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Loki on Biowulf & Helix

Loki is a linkage analysis package, primarily for large and complex pedigrees, which uses Markov chain Monte Carlo (MCMC) techniques to avoid many of the computational problems that prevent exact computational methods being used for large pedigrees. Loki was originally designed for linkage analysis of quantitative traits, though there is some limited support for qualitative trait linkage analysis.

Example files below can be copied :

$ mkdir /data/$USER/dir; cd /data/$USER/dir
$ cp -r /usr/local/apps/loki/sample .
$ cd /data/$USER/dir/sample

Running on Helix

$ module load loki
$ cd /data/$USER/dir/sample
$ loki lkmibd.loki > logfile

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 loki
cd /data/$USER/dir/sample
loki lkmibd.loki > logfile

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/$USER/dir1; loki lkmibd.loki > logfile
  cd /data/$USER/dir2; loki lkmibd.loki > logfile
  cd /data/$USER/dir2; loki lkmibd.loki > logfile
	[......]
  

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

  $ swarm -f swarmfile --module loki

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

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

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 loki
cn999$ cd /data/$USER/dir/sample
cn999$ loki lkmibd.loki > logfile
[...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

On helix/biowulf, make sure you have Xwindows connection, then type:

$ gs /usr/local/apps/loki/docs/loki_doc.ps