VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Apr 09 2015 - 09:40:36 CDT

I'm hoping to have updated builds today or tomorrow after I fix
one of the build machines....

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Apr 09, 2015 at 03:23:58PM +0200, andrea spitaleri wrote:
> 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 

-- 
NIH Center for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/