VMD-L Mailing List

From: Passerone, Daniele (Daniele.Passerone_at_empa.ch)
Date: Fri Nov 04 2011 - 00:31:15 CDT

Dear Vmd team

Vmd on Macosx (10.6.8, MBP 13'' 2010, Nvidia 320 with CUDA 4.0.50 Drivers) works really great. It is smooth, fast, and robust.
Unfortunately, I seem to have problems with big cubefiles (around 500 MB, 216x256x768 grid) when trying to handle
the "Volume slice" representation, or to color an isosurface using another cubefile as a color map (typical example: the electrostatic potential
of a molecule drawn on a density isosurface).
Such representations work perfectly with smaller cubefiles, but with larger cubefiles either I see everything black on the slice or the
isosurface, or, using the "Volume" coloring method and trying to "Autoscale" the colors, I get a "malloc" error on the console:

VMD(15755,0xa0587540) malloc: *** mmap(size=201326592) failed (error code=12)
*** error: can't allocate region
*** set a breakpoint in malloc_error_break to debug

My computer has 8 GB RAM, so I wonder whether it is possible to "force" VMD to use all available RAM or similar.
Some more information from the first lines (the same behavior is also observed in version 1.8.7, and decreasing the "resolution" of the grid in the Representation menu does not help):

Info) VMD for MACOSXX86, version 1.9 (March 14, 2011)
Info) http://www.ks.uiuc.edu/Research/vmd/
Info) Email questions and bug reports to vmd_at_ks.uiuc.edu<mailto: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, 2 CPUs detected.
Info) Creating CUDA device pool and initializing hardware...
Info) Detected 1 available CUDA accelerator:
Info) [0] GeForce 320M 6 SM_1.2 @ 0.95 GHz, 252MB RAM, KTO, OIO, ZCP
Info) OpenGL renderer: NVIDIA GeForce 320M OpenGL Engine
Info) Features: STENCIL MDE CVA MTX NPOT PP PS GLSL(OVF)
Info) Full GLSL rendering mode is available.
Info) Textures: 2-D (4096x4096), 3-D (2048x2048x2048), Multitexture (8)
Info) Dynamically loaded 2 plugins in directory:
Info) /Applications/VMD1.9.app/Contents/vmd/plugins/MACOSXX86/molfile

Thank you in advance for any help.
Regards,
Daniele Passerone
Empa, Switzerland