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== This FarmShare Documentation Is Not Current==
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This wiki is intended for the users of FarmShare, the Stanford shared research computing environment: the "cardinal" and "corn" and "barley" machines.
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Most useful pages: [[Special:AllPages]] and [[Special:RecentChanges]]
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'''This wiki describes a previous version of FarmShare.'''
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= How to connect  =
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Accurate documentation of the current system can be found at [https://srcc.stanford.edu/farmshare https://srcc.stanford.edu/farmshare]
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The machines are available for anyone with a SUNetID. Simply "ssh corn.stanford.edu" with your SUNetID credentials. The DNS name "corn.stanford.edu" actually goes to a load balancer and it will connect you to a particular corn machine (e.g. corn21) that has relatively low load.
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The "barley" machines are only accessible via a resource manager (currently Open Grid Engine). You can submit jobs from any corn. You'll need to ssh to corn-image-new.stanford.edu and a directory on /mnt/glusterfs will be created for you on non-AFS storage. E-mail the barley-alpha mailing list for more info.  
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FarmShare is Stanford’s community computing environment. It is primarily intended for use in coursework and unsponsored research (note that some software tools, like ANSYS, are only licensed for use on Farmshare for academic course use, not research); users participating in sponsored or departmental research should investigate the [https://sherlock.stanford.edu Sherlock] service or other, local alternatives, instead. FarmShare is ''not'' approved for use with [https://dataclass.stanford.edu high-risk] data, including protected health information and personally identifiable information, and is subject to University [[Policy | policies]] on acceptable use.
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= cardinal info  =
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For a description of the current environment, see [[FarmShare 2]]. More information can be found in the [https://srcc.stanford.edu/farmshare2 service documentation].
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The "cardinal" machines are older and slower and smaller and intended for long-running processes (on the order of days) that are not resource intensive. E.g. mail/chat clients. You could log in to a cardinal and run a screen/tmux session there to do things on other machines...  
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__NOTOC__
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{| width="100%" cellpadding="20"
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|-
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| style="width: 30%;" | __TOC__
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| style="width: 70%;" | <h3>Recent Messages on [https://mailman.stanford.edu/mailman/listinfo/farmshare-discuss/ farmshare-discuss]</h3><rss>http://web.stanford.edu/group/farmshare/wiki/rss/farmshare-discuss.rss</rss>
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|}
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= corn info  =
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== System Status ==
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FarmShare is online.
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The "corn" machines are general-purpose Ubuntu boxes and you can run whatever you want on them (so long as you don't negatively impact other users). Please read the policies and the motd first.
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== Getting Started ==
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*Policies: http://lelandpolicy.stanford.edu
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Any person with a [https://uit.stanford.edu/service/accounts/sunetids#eligibility full-service] SUNet ID can access FarmShare.
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*IT services page: https://itservices.stanford.edu/service/unixcomputing
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*VNC help: https://itservices.stanford.edu/service/unixcomputing/unix/vnc
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*Q? File HelpSU: http://helpsu.stanford.edu/
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*Future vision as of summer 2010: http://itservices.stanford.edu/strategy/sysadmin/timeshare
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Each of the 30 corn machines has 8 cores, 32GB RAM and ~70GB of local disk in /tmp.
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=== Connecting ===
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= barley info  =
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'''Do not connect to <code>farm.stanford.edu</code>.''' While there is such a system, it is ''not'' part of the FarmShare service.
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The "barley" machines are general-purpose newer Ubuntu boxes that can run jobs that you submit via the resource manager software.  
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Log into <code>rice.stanford.edu</code>. Authentication is by SUNet ID and password (or GSSAPI), and [https://uit.stanford.edu/service/webauth/twostep two-step] authentication is required.
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=== current barley policies  ===
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<source lang="sh">ssh sunetid@rice.stanford.edu</source>
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*100 max jobs per user
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SSH [https://srcc.stanford.edu/farmshare2/connecting-keys host keys and fingerprints] are available for verification.
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*3000 max jobs in the system
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*48hr max runtime for any job in regular queue
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*one week max runtime for the long queue
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*no memory/CPU limits yet
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=== Technical details  ===
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For light-duty, interactive work (e.g., e-mail, web browsing and development, file editing, and AFS access or file transfers), log into <code>cardinal.stanford.edu</code>, instead.
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*19 new machines, 24 cores each, 96GB RAM
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<source lang="sh">ssh sunetid@cardinal.stanford.edu</source>
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*1 new machine, 24 cores, 192GB RAM
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*~450GB local scratch on each
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*~3TB in /mnt/glusterfs
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*Grid Engine v6.2u5 (via standard Debian package)
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*10GbE interconnect (Juniper QFX3500 switch)
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=== how to use the barley machines  ===
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<code>cardinal</code> systems should ''not'' be used for long-running or compute- and/or memory-intensive work.
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To start using these new machines, you can check out the man page for 'sge_intro' or the 'qhost', 'qstat', 'qsub' and 'qdel' commands.  
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For more information, see [https://srcc.stanford.edu/farmshare2/connecting Getting Connected] and [[Advanced Connection Options]].
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Initial issues:
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=== User Guide ===
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*You are limited in space to your AFS homedir ($HOME) and local scratch disk on each node ($TMPDIR)
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The [[User Guide]] has information regarding storage, file-transfer, and cluster configuration. See the [[FAQ]] for common issues, and tips and tricks.
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*The execution hosts don't accept interactive jobs, only batch jobs for now.
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*You'll want to make sure you have your Kerberos TGT and your [[AFS]] token.
