From FarmShare

Revision as of 15:33, 24 May 2012 by Chekh (Talk | contribs)
Jump to: navigation, search

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:

Don't use /usr/pubsw

Maybe use /usr/sweet/bin, though we'll be installing new versions of software outside of AFS, use 'module avail' instead.


We use 'modules', a commonly used software package in HPC environments:

First, you will need to source the module env vars for your shell:

  If using sh/bash/ksh/zsh, add this to your .bashrc

     eval `tclsh /mnt/glusterfs/software/free/modules/tcl/modulecmd.tcl sh autoinit`

  If using csh/tcsh, add this to your .cshrc

     eval `tclsh /mnt/glusterfs/software/free/modules/tcl/modulecmd.tcl csh autoinit`

  If using perl, put this in your script

     eval `tclsh /mnt/glusterfs/software/free/modules/tcl/modulecmd.tcl perl autoinit`;

For example, try something like this at the end of your .bashrc:

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`

Then you can do something like:

module avail
module load stata

more complete example

[] ~ [0] 
$ module avail
------------------------------------------- /mnt/glusterfs/software/free/modules/tcl/modulefiles --------------------------------------------
MATLAB-R2009b     MATLAB-R2010b     MATLAB-R2011b     StatTransfer-10.1 StatTransfer-11.2 stata-v12         

[] ~ [0] 
$ module load StatTransfer-10.1

[] ~ [0] 
$ st --version
Stat/Transfer (c) 1986-2011 Circle Systems, Inc. 
Version 10.1.1847.0331 - 64 Bit Linux

User:	Pat Box (1) - Stanford University
License Type:	Linux - Single Machine Lease
Warning: Your annual license is in its last month.
Status:	License OK - Expires April 30, 2012
Stat/Transfer is running in a remote secure shell. A workgroup license covering all users may be required.
Please contact our sales department ( for more information.

[] ~ [0] 
$ module unload StatTransfer-10.1

[] ~ [0] 
$ module load StatTransfer-11.2

[] ~ [0] 
$ st --version
Stat/Transfer (c) 1986-2012 Circle Systems, Inc. 
Version 11.2.2013.0330 - 64 Bit Linux

User:	Jane Tansuwan - Stanford University
License Type:	Linux - 50 User Workgroup / Lease
Status:	License OK - Expires April 30, 2013

[] ~ [0] 
$ module help StatTransfer-11.2
Module Specific Help for /mnt/glusterfs/software/free/modules/tcl/modulefiles/StatTransfer-11.2:

	 ITS-maintained Stat/Transfer v11.2 (in GlusterFS)
	 use st for command-line version
	 use stattransfer for X11 GUI version
Personal tools