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
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.
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
> 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.
> On Wed, Feb 29, 2012 at 2:08 PM, Joshua Gross<grossj5(a)students.wwu.edu>
>> 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
>> 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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