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If you want to use the newer bigger storage:
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== Support ==
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#log into corn-image-new: "ssh sunetid@corn-image-new.stanford.edu"
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SRCC staff can be reached by e-mail at: [mailto:srcc-support@stanford.edu srcc-support@stanford.edu]. When reporting a problem, please let us know that you're running on FarmShare and report any relevant details, including the full text of any error message you're receiving, and the job ID and contents of your batch script (if applicable).
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#cd to /mnt/glusterfs/&lt;your username&gt; (or wait 5mins if it doesn't exist yet)
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#write a job script: "$EDITOR test_job.script"
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##see 'man qsub' for more info
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##use env var $TMPDIR for local scratch
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##use /mnt/glusterfs/&lt;your username&gt; for shared data directory
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#submit the job for processing: "qsub -cwd test_job.script"
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#monitor the jobs with "qstat -f -j JOBID"
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##see 'man qstat' for more info
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#check the output files that you specified in your job script (the input and output files must be in /mnt/glusterfs/)
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Any questions, please email 'barley-alpha@lists.stanford.edu'
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=== Course Instructors ===
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We plan to roll out to the full Stanford community on Jan 20.  
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If you are a course instructor using FarmShare for classwork and have any special requests or requirements please contact SRCC at least 30 days before the start of the academic quarter in which the class will be held. We try to accommodate reasonable requests but staff time is limited.
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== barley software  ==
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=== Discussion List ===
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=== stock software  ===
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Subscribe to the community discussion list, [https://mailman.stanford.edu/mailman/listinfo/farmshare-discuss farmshare-discuss], post questions and concerns to: [mailto:farmshare-discuss@lists.stanford.edu farmshare-discuss@lists.stanford.edu], or browse the [https://mailman.stanford.edu/pipermail/farmshare-discuss/ archives].
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The barley machines are running Ubuntu 11.04, and the software is from the Ubuntu repositories, e.g. do 'dpkg -l' to see the list of installed packages.
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=== SSDS Consulting ===
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*[[R]]
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The [https://ssds.stanford.edu SSDS] group supports statistical software, including R, Stata, and SAS. They are located in the Velma Denning Room in the Bing Wing of [https://campus-map.stanford.edu/?id=03-200&lat=37.42690686&lng=-122.16759602&zoom=17&srch=Green%20Library Green Library] and hold office hours Monday–Thursday, 2–5 PM, starting in the second week of each quarter and ending the last week of classes. SRCC staff are present on the third Tuesday of each month, from 2–4 PM. SSDS office hours are not held during the Summer Quarter.
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*[[OpenMPI]]
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*[[AFS]] / Kerberos
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*[[GridEngine]]
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=== licensed software ===
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== Software ==
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*/usr/sweet/bin - [[MATLAB]], SAS, [[Stata]], [[StataMP]], etc
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A variety of useful [[Software | software]], including some popular commercial software, is provided as part of the FarmShare environment. If something is missing, or a particular application, library, or utility needs updating, please let us know. We try to accommodate reasonable requests but staff time is limited.
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There is a group on campus called "SSDS" that can provide support for SAS and stata: http://www.stanford.edu/group/ssds/cgi-bin/drupal/content/who-we-are-what-we-do
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For more information, see [https://srcc.stanford.edu/farmshare2/software Software].
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= Monitoring / Status  =
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=== Packaged Software ===
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*Current status of farmshare machines: http://barley-monitor.stanford.edu/ganglia/
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FarmShare systems run Ubuntu 16.04 LTS, and most software is sourced from standard repositories.
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*More detailed graphs: http://barley-monitor.stanford.edu/munin/
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For important announcements, we plan to:
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=== Modules and Licensed Software ===
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*add it to this wiki
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Some software, including all licensed software, is built and/or installed manually and organized using the [https://lmod.readthedocs.io Lmod] environment module system.
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*modify /etc/motd on the corn machines
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*send a mail to farmshare-announce
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*duplicate that mail also to the farmshare "blog"
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= Mailing Lists  =
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<source lang="sh">
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module help
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module avail
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module load
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</source>
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We have several mailing lists, all @lists.stanford.edu
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'''Please note''' that commercial software is licensed for use on FarmShare ''only'' in coursework, and ''not'' for research.
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*barley-alpha - temp list till end of Oct/Nov 2011, for discussion around testing the barley machines
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=== User-installed Software ===
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*farmshare-announce - announcements list
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*farmshare-discuss - user discussion
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= Links  =
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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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Want to learn HPC? Free education materials available:
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=== Containers ===
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*http://shodor.org/petascale/materials/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.
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*http://hpcuniversity.org/roadmap/
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= Getting started with MediaWiki  =
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Consult the [http://meta.wikimedia.org/wiki/Help:Contents User's Guide] for information on using the wiki software.  
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*[http://www.mediawiki.org/wiki/Manual:Configuration_settings Configuration settings list]
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*[http://www.mediawiki.org/wiki/Manual:FAQ MediaWiki FAQ]
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*[http://lists.wikimedia.org/mailman/listinfo/mediawiki-announce MediaWiki release mailing list]
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Latest revision as of 12:39, 30 October 2023

