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# cd to /mnt/glusterfs/your_username | # cd to /mnt/glusterfs/your_username | ||
# write a job script: "$EDITOR test_job.script" | # write a job script: "$EDITOR test_job.script" | ||
| - | + | ##see 'man qsub' for more info | |
| - | + | ##use env var $TMPDIR for local scratch | |
| - | + | ##use /mnt/glusterfs/<your username> for shared data directory | |
# submit the job for processing: "qsub test_job.script" | # submit the job for processing: "qsub test_job.script" | ||
# monitor the jobs with "qstat -f -j JOBID" | # monitor the jobs with "qstat -f -j JOBID" | ||
| - | + | ##see 'man qstat' for more info | |
| - | # check the output files that you specified in your job script (the | + | # check the output files that you specified in your job script (the input and output files must be in /mnt/glusterfs/) |
| - | input and output files must be in /mnt/glusterfs/) | + | |
Technical details: | Technical details: | ||
Revision as of 17:56, 20 October 2011
This wiki is intended for the users of the Stanford shared research computing resources. E.g. the "cardinal" and "corn" and "barley" machines.
Contents |
How to connect
The machines are available for anyone with a SUNetID. Simply "ssh corn.stanford.edu" with your SUNetID credentials. The DNS name "corn.stanford.edu" actually goes to a load balancer and it will connect you to a particular corn machine that has relatively low load.
The "barley" machines are only accessible via a resource manager (currently Open GridEngine). You'll need to ssh to corn-image-new and a directory will be created for you on local (shared among barley) storage. e-mail barley-alpha for more info.
barley info
To start using the new machines, you can check out the 'qhost' and 'qstat' and 'qsub' commands on machine 'corn-image-new'.
So the procedure would look something like this:
- log into corn-image-new: "ssh corn-image-new.stanford.edu"
- cd to /mnt/glusterfs/your_username
- write a job script: "$EDITOR test_job.script"
- see 'man qsub' for more info
- use env var $TMPDIR for local scratch
- use /mnt/glusterfs/<your username> for shared data directory
- submit the job for processing: "qsub test_job.script"
- monitor the jobs with "qstat -f -j JOBID"
- see 'man qstat' for more info
- check the output files that you specified in your job script (the input and output files must be in /mnt/glusterfs/)
Technical details: 19 new machines, 24 cores each, 96GB RAM 1 new machine, 24 cores, 192GB RAM ~450GB local scratch on each ~3TB in /mnt/glusterfs Grid Engine v6.2u5 (via standard Debian package)
Initial issues: Kerberos and AFS don't work on the execution hosts You are limited in space to your AFS homedir ($HOME) and local scratch disk on each node ($TMPDIR) The execution hosts don't accept interactive jobs, only batch jobs for now.
Any questions, please email 'barley-alpha@lists.stanford.edu'
We plan to have "alpha" testing for a month or so, then rebuild the storage nodes using the information we learned, and also rebuild the execution hosts to Ubuntu 11.10. Then we'll have "beta testing" with more users in Nov and Dec and roll out to the full Stanford community on Jan 1.
Monitoring / Status
Current status of farmshare machines: http://barley-monitor.stanford.edu/ganglia/
Mailing Lists
We have several mailing lists, all @lists.stanford.edu, most are not used.
- barley-alpha - temp list till end of Oct/Nov 2011, for discussion around testing the barleys
- farmshare-announce - announce list (new service name)
- farmshare-discuss - users discussion (new service name)
- stanford-timeshare-users - users discussion list for the corn users, list to be retired
Getting started with MediaWiki
Consult the User's Guide for information on using the wiki software.
