VMD-L Mailing List

From: andrea spitaleri (andrea.spitaleri_at_iit.it)
Date: Thu Apr 09 2015 - 08:23:58 CDT

Indeed. I can load several pdb but as soon as I load two gro files
vmd1.9.2 crashes.

Perfect I will be stuck with 1.9.1 till you release the fixed version.
If it can help strace vmd says:

mmap(NULL, 8192, PROT_READ|PROT_WRITE, MAP_PRIVATE|MAP_ANONYMOUS, -1, 0)
= 0x7f48194cd000
write(17, "Segmentation fault (core dumped)"..., 33Segmentation fault
(core dumped)
) = 33
rt_sigprocmask(SIG_UNBLOCK, [INT], NULL, 8) = 0
rt_sigprocmask(SIG_BLOCK, [INT], NULL, 8) = 0
rt_sigprocmask(SIG_UNBLOCK, [INT], NULL, 8) = 0
rt_sigprocmask(SIG_BLOCK, [INT], NULL, 8) = 0
close(0) = -1 EBADF (Bad file descriptor)
dup(19) = 0
ioctl(0, FIONCLEX) = 0
close(1) = -1 EBADF (Bad file descriptor)
dup(17) = 1
ioctl(1, FIONCLEX) = 0
close(2) = -1 EBADF (Bad file descriptor)
dup(18) = 2
ioctl(2, FIONCLEX) = 0
close(0) = 0
close(1) = 0
close(2) = 0
rt_sigprocmask(SIG_UNBLOCK, [INT], NULL, 8) = 0
rt_sigprocmask(SIG_BLOCK, [INT], NULL, 8) = 0
rt_sigprocmask(SIG_UNBLOCK, [INT], NULL, 8) = 0
read(16, "", 1024) = 0
ioctl(16, SNDCTL_TMR_TIMEBASE or SNDRV_TIMER_IOCTL_NEXT_DEVICE or
TCGETS, 0x7fff381179f0) = -1 ENOTTY (Inappropriate ioctl for device)
rt_sigprocmask(SIG_UNBLOCK, [INT], NULL, 8) = 0
exit_group(0) = ?
+++ exited with 0 +++

On 09/04/2015 15:16, Axel Kohlmeyer wrote:
> 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
>>
>
> 

-- 
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