On 8/8/12 4:06 PM, "Nate Coraor" <n...@bx.psu.edu> wrote:

>On Aug 8, 2012, at 2:30 PM, Karger, Amir wrote:
>> Meanwhile, we're able to restart, and get happy log messages from the
>>jobrunner and two web "servers" (two servers running on different ports
>>of a Tomcat host). And I can do an upload, which runs locally. But when
>>I try to do a blast, which is supposed to submit to the cluster (and ran
>>just fine on our old install), it hangs and never starts. I would think
>>the database is working OK, since it shows me new history items when I
>>upload and stuff. The web Galaxy log shows that I went to the tool page,
>>and then has a ton of loads to root/history_item_updates, but nothing
>>else. The job handler Galaxy log has nothing since the PID messages when
>>the server started up most recently.
>> A quick search of the archives didn't find anything obvious. (I don't
>>have any obvious words to search for.) Any thoughts about where I should
>>start looking to track this down?
>Hi Amir,
>If you aren't setting job_manager and job_handlers in your config, each
>server will consider itself the manager and handler.  If not configured
>to run jobs, this may result in jobs failing to run.  I'd suggest
>explicitly defining a manager and handlers.

Sigh. We have both job_manager and job_handlers set to the same server.

It seems like our runner app may be getting into some kind of sleeping
state. I was unable to upload a file, which had worked before. However,
when I restarted the runner, it picked up the upload job and successfully
uploaded it AND picked up the previously queued tab2fasta job, and I
believe completed it successfully too. (There's an error due to a missing
filetype, which I guess makes stderr non-empty and makes Galaxy think it
was unsuccessful. But I can confirm that the job was in fact run on our
cluster.) Running paster.py ... --status claims that the process is still
running. So what would make the runner go to "sleep" like that and how do
I stop it from happening?



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