Software
From FarmShare
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<source lang="sh"> | <source lang="sh"> | ||
- | + | $ module avail | |
--------------------- /farmshare/software/free/lmod-5.0-install/lmod/lmod/modulefiles/Core ---------------------- | --------------------- /farmshare/software/free/lmod-5.0-install/lmod/lmod/modulefiles/Core ---------------------- | ||
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or to find out more information for a package: module spider matlab | or to find out more information for a package: module spider matlab | ||
- | + | $ module load matlab | |
- | + | $ module list | |
Currently Loaded Modules: | Currently Loaded Modules: | ||
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<source lang="sh"> | <source lang="sh"> | ||
- | + | $ module spider matlab | |
------------------------------------------------------------------------------------------------------------- | ------------------------------------------------------------------------------------------------------------- | ||
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------------------------------------------------------------------------------------------------------------- | ------------------------------------------------------------------------------------------------------------- | ||
- | + | $ module spider matlab/r2012b | |
------------------------------------------------------------------------------------------------------------- | ------------------------------------------------------------------------------------------------------------- | ||
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- | + | $ module load matlab/r2012b | |
- | + | $ module list | |
Currently Loaded Modules: | Currently Loaded Modules: |
Revision as of 12:32, 14 September 2013
Contents |
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 All have been replaced by /farmshare/software.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
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 ----------------------------------------- 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 $ 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 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