From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Mar 02 2017 - 14:25:30 CST

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

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