Barley info
From FarmShare
(Difference between revisions)
| Line 15: | Line 15: | ||
*1 new machine, AMD Magny Cours 24 cores, 192GB RAM | *1 new machine, AMD Magny Cours 24 cores, 192GB RAM | ||
*~450GB local scratch on each | *~450GB local scratch on each | ||
| - | |||
*~100TB in /farmshare/user_data shared across all barley and corn systems (introduced summer 2013) | *~100TB in /farmshare/user_data shared across all barley and corn systems (introduced summer 2013) | ||
| - | *Grid | + | *Open Grid Scheduler 2011.11p1 |
*10GbE interconnect (Juniper QFX3500 switch) | *10GbE interconnect (Juniper QFX3500 switch) | ||
| Line 32: | Line 31: | ||
If you want to use the newer bigger storage: | If you want to use the newer bigger storage: | ||
| - | #log into any FarmShare machine: | + | #log into any FarmShare machine: ssh sunetid@corn.stanford.edu |
| - | + | ||
#cd to /farmshare/user_data/<your username> (or wait 5mins if it doesn't exist yet) | #cd to /farmshare/user_data/<your username> (or wait 5mins if it doesn't exist yet) | ||
#write a job script: "$EDITOR test_job.script" | #write a job script: "$EDITOR test_job.script" | ||
Revision as of 20:31, 20 September 2013
Follow the FarmShare tutorial or the User Guide
current barley policies
- 480 max jobs per user (look for max_u_jobs in output of 'qconf -sconf')
- 3000 max jobs in the system (look for max_jobs in output of 'qconf -sconf')
- 48hr max runtime for any job in regular queue (look for h_rt in output of 'qconf -sq precise.q')
- 30 days max runtime for the long queue (look for h_rt in output of 'qconf -sq precise-long.q')
- 15min max runtime in test.q
- 4GB default mem_free request per slot ('qconf -sc |grep mem_free')
Technical details
- 19 new machines, AMD Magny Cours 24 cores each, 96GB RAM
- 1 new machine, AMD Magny Cours 24 cores, 192GB RAM
- ~450GB local scratch on each
- ~100TB in /farmshare/user_data shared across all barley and corn systems (introduced summer 2013)
- Open Grid Scheduler 2011.11p1
- 10GbE interconnect (Juniper QFX3500 switch)
how to use the barley machines
To start using these new machines, you can check out the man page for 'sge_intro' or the 'qhost', 'qstat', 'qsub' and 'qdel' commands.
Initial issues:
- 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.
- You'll want to make sure you have your Kerberos TGT and your AFS token.
If you want to use the newer bigger storage:
- log into any FarmShare machine: ssh sunetid@corn.stanford.edu
- cd to /farmshare/user_data/<your username> (or wait 5mins if it doesn't exist yet)
- write a job script: "$EDITOR test_job.script"
- see 'man qsub' for more info
- use env var $TMPDIR for local scratch
- use /farmshare/user_data/<your username> for shared data directory
- submit the job for processing: "qsub -cwd 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 /farmshare/user_data/)
Any questions, please email 'farmshare-discuss@lists.stanford.edu' Some good intro usage examples here: http://gridscheduler.sourceforge.net/howto/basic_usage.html
