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<seo metadescription="FarmShare shared computing and HPC resource for Stanford faculty, staff, and students, provided at no cost" metakeywords="farmshare, hpc, free, linux, ubuntu, cluster, matlab, R, MPI, SGE, grid engine, barley, corn, cardinal, timeshares, shared computing"/>
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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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== FarmShare ==
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This wiki is intended for the users of FarmShare, the Stanford shared research computing environment: the "'''cardinal'''",  "'''corn'''", and "'''barley'''" machines. For a general description of this service, and Stanford's shared computing policies, see the main [https://itservices.stanford.edu/service/sharedcomputing service catalog page].  
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'''Most useful pages: [[Special:AllPages]] and [[Special:RecentChanges]] and [[User Guide]] and [[FAQ]] and [[FarmShare tutorial]]'''
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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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__NOTOC__
{| width="100%" cellpadding="20"
{| width="100%" cellpadding="20"
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|
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|-
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| Last 10 messages on Farmshare-Discuss mail list (this month)
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| style="width: 30%;" | __TOC__
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|-
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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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| style="width: 30%;" | __TOC__
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|}
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| style="width: 40%;" | <rss>http://stanford.edu/group/farmshare/wiki/rss/farmshare-discuss.rss</rss>
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|}
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== FarmShare is in a rolling upgrade to Ubuntu 13.10 ==
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== System Status ==
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You can try connecting to corn-new instead of corn, which has Ubuntu 13.10 instead of Ubuntu 13.04.  But some programs may not work as expected. Docs will appear here: [[Ubuntu1310]]
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FarmShare is operational.
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Details and status from the last migration can be found here: [[Ubuntu13TransitionGuide]]
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== Getting Started ==
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= How to connect  =
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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 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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=== Connecting ===
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The "barley" machines are designed to be used for high performance computing (HPC) and only accessible via a resource manager (currently Open Grid Scheduler). You cannot log in directly, but you can submit jobs from any corn. Storage dedicated for jobs running on the barley cluster is available via /farmshare/user_data/ on all corn and barley nodes. Sign up and email the farmshare-discuss mailing list if you have any questions or would like any info not listed here.  
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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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corn SSH fingerprint is:
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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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  RSA key fingerprint is 0b:e7:b4:95:03:c1:1e:07:df:04:ca:a2:3d:8e:e3:37.
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= How to get help =
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<source lang="sh">ssh sunetid@rice.stanford.edu</source>
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== email support ==
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SSH [https://srcc.stanford.edu/farmshare2/connecting-keys host keys and fingerprints] are available for verification.
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[[Image:huangsmacc.png|frame]]
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*You can e-mail research-computing-support@stanford.edu
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**If you're e-mailing about a barley job, please mention that it's on barley and the job number.
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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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== SMACC office hours ==
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<source lang="sh">ssh sunetid@cardinal.stanford.edu</source>
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[[Image:smacctable.jpg|frame]]
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*You can come to office hours.  Every Wednesday from noon-2PM in [http://campus-map.stanford.edu/?id=&lat=37.43476699967559&lng=-122.17429865&zoom=15&srch=Huang%20Engineering%20Center Huang] basement in front of ICME door:
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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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**Have a computational or statistical problem that you need help with? Or maybe you have an account on Farmshare or Proclus, and so now what? You have a boatload of data to make sense of, but how? Wonder where you can do your research project, and who can help you? You know what you want to do – but how best to do it, you just aren’t sure. Help is here in the form of SMACC – Stat, Math, Algorithmic and Computational Consulting!  Technical consultants from ICME, Research Computing, Statistics and IRiSS will be available to work with you each Wednesday, from noon-2 pm, in the basement of Huang (in front of ICME). One stop shopping for your scientific computing needs.  Rather than poke around web sites and send mail to multiple groups, drop by to catch all of us at once.
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**Details are at [https://www.stanford.edu/group/su-hpc/cgi-bin/mediawiki/index.php/SMACC SMACC]
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Alternatively, the [http://www.stanford.edu/group/ssds/cgi-bin/drupal/content/who-we-are-what-we-do SSDS] campus group can provide one one one guidance for R, SAS and Stata.  Please [mailto:consult-ssds-software@stanford.edu contact them directly] if you have any questions about using those particular software packages.
