On Thu, Jun 14, 2012 at 6:15 PM, Dannon Baker <dannonba...@me.com> wrote:
> On Jun 14, 2012, at 12:48 PM, Peter Cock wrote:
>> In a separate example with 33 sub-tasks, there were two of these
>> inversions, while in yet another example with 33 sub-tasks there was
>> a trio submitted out of order. This non-deterministic behavior is a
>> little surprising, but in itself not an immediate problem.
> You're correct in that submission order shouldn't matter at all,
> but I'll take a look and see if I can come up with an explanation for why.


>> In what appears to be a separate (and more concerning) loss of order,
>> after merging the output file order appears randomized. I would expect
>> the output from task_0, then task_1, ..., finally task_16. I haven't yet
>> worked out what order I am getting, but it isn't this, and neither is it
>> the order from the SGE job numbers (e.g. correct bar one pair
>> switched round).
> This would be happening in the merge.  It looks like change set
 > c959d32f2405 might be the culprit for this -- it doesn't explicitly
> reorder by task number in the merge method, which would lead
> to (I'm guessing) an alphanumeric sort.  I'll test and fix this.

I hope you're right - I've not stuck any debugging code in to try
and pin point this yet (maybe tomorrow).

>> [*] P.S. I would like to see an upper bound on the sleep_time in method
>> run_job, say half an hour? Otherwise with a group of long running jobs
>> it seems Galaxy may end up waiting a very long time between checks
>> for their completion since it just doubles the wait at each point. I had
>> sometimes noticed a delay between the sub-jobs finishing according
>> to the cluster and Galaxy doing anything about merging it - this is
>> probably why.
> This sleep time should currently cap at 8 seconds.

Doh. Yes, that makes sense.


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