VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Aug 08 2012 - 16:32:20 CDT

Carolyn,
  I tried to reply to your note while I was traveling last weekend,
but apparently the email went into the bit bucket somewhere since I don't
see it in the mailing list archive... Anyway, if you can send me the
contents of your VMD configure.options file for the MacOS X build, I should
be able to figure out what went amiss there. The linkage error indicates to
me that there's a set of #ifdefs that aren't getting set, most likely due to
an incorrect configure.options setting. It should be easy to fix.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Sat, Aug 04, 2012 at 09:45:50AM -0500, Carolyn Phillips wrote:
> Hi,
>
> I am getting close (I think) to getting a compiled vmd to work. However I am encountering the following
>
> Linking vmd_MACOSXX86_64 ...
> ln: ./foobar: File exists
> Undefined symbols for architecture x86_64:
> "macosxvmdstart(int, char**)", referenced from:
> VMDinitialize(int*, char**) in vmd.o
> ld: symbol(s) not found for architecture x86_64
> clang: error: linker command failed with exit code 1 (use -v to see invocation)
> make: *** [vmd_MACOSXX86_64] Error 1
>
> It seems to me that this is a linking error to a file within the vmd code set. Any clue what is not being linked?
>
> Thanks for your help!
>
> -Carolyn
>
> On Jul 31, 2012, at 7:45 PM, John Stone <johns_at_ks.uiuc.edu> wrote:
>
> >
> > Carolyn,
> > Yes, you'll need to compile from source. Let us know if you have
> > any questions about compiling from source.
> >
> > Cheers,
> > John Stone
> > vmd_at_ks.uiuc.edu
> >
> > On Tue, Jul 31, 2012 at 07:00:26PM -0500, Carolyn Phillips wrote:
> >> A little deeper searching of the user list tells me that my version of VMD was compiled without python support.
> >>
> >> Looks like I will have to compile from source?
> >>
> >> -Carolyn
> >>
> >> On Jul 31, 2012, at 6:54 PM, Carolyn Phillips <phillicl_at_umich.edu> wrote:
> >>
> >>>
> >>>
> >>> I have VMD 1.9.1 installed on my MacOSX 10.8
> >>>
> >>> I launch vmd and at the prompt type "gopython"
> >>>
> >>> I get
> >>>
> >>>> invalid command name "gopython"
> >>>
> >>> Whats going on here?
> >>>
> >>> -Carolyn
> >>>
> >>>
> >>>
> >>
> >
> > --
> > 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
> 

-- 
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