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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