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For more information, see [https://srcc.stanford.edu/farmshare2/connecting Getting Connected] and [[Advanced Connection Options]].
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== FAQ ==
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=== User Guide ===
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*[[FAQ]]
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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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*[[FarmShare tutorial]]
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*VNC information: [[FarmVNC]]
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*[[Dotfiles|The official new-user bash/tcsh/zsh setup files]]
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== Support ==
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== Hardware Resources ==
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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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= cardinal info  =
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=== Course Instructors ===
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The "cardinal" machines are small VMs 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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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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Simply "ssh cardinal.stanford.edu" with your SUNetID credentials.
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=== Discussion List ===
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There are currently 3 cardinal machines: cardinal1, cardinal2 and cardinal3, load-balanced via cardinal.stanford.edu.  
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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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Things you can do on cardinal:
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=== Office Hours ===
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* text based email clients
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* transfer files to and from AFS and your desktop
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* access command line utilities
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= corn info  =
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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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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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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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Simply "ssh corn.stanford.edu" with your SUNetID credentials.
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SMACC office hours are not held during the Summer Quarter, or during inter-quarter periods.
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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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=== SSDS Consulting ===
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Things you can do on corn:
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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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* email to stanford addresses only. for general text based email please use the cardinal
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* access command line utilities
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* access desktop environment via [[FarmVNC|VNC]]
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* access developer toolchains (c/c++/java/python/go/julia/etc)
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* run licensed software (mathematica/stata/matlab/gaussian/sas/etc) as described [[FarmShare_software|here]]
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* submit jobs to the Barley cluster
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* basically anything you would do on a desktop Ubuntu system
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other info:
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== Software  ==
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*Policies: http://itservices.stanford.edu/service/sharedcomputing/policies
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*IT services page: https://itservices.stanford.edu/service/sharedcomputing
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*Q? E-mail research-computing-support@stanford.edu or file a HelpSU: http://helpsu.stanford.edu/?pcat=farmshare
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*Future vision as of summer 2010: http://itservices.stanford.edu/strategy/sysadmin/timeshare
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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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For more information, see [https://srcc.stanford.edu/farmshare2/software Software].
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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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= rye info =
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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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[[Image:pymolgiffy.gif|frame]]
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The "rye" machines are general purpose Ubuntu (same as corn) but have 8 Nvidia GPU's each.
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Things you can do on rye:
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* anything you can do on a corn
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* run CUDA 5.5/OpenCL programs (text based or GUI)
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* run 3D graphics programs such as PyMOL    ------>
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*Detailed [[Rye-GPU|Rye info]]
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= barley info  =
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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. You should not log in to any barley directly, but can do so to troubleshoot your jobs.
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Things you can do on barley:
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* cpu intensive jobs
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* large memory jobs (up to 192GB)
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* lots of cpu intensive jobs
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* thousands of cpu intensive jobs
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*Detailed [[Barley info]]
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= Examples of using the barley cluster  =
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#Introductory examples:
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##[[FlacLikeABoss|Flac Like a Boss]]
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##[[CheapFlights|Cheap Flights]]
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##[[SFOtoHKGin5min|San Francisco to Hong Kong in 5 minutes]]
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##[[MatCarlo|Monte Carlo Simulations in Matlab]]
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#[[R]]
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#[[MATLAB]]
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#[[MatlabMysql|Access Mysql from Matlab]]
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#[[Abinit|MPI Abinit]]
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#[[Rmpi]]
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#[[Gaussian]]
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#[[Ipython]]
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#[[ANSYS]]
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#Gaussview:&nbsp;[[Automated Submission Script Creation & Submission]]
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== FarmShare software ==
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=== questions or requests about installed software ===
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If you have a question or request about the installed software on FarmShare please email us: research-computing-support@stanford.edu
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=== questions about how to use installed software ===
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If you need help on usage we would suggest:
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* FarmShare mail list.  FarmShare maillist has hundreds of other FarmShare users.  It is quite likely somebody will be able to help.  Please [mailto:farmshare-discuss@lists.stanford.edu e-mail] the [https://mailman.stanford.edu/mailman/listinfo/farmshare-discuss FarmShare user community]
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*SMACC.  SMACC office hours is an excellent place to start if you would like to discuss or ask a question in-person.  see [[Main_Page#SMACC_office_hours|SMACC]]
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== stock software  ==
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The FarmShare machines are running Ubuntu 13.04, and the software is from the Ubuntu repositories, e.g. run '''dpkg -l | grep ^i''' to see the list of installed packages.
