Overview

On the SCC, software and application environments are often controlled using “modules.” This page will cover the basics of choosing, loading and using modules on the cluster. For complete information on modules, see the module page. Information about available software packages is available in our software pages.

Start Application Without Modules

Some applications on the Shared Computing Cluster do not require modules. Notable examples are matlab and sas. To run these applications and basic system commands, simply type the application name.
[username@scc1 ~]$ matlab

[username@scc1 ~]$ sas
Note: Both MATLAB and SAS have graphical user interfaces. X Forwarding is required to use either of these applications.

Start Applications With Modules

Most applications on the Shared Computing Cluster require the use of 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@scc1 ~]$ module list
    Currently Loaded Modulefiles:
      1) pgi/13.5
    
  • Most applications will not run without being loaded.
    [username@scc1 ~]$ merlin
    -bash: merlin: command not found
    
  • To list available packages use the module command with the “avail” argument
    [username@scc1 ~]$ 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@scc1 ~]$ module load merlin
    
  • To run the application, type the application command.
    [username@scc1 ~]$ merlin --help
    
    MetaAnalysis Helper - (c) 2007 - 2009 Goncalo Abecasis
    This version released on 2011-03-25
    
    # This program faciliates 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@scc1 ~]$ module unload merlin
    

For more information, including other module commands, automatic loading of modules and personal module creation, please see our module page. Information about available software packages is provided in our software pages.


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