From FarmShare

Revision as of 12:14, 14 September 2013

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 All have been replaced by /farmshare/software.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

bishopj@scorn:~$ 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

bishopj@scorn:~$ module load matlab
bishopj@scorn:~$ module list

Currently Loaded Modules:
  1) matlab/r2013a

$ matlab -nodesktop

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

$ module load 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

$ module spider stattransfer
bishopj@scorn:~$ module spider stattransfer

  -------------------------------------------------------------------------------------------------------------
  stattransfer: stattransfer/12
  -------------------------------------------------------------------------------------------------------------
    Description:
      File conversion utility

    This module can be loaded directly: module load stattransfer/12

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

modules

We use 'modules', a commonly used software package in HPC environments: http://modules.sourceforge.net/

The 'module' command has been added to your environment, but if you have modified your environment away from the defaults, you may need to source the module env vars for your shell.

For example, you may need to try something like this at the end of your .bashrc:

HOSTNAME=$(hostname)
if [ "${HOSTNAME:0:4}" = "corn" ]; then
  #source farmshare modules
  echo "on a corn! try module avail"
  eval `tclsh /mnt/glusterfs/software/free/modules/tcl/modulecmd.tcl sh autoinit`
fi

Then you can do something like:

module avail
module load stata
stata

Link: https://www.stanford.edu/group/hpcc/cgi-bin/mediawiki/index.php/Modules