zong-pei.han@imm.ox.ac.uk wrote:
"use_heartbeat = True" is set. No heartbeat log files are generated after restarting Galaxy service and running a queue job.
I'm not sure how this can occur. They should be created in Galaxy's root directory since this is the working directory when Galaxy runs. --nate
Zong-Pei
On Thu, 29 Apr 2010, Nate Coraor wrote: Date: Thu, 29 Apr 2010 16:03:59 +0100 From: Nate Coraor <nate@bx.psu.edu> To: Stephen Taylor <stephen.taylor@imm.ox.ac.uk> Cc: "galaxy-dev@bx.psu.edu" <galaxy-dev@bx.psu.edu>, "zph@herald.ox.ac.uk" <zph@herald.ox.ac.uk> Subject: Re: [galaxy-dev] Job Control in Galaxy
Steve Taylor wrote:
Yes it says:
galaxy.jobs.runners.sge DEBUG 2010-04-29 15:33:33,133 (136/1221) state change: job finished normally
but in Galaxy it still is showing it as running.
After this you should also see 'job 136 ended'. This means that Galaxy has finished all post-processing.
If this never happens, please try enabling this option:
use_heartbeat = True
This will create two files:
heartbeat.log heartbeat.log.nonsleeping
Watching the latter will show what the threads are up to when this is happening. I suspect it's setting metadata, but this should tell us for sure.
--nate
Steve