Main Page
From FarmShare
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#Gaussview: [[Automated Submission Script Creation & Submission]] | #Gaussview: [[Automated Submission Script Creation & Submission]] | ||
- | + | = FarmShare software = | |
Please note that we provide suppport on the installation and availability of software packages, but we generally don't provide support on the '''usage''' of the software. If you need help on usage, please [mailto:farmshare-discuss@lists.stanford.edu e-mail] the [https://mailman.stanford.edu/mailman/listinfo/farmshare-discuss FarmShare user community] or submit a support ticket with the appropriate vendor. Alternatively, the [http://www.stanford.edu/group/ssds/cgi-bin/drupal/content/who-we-are-what-we-do SSDS] campus group can provide 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. | Please note that we provide suppport on the installation and availability of software packages, but we generally don't provide support on the '''usage''' of the software. If you need help on usage, please [mailto:farmshare-discuss@lists.stanford.edu e-mail] the [https://mailman.stanford.edu/mailman/listinfo/farmshare-discuss FarmShare user community] or submit a support ticket with the appropriate vendor. Alternatively, the [http://www.stanford.edu/group/ssds/cgi-bin/drupal/content/who-we-are-what-we-do SSDS] campus group can provide 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. | ||
- | + | == stock software == | |
- | + | ||
The FarmShare machines are running Ubuntu, and the software is from the Ubuntu repositories, e.g. run '''dpkg -l | grep ^i''' to see the list of installed packages. | The FarmShare machines are running Ubuntu, 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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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. | 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. | ||
- | + | == licensed software == | |
As of April 2012, we're transitioning the location of licensed software into /mnt/glusterfs/software/ and using [[FarmShare software | modules]]. As of July 2, 2012, the software that is available is: | As of April 2012, we're transitioning the location of licensed software into /mnt/glusterfs/software/ and using [[FarmShare software | modules]]. As of July 2, 2012, the software that is available is: | ||
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*add it to this wiki | *add it to this wiki | ||
*modify /etc/motd on the corn machines | *modify /etc/motd on the corn machines | ||
- | *send a mail to farmshare- | + | *send a mail to farmshare-discuss |
= Mailing Lists = | = Mailing Lists = |
Revision as of 13:29, 8 January 2013
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 service catalog page.
Most useful pages: Special:AllPages and Special:RecentChanges and User Guide and FAQ and FarmShare tutorial
Last 10 messages on Farmshare-Discuss mail list (this month) | ||
| |
How to connect
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.
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 /mnt/glusterfs on all corn and barley nodes. Login to senpai1.stanford.edu and a directory will be created for you as /mnt/glusterfs/<your user name> (can take up to 5 minutes). Sign up and email the farmshare-discuss mailing list if you have any questions or would like any info not listed here.
How to get help
You can e-mail research-computing-support@stanford.edu
cardinal info
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.
Simply "ssh cardinal.stanford.edu" with your SUNetID credentials.
There are currently 3 cardinal machines: cardinal1, cardinal2 and cardinal3, load-balanced via cardinal.stanford.edu.
corn info
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.
- Policies: http://itservices.stanford.edu/service/sharedcomputing/policies
- IT services page: https://itservices.stanford.edu/service/sharedcomputing
- VNC help: https://itservices.stanford.edu/service/sharedcomputing/vnc
- Q? E-mail research-computing-support@stanford.edu or file a HelpSU: http://helpsu.stanford.edu/?pcat=farmshare
- Future vision as of summer 2010: http://itservices.stanford.edu/strategy/sysadmin/timeshare
Each of the 30 corn machines has 8 cores, 32GB RAM and ~70GB of local disk in /tmp.
barley info
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.
- Q? E-mail research-computing-support@stanford.edu or file a HelpSU: http://helpsu.stanford.edu/?pcat=farmshare
Examples of using the barley cluster
- Introductory examples: Examples Ready to Make
- R
- MATLAB
- Access Mysql from Matlab
- Rmpi
- Gaussian
- Ipython
Please note that we provide suppport on the installation and availability of software packages, but we generally don't provide support on the usage of the software. If you need help on usage, please e-mail the FarmShare user community or submit a support ticket with the appropriate vendor. Alternatively, the SSDS campus group can provide guidance for R, SAS and Stata. Please contact them directly if you have any questions about using those particular software packages.
stock software
The FarmShare machines are running Ubuntu, and the software is from the Ubuntu repositories, e.g. run dpkg -l | grep ^i to see the list of installed packages.
