Re: Segmentation violation with adaptive tempering.

From: johan strumpfer (johanstr_at_ks.uiuc.edu)
Date: Mon Nov 21 2011 - 12:20:28 CST

Hi Nicholas,

No problem. That's another bug that I've ironed out already too. The testing and
fixes should be into the CVS by the end of the week.

Cheers,
Johan

------------------------------------------------------------------------------------------------------
Johan Strumpfer:         johanstr_at_ks.uiuc.edu        www.ks.uiuc.edu/~johanstr
Theoretical and Computational Biophysics Group
3115 Beckman Institute
University of Illinois at Urbana-Champaign
405 N. Mathews
Urbana, IL 61801, USA
------------------------------------------------------------------------------------------------------

2011/11/21 Nicholas M Glykos <glykos_at_mbg.duth.gr>:
>
> Hi Johan,
>
> Thanks for the quick reply. I have another one for you : I couldn't get a
> restart to work using adaptTempInFile. I assume that all I need is
>
> adaptTempMD     on
> adaptTempInFile myfile
>
> but initialization fails with a message in the spirit of 'you can not
> define both adaptTempInFile and adaptTempTmin, adaptTempTmax,
> adaptTempBins, ... (which I didn't define).
>
> Thanks again,
> Nicholas
>
>
>
> On Mon, 21 Nov 2011, johan strumpfer wrote:
>
>> Hi Nicholas,
>>
>> Thanks for posting - there was a bug in the code that I've been
>> tracking down. I've found the one you mentioned (an uninitialized int)
>> but I'm busy testing the code some more before committing the changes
>> to cvs.
>>
>> Cheers,
>> Johan
>>
>> ------------------------------------------------------------------------------------------------------
>> Johan Strumpfer:         johanstr_at_ks.uiuc.edu        www.ks.uiuc.edu/~johanstr
>> Theoretical and Computational Biophysics Group
>> 3115 Beckman Institute
>> University of Illinois at Urbana-Champaign
>> 405 N. Mathews
>> Urbana, IL 61801, USA
>> ------------------------------------------------------------------------------------------------------
>>
>>
>>
>> On Sun, Nov 20, 2011 at 6:13 AM, Nicholas M Glykos <glykos_at_mbg.duth.gr> wrote:
>> >
>> >
>> > Dear Developers,
>> >
>> > Using CVS-2011-11-20 for Linux-x86_64 we get sporadic segmentation
>> > violations when using adaptive tempering. Sporadic means that
>> > re-submitting the same job without changing anything eventually leads to
>> > an apparently stably-running job. I attach the log files from one job that
>> > failed and the initial portion from a job that is stable. The problem only
>> > surfaced when using multiple nodes (the multicore version running on a
>> > single node was ok).
>> >
>> > Best regards,
>> > Nicholas
>> >
>> >
>> >
>> > --
>> >
>> >
>> >            Nicholas M. Glykos, Department of Molecular Biology
>> >     and Genetics, Democritus University of Thrace, University Campus,
>> >  Dragana, 68100 Alexandroupolis, Greece, Tel/Fax (office) +302551030620,
>> >    Ext.77620, Tel (lab) +302551030615, http://utopia.duth.gr/~glykos/
>> >
>>
>
> --
>
>
>            Nicholas M. Glykos, Department of Molecular Biology
>     and Genetics, Democritus University of Thrace, University Campus,
>  Dragana, 68100 Alexandroupolis, Greece, Tel/Fax (office) +302551030620,
>    Ext.77620, Tel (lab) +302551030615, http://utopia.duth.gr/~glykos/
>

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