Biowulf High Performance Computing at the NIH
Viennarna on HPC

The ViennaRNA Package consists of a C code library and several stand-alone programs for the prediction and comparison of RNA secondary structures.

References:

Documentation
Important Notes

Interactive job
Interactive jobs should be used for debugging, graphics, or applications that cannot be run as batch jobs.

Allocate an interactive session and run the program. Sample session:

[user@biowulf]$ sinteractive
salloc.exe: Pending job allocation 46116226
salloc.exe: job 46116226 queued and waiting for resources
salloc.exe: job 46116226 has been allocated resources
salloc.exe: Granted job allocation 46116226
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3144 are ready for job

[user@cn3144 ~]$ module load viennarna
[user@cn3144 ~]$ RNAfold < INPUT.fa

[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

Batch job
Most jobs should be run as batch jobs.

Create a batch input file (e.g. batch.sh). For example:

#!/bin/bash
set -e
module load viennarna
RNAfold < INPUT.fa

Submit this job using the Slurm sbatch command.

sbatch batch.sh
Swarm of Jobs
A swarm of jobs is an easy way to submit a set of independent commands requiring identical resources.

Create a swarmfile (e.g. job.swarm). For example:

cd dir1; RNAfold < INPUT.fa
cd dir2; RNAfold < INPUT.fa
cd dir3; RNAfold < INPUT.fa

Submit this job using the swarm command.

swarm -f job.swarm --module viennarna
where
--module Loads the module for each subjob in the swarm