[gmx-users] Segmentation fault in g_hbond

[Erik Marklund]

Erik Marklund skrev 2010-12-18 16.36:
> Erik Marklund skrev 2010-12-18 16.23:
>> leila karami skrev 2010-12-18 16.18:
>>> Dear Erik
>>>
>>> excuse me, I sent .xtc and .tpr file your e-mail.
>>>
>>>
>>>
>>> -- 
>>> Leila Karami
>>> Ph.D. student of Physical Chemistry
>>>
>>> K.N. Toosi University of Technology
>>> Theoretical Physical Chemistry Group
>>>
>> I can reproduce the segfault. It doesn't happen without -hbn. I'll 
>> have a crack at fixing it. I won't promise to have it done before 
>> christmas, but I'll try.
> Fixed it. There's a call to clearPshift in do_merge which causes a 
> segfault if g_hbond is run without -geminate. Here's what you do:
>
> In gmx_hbond.c, enclose the call in an if-statement:
>
> if (hb->per->pHist)
> {
>     clearPshift(&(hb->per->pHist[a1][a2]));
> }
>
> I'll push this to the master and release branches some time today.
>
> Thanks for reporting this.
>
> Regards,
>
> Erik
As it turns out, I (or possibly someone else) had already fixed this 
issue in the master and release branches. Hence the solution is again to 
update your gromacs installation.

Erik
>>
>> -- 
>> -----------------------------------------------
>> Erik Marklund, PhD student
>> Dept. of Cell and Molecular Biology, Uppsala University.
>> Husargatan 3, Box 596,    75124 Uppsala, Sweden
>> phone:    +46 18 471 4537        fax: +46 18 511 755
>> erikm at xray.bmc.uu.se     http://folding.bmc.uu.se/
>
>
> -- 
> -----------------------------------------------
> Erik Marklund, PhD student
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596,    75124 Uppsala, Sweden
> phone:    +46 18 471 4537        fax: +46 18 511 755
> erikm at xray.bmc.uu.se     http://folding.bmc.uu.se/


-- 
-----------------------------------------------
Erik Marklund, PhD student
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,    75124 Uppsala, Sweden
phone:    +46 18 471 4537        fax: +46 18 511 755
erikm at xray.bmc.uu.se    http://folding.bmc.uu.se/

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