Software

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==FarmShare software managed with modules==
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==Packaged Software==
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There is a lot of software available on the FarmShare systems.  The systems run Ubuntu, so a lot of [[Packages | Ubuntu packages]] are installed.
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FarmShare systems run Ubuntu, and most software is installed using [[Packaged Software | packages]] available from the standard Ubuntu repositories. Select external repositories are used to provide more frequently updated versions of very commonly used software (''e.g.'', [[R]]).
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There is also some licensed software installed: https://itservices.stanford.edu/service/sharedcomputing/software
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==Commercial Software==
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Notice: /usr/pubsw, /usr/sweet/bin, and /mnt/glusterfs/software have been deprecated.  All have been replaced by /farmshare/software.
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A selection of commercial software is also available, but '''please note''' that this software is licensed for use on FarmShare ''only'' in coursework, and ''not'' for research. Licensed software is made available using environment modules, and can be accessed using the <code>module</code> command.
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/farmshare/software can be accessed as follows:
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==Software Modules==
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===using latest version of matlab===
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Software not installed from packages is managed using [https://lmod.readthedocs.io/en/latest/010_user.html Lmod] environment modules. Use the <code>module avail</code> and <code>module spider</code> commands to list available software, and <code>module load</code> to load desired modules. You can unload modules and restore a previous environment using the <code>module unload</code> and <code>module purge</code> commands.
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To run the latest version of matlab, execute these commands:
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===An Example: Using MATLAB===
<source lang="sh">
<source lang="sh">
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$ module avail
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which matlab
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$ module load matlab
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module avail
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$ module list
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module spider matlab
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$ matlab -nodesktop
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module load matlab
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module list
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which matlab
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matlab
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module unload matlab
 +
which matlab
</source>
</source>
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For example
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== User-installed Software ==
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<source lang="sh">
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New or updated software can often be built and/or installed by users in their own home directories, and local package managers like [http://linuxbrew.sh Linuxbrew] and [https://spack.io Spack] can help. Local package managers are also available for many programming languages (e.g., [https://pip.pypa.io <code>pip</code>], [https://virtualenv.pypa.io <code>virtualenv</code>], and [https://conda.io Conda] for [https://www.python.org Python], <code>local::lib</code> and [https://perlbrew.pl Perlbrew] for [https://www.perl.org Perl], and [https://luarocks.org Luarocks] for [https://www.lua.org Lua]), and some of these provide tools for managing entire local programming environments.
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$ module avail
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---------------------------------- /farmshare/software/free/lmod-5.0-install/lmod/lmod/modulefiles/Core -----------------------------------
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  lmod/lmod    settarg/settarg
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------------------------------------------------------ /farmshare/software/mf/raring ------------------------------------------------------
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  abinit/7.4.2      cudasamples/5.5                  julia/git11262013          povray/3.6.1                    statamp/12.1
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  acml/5.3.1        farmvnc/0.1                      mathematica/9.0            sagemath/5.11                  statase/12.1
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  ampl/20120629      farmvnc/0.2              (D)    matlab/r2012b              sas/9.2                        stattransfer/12
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  atompaw/4.0.0.3    gams/24.1                        matlab/r2013a      (D)    sas/9.3
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  cplex/12.4        gaussian/g09gview50      (D)    mzmine/2.10                sas/9.4                  (D)
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  cuda/5.5          gaussian/g09sse4gview50          openmpi/1.6.5              sentarus/H_2013.03-SP1
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-------------------------------------------------- /farmshare/software/mf/raring-compat ---------------------------------------------------
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  ANSYS        GAMS-24.1        MATLAB-R2013a      SAS-v9.2            StataMP-12.1
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  CPLEX-12.4    MATLAB-R2012b    Mathematica-9.0    StatTransfer-v12    StataSE-12.1
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  Where:
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  (D):  Default Module
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See https://www.stanford.edu/group/farmshare/cgi-bin/wiki/index.php/FarmShare_software for description of how to use modules.
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A few commands to get you started:
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To load latest version of matlab: module load matlab
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You can load a specific version by: module load matlab/r2012b or module load MATLAB-R2012b
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or to find out more information for a package: module spider matlab
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$ module load matlab
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$ module list
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Currently Loaded Modules:
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  1) matlab/r2013a
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$ matlab -nodesktop
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</source>
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===using a specific version of matlab===
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You can run a specific version of matlab by running these commands:
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<source lang="sh">
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$ module spider matlab
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$ module spider matlab/r2012b
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$ module load matlab/r2012b
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$ module list
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$ matlab -nodesktop
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</source>
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Example session
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<source lang="sh">
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$ module spider matlab
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  -------------------------------------------------------------------------------------------------------------
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  matlab:
