Well, I didn't move it to a grid configuration using PBS recently, it was
already using a grid configuration with PBS before I moved it to the NFS
volume and no such an error ever happened :) So it must be related to NFS.


Thanks for you great suggestions! I will try them out and see how they work
on my system.

Thanks,
Luobin

On Mon, Oct 17, 2011 at 12:45 PM, Duddy, John <jdu...@illumina.com> wrote:

>  You mention that you moved it to an NFS volume – but it seems you also
> moved to a grid configuration using PBS?****
>
> ** **
>
> If that’s the case, what you are seeing might be an issue with NFS
> attribute caching or write caching, which causes files created from one
> machine to not appear until some time later (from the perspective of other
> machines). The PBS job notifications are not impacted by the filesystem
> latencies.****
>
> ** **
>
> You can prove this by experiment if you alter the finish_job method in
> lib/galaxy/jobs/runners/pbs.py to do a sleep/wait loop, waiting up to 60
> seconds for the files to be readable. If that hack works, latency is your
> problem.****
>
> ** **
>
> The solution is either to:****
>
> **-          **Configure your mounts not to use attribute caching (has
> performance impacts), or****
>
> **-          **Make the hack permanent.****
>
> ** **
>
> This happened to us on SGE, which is why I know these details ;-} ****
>
> ** **
>
> *John Duddy
> Sr. Staff Software Engineer
> Illumina, Inc.
> *9885 Towne Centre Drive
> San Diego, CA 92121
> Tel: 858-736-3584
> E-mail: jdu...@illumina.com****
>
> ** **
>
> *From:* galaxy-dev-boun...@lists.bx.psu.edu [mailto:
> galaxy-dev-boun...@lists.bx.psu.edu] *On Behalf Of *Luobin Yang
> *Sent:* Monday, October 17, 2011 10:31 AM
> *To:* galaxy-dev@lists.bx.psu.edu
> *Subject:* [galaxy-dev] What's causing this error?****
>
> ** **
>
> Hi, ****
>
> ** **
>
> Recently I moved my locally installed Galaxy from a local hard drive to an
> NFS mounted hard drive, when I run some tools, I go the following error from
> the log file:****
>
> ** **
>
> Job output not returned by PBS: the output datasets were deleted while the
> job was running, the job was manually dequeued or there was a cluster error.
> ****
>
> ** **
>
> I am pretty sure the job was not manually dequeued. Any idea how this
> happened and how this can be fixed?****
>
> ** **
>
> Thanks,****
>
> Luobin****
>
> ** **
>
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