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?

Thanks, Thon ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/

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 >> >> ___________________________________________________________ >> Please keep all replies on the list by using "reply all" >> in your mail client. To manage your subscriptions to this >> and other Galaxy lists, please use the interface at: >> >> http://lists.bx.psu.edu/ > > > ___________________________________________________________ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > > http://lists.bx.psu.edu/ >

I created the index but that did not change anything... I had sent James Taylor the schema as he requested, but I never heard anything so I guess he must not have found anything weird... I am waiting to move my Galaxy server off to a three server configuration, so I am hoping the problem will not return, although your issue does not bode well for this issue...

Regards, Thon de Boer, Ph.D. Bioinformatics Guru +1-650-799-6839 thondeboer(a)me.com LinkedIn Profile On Oct 23, 2012, at 4:14 AM, Hans-Rudolf Hotz <hrh(a)fmi.ch&gt; 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 >>> >>> ___________________________________________________________ >>> Please keep all replies on the list by using "reply all" >>> in your mail client. To manage your subscriptions to this >>> and other Galaxy lists, please use the interface at: >>> >>> http://lists.bx.psu.edu/ >> >> >> ___________________________________________________________ >> Please keep all replies on the list by using "reply all" >> in your mail client. To manage your subscriptions to this >> and other Galaxy lists, please use the interface at: >> >> http://lists.bx.psu.edu/ >>