Hello Nate,<br><br>Yeah, the day I wrote this, it was dying horribly all over the place. However the first thing I tried was to switch Galaxy to use Python 2.6.4. Indeed it has been stable ever since!<br>Unfortunately I wasn&#39;t able to dig any further into (what was) the root cause. Since the change, we&#39;ve just been rolling forward. But at least it&#39;s good to know the Python upgrade did the trick.<br>

<br>Thanks<br>Chris<br><br><br><div class="gmail_quote">On Thu, May 20, 2010 at 3:06 PM, Nate Coraor <span dir="ltr">&lt;<a href="mailto:nate@bx.psu.edu">nate@bx.psu.edu</a>&gt;</span> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">

<div><div></div><div class="h5">Chris Zaleski wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Greetings,<br>
<br>
I&#39;m unfortunately having problems with segfaults on my server. The server runs CentOS, with python version 2.4.3. After installing &amp; setting up Galaxy, there have been an increasing number of segfaults thrown by multiple processes. Originally there were 2 distinct tools (which were run by Galaxy) that had thrown segfaults, *and* Galaxy&#39;s own python process was throwing segfaults as well. This is happening with increasing frequency.<br>


Most recently python is throwing the segfault (and galaxy dies) before we can even run any tools. Syslog eg:<br>
May 18 13:29:12 florence kernel: python[10657]: segfault at 00002aab33ff1000 rip 00000033a427bf0b rsp 000000004942ac38 error 6<br>
<br>
Notes:<br>
1) We ran a full spectrum of hardware diagnostics which found no problems.<br>
2) This morning while in the process of troubleshooting, I rebooted the server. Galaxy started as a service, and /threw another segfault shortly after instantiating/ - long before anyone could have interacted with the server. This leads me to believe the problem is python related.<br>


<br>
I plan to upgrade python, possibly go through some core dumps, etc. However before going any further, I wanted to see if any had experience with a similar problem. Any information is appreciated.<br>
</blockquote>
<br></div></div>
Hi Chris,<br>
<br>
Although Python has segfaulted on me before, it&#39;s never done it with this sort of frequency.  I&#39;d be interested to see what happens after upgrading Python (have you checked closed bug reports for this release on CentOS to see if there are any hints there?).<br>


<br>
--nate<br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div class="im">
<br>
Thanks very much,<br>
Chris Zaleski<br>
CSHL<br>
<br>
<br></div>
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