From FarmShare

Revision as of 16:24, 6 April 2012 (view source) Chekh (Talk | contribs) (→mem_free) ← Older edit		Revision as of 16:42, 6 April 2012 (view source) Chekh (Talk | contribs) (→useful commands) Newer edit →
Line 21:		Line 21:
	*see all jobs: '''qstat -f -u "*"'''		*see all jobs: '''qstat -f -u "*"'''
	*see all host attributes: '''qstat -f -F -u "*"'''		*see all host attributes: '''qstat -f -F -u "*"'''
		+	*explain state 'a': '''qstat -explain a'''
	==queues==		==queues==

---

Revision as of 16:42, 6 April 2012

We're using the Debian packages of "Sun Grid Engine" which isn't quite "Sun" anymore since Oracle bought Sun, and the Debian packages are a bit behind the current forks of Open Grid Engine or Son of Grid Engine or Univa Grid Engine.

Contents 1 documentation 2 shell mode 3 useful commands 4 queues 5 Grid Engine settings on farmshare 5.1 main.q 5.2 bigmem.q 5.3 long.q 5.4 test.q 5.5 starter method 5.6 making the test.q 5.7 mem_free

documentation

Start with 'man sge_intro'. Move on to 'man qsub'. Try submitting a simple job with 'echo "sleep 3600" | qsub", then run 'qstat' and 'qdel'.

shell mode

GE can run in "POSIX mode" or "Unix mode". See the "shell_start_mode" section of 'man sge_conf'

 # qconf -sconf|grep shell
 shell_start_mode             unix_behavior
 login_shells                 bash,sh,ksh,csh,tcsh

So you'll want to explicitly specify your shell with the -S flag to qsub. E.g.

 # get rid of spurious messages about tty/terminal types
 #$ -S /bin/sh

useful commands

• see all hosts: qhost
• see which jobs are on which hosts: qhost -j
• see all jobs: qstat -f -u "*"
• see all host attributes: qstat -f -F -u "*"
• explain state 'a': qstat -explain a

queues

Under SGE, a 'queue' is a set of settings that get applied to jobs that are assigned to that queue.

Grid Engine settings on farmshare

We are using pretty much the default settings. This page should contain a description of all of the settings we've changed away from the defaults along with a reason for doing so.

We created four queues: bigmem.q, long.q, main.q and test.q. Use 'qconf -sql' to list queues, 'qconf -sq queue_name' to see the queue settings.

main.q

Most jobs end up here. Time limit is 48hrs.

bigmem.q

This queue is explicitly tied to the machine with more physical memory. Same settings as main.q

long.q

2week time limit instead of 48hrs

test.q

15min time limit instead of 48hrs

If you want to submit a job to this test queue, you must use '-l testq=1' flag to qsub.

starter method

There is a file /usr/local/libexec/gridengine/job_start.sh which sets up the checkpointing environment if you specified checkpointing for your job.

making the test.q

• add testq to the global complex attributes list (qconf -mc)

 senpai1:/root# qconf -sc |grep testq
 testq               testq      BOOL        ==    FORCED         NO         0        0

"requestable" is set to FORCED to make that attribute required (per 'man 5 complex')

• add testq to the complex attributes of the queue (qconf -sq test.q)

 senpai1:/root# qconf -sq test.q|grep testq
 hostlist              barley-testq.stanford.edu
 complex_values        testq=1

• users now need to use the qsub parameter "-l testq=1" to have the job go to that queue instance. no jobs without testq=1 will go in that queue.

relevant thread: http://gridengine.org/pipermail/users/2012-March/002972.html

mem_free

Each node has a "load value" named "mem_free" that tracks actual free memory available.

Each node has a requestable and consumable "complex value" named "mem_free" that is set to 95G (190G for barley05).

Each job requests 4G of mem_free by default (unless uses specifies a different value). (qconf -sc)

You can see current values for the execution hosts with qstat -F, e.g. 'qstat -F -f -u "*"' and then search for mem_free.

 #request 37GB RAM for this job
 qsub -l mem_free=37G job.script