https://rna.urmc.rochester.edu/RNAstructureWeb/Information/Help.html
Allocate an interactive session and run the interactive job there.
[biowulf]$ sinteractive --mem=5g salloc.exe: Granted job allocation 789523 salloc.exe: Waiting for resource configuration salloc.exe: Nodes cn0135 are ready for job [cn0135]$ cd /data/$USER/ [cn0135]$ module load rnastructure [cn0135]$ bifold query.fasta target.fasta query-target.ct [cn0135]$ exit salloc.exe: Job allocation 789523 has been revoked. [biowulf]$
1. Create a script file (myscript) similar to the one below
#! /bin/bash # myscript set -e module load rnastructure || exit 1 cd /data/$USER/ bifold query.fasta target.fasta query-target.ct
2. Submit the script on biowulf:
[biowulf]$ sbatch --mem=5g myscript
Using the 'swarm' utility, one can submit many jobs to the cluster to run concurrently.
Set up a swarm command file (eg /data/$USER/cmdfile).
cd /data/$USER/dir1; bifold query.fasta target.fasta query-target.ct cd /data/$USER/dir2; bifold query.fasta target.fasta query-target.ct cd /data/$USER/dir3; bifold query.fasta target.fasta query-target.ct ... cd /data/$USER/dir20; bifold query.fasta target.fasta query-target.ct
submit the swarm job:
$ swarm -f cmdfile --module rnastructure -g 5
For more information regarding running swarm, see swarm.html