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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==Packaged Software==
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There is also some licensed software installed: https://itservices.stanford.edu/service/sharedcomputing/software
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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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Notice: /usr/pubsw, /usr/sweet/bin, and /mnt/glusterfs/software have been deprecated.  All have been replaced by /farmshare/software.
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==Commercial Software==
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/farmshare/software can be accessed as follows:
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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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===using latest version of matlab===
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==Software Modules==
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To run the latest version of matlab, execute these commands:
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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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<source lang="sh">
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===An Example: Using MATLAB===
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$ module avail
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$ module load matlab
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$ module list
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$ matlab -nodesktop
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</source>
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For example
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<source lang="sh">
<source lang="sh">
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which matlab
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bishopj@scorn:~$ module avail
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module avail
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module spider matlab
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--------------------- /farmshare/software/free/lmod-5.0-install/lmod/lmod/modulefiles/Core ----------------------
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module load matlab
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  lmod/lmod    settarg/settarg
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module list
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which matlab
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----------------------------------------- /farmshare/software/mf/raring -----------------------------------------
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matlab
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  cplex/12.4    gaussian/g09gview50    matlab/r2013a  (D)    statase/12.1
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module unload matlab
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  cuda/5.5      mathematica/9.0        sas/9.2                stattransfer/12
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which matlab
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  gams/24.1    matlab/r2012b          statamp/12.1
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------------------------------------- /farmshare/software/mf/raring-compat --------------------------------------
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  CPLEX-12.4    MATLAB-R2012b    Mathematica-9.0    StatTransfer-v12    StataSE-12.1
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  GAMS-24.1    MATLAB-R2013a    SAS-v9.2          StataMP-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
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use modules.
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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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bishopj@scorn:~$ module load matlab
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bishopj@scorn:~$ 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>
</source>
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===using a specific version of matlab===
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== User-installed Software ==
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<source lang="sh">
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bishopj@scorn:~$ module spider matlab
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  -------------------------------------------------------------------------------------------------------------
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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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  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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bishopj@scorn:~$ 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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bishopj@scorn:~$ module load matlab/r2012b
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bishopj@scorn:~$ 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 load 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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==modules==
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We use 'modules', a commonly used software package in HPC environments: http://modules.sourceforge.net/
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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 source the module env vars for your shell.
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For example, you may need to try something like this at the end of your .bashrc:
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<source lang="sh">
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HOSTNAME=$(hostname)
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if [ "${HOSTNAME:0:4}" = "corn" ]; then
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  #source farmshare modules
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  echo "on a corn! try module avail"
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  eval `tclsh /mnt/glusterfs/software/free/modules/tcl/modulecmd.tcl sh autoinit`
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fi
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</source>
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Then you can do something like:
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<source lang="sh">
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module avail
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module load stata
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stata
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</source>
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== Containers ==
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Link: https://www.stanford.edu/group/hpcc/cgi-bin/mediawiki/index.php/Modules
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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 09:39, 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.

Personal tools
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