VMD-L Mailing List

From: Peter C. Lai (pcl_at_uab.edu)
Date: Wed Dec 07 2011 - 01:47:12 CST

You won't be able to install Linux packages on MacOSX they are not ABI
compatible (and it won't even know where to find the libraries like tcl/tk
etc.)

Building from source would appear to be difficult, for OS X...
You might try asking whoever built the official version to tell you the
toolchain they used and how they did it and then go off of that. Or try to
use a combination of MacPorts (for tcl/tk/fltk/py-numeric) and link to
those...

As a workaround for now, split your trajectory into smaller pieces or post-
process the trajectory file to skip every Nth frame so that the total memory
size is under 4GB (however you do that in NAMD; in gromacs it's trjconv -skip)
- it's what I do even in 64bit linux version since I have 6gb of ram and I
start using a lot of swap when trying to load more than 5000 frames of a
100k atom simulation.

On 2011-12-06 11:25:17PM -0600, Anthony Rey wrote:
> Dear VMD experts,
>
> I am using VMD1.9 on Mac OS X 10.6.8.
>
> I ran a 10ns simulation on a server and want to analyze it on my
> computer. I have the following error message while loading psf+dcd file.
>
>
> --------------------------------------------------------------------------------------
> >VMD(1542,0xa0b08540) malloc: *** mmap(size=1822720) 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
> >/Applications/VMD 1.9.app/Contents/MacOS/startup.command: line 7:
> > 1542 Abort trap
> > "$p/../Resources/VMD.app/Contents/MacOS/VMD" $*
> --------------------------------------------------------------------------------------
>
> I've seen that many people seem to have the same problem, and it seems
> to be a 32-bitness issue. I am running on a 64-bit OS but it seems that
> VMD package for Mac are only available in 32-bits. Is this correct?
>
> If so, which version can I install to get a 64-bits version? If I
> download the package for linux (LINUX_64 OpenGL, CUDA (Linux (64-bit
> Intel/AMD x86) with CUDA)), do you know if I could install this on Mac
> OS X?
>
> Otherwise, should I start from scratch, and get the source and compile
> it on my OS? I mean, surely there might be a way to analyze a 10ns
> simulation on Mac....Has anyone seen this problem before? :-)
>
> Thanks very much for your help.
>
> Tony
>
> 

-- 
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Peter C. Lai			| University of Alabama-Birmingham
Programmer/Analyst		| KAUL 752A
Genetics, Div. of Research	| 705 South 20th Street
pcl_at_uab.edu			| Birmingham AL 35294-4461
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