Software
From FarmShare
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 All have been replaced by /farmshare/software.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:
more complete 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 gams/24.1 mathematica/9.0 matlab/r2013a (D) statamp/12.1 stattransfer/12 cuda/5.5 gaussian/g09gview50 matlab/r2012b sas/9.2 statase/12.1 -------------------------------------------------------- /farmshare/software/mf/raring-compat --------------------------------------------------------- CPLEX-12.4 GAMS-24.1 MATLAB-R2012b MATLAB-R2013a Mathematica-9.0 SAS-v9.2 StatTransfer-v12 StataMP-12.1 StataSE-12.1 Where: (D): Default Module See http://farmshare.stanford.edu 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
$ module load StatTransfer-v12 bishopj@scorn:~$ 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 [chekh@corn24.stanford.edu] ~ [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 -------------------------------------------------------------------
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