to use pip3.
Usage example with bash submission script, openmm run python script, and input files can be downloaded below.
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