Hi Thon
Have you made any progress regarding the delays you've experienced?
I had some time this morning and was digging in the code a little
bit....in '~/lib/galaxy/jobs/manager.py' there is on line 155:
time.sleep( 5 )
and I am wondering is this delay really necessary? - needless to say,
if I remove it, jobs are executed ~5 seconds faster, and the time now
roughly corresponds to the numbers I have seen before the upgrade.
I doubt, there is a connection to the delays in minutes you've
experienced, but I am pretty happy with the speed up in our case. Now.
the big question: how safe is it to remove.... (or at least set to 1
sec)? - that's where my python and/or galaxy code knowledge comes to the
end.
Any comments from the developers appreciated.
Thank you very much
Hans-Rudolf
On 10/23/2012 01:14 PM, Hans-Rudolf Hotz wrote:
Hi Thon
Sorry for re-activating an old e-mail thread. I am just curious, whether
Nate's suggestion solved your problem?
After our upgrade (from the "March 12th changeset 6799:40f1816d6857" to
the "October 5th changeset 7824:b5bda7a5c345") we see long delays in the
jobs going from queued to running.
For our server, switching from "set_metadata_externally = False" to
"set_metadata_externally = True" did not speed up anything.
Regards, Hans-Rudolf
On 09/19/2012 04:27 PM, Nate Coraor wrote:
On Sep 18, 2012, at 6:31 PM, Anthonius deBoer wrote:
Hi,
Jobs that I start on my in-house Galaxy instance now take up to 3-4
min to go from queued to Running, even though there is nothing much
going on on the galaxy server...
I have been running this instance since June and use a relatively new
version of Galaxy-central (Last update, 22-Aug changeset:
7535:bf6517b2b336)
I have noticed that my jobs table in the galaxy Postgres database
contains about 60,000 jobs...
Could that be the culprit? Does it slow to the complete database to
see if there are any jobs that need to run?
Could I purge the jobs and related tables to speed up the submissions?
Hi Thon,
It's not really possible to remove things from the database since
there are a lot of interdependencies.
The first thing to check would be whether set_metadata_externally =
True in your Galaxy config.
--nate
Thanks,
Thon
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