Software
From FarmShare
Line 7: | Line 7: | ||
/farmshare/software can be accessed as follows: | /farmshare/software can be accessed as follows: | ||
- | === | + | ===using latest version of matlab=== |
<source lang="sh"> | <source lang="sh"> | ||
Line 40: | Line 40: | ||
Currently Loaded Modules: | Currently Loaded Modules: | ||
1) matlab/r2013a | 1) matlab/r2013a | ||
+ | |||
+ | $ matlab -nodesktop | ||
+ | </source> | ||
+ | |||
+ | ===using a specific version of software (StatTransfer version 12 in this case)=== | ||
<source lang="sh"> | <source lang="sh"> | ||
$ module load StatTransfer-v12 | $ module load StatTransfer-v12 | ||
- | + | $ st --version | |
Stat/Transfer (c) 1986-2013 Circle Systems, Inc. | Stat/Transfer (c) 1986-2013 Circle Systems, Inc. | ||
www.stattransfer.com | www.stattransfer.com | ||
Line 54: | Line 59: | ||
Status: License OK - Expires April 30, 2014 | Status: License OK - Expires April 30, 2014 | ||
- | + | $ module spider stattransfer | |
- | $ module | + | bishopj@scorn:~$ module spider stattransfer |
- | ------------------------------------------------------------------- | + | |
- | + | ------------------------------------------------------------------------------------------------------------- | |
+ | stattransfer: stattransfer/12 | ||
+ | ------------------------------------------------------------------------------------------------------------- | ||
+ | Description: | ||
+ | File conversion utility | ||
+ | |||
+ | This module can be loaded directly: module load stattransfer/12 | ||
- | + | Help: | |
- | + | This is Stat/Transfer version 12 | |
- | + | ||
- | + | call 'st' for CLI | |
+ | |||
</source> | </source> | ||
Revision as of 12:14, 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 All have been replaced by /farmshare/software.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:
using latest version of matlab
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 software (StatTransfer version 12 in this case)
$ 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 $ module spider stattransfer bishopj@scorn:~$ module spider stattransfer ------------------------------------------------------------------------------------------------------------- stattransfer: stattransfer/12 ------------------------------------------------------------------------------------------------------------- Description: File conversion utility This module can be loaded directly: module load stattransfer/12 Help: This is Stat/Transfer version 12 call 'st' for CLI
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