Biowulf High Performance Computing at the NIH
MUMmer on Biowulf

MUMmer is a system for rapidly aligning entire genomes.

Versatile and open software for comparing large genomes S. Kurtz, A. Phillippy, A.L. Delcher, M. Smoot, M. Shumway, C. Antonescu, and S.L. Salzberg. Genome Biology (2004), 5:R12.
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 mummer

[user@cn3144 ~]$ mummer /fdb/genome/hg19/chr_all.fa /fdb/genome/hg19/chrX.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. For example:

set -e
module load mummer
mummer /fdb/genome/hg19/chr_all.fa /fdb/genome/hg19/chrX.fa

Submit this job using the Slurm sbatch command.

sbatch --mem=10g
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. MUMmer.swarm). For example:

mummer    /fdb/genome/hg19/chr_all.fa     file1.fa
mummer    /fdb/genome/hg19/chr_all.fa     file2.fa
mummer    /fdb/genome/hg19/chr_all.fa     file3.fa

Submit this job using the swarm command.

swarm -f MUMmer.swarm -g 1-0 [-t #] --module MUMmer
-g # Number of Gigabytes of memory required for each process (1 line in the swarm command file)
-t # Number of threads/CPUs required for each process (1 line in the swarm command file).
--module MUMmer Loads the MUMmer module for each subjob in the swarm