VMD-L Mailing List

From: andrea spitaleri (andrea.spitaleri_at_iit.it)
Date: Thu Apr 09 2015 - 08:14:50 CDT

Running with -debug I get this in loading second molecule gro:

Program received signal SIGSEGV, Segmentation fault.
0x0000000000790bbd in stringdup(char const*) ()

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