If the package you're looking for isn't installed, search the Ubuntu Packages page and submit a HelpSU with the package name(s) you want.
licensed software
As of April 2012, we're transitioning the location of licensed software into /mnt/glusterfs/software/ and using modules. As of July 2, 2012, the software that is available is:
# module avail ------------------------ /mnt/glusterfs/software/free/modules/tcl/modulefiles ------------------------- CPLEX_Studio-12.4 MATLAB-R2010b NAG-gfortran-23 StataMP-12.1 GAMS-23.8.1-AFS MATLAB-R2011b R-2.15.0 StataSE-12.1 GAMS-23.8.2-GlusterFS MATLAB-R2012a R-2.15.1-notyet IMSL NAG-C-23 StatTransfer-11.2
Licensed software that hasn't been transitioned yet is still available in /usr/sweet/bin. Older versions of some of the same programs as above may also be available here.
# ls /usr/sweet/bin/ MathKernel@ cplexamp@ g03@ hlm2@ lmutil@ mex@ sicstus@ stata@ Mathematica@ cplexconvert@ g09@ hlm3@ maple@ mint@ spdet@ stata-se@ Splus@ dbmscopy@ gams@ hmlm@ math@ rats@ spld@ tracker@ ampl@ dbmsnox@ gamsbatch@ hmlm2@ mathematica@ ratsgraph@ splfr@ xdisplay@ anshelp@ eqs@ gamslib@ launcher@ matlab@ rcomp@ splm@ xmaple@ ansys@ f95@ gview@ limdep@ mbuild@ rgf2pst@ splus@ xstata@ cplex@ f95mcheck@ hcm2@ lmgrd@ mcc@ sas@ spxref@ xstata-se@
Monitoring / Status
- Current status of farmshare machines: http://barley-monitor.stanford.edu/ganglia/
- More detailed graphs: http://barley-monitor.stanford.edu/munin/
- File a help ticket for farmshare problems: http://helpsu.stanford.edu/?pcat=farmshare
For important announcements, we plan to:
- add it to this wiki
- modify /etc/motd on the corn machines
- send a mail to farmshare-discuss
Mailing Lists
We have mailing lists, @lists.stanford.edu - https://itservices.stanford.edu/service/mailinglists/tools
- farmshare-announce - announcements list - Archives
- farmshare-discuss - user discussion - Archives
Links
Want to learn HPC? Free education materials available:
GPUs! We don't have any GPUs as part of FarmShare, but there are other campus resources available:
- http://icme.stanford.edu/Computer%20Resources/gpu.php
- http://classx.stanford.edu/ClassX/system/users/web/pg/view_subject.php?subject=NVIDIA_ICME_SPRING_2010_2011
- Engineering / Computer Science computer labs: myth20 through myth32 have nVidia GPU modules for development: http://cs.stanford.edu/computing-guide/overview/computer-systems/myth
Other similar wikis/clusters on campus (you might not have access to these):
- Engineering / Computer Science computer labs (myth.stanford.edu), open to all fully sponsored SunetIDs: http://cs.stanford.edu/computing-guide/overview/computer-systems/myth
- Statistics cluster: https://www.stanford.edu/dept/statistics/cgi-bin/projects/stat-sysadminwiki/index.php/Cluster_Help
- Genetics cluster: https://www.stanford.edu/group/scgpm/cgi-bin/informatics/wiki/index.php/Main_Page
- SU-HPC group: https://www.stanford.edu/group/su-hpc/cgi-bin/mediawiki/index.php/Special:Recentchanges
- HPCC wiki: https://www.stanford.edu/group/hpcc/cgi-bin/mediawiki/index.php/Main_Page
- Proclus (H&S cluster): https://www.stanford.edu/group/proclus/cgi-bin/mediawiki/index.php/Main_Page
Vision
The Farmshare resources are being made available to students, faculty and staff with fully sponsored SunetIDs to facilitate research at Stanford University. 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. The Farmshare resources are focused on making it easier to learn how to parallelize research computing tasks and use research software including a "scheduler" or "distributed resource management system" to submit compute jobs.
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.