From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Sep 11 2015 - 11:35:35 CDT

Hi,
  I think the cause of your problem is that VMD is obtaining 4096-byte
page-sized memory allocations for each timestep (for performance reasons),
however for your 44-atom trajectory, the ideal allocation size would only
be 528-bytes per frame. The outcome of this is that you're unable to
load the entire trajectory within the 32-bit 4GB memory limit enforced
by MacOS X. For the time being, I would suggest loading a subset of your
frames, either by limiting the start/end frame indices, or by setting a
frame stride greater than 1 when loading the trajectory.

If you are willing to try an experimental VMD build, I should be able to
give you a new build in a week or so that should prevent this issue from
occuring with very small molecular structures like yours, which far
fall below the size of a single 4KB memory page.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Fri, Sep 11, 2015 at 02:35:12AM -0700, Lee-Ping Wang wrote:
> Hi everyone,
>
> I've recently encountered a problem where VMD will crash when loading a
> rather large trajectory file (.xyz format, 700 MB, 44 atoms, 293360
> frames). The error message is attached at the end of this email. This
> happens on a new Mac laptop that I recently purchased with 16 GB of memory
> with no other programs running.
>
> I'm puzzled because my previous Mac laptop with 8 GB of memory was able to
> load a trajectory of this size with no issues. The "activity monitor"
> reports a small amount of memory used (about 1 GB allocated to VMD) when
> this crash occurs. I confirmed this error still happens with VMD 1.9.1,
> which is the version I had on my previous laptop.
>
> If anyone could help me troubleshoot, I'd greatly appreciate it.
>
> Thanks a lot,
>
> - Lee-Ping
>
> leeping_at_campus-003-211:~/projects/LPW07-Acetone/Dimer/rhf-631gs/Consolidated$
> vmd all-coors.xyz
>
> Info) VMD for MACOSXX86, version 1.9.2 (December 29, 2014)
>
> Info) http://www.ks.uiuc.edu/Research/vmd/
>
> Info) Email questions and bug reports to vmd_at_ks.uiuc.edu
>
> Info) Please include this reference in published work using VMD:
>
> Info) Humphrey, W., Dalke, A. and Schulten, K., `VMD - Visual
>
> Info) Molecular Dynamics', J. Molec. Graphics 1996, 14.1, 33-38.
>
> Info) -------------------------------------------------------------
>
> Info) Multithreading available, 8 CPUs detected.
>
> Info) OpenGL renderer: ATI Radeon R9 M370X OpenGL Engine
>
> Info) Features: STENCIL MDE CVA MTX NPOT PP PS GLSL(OVF)
>
> Info) Full GLSL rendering mode is available.
>
> Info) Textures: 2-D (16384x16384), 3-D (16384x16384x16384), Multitexture
> (8)
>
> Info) Dynamically loaded 2 plugins in directory:
>
> Info) /Applications/VMD 1.9.2.app/Contents/vmd/plugins/MACOSXX86/molfile
>
> Info) File loading in progress, please wait.
>
> Info) Using plugin xyz for structure file all-coors.xyz
>
> Info) Using plugin xyz for coordinates from file all-coors.xyz
>
> Info) Determining bond structure from distance search ...
>
> vmd_MACOSXX86(61772,0xa0f2f1d4) malloc: *** mach_vm_map(size=8388608)
> failed (error code=3)
>
> *** error: can't allocate region
>
> *** set a breakpoint in malloc_error_break to debug
>
> Segmentation fault: 11 (core dumped)

-- 
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/