Random Jungle on the Biowulf Linux CLuster

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Random Jungle on Biowulf

Random Jungle was developed by Daniel F. Schwarz and provides a free random forest implementation for high dimensional data. It is intended to be widely useful, and usable across a broad spectrum of applications.

Random Jungle website.
On Safari to Random Jungle: A fast implementation of Random Forests for high dimensional data.. Schwarz DF, Konig IR, Ziegler A., Bioinformatics. 2010 May 26.

Usage

There are two executables: rjungle and rjunglesparse. Several versions of Random Jungle are available on Helix/Biowulf in /usr/local/apps/rjungle. The easiest way to select a particular version is to use the modules commands, as in the example below:

[user@biowulf]$ module avail rjungle

----------------------- /usr/local/Modules/3.2.9/modulefiles --------------
rjungle/1.0.359        rjungle/1.2.362-mpi    rjungle/1.2.365        
rjungle/1.3.0(default) rjungle/1.3.0-mpi

[user@biowulf]$ module load rjungle/1.2.365

[user@biowulf]$ module list
Currently Loaded Modulefiles:
  1) rjungle/1.2.365

If you type 'module load rjungle' without specifying a version, the default version will be loaded.

To submit a swarm of randomjungle jobs, set up a swarm command script along the following lines:

#this file is rjswarm
cd /data/user/mydir1; rjungle [...options...]
cd /data/user/mydir2; rjunglesparse [...options...]
cd /data/user/mydir3; rjungle [...options...]
...

Submit this swarm with the command:

swarm -f rjswarm --module rjungle/1.2.365

Alternatively, you can add 'module load rjungle/1.2.365;' at the beginning of each line of your swarm command file, and then submit with 'swarm -f rjswarm'.

Submitting a single Random Jungle batch job

Sample batch script for a single randomjungle job:

#!/bin/bash

# load the latest (default) version of Random Jungle
module load rjungle

cd /data/user/mydir
rjungle [...options]

This job can be submitted with the command:

qsub -l nodes=1 rjscript

Documentation

Random Jungle website