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Merlin on Biowulf & Helix

MERLIN uses sparse trees to represent gene flow in pedigrees and is one of the fastest pedigree analysis packages around (Abecasis et al, 2002).

Running on Helix

$ module load merlin
$ cd /data/$USER/dir
$ merlin merlin.dat

Running a single batch job on Biowulf

1. Create a script file. The file will contain the lines similar to the lines below.

#!/bin/bash


module load merlin
cd /data/$USER/merlin
merlin merlin.dat

2. Submit the script on biowulf:

$ sbatch jobscript

If more momory is required (default 4gb), specify --mem=Mg, for example

$ sbatch --mem=10g jobscript

Running a swarm of jobs on Biowulf

Setup a swarm command file:

  cd /data/$USER/dir1; merlin merlin.dat
  cd /data/$USER/dir2; merlin merlin.dat
  cd /data/$USER/dir3; merlin merlin.dat
	[......]
  

Submit the swarm file, -f specify the swarmfile name, and --module will be loaded the required module for each command line in the file:

  $ swarm -f swarmfile --module merlin

If more memory is needed for each line of commands, the below example allocate 10g for each command:

  $ swarm -f swarmfile -g 10 --module merlin

For more information regarding running swarm, see swarm.html

Running an interactive job on Biowulf

It may be useful for debugging purposes to run jobs interactively. Such jobs should not be run on the Biowulf login node. Instead allocate an interactive node as described below, and run the interactive job there.

biowulf$ sinteractive 
salloc.exe: Granted job allocation 16535

cn999$ module load merlin
cn999$ cd /data/$USER/dir
cn999$ merlin merlin.dat
[...etc...]

cn999$ exit
exit

biowulf$

Make sure to exit the job once finished.

If more memory is needed, use --mem. For example

biowulf$ sinteractive --mem=8g

Documentation

http://www.sph.umich.edu/csg/abecasis/Merlin/tour/linkage.html