We've experience memory-leak symptoms and we also use the PBS job runner here. We did not try to locate the leak, but instead installed monit as a work-around

http://mmonit.com/monit/
Todd Oakley

On 3/6/2012 11:10 AM, Nate Coraor wrote:
There is also a memory leak that occurs when using the pbs job runner.  I 
believe the leak is somewhere in libtorque or pbs_python but I have not yet 
tracked it down.

--nate

On Feb 29, 2012, at 3:28 PM, John Chilton wrote:

We had intermittent issues like this for an embarrassingly long time
at MSI, but since we applied this patch
https://bitbucket.org/galaxy/galaxy-central/pull-request/36/fix-for-dynamic_optionspy
Galaxy has been running smoothly for weeks. Seems unlikely this is the
problem in your case (unless you have pulled in tools with make use of
dynamic options), but it something to consider.

-John

On Wed, Feb 29, 2012 at 2:08 PM, Joshua Gross<gros...@students.wwu.edu>  wrote:
Hi all--

Our group is running a local instance of Galaxy on a Linux box.  We have
been noticing a memory issue, where if we leave the server running for a few
days, soon all available memory (~8gb) will be used up to the point where
the tools fail because they are unable to allocate new memory.

While we haven't done any rigorous testing, this issue seems to be
independent of the specific tools we run, and actually seems to still appear
if we do not run any tools at all.  The process "python" is what is taking
up all the memory, and the issue is not instantaneous but happens over
time.  Restarting the server frees the memory immediately.

Is this a known issue?  If so, is there a known fix for it?  Any insight on
this would be much appreciated, as it is complicating our efforts to
automate long work-flows.

Thank you so much for your time

Josh Gross, Western Washington University.

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--
*************************************
Todd Oakley, Professor
Ecology Evolution and Marine Biology
University of California, Santa Barbara
Santa Barbara, CA 93106 USA

NEWLY UPDATED LAB WEBSITE: http://labs.eemb.ucsb.edu/oakley/todd/
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