Software
From FarmShare
Line 1: | Line 1: | ||
- | ==FarmShare software | + | ==FarmShare software installed with the OS== |
There is a lot of software available on the FarmShare systems. The systems run Ubuntu, so a lot of [[Packages | Ubuntu packages]] are installed. | There is a lot of software available on the FarmShare systems. The systems run Ubuntu, so a lot of [[Packages | Ubuntu packages]] are installed. | ||
+ | |||
+ | ==FarmShare proprietary/commercial software== | ||
There is also some licensed software installed: https://itservices.stanford.edu/service/sharedcomputing/software | There is also some licensed software installed: https://itservices.stanford.edu/service/sharedcomputing/software | ||
Line 7: | Line 9: | ||
Notice: /usr/pubsw, /usr/sweet/bin, and /mnt/glusterfs/software have been deprecated. All have been replaced by /farmshare/software. | Notice: /usr/pubsw, /usr/sweet/bin, and /mnt/glusterfs/software have been deprecated. All have been replaced by /farmshare/software. | ||
- | + | All the software is now available via the 'module' command, with examples below. | |
+ | |||
+ | ==FarmShare software managed with modules== | ||
===using latest version of matlab=== | ===using latest version of matlab=== |
Revision as of 12:25, 16 January 2015
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 All have been replaced by /farmshare/software.
All the software is now available via the 'module' command, with examples below.
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 ------------------------------------------------------ abinit/7.4.2 cudasamples/5.5 julia/git11262013 povray/3.6.1 statamp/12.1 acml/5.3.1 farmvnc/0.1 mathematica/9.0 sagemath/5.11 statase/12.1 ampl/20120629 farmvnc/0.2 (D) matlab/r2012b sas/9.2 stattransfer/12 atompaw/4.0.0.3 gams/24.1 matlab/r2013a (D) sas/9.3 cplex/12.4 gaussian/g09gview50 (D) mzmine/2.10 sas/9.4 (D) cuda/5.5 gaussian/g09sse4gview50 openmpi/1.6.5 sentarus/H_2013.03-SP1 -------------------------------------------------- /farmshare/software/mf/raring-compat --------------------------------------------------- ANSYS GAMS-24.1 MATLAB-R2013a SAS-v9.2 StataMP-12.1 CPLEX-12.4 MATLAB-R2012b Mathematica-9.0 StatTransfer-v12 StataSE-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. A few commands to get you started: 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 spider StatTransfer-v12 ------------------------------------------------------------------------------------------------------------- StatTransfer-v12: StatTransfer-v12 ------------------------------------------------------------------------------------------------------------- Description: File conversion utility This module can be loaded directly: module load StatTransfer-v12 Help: This is Stat/Transfer version 12 call 'st' for CLI $ module load StatTransfer-v12 $ module list Currently Loaded Modules: 1) 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
switching between versions of software packages
If you wish to switch between versions it is quite easy. In this case we switch from matlab 2013a back to 2012b
$ module list Currently Loaded Modules: 1) matlab/r2013a $ module purge $ module list Lmod Warning: No modules installed $ module load matlab/r2012b $ module list Currently Loaded Modules: 1) matlab/r2012b $ matlab -nodesktop
automatic loading of packages at login
If you wish to have a set of modules loaded automatically at login time you can follow these steps. Once you have saved the module list, you not need to do anything further, the list will be loaded each time you login.
first, check our current environment. Ok good, I don't have anything loaded
$ module list
Lmod Warning: No modules installed
Now let's select a few modules we want to load. Then we save them
$ module avail ------------------------------ /farmshare/software/free/lmod-5.0-install/lmod/lmod/modulefiles/Core ------------------------------- lmod/lmod settarg/settarg -------------------------------------------------- /farmshare/software/mf/raring -------------------------------------------------- abinit/7.4.2 cudasamples/5.5 matlab/r2012b sas/9.3 (D) acml/5.3.1 farmvnc/0.1 matlab/r2013a (D) sentarus/H_2013.03-SP1 ampl/20120629 gams/24.1 openmpi/1.6.5 statamp/12.1 atompaw/4.0.0.3 gaussian/g09gview50 (D) povray/3.6.1 statase/12.1 cplex/12.4 gaussian/g09sse4gview50 sagemath/5.11 stattransfer/12 cuda/5.5 mathematica/9.0 sas/9.2 ---------------------------------------------- /farmshare/software/mf/raring-compat ----------------------------------------------- ANSYS GAMS-24.1 MATLAB-R2013a SAS-v9.2 StataMP-12.1 CPLEX-12.4 MATLAB-R2012b Mathematica-9.0 StatTransfer-v12 StataSE-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. A few commands to get you started: 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 farmvnc matlab statase $ module save Saved current collection of modules to: default $ logout Connection to corn-image closed.
Now, upon logging in, the saved modules are loaded automatically
$ ssh corn.stanford.edu corn-image.stanford.edu - Ubuntu 13.04, amd64 4-core Xeon E5620 @ 2.40GHz (vmware); 15.67GB RAM, 1024MB swap Puppet environment: rec_master; kernel 3.8.0-31-generic (x86_64) --*-*- Stanford University Research Computing -*-*-- _____ ____ _ | ___|_ _ _ __ _ __ ___ / ___|| |__ __ _ _ __ ___ | |_ / _` | '__| '_ ` _ \\___ \| '_ \ / _` | '__/ _ \ | _| (_| | | | | | | | |___) | | | | (_| | | | __/ |_| \__,_|_| |_| |_| |_|____/|_| |_|\__,_|_| \___| http://farmshare.stanford.edu ### ## # new to Ubuntu 13.04 Farmshare? # follow this link to get started: # https://www.stanford.edu/group/farmshare/cgi-bin/wiki/index.php/Ubuntu13TransitionGuide ## ### Last login: Fri Nov 1 14:03:05 2013 from barley-storage01.stanford.edu Restoring modules to users default $ module list Currently Loaded Modules: 1) farmvnc/0.1 2) matlab/r2013a 3) statase/12.1
modules
We use 'lmod', a variant of commonly used software package 'modules' in HPC environments: http://www.tacc.utexas.edu/tacc-projects/mclay/lmod
If this your first time using modules, this is a good introduction: http://www.tacc.utexas.edu/tacc-projects/mclay/lmod/user-guide/users-tour-of-module-command
The 'module' command has been added to your environment, but if you have modified your environment away from the defaults, you may need to make some configuration changes.
Email us and we will be happy to help: research-computing-support@stanford.du