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.
Joseph Hargitai wrote:Ah, I suspect this is attribute caching in NFS. Try mounting with the
> 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.
option 'noac' and see if it solves the problem.
The filename is unimportant, but I doubt it's the cause.
> Could we suppress e and o SGE style to resolve this issue, or Galaxy wants the o?
Not off the top of my head. I have this message marked, I'll take a
> Do you have an idea about the url build for galaxy - ucsc page return when the url is :8080/galaxy and not just /galaxy?
look as soon as I have time.
--nate
>
> thanks,
> joe
>
> ________________________________________
> From: Nate Coraor [nate@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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