This FarmShare Documentation Is Not Current

This wiki describes a previous version of FarmShare.

Accurate documentation of the current system can be found at https://srcc.stanford.edu/farmshare

FarmShare is Stanford’s community computing environment. It is primarily intended for use in coursework and unsponsored research (note that some software tools, like ANSYS, are only licensed for use on Farmshare for academic course use, not research); users participating in sponsored or departmental research should investigate the Sherlock service or other, local alternatives, instead. FarmShare is not approved for use with high-risk data, including protected health information and personally identifiable information, and is subject to University policies on acceptable use.

For a description of the current environment, see FarmShare 2. More information can be found in the service documentation.


Contents

Recent Messages on farmshare-discuss

    System Status

    FarmShare is online.

    Getting Started

    Any person with a full-service SUNet ID can access FarmShare.

    Connecting

    Do not connect to farm.stanford.edu. While there is such a system, it is not part of the FarmShare service.

    Log into rice.stanford.edu. Authentication is by SUNet ID and password (or GSSAPI), and two-step authentication is required. 

    ssh sunetid@rice.stanford.edu

    SSH host keys and fingerprints are available for verification.

    For light-duty, interactive work (e.g., e-mail, web browsing and development, file editing, and AFS access or file transfers), log into cardinal.stanford.edu, instead. 

    ssh sunetid@cardinal.stanford.edu

    cardinal systems should not be used for long-running or compute- and/or memory-intensive work.

    For more information, see Getting Connected and Advanced Connection Options.

    User Guide

    The User Guide has information regarding storage, file-transfer, and cluster configuration. See the FAQ for common issues, and tips and tricks.

    Support

    SRCC staff can be reached by e-mail at: srcc-support@stanford.edu. When reporting a problem, please let us know that you're running on FarmShare and report any relevant details, including the full text of any error message you're receiving, and the job ID and contents of your batch script (if applicable).

    Course Instructors

    If you are a course instructor using FarmShare for classwork and have any special requests or requirements please contact SRCC at least 30 days before the start of the academic quarter in which the class will be held. We try to accommodate reasonable requests but staff time is limited.

    Discussion List

    Subscribe to the community discussion list, farmshare-discuss, post questions and concerns to: farmshare-discuss@lists.stanford.edu, or browse the archives.

    SSDS Consulting

    The SSDS group supports statistical software, including R, Stata, and SAS. They are located in the Velma Denning Room in the Bing Wing of Green Library and hold office hours Monday–Thursday, 2–5 PM, starting in the second week of each quarter and ending the last week of classes. SRCC staff are present on the third Tuesday of each month, from 2–4 PM. SSDS office hours are not held during the Summer Quarter.

    Software

    A variety of useful software, including some popular commercial software, is provided as part of the FarmShare environment. If something is missing, or a particular application, library, or utility needs updating, please let us know. We try to accommodate reasonable requests but staff time is limited.

    For more information, see Software.

    Packaged Software

    FarmShare systems run Ubuntu 16.04 LTS, and most software is sourced from standard repositories.

    Modules and Licensed Software

    Some software, including all licensed software, is built and/or installed manually and organized using the Lmod environment module system. 

    module help
module avail
module load

    Please note that commercial software is licensed for use on FarmShare only in coursework, and not for research.

    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/Main_Page"
    Personal tools
    Toolbox
    LANGUAGES