Hi All,
After changing the sleep in manager.py from 5 seconds to 0.2 seconds, the job
start is very snappy. I did not touch the various sleep(10)s that don't seem
to be relevant.
I'm testing how long it takes to sort a short bed file in galaxy.
After the fix, the problem seems to be at the end of the process. In the
timeline below the gap between the job ending on the server and the client
getting the update is 5 seconds.
Is that a built in sleep or something else? Can I turn off metadata for tools
that don't generate it?
BTW: thousands of seconds are on in the manager and handler logs and should be
turned on in the main.log.
Rather than 2 round trips to the server. I think we need a special class of
tools that run in a single round trip (like the eyeball viz). The max run time
for this class of jobs should be no more than a few seconds. Is that is the
roadmap somewhere?
-Robert Baertsch
UC Santa Cruz
https://medbook.ucsc.edu
RUN1 - 9 seconds (1 sec to start, 0.2 sec to run , 2 sec metadata, 5.5 secs to
update client)
12:08:12.? main: log job on main thread
12:08:12.8 manager : galaxy.jobs.manager DEBUG 2013-03-30 12:08:12,867
(2308) Job assigned to handler 'handler2'
12:08:13.26 handler:start handler
12:08:13.35 handler:job dispatched
12:08:13,44 handler:job runner started
12:08:13,72 handler:python tool started
12:08:13,91 handler: python tool finished
12:08:13,98 handler: set_metadata.sh started
12:08:15,70 handler:metadata ended
12:08:15,85 handler:job Ended
12:08:21main: /api/histories - update on client
RUN2 - 9 seconds (1.8 sec to start, 0.2 sec to run, 2 sec metadata, 4.5 sec to
update client)
12:23:00.? main: log job on main thread
12:23:00,60 manager : galaxy.jobs.manager DEBUG 2013-03-30 12:08:12,867
(2308) Job assigned to handler 'handler2'
12:23:01,63 handler:start handler
12:23:01,72 handler:job dispatched
12:23:01,81 handler:job runner started
12:23:02,44 handler:python tool started
12:23:02,64 handler: python tool finished
12:23:02,72 handler: set_metadata.sh started
12:23:04,64 handler:metadata ended
12:23:04,71 handler:job Ended
12:23:09main: /api/histories - update on client
___
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/
To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/mailinglists/
