VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Nov 02 2015 - 10:35:29 CST

Hi,
  The current VMD builds for MacOS X are 32-bit (long story with
cross-platform GUI toolkits not working well enough with the new Cocoa APIs).
As such, the data size that you can load and work with is limited by 32-bit
addressing even though you're running on a 64-bit machine with large physical
memory. You will need to limit the size of the data you load to fit within
the addressing limit, under 4GB. You can do this by having VMD load a subset
of trajectory frames at a time, either by changing the first/last frames
loaded, or by changing the stride it uses when loading the frames.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Mon, Nov 02, 2015 at 09:35:36AM +0000, Eiros Zamora, Juan wrote:
> Dear VMD users,
>
> I recently installed VMD 1.9.2
> ??? MacOS X OpenGL (32-bit Intel x86) (Apple MacOS-X (10.4.7 or later) with hardware OpenGL (native bundle))
> on a new iMac with the following specs:
>
> OS X El Capitan
> Version 10.11.1
> Processor 4 GHz Intel Core i7
> Memory 8 GB 1867 MHz DDR3
> Graphics AMD Radeon R9 M395 2048 MB
>
> I tried loading a netcdf trajectory that I obtained with AMBER split in chunks, in total its around 6GB of data.
>
> I got the following error
>
> > VMD(63006,0xa344c000) malloc: *** mach_vm_map(size=8388608) failed (error code=3)
> > *** error: can't allocate region
> > *** set a breakpoint in malloc_error_break to debug
> > putget.c:3593: failed assertion `value != NULL'
> > Abort trap: 6
>
> I tried to attach a more complete error message on a 54 KB text file, but the message didn???t reach the mailing list, so I can email it off-list if need be.
>
> I googled the error and saw some similar problems on this mailing list, but they were from 2007 to 2011.
> I understand that this is related to the 32-bit version of VMD for Mac, is there any solution to this now (as in, can I get a 64-bit version)? Also, would installing the CUDA version make any difference? I presume not, but just to be sure that I am installing the most appropriate version of VMD for this machine???
>
> Thanks for any suggestions,
>
> Juan Eiros 

-- 
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/