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  -------------------------------------------------------------------------------------------------------------
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    Description:
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      MATLAB and toolboxes
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    Versions:
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        matlab/r2012b
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        matlab/r2013a
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  -------------------------------------------------------------------------------------------------------------
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  To find detailed information about matlab please enter the full name.
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  For example:
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    $ module spider matlab/r2013a
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  -------------------------------------------------------------------------------------------------------------
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$ module spider matlab/r2012b
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  -------------------------------------------------------------------------------------------------------------
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  matlab: matlab/r2012b
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  -------------------------------------------------------------------------------------------------------------
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    Description:
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      MATLAB and toolboxes
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    This module can be loaded directly: module load matlab/r2012b
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    Help:
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      This is MATLAB R2012b
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      call matlab -nosplash -nodesktop to get the CLI
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$ module load matlab/r2012b
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$ module list
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Currently Loaded Modules:
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  1) matlab/r2012b
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$ matlab -nodesktop
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</source>
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===using a specific version of software (StatTransfer version 12 in this case)===
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An alternate form of the above
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<source lang="sh">
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$ module spider StatTransfer-v12
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  -------------------------------------------------------------------------------------------------------------
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  StatTransfer-v12: StatTransfer-v12
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  -------------------------------------------------------------------------------------------------------------
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    Description:
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      File conversion utility
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    This module can be loaded directly: module load StatTransfer-v12
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    Help:
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      This is Stat/Transfer version 12
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      call 'st' for CLI
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$ module load StatTransfer-v12
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$ module list
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Currently Loaded Modules:
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  1) StatTransfer-v12
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$ st --version
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Stat/Transfer (c) 1986-2013 Circle Systems, Inc.
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www.stattransfer.com
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Version 12.0.56.0613 - 64 Bit Linux
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Serial: B2CNR-FZAS7-LPHI
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User: Software Licensing - Stanford University
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License Type: 25 User Workgroup / Lease
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Status: License OK - Expires April 30, 2014
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</source>
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===switching between versions of software packages===
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If you wish to switch between versions it is quite easy. In this case we switch from matlab 2013a back to 2012b
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<source lang="sh">
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$ module list
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Currently Loaded Modules:
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  1) matlab/r2013a
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$ module purge
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$ module list
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Lmod Warning: No modules installed
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$ module load matlab/r2012b
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$ module list
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Currently Loaded Modules:
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  1) matlab/r2012b
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$ matlab -nodesktop
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</source>
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===automatic loading of packages at login===
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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.
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first, check our current environment.  Ok good, I don't have anything loaded
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<source lang="sh">
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$ module list
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Lmod Warning: No modules installed
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</source>
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Now let's select a few modules we want to load.  Then we save them
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<source lang="sh">
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$ module avail
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------------------------------ /farmshare/software/free/lmod-5.0-install/lmod/lmod/modulefiles/Core -------------------------------
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  lmod/lmod    settarg/settarg
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-------------------------------------------------- /farmshare/software/mf/raring --------------------------------------------------
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  abinit/7.4.2      cudasamples/5.5                  matlab/r2012b          sas/9.3                  (D)
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  acml/5.3.1        farmvnc/0.1                      matlab/r2013a  (D)    sentarus/H_2013.03-SP1
+
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  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
+
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  cplex/12.4        gaussian/g09sse4gview50          sagemath/5.11          stattransfer/12
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  cuda/5.5          mathematica/9.0                  sas/9.2
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---------------------------------------------- /farmshare/software/mf/raring-compat -----------------------------------------------
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  ANSYS        GAMS-24.1        MATLAB-R2013a      SAS-v9.2            StataMP-12.1
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  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
+
-
 
