VMD-L Mailing List

From: yjcoshc_at_gmail.com
Date: Tue Feb 28 2017 - 22:11:21 CST

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

在 2017年03月01日 02:57, John Stone 写道:
> 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