Software

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FarmShare software managed with modules

There is a lot of software available on the FarmShare systems. The systems run Ubuntu, so a lot of Ubuntu packages are installed.

There is also some licensed software installed: https://itservices.stanford.edu/service/sharedcomputing/software

Notice: /usr/pubsw, /usr/sweet/bin, and /mnt/glusterfs/software have been deprecated. All have been replaced by /farmshare/software.

/farmshare/software can be accessed as follows:

using latest version of matlab

To run the latest version of matlab, execute these commands:

$ module avail
$ module load matlab
$ module list
$ matlab -nodesktop

For example

$ module avail

--------------------- /farmshare/software/free/lmod-5.0-install/lmod/lmod/modulefiles/Core ----------------------
   lmod/lmod    settarg/settarg

----------------------------------------- /farmshare/software/mf/raring -----------------------------------------
   cplex/12.4    gaussian/g09gview50    matlab/r2013a   (D)    statase/12.1
   cuda/5.5      mathematica/9.0        sas/9.2                stattransfer/12
   gams/24.1     matlab/r2012b          statamp/12.1

------------------------------------- /farmshare/software/mf/raring-compat --------------------------------------
   CPLEX-12.4    MATLAB-R2012b    Mathematica-9.0    StatTransfer-v12    StataSE-12.1
   GAMS-24.1     MATLAB-R2013a    SAS-v9.2           StataMP-12.1

  Where:
   (D):  Default Module

See https://www.stanford.edu/group/farmshare/cgi-bin/wiki/index.php/FarmShare_software for description of how to
use modules. 

To load latest version of matlab: module load matlab 
You can load a specific version by: module load matlab/r2012b or module load MATLAB-R2012b

or to find out more information for a package: module spider matlab

$ module load matlab
$ module list

Currently Loaded Modules:
  1) matlab/r2013a

$ matlab -nodesktop

using a specific version of matlab

You can run a specific version of matlab by running these commands:

$ module spider matlab
$ module spider matlab/r2012b
$ module load matlab/r2012b
$ module list
$ matlab -nodesktop

Example session

$ module spider matlab

  -------------------------------------------------------------------------------------------------------------
  matlab:
  -------------------------------------------------------------------------------------------------------------
    Description:
      MATLAB and toolboxes

     Versions:
        matlab/r2012b
        matlab/r2013a

  -------------------------------------------------------------------------------------------------------------
  To find detailed information about matlab please enter the full name.
  For example:

     $ module spider matlab/r2013a
  -------------------------------------------------------------------------------------------------------------

$ module spider matlab/r2012b 

  -------------------------------------------------------------------------------------------------------------
  matlab: matlab/r2012b
  -------------------------------------------------------------------------------------------------------------
    Description:
      MATLAB and toolboxes

    This module can be loaded directly: module load matlab/r2012b

    Help:
      This is MATLAB R2012b
      
      call matlab -nosplash -nodesktop to get the CLI
      
      
$ module load matlab/r2012b
$ module list

Currently Loaded Modules:
  1) matlab/r2012b

$ matlab -nodesktop

using a specific version of software (StatTransfer version 12 in this case)

An alternate form of the above

$ module spider StatTransfer-v12 

  -------------------------------------------------------------------------------------------------------------
  StatTransfer-v12: StatTransfer-v12
  -------------------------------------------------------------------------------------------------------------
    Description:
      File conversion utility

    This module can be loaded directly: module load StatTransfer-v12

    Help:
      This is Stat/Transfer version 12
      
      call 'st' for CLI
      

$ module load StatTransfer-v12
$ module list

Currently Loaded Modules:
  1) StatTransfer-v12

$ st --version
Stat/Transfer (c) 1986-2013 Circle Systems, Inc.
www.stattransfer.com 
Version 12.0.56.0613 - 64 Bit Linux

Serial:	B2CNR-FZAS7-LPHI
User:	Software Licensing - Stanford University
License Type:	25 User Workgroup / Lease
Status:	License OK - Expires April 30, 2014

switching between versions of software packages

If you wish to switch between versions it is quite easy. In this case we switch from matlab 2013a back to 2012b

$ module list

Currently Loaded Modules:
  1) matlab/r2013a

$ module purge
$ module list

Lmod Warning: No modules installed

$ module load matlab/r2012b
$ module list

Currently Loaded Modules:
  1) matlab/r2012b

$ matlab -nodesktop


modules

We use 'lmod', a variant of commonly used software package 'modules' in HPC environments: http://www.tacc.utexas.edu/tacc-projects/mclay/lmod

If this your first time using modules, this is a good introduction: http://www.tacc.utexas.edu/tacc-projects/mclay/lmod/user-guide/users-tour-of-module-command

The 'module' command has been added to your environment, but if you have modified your environment away from the defaults, you may need to make some configuration changes.

Email us and we will be happy to help: research-computing-support@stanford.du

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