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<pre>
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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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</pre>
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This wiki is intended for the users of the Stanford shared research computing resources. E.g. the "cardinal" and "corn" and "barley" machines.
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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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= How to connect =
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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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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 that has relatively low load.  
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== System Status ==
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FarmShare is operational.
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The "barley" machines are only accessible via a resource manager (currently Open GridEngine). You'll need to ssh to corn-image-new.stanford.edu and a directory will be created for you on local (shared among barley) storage. E-mail the barley-alpha mailing list for more info.
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== Getting Started ==
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=cardinal info=
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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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The "cardinal" machines are older and slower and smaller and intended for long-running processes 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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=corn info=
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=== Connecting ===
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*Policies: http://lelandpolicy.stanford.edu
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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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'''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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=barley info=
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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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Job submission now works from any corn.
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<source lang="sh">ssh sunetid@rice.stanford.edu</source>
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Technical details:
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SSH [https://srcc.stanford.edu/farmshare2/connecting-keys host keys and fingerprints] are available for verification.
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*19 new machines, 24 cores each, 96GB RAM
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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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To start using the 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 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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Initial issues:
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<source lang="sh">ssh sunetid@cardinal.stanford.edu</source>
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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 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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<code>cardinal</code> systems should ''not'' be used for long-running or compute- and/or memory-intensive work.
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# log into corn-image-new: "ssh sunetid@corn-image-new.stanford.edu"
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# cd to /mnt/glusterfs/<your username> (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/<your username> 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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For more information, see [https://srcc.stanford.edu/farmshare2/connecting Getting Connected] and [[Advanced Connection Options]].
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We plan to have "alpha" testing for a month or so, then rebuild the
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=== User Guide ===
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storage nodes using the information we learned, and also rebuild the
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execution hosts to Ubuntu 11.10.  Then we'll have "beta testing" with
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more users in Nov and Dec and roll out to the full Stanford community on
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Jan 1.
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== barley software ==
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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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=== stock software ===
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== Support ==
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The barley machines are running Ubuntu 11.04, and the software is from the Ubuntu repositories
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* [[R]]
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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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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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* /usr/sweet/bin - [[MATLAB]], SAS, [[stata]], [[stataMP]], etc
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=== current barley policies ===
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=== Course Instructors ===
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* 100 max jobs per user
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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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* 3000 max jobs in the system
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* 48hr max runtime for any job
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* no memory/CPU limits yet
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If you have any concerns or suggestions, please mail barley-alpha.
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=== Discussion List ===
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= Monitoring / Status =
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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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Current status of farmshare machines: http://barley-monitor.stanford.edu/ganglia/
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=== Office Hours ===
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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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<span style="color: red">In accordance with guidance from the University regarding COVID-19, SMACC office hours have been suspended until further notice.</span> If you need assistance with FarmShare please contact us at srcc-support@stanford.edu.
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* modify /etc/motd on the corns
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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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SRCC participates in [https://web.stanford.edu/group/su-hpc/cgi-bin/mediawiki/index.php/SMACC SMACC] (C2) office hours, held weekly in the basement of [https://campus-map.stanford.edu/?id=04-080&lat=37.42787956&lng=-122.17429865&zoom=17&srch=Huang%20Engineering%20Center Huang Engineering Center], near the [https://icme.stanford.edu ICME] offices.
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We have several mailing lists, all @lists.stanford.edu, most are not used.
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SMACC office hours are not held during the Summer Quarter, or during inter-quarter periods.
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* barley-alpha - temp list till end of Oct/Nov 2011, for discussion around testing the barleys
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* farmshare-announce -  announce list (new service name)
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* farmshare-discuss - users discussion (new service name)
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* stanford-timeshare-users - users discussion list for the corn users, list to be retired
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=== SSDS Consulting ===
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= Links =
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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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Want to learn HPC?  Free education materials available:
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* http://shodor.org/petascale/materials/modules/
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* http://hpcuniversity.org/roadmap/
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= Getting started with MediaWiki =
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== Software  ==
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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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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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* [http://www.mediawiki.org/wiki/Manual:Configuration_settings Configuration settings list]
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For more information, see [https://srcc.stanford.edu/farmshare2/software Software].
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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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=== Packaged Software ===
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FarmShare systems run Ubuntu 16.04 LTS, and most software is sourced from standard repositories.
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=== Modules and Licensed Software ===
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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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<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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'''Please note''' that commercial software is licensed for use on FarmShare ''only'' in coursework, and ''not'' for research.
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=== User-installed Software ===
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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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=== Containers ===
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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.

Revision as of 10:01, 17 September 2021

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 operational.

    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.

    Office Hours

    In accordance with guidance from the University regarding COVID-19, SMACC office hours have been suspended until further notice. If you need assistance with FarmShare please contact us at srcc-support@stanford.edu.

    SRCC participates in SMACC (C2) office hours, held weekly in the basement of Huang Engineering Center, near the ICME offices.

    SMACC office hours are not held during the Summer Quarter, or during inter-quarter periods.

    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
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