VMD-L Mailing List

From: Reid Van Lehn (rvanlehn_at_gmail.com)
Date: Sun Jun 06 2010 - 14:53:58 CDT

Last message - I resolved the issue by recompiling everything with MACOSXX86
instead of the _64 architecture. Things seem to be working now - thanks for
the help!

Reid

On Sat, Jun 5, 2010 at 12:36 AM, Reid Van Lehn <rvanlehn_at_gmail.com> wrote:

> 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
> 

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