[gridengine users] suspend_threshold depending on job I/O

Txema Heredia Genestar txema.heredia at upf.edu
Tue Nov 13 17:27:40 UTC 2012

Well, our main problem (for now) is not a single huge_io job, but lots 
(50+ maybe?) big_io jobs running at once scattered through the 26 nodes 
of our cluster.

My only hope is creating a cron job that reads the qstat info for all 
running jobs, parses all the jobs "io" values, saves them, compares them 
against the "io" value from the last cron run, and, if in trouble, 
suspends the jobs with the highest "now_io - old_io". But I don't expect 
it to hit the nail very often...

By the way... what does that "io" really measure?


El 13/11/12 18:05, Reuti escribió:
> Am 13.11.2012 um 15:24 schrieb Txema Heredia Genestar:
>> we have a 300-core cluster with a ~150Tb shared directory (GPFS). Our users run some genomic analysis that use huge files and usually cannot fit the 500Gb internal HDD of the nodes. As you can imagine, sometimes things get pretty intense and all the nagios disk alarms start going off (the disk "works" but we got 10+ sec timeouts).
>> Knowing that I cannot trust our users to request any "disk_intensive" parameter/flag, I was pondering on setting a suspend_threshold in the queues, watching the shared disk status (e.g. timing an ls to the shared disk) and start suspending jobs when the disk has, say, a 3 sec delay. This would be a nice fix for our issue, but it has some problems: When there are both "IO-intensive" and "normal" jobs, and the suspend_threshold kicks in, SGE will start suspending jobs ¿without any particular criteria? (I don't know this part)
> Yes.
>> , and lots of innocent "normal" jobs will be suspended through all the nodes before the disk load is stabilized.
> You would need another queue for the normal jobs without a suspend_threshold, but then you are where you started: users won't add a proper flag or request a proper queue.
> And: suspending a "bigio" job would only help if there is another "bigio" job on the same node, as otherwise it will have this "bigio" a little bit later again...
> -- Reuti
>> Does anyone have any idea/workaround to solve this? Or should I ignore/relax all the disk alarms?
>> Thanks in advance,
>> Txema
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