[galaxy-dev] Job output not returned from cluster

[Edward Kirton]

yes, i think galaxy already grabs these files.  i seem to recall this
process would get stuck if the output was too large (i was running
something with a --debug/verbose option and galaxy would not finish the job
even though it was off the cluster -- had to redirect to a log file).

so i guess others aren't having the same problems as i had, which is good
news

On Thu, Dec 1, 2011 at 10:01 AM, Nate Coraor <nate at bx.psu.edu> wrote:

>
> On Nov 29, 2011, at 9:22 PM, Fields, Christopher J wrote:
>
> > On Nov 29, 2011, at 3:13 AM, Peter Cock wrote:
> >
> >> On Monday, November 28, 2011, Joseph Hargitai <
> joseph.hargitai at einstein.yu.edu> wrote:
> >>> Ed,
> >>>
> >>> we had the classic goof on our cluster with this. 4 nodes could not
> see the /home/galaxy folder due to a missing entry in /etc/fstab. When the
> jobs hit those nodes (which explains the randomness) we got the error
> message.
> >>>
> >>> Bothersome was the lack of good logs to go on. The error message was
> too generic - however I discovered that Galaxy was depositing the error and
> our messages in the /pbs folder and you could briefly read them before they
> got deleted. There the message was the classic SGE input/output message -
> /home/galaxy.... file not found.
> >>>
> >>> Hence my follow up question - how can I have galaxy NOT to delete
> these SGE error and out files?
> >>>
> >>> best,
> >>> joe
> >>
> >> Better yet, Galaxy should read the SGE o and e files and record their
> contents as it would for a directly executed tools stdout and stderr.
> >>
> >> Peter
> >
> > ...or at least have the option to do so, maybe a level of verbosity.  I
> have been bitten by lack of stderr output myself, where having it might
> have saved some manual debugging.
>
> Unless I'm misunderstanding, this is what Galaxy already does.
>  stdout/stderr up to 32K are read from .o and .e and stored in
> job.stdout/job.stderr.  We do need to just store them as files and make
> them accessible for each tool run, this will hopefully happen sometime
> soonish.
>
> --nate
>
> >
> > chris
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