VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Nov 11 2011 - 10:12:57 CST

Hi,
  The 32-bit version of VMD can't use more than 4GB of RAM (and usually less),
but I have a new 64-bit test version of VMD for MacOS X 10.6.x or later, which
you can try out if you like. You can download it by following the instructions
on this page:
  http://www.ks.uiuc.edu/Research/vmd/alpha/

Let me know if you need help. I would be curious to hear how the
64-bit test version of VMD works for you.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Fri, Nov 04, 2011 at 06:31:15AM +0100, Passerone, Daniele wrote:
> 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
> 

-- 
NIH Resource 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/       Fax: 217-244-6078