VMD-L Mailing List

From: yjcoshc_at_gmail.com
Date: Fri Feb 24 2017 - 20:54:27 CST

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