VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Sep 24 2012 - 15:03:56 CDT

Hi,
  I think that the MacOS X 10.8 build platform is at least part of the
problem here. They just deprecated some of the SMP hardware query functions
as of 10.7, and so for MPProcessorsScheduled() we'll have to make an
alternative function call that provides the same information. I don't know
if 10.8 supports queries through sysconf(), but that would be the first
place I'd look, since almost every other Unix platform does it that way.
Let me dig into that particular issue, as that's going to require a code change
in order to work on 10.8... I'll get back to you on this.

I'm not sure what the problem with the STL string find operation is, that
may be some sort of compiler issue there. If needed, you could just skip
compiling dtrplugin, unless you know that you're going to be working with
trajectories from Desmond or Anton simulations...

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Mon, Sep 24, 2012 at 11:45:25AM -0400, Stephen Herbein wrote:
> Hi,
>
> I'm trying to compile VMD mixed with custom code for Mac OS X 10.8. It
> compiles fine in Linux, but Mac seems to be a different story. Everything
> compiles, but ld errors out as soon as it starts to link all the files
> together. The error output is:
>
> Undefined symbols for architecture x86_64:
> "_MPProcessorsScheduled", referenced from:
> _vmd_thread_numphysprocessors in VMDThreads.o
> "macosxvmdstart(int, char**)", referenced from:
> VMDinitialize(int*, char**) in vmd.o
> "std::string::find(char, unsigned long) const", referenced from:
> framefile(std::string const&, unsigned long, unsigned long, int,
> int) in libmolfile_plugin.a(dtrplugin-s.o)
> "std::string::rfind(char const*, unsigned long, unsigned long) const",
> referenced from:
> open_file_read(char const*, char const*, int*) in
> libmolfile_plugin.a(dtrplugin-s.o)
> [with another 8 screens full of errors stemming from libmolfile_plugin.a]
>
> I compiled the plugins using "make MACOSXX86_64". (Compiled using default
> makefile, thus CC was used).
> I compiled the VMD and custom source files using an altered Makefile and
> clang[++].
>
> I'm at a loss for what to do next. Any help or advice would be very much
> appreciated.
> -Stephen 

-- 
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