[GE users] Sporadic errors in array tasks with a PE

elauzier elauzier2 at perlstar.com
Mon Apr 19 20:16:01 BST 2010


Use the "-b y" qsub switch.  This is stated in the docs, but I missed it too the first time I ran into this issue.

The problem is that when using array jobs and pe spreading over many hosts, there is a race condition that goes on and for large jobs spread across many hosts, you will see this especially if SGE is very busy...

To get around this, eliminate the need for the job file... use "-b y"...but...

You cannot use the embedded SGE options in your scriptfile...

Takes a bit of adjustment, but it is very doable and once done works very well...

Ed Lauzier

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