Software

From FarmShare

(Difference between revisions)
Jump to: navigation, search
Line 8: Line 8:
===using latest version of matlab===
===using latest version of matlab===
 +
 +
To run the latest version of matlab, execute these commands:
 +
 +
<source lang="sh">
 +
$ module avail
 +
$ module load matlab
 +
$ module list
 +
$ matlab -nodesktop
 +
</source>
 +
 +
For example
 +
<source lang="sh">
<source lang="sh">

Revision as of 11:24, 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 All have been replaced by /farmshare/software.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:

Contents

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

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 matlab

bishopj@scorn:~$ 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
  -------------------------------------------------------------------------------------------------------------

bishopj@scorn:~$ 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
      
      
bishopj@scorn:~$ module load matlab/r2012b
bishopj@scorn:~$ 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 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

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

Personal tools
Toolbox
LANGUAGES