Biowulf High Performance Computing at the NIH
RNAstructure on Biowulf
RNAstructure is a complete package for RNA and DNA secondary structure prediction and analysis.

Documentation

https://rna.urmc.rochester.edu/RNAstructureWeb/Information/Help.html

Important Notes
Submitting an interactive job

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salloc.exe: Job allocation 789523 has been revoked.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]$

Submitting a single batch job

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 Swarm

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