Further to my email below.

I have a data library that contains many ~117Gb of NGS data, uploaded via file system path. This library was always slow to open (about 10s) but now takes several minutes or not at all.

Thanks for any help on this. I am still experiencing a memory leak that I can't pinpoint and it is only dissipated by restarting the server. At the moment my debugging level is set to INFO. Is there anything I can change in the universe file to try to trace this.

Thanks!
Shaun


----- Forwarded message from swe...@staffmail.ed.ac.uk -----
    Date: Wed, 09 Mar 2011 10:15:13 +0000
    From: SHAUN WEBB <swe...@staffmail.ed.ac.uk>
 Subject: Galaxy process
      To: galaxy dev <galaxy-...@bx.psu.edu>



Hi,

since making the last update I have found some new warnings in my paster.log, it also seems as though the galaxy process starts to gather memory and eventually hang (35% of 64G memory).

I've posted the entries below.

If anyone could help me understand what is going on that would be great.

Thanks.
Shaun Webb



paste.httpserver.ThreadPool INFO 2011-03-09 09:49:49,962 No idle tasks, and only 0 busy tasks; adding 5 more workers paste.httpserver.ThreadPool INFO 2011-03-09 09:49:58,754 No idle tasks, and only 4 busy tasks; adding 1 more workers paste.httpserver.ThreadPool INFO 2011-03-09 09:51:47,301 Culling 6 extra workers (5 idle workers present) paste.httpserver.ThreadPool INFO 2011-03-09 09:55:17,163 No idle tasks, and only 0 busy tasks; adding 5 more workers 129.215.14.72 - - [09/Mar/2011:09:48:40 +0100] "GET /history HTTP/1.1" 500 - "http://bifx-core.bio.ed.ac.uk:8080/"; "Mozilla/5.0 (Windows; U; Windows NT 5.1; en-GB; rv:1.9.2.13) Gecko/20101203 Firefox/3.6.13 (.NET CLR 2.0.50727; .NET CLR 1.1.4322; .NET CLR 3.0.4506.2152; .NET CLR 3.5.30729)" paste.httpserver.ThreadPool INFO 2011-03-09 10:13:16,956 Culling 5 extra workers (7 idle workers present) 212.183.140.59 - - [09/Mar/2011:10:13:17 +0100] "GET / HTTP/1.1" 200 - "-" "Mozilla/5.0 (Macintosh; U; Intel Mac OS X 10_6_6; en-US) AppleWebKit/534.13 (KHTML, like Gecko) Chrome/9.0.597.102 Safari/534.13" paste.httpserver.ThreadPool INFO 2011-03-09 10:14:35,715 No idle tasks, and only 2 busy tasks; adding 3 more workers paste.httpserver.ThreadPool WARNING 2011-03-09 10:15:15,104 Thread 140283224094464 hung (working on task for 3096 seconds)
----------------------------------------
Exception happened during processing of request from ('212.183.140.59', 10871)
Traceback (most recent call last):
File "/usr/lib/python2.6/SocketServer.py", line 281, in _handle_request_noblock
    self.process_request(request, client_address)
File "/storage/home/galaxy/galaxy_dist/eggs/Paste-1.6-py2.6.egg/paste/httpserver.py", line 1037, in process_request
    lambda: self.process_request_in_thread(request, client_address))
File "/storage/home/galaxy/galaxy_dist/eggs/Paste-1.6-py2.6.egg/paste/httpserver.py", line 617, in add_task
    self.kill_hung_threads()
File "/storage/home/galaxy/galaxy_dist/eggs/Paste-1.6-py2.6.egg/paste/httpserver.py", line 778, in kill_hung_threads
    self.kill_worker(worker.thread_id)
File "/storage/home/galaxy/galaxy_dist/eggs/Paste-1.6-py2.6.egg/paste/httpserver.py", line 705, in kill_worker
    killthread.async_raise(thread_id, SystemExit)
File "/storage/home/galaxy/galaxy_dist/eggs/Paste-1.6-py2.6.egg/paste/util/killthread.py", line 22, in async_raise
    raise ValueError("invalid thread id")
ValueError: invalid thread id
----------------------------------------


--
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.



----- End forwarded message -----


--
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.


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