Biowulf High Performance Computing at the NIH
Mega2 on Biowulf

“Manipulation Environment for Genetic Analyses” A data-handling program for facilitating genetic linkage and association analyses

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 input in bold):

[user@biowulf]$ sinteractive --mem=5g
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 mega2
[user@cn3144 ~]$ mega2 --help
Usage: mega2 [options] [batch-file-name] {arguments}
  acceptable options:
  DB         --DBfile 
                change the database name from dbmega2.db to .
                dump the database and if --DBread is also present,
                then exec’s a new copy of Mega2 to process the database.
                read an existing database file and do an analysis.
                set database compression level: 0 == off; 1 == gzip; (default == 1).
[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 mega2
cd /data/$USER
mega2 command

Submit this job using the Slurm sbatch command.

sbatch --mem=5g
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. mega2.swarm). For example:

cd dir1; mega2 command
cd dir2; mega2 command
cd dir10; mega2 command

Submit this job using the swarm command.

swarm -f mega2.swarm -g 5 --module mega2
-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 mega2 Loads the mega2 module for each subjob in the swarm