hi, we've had this issue too -- in short, the cluster node(s) finish
writing outfiles to disk, but the file system (inode metadata) isn't
updated at the galaxy server yet when galaxy checks for the files.

turning the metadata caching off (as recommended on the galaxy wiki) isn't
an option for me (and the performance hit would be significant), so i added
some loops around the file checking (5sec sleep and retry up to 6 times).
 there were a couple of places this probably should be done (not just
.[eo]* log files but also the outfiles).

i am testing these hacks now but due to the intermittent nature of these
errors, it'll be a few days before i know if this is working as expected.
 once vetted, i will put these minor edits in a clone of galaxy-central so
the changes can be picked up.

ed

On Mon, Oct 24, 2011 at 10:24 AM, Nate Coraor <n...@bx.psu.edu> wrote:

> Joseph Hargitai wrote:
> > Nate,
> >
> > this error is intermittent. You resubmit the same job twice or three
> time and then it works.  Once we are over the midterm exams - which use
> galaxy - we will try to switch the filesystem from autofs to hard mount. We
> suspect this to be the issue.
>
> Ah, I suspect this is attribute caching in NFS.  Try mounting with the
> option 'noac' and see if it solves the problem.
>
> > Could we suppress e and o SGE style to resolve this issue, or Galaxy
> wants the o?
>
> The filename is unimportant, but I doubt it's the cause.
>
> > Do you have an idea about the url build for galaxy - ucsc page return
> when the url is :8080/galaxy and not just /galaxy?
>
> Not off the top of my head.  I have this message marked, I'll take a
> look as soon as I have time.
>
> --nate
>
> >
> > thanks,
> > joe
> >
> > ________________________________________
> > From: Nate Coraor [n...@bx.psu.edu]
> > Sent: Friday, October 21, 2011 10:26 AM
> > To: Joseph Hargitai
> > Cc: galaxy-dev@lists.bx.psu.edu
> > Subject: Re: [galaxy-dev] Job output not returned from cluster
> >
> > Joseph Hargitai wrote:
> > >
> > > Hi,
> > >
> > > i was browsing through the list and found many entries for this issue
> but not a definite answer.
> > >
> > > We are actually running into this error for simple file uploads from
> the internal filesystem.
> >
> > Hi Joe,
> >
> > This error occurs when the job's standard output and error files are not
> > found where Galaxy expects them, namely:
> >
> >     <cluster_files_directory>/<job_id>.o
> >     <cluster_files_directory>/<job_id>.e
> >
> > Please check your queueing system to make sure it can correctly deliver
> > these back from the execution hosts to the specified filesystem.
> >
> > --nate
> >
> > >
> > > thanks,
> > > joe
> > >
> >
> > > ___________________________________________________________
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> >
> >
> >
> >
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