Biowulf High Performance Computing at the NIH
Probabel on HPC

ProbABEL is a Tool for genome-wide association analysis of imputed genetic data. It was designed to perform such regression in fast, memory-efficient and consequently genome-wide feasible manner. Currently, ProbABEL implements linear, logistic regression, and Cox proportional hazards models.


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 probabel
[user@cn3144 ~]$ cp -rp /usr/local/apps/probabel/0.4.3/examples /data/$USER
[user@cn3144 ~]$ cd /data/$USER/examples
[user@cn3144 ~]$ export padir=/usr/local/apps/probabel/0.4.3/bin/
[user@cn3144 ~]$ ./

[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 probabel
probabel commands

Submit this job using the Slurm sbatch command.

sbatch [--mem=#]
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; probabel commands
cd dir2; probabel commands
cd dir3; probabel commands

Submit this job using the swarm command.

swarm -f job.swarm [-g #] --module probabel
-g # Number of Gigabytes of memory required for each process (1 line in the swarm command file)
--module Loads the module for each subjob in the swarm