VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Thu Apr 09 2015 - 08:16:24 CDT

On Thu, Apr 9, 2015 at 9:14 AM, andrea spitaleri
<andrea.spitaleri_at_iit.it> wrote:
> Running with -debug I get this in loading second molecule gro:
>
> Program received signal SIGSEGV, Segmentation fault.
> 0x0000000000790bbd in stringdup(char const*) ()

well, that is not a complete stack trace, but since it is happening
when loading the .gro file, you are confirming that this is the
already fixed bug.

>
> cheers
>
> and
>
>
>
> On 09/04/2015 14:44, Axel Kohlmeyer wrote:
>>
>> On Thu, Apr 9, 2015 at 8:14 AM, andrea spitaleri
>> <andrea.spitaleri_at_iit.it> wrote:
>>>
>>> Hi there,
>>>
>>> I am facing continuous crashes when I load two or more files, including
>>> gro,
>>> pdb, with or without trajectory. This happens only with vmd 1.9.2 and not
>>> with 1.9.1. As soon as I load the second file I get seg fault (core
>>> dumped).
>>> dmesg says:
>>>
>>> [Wed Apr 8 18:45:32 2015] vmd_LINUXAMD64[26513]: segfault at 7400040400
>>> ip
>>> 0000000000790bbd sp 00007fff17c32740 error 4 in
>>> vmd_LINUXAMD64[400000+d47000]
>>> [Wed Apr 8 18:46:08 2015] traps: vmd_LINUXAMD64[26705] general
>>> protection
>>> ip:790bbd sp:7fffc9c63ae0 error:0 in vmd_LINUXAMD64[400000+d47000]
>>> [Wed Apr 8 18:46:39 2015] traps: vmd_LINUXAMD64[26727] general
>>> protection
>>> ip:790bbd sp:7fffe72e97e0 error:0 in vmd_LINUXAMD64[400000+d47000]
>>> [Wed Apr 8 18:48:16 2015] traps: vmd_LINUXAMD64[29404] general
>>> protection
>>> ip:790bbd sp:7fff8121c060 error:0 in vmd_LINUXAMD64[400000+d47000]
>>>
>>> any reason why it is happening?
>>
>> to be certain, you would have to report a proper stack trace obtained
>> with vmd -debug (see VMD docs for details).
>>
>> there have been a few bugs in the gromacs plugin that crept into the
>> code with some updated features to it late in the VMD 1.9.2
>> development cycle. so chances are that this is related. the bugs have
>> been detected and fixed in the development sources.
>>
>> axel.
>>
>>
>>> cheers
>>>
>>> and
>>>
>>> --
>>> Andrea Spitaleri PhD
>>> D3 - Drug Discovery & Development
>>> Istituto Italiano di Tecnologia
>>> Via Morego, 30 16163 Genova
>>> cell: +39 3485188790
>>> http://www.iit.it/en/d3-people/andrea-spitaleri.html
>>> ORCID: http://orcid.org/0000-0003-3012-3557
>>>
>>
>>
>
> --
> Andrea Spitaleri PhD
> D3 - Drug Discovery & Development
> Istituto Italiano di Tecnologia
> Via Morego, 30 16163 Genova
> cell: +39 3485188790
> http://www.iit.it/en/d3-people/andrea-spitaleri.html
> ORCID: http://orcid.org/0000-0003-3012-3557
> 

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.