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*[[R]]
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*[[OpenMPI]]
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*[[AFS]] / [https://itservices.stanford.edu/service/kerberos Kerberos]  
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*[[GridEngine]]
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If the package you're looking for isn't installed, search the [http://packages.ubuntu.com/ Ubuntu Packages] page and submit a [http://helpsu.stanford.edu/?pcat=farmshare HelpSU] with the package name(s) you want.
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== licensed software  ==
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In addition to Ubuntu packages, the following packages are installed and are available via the "module" command:
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See [[FarmShare_software]] for detailed examples.
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<source lang="sh">
<source lang="sh">
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$ module avail
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module help
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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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module load
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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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</source>
</source>
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= Monitoring / Status  =
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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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You probably want to try these commands:
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  qstat -g c #cluster slots summary by queue
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  qhost -F mem_free #show available memory on each host
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  qstat -f -u \* #show all jobs in the system
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*Current status of farmshare machines: http://barley-monitor.stanford.edu/ganglia/
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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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*add it to this wiki
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*modify /etc/motd on the corn machines
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*send a mail to farmshare-discuss
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= Mailing Lists  =
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We have mailing lists, @lists.stanford.edu - https://itservices.stanford.edu/service/mailinglists/tools
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*[https://mailman.stanford.edu/mailman/listinfo/farmshare-announce farmshare-announce] - announcements list - [https://mailman.stanford.edu/pipermail/farmshare-announce/ Archives]
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*[https://mailman.stanford.edu/mailman/listinfo/farmshare-discuss farmshare-discuss] - user discussion - [https://mailman.stanford.edu/pipermail/farmshare-discuss/ Archives]
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= Links  =
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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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FarmShare has GPUs, but if you need to scale up to a cluster ICME is an excellent resource:
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*http://icme.stanford.edu/Computer%20Resources/gpu.php
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Other GPU resources are:
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*http://classx.stanford.edu/ClassX/system/users/web/pg/view_subject.php?subject=NVIDIA_ICME_SPRING_2010_2011
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*Engineering / Computer Science computer labs: myth20 through myth32 have nVidia GPU modules for development: http://cs.stanford.edu/computing-guide/overview/computer-systems/myth
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Other similar wikis/clusters on campus (you might not have access to these):
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*Engineering / Computer Science computer labs (myth.stanford.edu), open to all fully sponsored SunetIDs: http://cs.stanford.edu/computing-guide/overview/computer-systems/myth
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=== User-installed Software ===
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*Statistics cluster: https://www.stanford.edu/dept/statistics/cgi-bin/projects/stat-sysadminwiki/index.php/Cluster_Help
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*Genetics cluster: https://www.stanford.edu/group/scgpm/cgi-bin/informatics/wiki/index.php/Main_Page
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*SU-HPC group: https://www.stanford.edu/group/su-hpc/cgi-bin/mediawiki/index.php/Special:Recentchanges
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*HPCC wiki: https://www.stanford.edu/group/hpcc/cgi-bin/mediawiki/index.php/Main_Page
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*Proclus (H&S cluster): https://www.stanford.edu/group/proclus/cgi-bin/mediawiki/index.php/Main_Page
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= Vision =
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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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The Farmshare resources are being made available to students, faculty and staff with fully sponsored SunetIDs to facilitate research at Stanford University.&nbsp; This resource is designed so that those doing research will have a place to experiment and learn about technical solutions to assist in reaching their research goals without needing to write a grant for a cluster.&nbsp; The Farmshare resources are focused on making it easier to learn how to parallelize research computing tasks and use research software including a "scheduler"&nbsp;or "distributed resource management system" to submit compute jobs.<br>
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=== Containers ===
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By using Farmshare, new researchers can more easily adapt to using larger clusters when they have big projects that involve using federally funded resources, shared Stanford clusters, or on a small grant funded cluster.<br>
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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 15:49, 15 July 2020

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.

    Personal tools
    Toolbox
    LANGUAGES