Starting Software and Applications - mghpcc-projects/c3ddb GitHub Wiki

On c3ddb, software and application environments are often controlled using “modules.” This page will cover the basics of choosing, loading and using modules on the cluster.

Start Applications With Modules:

Modules set the appropriate environment variables for the application and prevent version and other application conflicts from occurring on the cluster. Applications should be loaded and unloaded as needed.

To list your loaded modules:

[username@[email protected]/]$ module list

      Currently Loaded Modulefiles:
      1) gcc/6.3.0

Most applications will not run without being loaded.

[username@[email protected]/]$ merlin

      -bash: merlin: command not found

To list available packages use the module command with the “avail” argument

[username@[email protected]/]$ module avail

    ---------------------------- /share/etc/modulefiles ----------------------------
    BEAGLE/BEAGLE-3.3.2_jar_x86_64           locuszoom/1.2
    CASAVA/CASAVA_v1.8.2_gnu446              log4perl/v1.43
    CPAT/CPAT-1.2.1_Python-2.7.3_gnu446      mach/mach-1.0.18.c_gnu446
    DELLY/0.0.11                             merlin/merlin-1.1.2_gnu446
    EIGENSOFT/EIGENSOFT-4.2_gnu447           metal/metal_2011-03-25_gnu447
    ...                                   ...

To load an application, invoke the module command with the “load” argument.

[username@[email protected]/]$ module load merlin

To run the application, type the application command.

[username@[email protected]/]$ merlin --help

     MetaAnalysis Helper - (c) 2007 - 2009 Goncalo Abecasis
     This version released on 2011-03-25

     #This program facilitates meta-analysis of genome-wide association studies.
     #Commonly used commands are listed below:
     #Options for describing input files ...
     #SEPARATOR        [WHITESPACE|COMMA|BOTH|TAB] (default = WHITESPACE)
     #COLUMNCOUNTING   [STRICT|LENIENT]            (default = 'STRICT')
     #MARKERLABEL      [LABEL]                     (default = 'MARKER')

To unload a module, invoke the module command with the “unload” argument.

[username@[email protected]/]$ module unload merlin

Note: Both MATLAB and SAS have graphical user interfaces. X Forwarding is required to use either of these applications.