Biowulf High Performance Computing at the NIH
Schism on Biowulf

Subclonal Hierarchy Inference from Somatic Mutations

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 schism
[user@cn3144 ~]$ cp -r /usr/local/apps/schism/example/E1 /data/$USER/
[user@cn3144 ~]$ cd /data/$USER/E1
[user@cn3144 ~]$ runSchism analyze --config E1.yaml [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. schism.sh). For example:

#!/bin/bash
set -e
module load schism
cd dir
runSchism analyze --config E1.yaml

Submit this job using the Slurm sbatch command.

sbatch [--mem=#] schism.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. schism.swarm). For example:

cd dir1; runSchism analyze --config E1.yaml
cd dir1; runSchism analyze --config E1.yaml
cd dir1; runSchism analyze --config E1.yaml

Submit this job using the swarm command.

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