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: email@example.com > 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 > > > > > ___________________________________________________________ > > Please keep all replies on the list by using "reply all" > > in your mail client. To manage your subscriptions to this > > and other Galaxy lists, please use the interface at: > > > > http://lists.bx.psu.edu/ > > > > ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/