[Biopython-dev] curious error from HMM unit test

[Tiago Antão]

Sorry, I am drenched in work (writing up my PhD thesis) and had no
time to attend to this. Maybe it is the Jython version? It is still a
release candidate. I think the one installed is RC2, I am going to
upgrade to the new RC3 and try again.

Tiago

On Mon, Jan 24, 2011 at 11:50 AM, Peter <biopython at maubp.freeserve.co.uk> wrote:
> 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,
> http://events.open-bio.org:8010/builders/Linux%2064%20-%20Jython%202.5.2/builds/16/steps/shell/logs/stdio
> http://events.open-bio.org:8010/builders/Linux%2064%20-%20Jython%202.5.2/builds/18/steps/shell/logs/stdio
>
> # 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.
>
> Peter
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