View source for Using modules on cyclone

== Using modules on cyclone==

This page documents how to use Modulefiles on the Abel (HPC for UiO) and Colossus (HPC for TSD) clusters. Same procedure applies on cyclone.

To simplify setting up environments for compilers, MPI-versions and some installed applications, the clusters have the [http://modules.sourceforge.net Environment Modules package] installed. This provides means for dynamic modification of a user's environment via modulefiles.

Each modulefile contains the information needed to configure the shell for an environment. Typically, a modulefile modifies environment variables like PATH, MANPATH, LD_LIBRARY_PATH, CPATH and PKG_CONFIG_PATH to give access to an application or library.

Modulefiles can be used from most shells, as well as Perl and Python. Modulefiles can be loaded/unloaded on the command line or within your scripts by typing:

<code>
module load modulefile

module unload modulefile
</code>

(On Colossus, the module commands can only be used in job scripts.)  You can also ask for a specific version of a modulefile:

<code>
module load modulefile/version
</code>

For the purpose of reproducability, we encourage users to load specific versions of modulefiles.  Also, we recommend using

<code>
module purge
</code>

prior to any module load commands in job scripts, to prevent inheriting environment variables set by module commands in the shell used when submitting the job.

The available modulefiles can be listed by module avail. Example output:

 <nowiki>
$ module avail 
------------------------ /usr/share/Modules/modulefiles -------------------------
dot         module-cvs  module-info modules     null        use.own

--------------------------- /cluster/etc/modulefiles ----------------------------
454apps/2.8(default)             mcmcphase/2.0(default)
R/2.15.1(default)                microbiomeutil/20110519(default)
R/2.15.1.shlib                   migrate/3.3.2(default)
abyss/1.3.4(default)             mothur/1.26.0(default)
adf/2010.02b(default)            mrbayes/3.2.1(default)
adf/2012.01b                     muscle/3.8.31(default)
ampliconnoise/1.25(default)      ncl/2.1.18(default)
beagle/1.0(default)              newbler/2.8(default)
[...]
</nowiki>

You can also specify a name:

 <nowiki>
$ module avail blast
--------------------------- /cluster/etc/modulefiles ----------------------------
blast/2.2.26(default)  blast+/2.2.26(default)
</nowiki>

You will get a list of current loaded modulefiles by

 <nowiki>
$ module list
Currently Loaded Modulefiles:
 1) intel/2011.10   2) R/2.15.1
</nowiki>

A help text exists for most of the modulefiles; to view it, type

<code>
module help modulefile
</code>

To view exactly what a modulefile is doing to your environment, type

<code>
module show modulefile
</code>

For further documentation, please refer to the [http://modules.sourceforge.net Environment Modules homepage]

Personalize default modulefiles

You may add loading of modulefiles to your .bash_profile file to make sure your favorite modulefile is always loaded when logging in. For instance, to always have the intel modulefile load on login, add:

<code>
module load intel
</code>

to the .bash_profile file.