VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Sep 08 2010 - 19:58:19 CDT

Hi,
  The existing MacOS versions of VMD are all 32-bit binaries due to
the fact that Apple doesn't provide a 64-bit version of the Carbon APIs
that are used by FLTK, Tcl/TK, and other libraries required by VMD.
This means that in practice, the standard MacOS versions of VMD are
limited to working with datasets that fit within the user-mode-accessible
32-bit addressing range provided by MacOS X.

At the moment, the only way to build a 64-bit version of VMD on MacOS X
would be to compile it to use the X-windows API rather than using the
native MacOS X Aqua GUI interfaces. I've done a few experiments with this
and it should be possible to do such a build but it requires some tricky
steps in compiling FLTK, Tcl/Tk and other libraries that want to use the
native MacOS APIs by default (which are 32-bit only at present).

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Sep 08, 2010 at 05:04:38PM -0700, Patrick Burney wrote:
> Hey guys,
>
> I just upgraded my workstation's ram so that I could view larger trajectories in vmd. However, now that I have 8gbs of ram, I still find I can only load dcds smaller than about 3.0gb without running into the usual error code 12 (see below). I've been watching some plots of the system's memory allocation and noticed that I get the error (see below) right after the vmd program is being allocated 2.96gb of memory. This is strange to me because at the moment, the system has 6.9gb of memory "Free".
> I've run a few different memtests and also tried this on another workstation we upgraded with the old memory from mine to no avail. It may help to know that I'm using a 27'' iMac (intel x86_64) running snow leopard. If this problem winds up being a consequence of my operating system, I applogize for wasting your time.
>
> vmd > animate delete all
> vmd > animate read dcd wtbound_smaller.dcd beg 0 end -1 waitfor all
> dcdplugin) detected standard 32-bit DCD file of native endianness
> dcdplugin) CHARMM format DCD file (also NAMD 2.1 and later)
> Info) Using plugin dcd for coordinates from file wtbound_smaller.dcd
> VMD(42925,0xa0703500) malloc: *** mmap(size=16777216) failed (error code=12)
> *** error: can't allocate region
> *** set a breakpoint in malloc_error_break to debug
> terminate called after throwing an instance of 'std::bad_alloc'
> what(): std::bad_alloc
> Abort trap
>
>
>
> Thanks for the help,
> Patrick Burney
> University of Washington
> Department of Chemical Engineering
>
> 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078