VMD-L Mailing List

From: Reid Van Lehn (rvanlehn_at_gmail.com)
Date: Fri Jun 04 2010 - 23:36:13 CDT

Sorry to keep spamming the list - if I remove the -x11 extensions from the
libraries listed by default in the Makefile (e.g. change -ltcl8.5-x11 to
-ltcl8.5) then compilation fails with a ton of errors like:

Undefined symbols:
  "_molfile_phiplugin_fini", referenced from:
      PluginMgr::~PluginMgr()in PluginMgr.o
      PluginMgr::~PluginMgr()in PluginMgr.o
  "_molfile_rst7plugin_register", referenced from:
      PluginMgr::load_static_plugins() in PluginMgr.o
  "_Tcl_WriteChars", referenced from:
      TclTextInterp::evalFile(char const*)in TclTextInterp.o
      TclTextInterp::evalFile(char const*)in TclTextInterp.o
      TclTextInterp::doEvent() in TclTextInterp.o
      TclTextInterp::doEvent() in TclTextInterp.o
      TclTextInterp::doEvent() in TclTextInterp.o
... many more ....

Hence I think linking is the issue, but I'm not sure how to fix this.

Thanks!
Reid

On Sat, Jun 5, 2010 at 12:11 AM, Reid Van Lehn <rvanlehn_at_gmail.com> wrote:

> Hey guys,
>
> Thank you for the help so far! I'm still not sure what caused all of those
> errors but I started the compilation process over. I was using the incorrect
> system architecture on my previous builds (MACOSX, whereas now I'm using
> MACOSXX86_64) and recreated the plugin directory, and configured using the
>
> MACOSXX86_64 FLTK TK TCL SILENT
>
> options. Now, upon running 'make' in the vmd/src directory it seems to
> compile all of the files successfully, but fails with:
>
> Linking vmd_MACOSXX86_64 ...
> ln: ./foobar: File exists
> ld: library not found for -ltk8.5-x11
> collect2: ld returned 1 exit status
> make: *** [vmd_MACOSXX86_64] Error 1
>
> where -ltk8.5-x11 is the first library listed in the LIBS line of the
> Makefile. I previously installed tcl and tk to the vmd/lib directory using
> the unix installation (not macosx one) with the --enable-64bit flag on. I
> can't seem to find any libraries that correspond to the one sought for (the
> libtk8.5.dylib file is there, however). I figure this is an issue with my
> tcl/tk installation but thought you might be able to offer advice since I
> haven't had any luck yet. I do have X11 installed, and the -lx11 library was
> found successfully (after modifying my LIBDIRS slightly).
>
> Any advice on this problem would be much appreciated!
>
> Thanks,
> Reid
>
>
> On Fri, Jun 4, 2010 at 6:08 PM, John Stone <johns_at_ks.uiuc.edu> wrote:
>
>> Reid,
>> I'm puzzled by the error you are getting. What compiler and
>> version are you using? This error seems to indicate that the
>> compiler you're using doesn't like forward class declarations,
>> but I see nothing wrong there.
>>
>> Cheers,
>> John Stone
>> vmd_at_ks.uiuc.edu
>>
>> On Fri, Jun 04, 2010 at 12:36:54PM -0400, Reid Van Lehn wrote:
>> > Hi everyone,
>> >
>> > I'm having an issue compiling from source on Mac OS X. I was able to
>> > successfully make the plugins directory using the instructions on the
>> > website. I next configure a bare-bones installation using:
>> >
>> > MACOSX OPENGL FLTK TK NETCDF TCL SILENT
>> >
>> > as my flags. I have the FLTK, Tcl/Tk and NetCDF packages installed in
>> > /vmd/lib, mimicking the set ups in the plugins/build.csh file.
>> >
>> > However, when I run 'gmake' in the /vmd/src directory, make fails
>> with a
>> > number of errors in MolFilePlugin.c:
>> >
>> > ***********
>> >
>> > Compiling MoleculeGraphics.C --> MoleculeGraphics.o ...
>> > Compiling MolFilePlugin.c --> MolFilePlugin.o ...
>> > In file included from MolFilePlugin.c:31:
>> > MolFilePlugin.h:30: error: syntax error before *Molecule*
>> > MolFilePlugin.h:30: warning: data definition has no type or storage
>> class
>> > MolFilePlugin.h:31: error: syntax error before *Timestep*
>> > MolFilePlugin.h:31: warning: data definition has no type or storage
>> class
>> > MolFilePlugin.h:32: error: syntax error before *AtomSel*
>> > MolFilePlugin.h:32: warning: data definition has no type or storage
>> class
>> > MolFilePlugin.h:33: error: syntax error before *Scene*
>> > MolFilePlugin.h:33: warning: data definition has no type or storage
>> class
>> > MolFilePlugin.h:34: error: syntax error before *QMData*
>> > MolFilePlugin.h:34: warning: data definition has no type or storage
>> class
>> > In file included from MolFilePlugin.c:31:
>> > MolFilePlugin.h:42: error: syntax error before *MolFilePlugin*
>> >
>> > plus many more, also in files utilities.h, Matrix4.h, QMData.h, and
>> more
>> >
>> > *************
>> >
>> > Looking at the errors, it seems like a lot of the C++ keywords aren't
>> > being recognized, and the origin of the errors are all tied to the
>> > MolFilePlugin.c/.h and Molecule.h files. I've also tried following
>> the
>> > directions from
>> http://www.debianclusters.org/index.php/NAMD:_Building_vmd
>> > with the same results.
>> >
>> > Does anyone have an idea of what may be wrong? I can send more
>> information
>> > as needed.
>> >
>> > Thank you!
>> > Reid Van Lehn
>>
>> --
>> 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/ <http://www.ks.uiuc.edu/%7Ejohns/>
>> Fax: 217-244-6078
>>
>
>
>
> --
> Reid Van Lehn
> NSF/MIT Presidential Fellow
> Alfredo Alexander-Katz Research Group
> Ph.D Candidate - Materials Science
> 

-- 
Reid Van Lehn
NSF/MIT Presidential Fellow
Alfredo Alexander-Katz Research Group
Ph.D Candidate - Materials Science