+
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or to find out more information for a package: module spider matlab
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$ module load farmvnc matlab statase
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$ module save
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Saved current collection of modules to: default
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$ logout
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Connection to corn-image closed.
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</source>
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Now, upon logging in, the saved modules are loaded automatically
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<source lang="sh">
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$ ssh corn.stanford.edu
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corn-image.stanford.edu - Ubuntu 13.04, amd64
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4-core Xeon E5620 @ 2.40GHz (vmware); 15.67GB RAM, 1024MB swap
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Puppet environment: rec_master; kernel 3.8.0-31-generic (x86_64)
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--*-*- Stanford University Research Computing -*-*--
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  _____                    ____  _
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|  ___|_ _ _ __ _ __ ___ / ___|| |__  __ _ _ __ ___
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| |_ / _` | '__| '_ ` _ \\___ \| '_ \ / _` | '__/ _ \
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|  _| (_| | |  | | | | | |___) | | | | (_| | | |  __/
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|_|  \__,_|_|  |_| |_| |_|____/|_| |_|\__,_|_|  \___|
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    http://farmshare.stanford.edu
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###
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##
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# new to Ubuntu 13.04 Farmshare?
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# follow this link to get started:
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# https://www.stanford.edu/group/farmshare/cgi-bin/wiki/index.php/Ubuntu13TransitionGuide
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##
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###
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Last login: Fri Nov  1 14:03:05 2013 from barley-storage01.stanford.edu
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Restoring modules to users default
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$ module list
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Currently Loaded Modules:
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  1) farmvnc/0.1  2) matlab/r2013a  3) statase/12.1
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</source>
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==modules==
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We use 'lmod', a variant of commonly used software package 'modules' in HPC environments: http://www.tacc.utexas.edu/tacc-projects/mclay/lmod
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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
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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.
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== Containers ==
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Email us and we will be happy to help: research-computing-support@stanford.du
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[http://singularity.lbl.gov Singularity] containers are supported, but bootstrapping an image requires <code>root</code> access, so you'll need to create your containers elsewhere and copy them to FarmShare to run.

Latest revision as of 10:39, 4 September 2018

Contents

Packaged Software

FarmShare systems run Ubuntu, and most software is installed using packages available from the standard Ubuntu repositories. Select external repositories are used to provide more frequently updated versions of very commonly used software (e.g., R).

Commercial Software

A selection of commercial software is also available, but please note that this software is licensed for use on FarmShare only in coursework, and not for research. Licensed software is made available using environment modules, and can be accessed using the module command.

Software Modules

Software not installed from packages is managed using Lmod environment modules. Use the module avail and module spider commands to list available software, and module load to load desired modules. You can unload modules and restore a previous environment using the module unload and module purge commands.

An Example: Using MATLAB

which matlab
module avail
module spider matlab
module load matlab
module list
which matlab
matlab
module unload matlab
which matlab

User-installed Software

New or updated software can often be built and/or installed by users in their own home directories, and local package managers like Linuxbrew and Spack can help. Local package managers are also available for many programming languages (e.g., pip, virtualenv, and Conda for Python, local::lib and Perlbrew for Perl, and Luarocks for Lua), and some of these provide tools for managing entire local programming environments.

Containers

Singularity containers are supported, but bootstrapping an image requires root access, so you'll need to create your containers elsewhere and copy them to FarmShare to run.

Retrieved from "https://web.stanford.edu/group/farmshare/cgi-bin/wiki/index.php/Software"
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