VMD-L Mailing List

From: Joshua A. Anderson (joaander_at_umich.edu)
Date: Thu Sep 09 2010 - 06:50:43 CDT

I successfully built VMD for Mac OS X x86_64 against FLTK's trunk
(which now has support for the 64-bit library that replaced Carbon).
This isn't something John would do for a release version, but it is a
pathway for those of us building for our own use.

I didn't run into any tcl/tk 32/64 issues, but I did install those
with macports - perhaps they have already solved the tricky issues.
--------
Joshua A. Anderson, Ph.D.
Chemical Engineering Department, University of Michigan

On Sep 8, 2010, at 8:58 PM, John Stone wrote:

>
> 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
>
>