Biowulf High Performance Computing at the NIH
minimac on Biowulf

Minimac is a low memory, computationally efficient implementation of the MaCH algorithm for genotype imputation.

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 input in bold):

[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 minimac/minimac3

[user@cn3144 ~]$  minimac --refHaps refPanel.vcf \ 
                --haps targetStudy.vcf \
                --prefix testRun

[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. minimac.sh). For example:

#!/bin/bash
set -e
module load minimac/minimac3
minimac-omp --cpus $SLURM_CPUS_PER_TASK --refHaps refPanel.vcf \ 
                --haps targetStudy.vcf \
                --prefix testRun

Submit this job using the Slurm sbatch command.

sbatch --cpus-per-task=4 [--mem=#] minimac.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. minimac.swarm). For example:

minimac-omp --cpus $SLURM_CPUS_PER_TASK -refHaps ref1.vcf --haps target1.vcf --prefix test1
minimac-omp --cpus $SLURM_CPUS_PER_TASK -refHaps ref2.vcf --haps target2.vcf --prefix test2
minimac-omp --cpus $SLURM_CPUS_PER_TASK -refHaps ref3.vcf --haps target3.vcf --prefix test3

Submit this job using the swarm command.

swarm -f minimac.swarm [-g #] [-t 4] --module minimac
where
-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). 4 or 8 threads max is recommended.
--module minimac Loads the minimac module for each subjob in the swarm