[Biopython-dev] curious error from HMM unit test

Peter biopython at maubp.freeserve.co.uk
Mon Jan 24 11:50:21 UTC 2011

On Thu, Jan 20, 2011 at 12:04 PM, Peter <biopython at maubp.freeserve.co.uk> wrote:
> On Mon, Jan 17, 2011 at 4:37 PM, Peter <biopython at maubp.freeserve.co.uk> wrote:
>> On Mon, Jan 17, 2011 at 4:17 PM, Eric Talevich <eric.talevich at gmail.com> wrote:
>>> It could have been an exotic bug in Jython (or its interactions with the
>>> JVM) where the JIT or garbage collector is removing local variables too
>>> early. I don't see how you could provide a "fix" for it in Biopython, since
>>> k definitely exists at that point in the loop in any valid Python and Jython
>>> almost always handles it correctly.
>> Good point - maybe that is the most likely explanation.
> It has happened again on the same install of Jython 2.5.2rc3 on 64bit Linux,
> previously on build 6, now on build 12:
> http://events.open-bio.org:8010/builders/Linux%2064%20-%20Jython%202.5.2/builds/12/steps/shell/logs/stdio
> Again, repeating the build made the error go away - but the load on the
> machine would have been different etc.

And a more interesting variant,

# A fatal error has been detected by the Java Runtime Environment:
#  SIGSEGV (0xb) at pc=0x00002aaaab54c400, pid=13422, tid=1078704448
# JRE version: 6.0_17-b17
# Java VM: OpenJDK 64-Bit Server VM (14.0-b16 mixed mode linux-amd64 )
# Derivative: IcedTea6 1.7.5
# Distribution: Custom build (Wed Oct 13 13:04:40 EDT 2010)
# Problematic frame:
# j  Bio.HMM.Trainer$py.update_emissions$12(Lorg/python/core/PyFrame;Lorg/python/core/ThreadState;)Lorg/python/core/PyObject;+555
# An error report file with more information is saved as:
# /home/buildslave/BuildBot/jython252lin64/build/Tests/hs_err_pid13422.log
# If you would like to submit a bug report, please include
# instructions how to reproduce the bug and visit:
#   http://icedtea.classpath.org/bugzilla

Looking at the log suggests this could be a low memory issue,
perhaps from running multiple test builds at once.


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