Software

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FarmShare software installed with the OS

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

FarmShare proprietary/commercial software

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 All have been replaced by /farmshare/software.

All the software is now available via the 'module' command, with examples below.

FarmShare software managed with modules

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 ------------------------------------------------------
   abinit/7.4.2       cudasamples/5.5                  julia/git11262013          povray/3.6.1                    statamp/12.1
   acml/5.3.1         farmvnc/0.1                      mathematica/9.0            sagemath/5.11                   statase/12.1
   ampl/20120629      farmvnc/0.2               (D)    matlab/r2012b              sas/9.2                         stattransfer/12
   atompaw/4.0.0.3    gams/24.1                        matlab/r2013a       (D)    sas/9.3
   cplex/12.4         gaussian/g09gview50       (D)    mzmine/2.10                sas/9.4                  (D)
   cuda/5.5           gaussian/g09sse4gview50          openmpi/1.6.5              sentarus/H_2013.03-SP1

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

A few commands to get you started: 

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

automatic loading of packages at login

If you wish to have a set of modules loaded automatically at login time you can follow these steps. Once you have saved the module list, you not need to do anything further, the list will be loaded each time you login.

first, check our current environment. Ok good, I don't have anything loaded

$ module list

Lmod Warning: No modules installed

Now let's select a few modules we want to load. Then we save them

$ module avail

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

-------------------------------------------------- /farmshare/software/mf/raring --------------------------------------------------
   abinit/7.4.2       cudasamples/5.5                  matlab/r2012b          sas/9.3                  (D)
   acml/5.3.1         farmvnc/0.1                      matlab/r2013a   (D)    sentarus/H_2013.03-SP1
   ampl/20120629      gams/24.1                        openmpi/1.6.5          statamp/12.1
   atompaw/4.0.0.3    gaussian/g09gview50       (D)    povray/3.6.1           statase/12.1
   cplex/12.4         gaussian/g09sse4gview50          sagemath/5.11          stattransfer/12
   cuda/5.5           mathematica/9.0                  sas/9.2

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

A few commands to get you started: 

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 farmvnc matlab statase
$ module save
Saved current collection of modules to: default
$ logout
Connection to corn-image closed.


Now, upon logging in, the saved modules are loaded automatically

$ ssh corn.stanford.edu
corn-image.stanford.edu - Ubuntu 13.04, amd64
4-core Xeon E5620 @ 2.40GHz (vmware); 15.67GB RAM, 1024MB swap
Puppet environment: rec_master; kernel 3.8.0-31-generic (x86_64)
 --*-*- Stanford University Research Computing -*-*--

  _____                    ____  _
 |  ___|_ _ _ __ _ __ ___ / ___|| |__   __ _ _ __ ___
 | |_ / _` | '__| '_ ` _ \\___ \| '_ \ / _` | '__/ _ \
 |  _| (_| | |  | | | | | |___) | | | | (_| | | |  __/
 |_|  \__,_|_|  |_| |_| |_|____/|_| |_|\__,_|_|  \___|


    http://farmshare.stanford.edu

###
##
# new to Ubuntu 13.04 Farmshare?
# follow this link to get started:
# https://www.stanford.edu/group/farmshare/cgi-bin/wiki/index.php/Ubuntu13TransitionGuide
##
###

Last login: Fri Nov  1 14:03:05 2013 from barley-storage01.stanford.edu
Restoring modules to users default
$ module list

Currently Loaded Modules:
  1) farmvnc/0.1   2) matlab/r2013a   3) statase/12.1


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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