VMD-L Mailing List

From: Lee-Ping Wang (leeping_at_stanford.edu)
Date: Fri Sep 11 2015 - 04:35:12 CDT

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)