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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Don't use /usr/pubsw
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==Commercial Software==
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Maybe use /usr/sweet/bin, though we'll be installing new versions of software outside of AFS, use '''module avail''' instead.
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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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===more complete example===
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==Software Modules==
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<pre>
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[chekh@corn24.stanford.edu] ~ [0]
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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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$ module avail
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------------------------------------------- /mnt/glusterfs/software/free/modules/tcl/modulefiles --------------------------------------------
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MATLAB-R2009b    MATLAB-R2010b    MATLAB-R2011b    StatTransfer-10.1 StatTransfer-11.2 stata-v12       
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===An Example: Using MATLAB===
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[chekh@corn24.stanford.edu] ~ [0]
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<source lang="sh">
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$ module load StatTransfer-10.1
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which matlab
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module avail
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module spider matlab
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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
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which matlab
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</source>
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[chekh@corn24.stanford.edu] ~ [0]
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== User-installed Software ==
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$ st --version
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Stat/Transfer (c) 1986-2011 Circle Systems, Inc.
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www.stattransfer.com
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Version 10.1.1847.0331 - 64 Bit Linux
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Serial: BUNLM-VEAN7-JMC8
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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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User: Pat Box (1) - Stanford University
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License Type: Linux - Single Machine Lease
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Warning: Your annual license is in its last month.
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Status: License OK - Expires April 30, 2012
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Stat/Transfer is running in a remote secure shell. A workgroup license covering all users may be required.
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Please contact our sales department (sales@circlesys.com) for more information.
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[chekh@corn24.stanford.edu] ~ [0]
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== Containers ==
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$ module unload StatTransfer-10.1
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[chekh@corn24.stanford.edu] ~ [0]
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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.
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$ module load StatTransfer-11.2
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[chekh@corn24.stanford.edu] ~ [0]
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$ st --version
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Stat/Transfer (c) 1986-2012 Circle Systems, Inc.
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www.stattransfer.com
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Version 11.2.2013.0330 - 64 Bit Linux
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Serial: BOC59-BUAAN-ZCYF
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User: Jane Tansuwan - Stanford University
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License Type: Linux - 50 User Workgroup / Lease
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Status: License OK - Expires April 30, 2013
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[chekh@corn24.stanford.edu] ~ [0]
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$ module help StatTransfer-11.2
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-------------------------------------------------------------------
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Module Specific Help for /mnt/glusterfs/software/free/modules/tcl/modulefiles/StatTransfer-11.2:
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ITS-maintained Stat/Transfer v11.2 (in GlusterFS)
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use st for command-line version
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use stattransfer for X11 GUI version
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-------------------------------------------------------------------
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</pre>
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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 will need to source the module env vars for your shell:
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<pre>
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  If using sh/bash/ksh/zsh, add this to your .bashrc
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    eval `tclsh /mnt/glusterfs/software/free/modules/tcl/modulecmd.tcl sh autoinit`
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  If using csh/tcsh, add this to your .cshrc
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    source /mnt/glusterfs/software/free/modules/tcl/init/csh
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  If using perl, put this in your script
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    eval `tclsh /mnt/glusterfs/software/free/modules/tcl/modulecmd.tcl perl autoinit`;
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</pre>
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For example, 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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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.

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