zong-pei.han@imm.ox.ac.uk wrote:
Hi Nate,
Our local Galaxy root directory is /wwwdata/galaxy, and I have to hardwire the filename
/wwwdata/galaxy/log/heartbeat.log
in /wwwdata/galaxy/lib/galaxy/util/heartbeat.py for log files to be created.
With "use_heartbeat = True", now Galaxy no longer getting job running or finished status - just sits there saying "Job is waiting to run". In fact the queued jobs are finished! I have put log files below for you to look at:
http://sara.molbiol.ox.ac.uk/userweb/zph/galaxy.log http://sara.molbiol.ox.ac.uk/userweb/zph/heartbeat.log http://sara.molbiol.ox.ac.uk/userweb/zph/heartbeat.log.nonsleeping
Galaxy is setting metadata on one of the datasets, which is causing other job operations to move very slowly. I suspect it's job 141 - could this job have been created before you enabled set_metadata_externally? --nate
Regards, Zong-Pei
On Thu, 29 Apr 2010, Nate Coraor wrote: Date: Thu, 29 Apr 2010 18:27:59 +0100 From: Nate Coraor <nate@bx.psu.edu> To: Zong-Pei Han <zong-pei.han@imm.ox.ac.uk> Cc: Stephen Taylor <stephen.taylor@imm.ox.ac.uk>, "galaxy-dev@bx.psu.edu" <galaxy-dev@bx.psu.edu> Subject: Re: [galaxy-dev] Job Control in Galaxy
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
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