VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed May 31 2017 - 16:33:16 CDT

Hi,
  I have found and fixed the issue that caused the crash that
you observe, but I don't quite understand what the issue is with the file.
It seems that some of the timesteps in the file you provided don't contain
coordinates, and that upsets the VMD gromacs plugin. I have made the VMD
Gromacs plugin tolerate such files, but I'm puzzled why you would want a
trajectory that periodically has a sequence of frame without any coordinates.
The next test versions of VMD we make available on the web site will contain
the new plugin. If you would like to try out a new version soon, send me a
note in about a week (I'm away from the office traveling until then anyway)
and I can see about getting you a build. During the time while I'm away
a bunch of our build machines are down due to building construction projects
underway here, so I can't do VMD builds remotely.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Sat, Apr 29, 2017 at 07:43:53PM +0800, yjcoshc wrote:
> Hi,
>
> Any ideas? I managed to generate a small(36M) trr file that could
> crash the VMD. You can download it at:
>
> http://chinfo.nankai.edu.cn/files/vmdtrr/traj.trr
>
> The gmx check result is:
>
> Command line:
> gmx check -f ./traj.trr -s1 ./eq.tpr
>
> Reading file ./eq.tpr, VERSION 2016.3 (single precision)
> Checking file ./traj.trr
> trr version: GMX_trn_file (single precision)
> Reading frame 0 time 0.000
> # Atoms 43044
> Last frame 50 time 100.000
>
>
> Item #frames Timestep (ps)
> Step 51 2
> Time 51 2
> Lambda 51 2
> Coords 11 10
> Velocities 11 10
> Forces 51 2
> Box 51 2
>
> The gromacs running tpr file is at
> http://chinfo.nankai.edu.cn/files/vmdtrr/eq.tpr. I ran it 50000
> steps.
>
> Thanks,
>
> yjcoshc
>
>
> ??? 2017???03???03??? 04:25, John Stone ??????:
> >Hi,
> > Looking at the source code it seems that this is an unusual .trr file.
> >Would it be possible for you to post this file somewhere where
> >I could download it? That would allow me to debug the problem in more
> >detail. It is conceivable that this file triggers an extremely unusual
> >path through the code, which could explain the segfault you observe, but
> >I need access to the input file to be certain. If you can post the file
> >somewhere, I should be able to fix it and provide an updated plugin for
> >VMD 1.9.3 that will address this issue.
> >
> >Cheers,
> > John Stone
> > vmd_at_ks.uiuc.edu
> >
> >On Wed, Mar 01, 2017 at 12:11:21PM +0800, yjcoshc_at_gmail.com wrote:
> >>Hi,
> >>
> >>I ran gmx check on my trr file:
> >>
> >>Checking file ./traj.trr
> >>trr version: GMX_trn_file (single precision)
> >>Reading frame 0 time 0.000
> >># Atoms 2422
> >>Last frame 50000 time 50000.000
> >>WARNING: Incomplete header: nr 50001 time 50000
> >>
> >>
> >>Item #frames Timestep (ps)
> >>Step 50001 1
> >>Time 50001 1
> >>Lambda 50001 1
> >>Coords 5001 10
> >>Velocities 5001 10
> >>Forces 50001 1
> >>Box 50001 1
> >>
> >>The machine has 32G memory and 29G available.
> >>
> >>Thanks,
> >>
> >>yjcoshc
> >>
> >>
> >>??? 2017???03???01??? 02:57, John Stone ??????:
> >>>Hi,
> >>> How much memory does your machine have? Are you certain that
> >>>you have enough physical memory for the trajectory to be loaded
> >>>within VMD? The backtrace shows it dies in an optimized memmove()
> >>>call which indicates to me that it ran beyond a buffer boundary,
> >>>perhaps because a previous memory allocation had failed. Ignoring
> >>>the on-disk size of your TRR file, how many atoms are in the structure
> >>>and how many frames are you trying to load into RAM?
> >>>
> >>>Cheers,
> >>> John Stone
> >>> vmd_at_ks.uiuc.edu
> >>>
> >>>On Sat, Feb 25, 2017 at 10:54:27AM +0800, yjcoshc_at_gmail.com wrote:
> >>>>Hello everyone,
> >>>>
> >>>>I am using VMD 1.9.3 and trying to load a trr trajectory from
> >>>>GROMACS 2016.1 in linux(opensuse tumbleweed). The VMD crashes with
> >>>>Segmentation fault. I have tried attaching the gdb to it and print
> >>>>the backtrace as follow:
> >>>>
> >>>>Thread 1 "vmd_LINUXAMD64" received signal SIGSEGV, Segmentation fault.
> >>>>0x00007fd1e406372f in __memmove_avx_unaligned_erms () from /lib64/libc.so.6
> >>>>(gdb) backtrace
> >>>>#0 0x00007fd1e406372f in __memmove_avx_unaligned_erms () from
> >>>>/lib64/libc.so.6
> >>>>#1 0x00000000007a24e6 in read_trr_timestep(void*, int,
> >>>>molfile_timestep_t*) ()
> >>>>#2 0x0000000000685181 in MolFilePlugin::next(Molecule*) ()
> >>>>#3 0x00000000005eecd4 in CoorPluginData::next(Molecule*) ()
> >>>>#4 0x00000000006755b0 in Molecule::get_new_frames() ()
> >>>>#5 0x0000000000676879 in Molecule::prepare() ()
> >>>>#6 0x00000000005f4d4a in Displayable::draw_prepare() ()
> >>>>#7 0x00000000006d0e83 in Scene::prepare() ()
> >>>>#8 0x00000000006e37f2 in VMDApp::VMDupdate(int) [clone .part.106] ()
> >>>>#9 0x000000000049ea32 in main ()
> >>>>
> >>>>It seems a bug in the molfile plugin because I have failed to load
> >>>>the trajectory in the latest pymol(also segfault).
> >>>>
> >>>>The trr file is 1.6G. Both the text version and the GUI version of
> >>>>vmd in linux crash but the windows version doesn't have the problem.
> >>>>
> >>>>Thanks,
> >>>>
> >>>>yjcoshc 

-- 
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/