VMD-L Mailing List

From: David Tanner (dtanner_at_ks.uiuc.edu)
Date: Fri May 29 2009 - 13:18:28 CDT

I had been using g++ but was getting similar errors also (shown below), so I
gave gcc a whirl.

gcc -I./inc -Ilib/lib_LINUX -Llib/lib_LINUX -m32 -Wall -o obj/main.o -c
src/Main.C
gcc -I./inc -Ilib/lib_LINUX -Llib/lib_LINUX -m32 -Wall -o obj/configio.o -c
src/ConfigIO.C
gcc -I./inc -Ilib/lib_LINUX -Llib/lib_LINUX -m32 -Wall -o obj/molfileapi.o
-c src/MolfileAPI.C
gcc -I./inc -Ilib/lib_LINUX -Llib/lib_LINUX -m32 -Wall -o obj/hash.o -c
src/hash.c
gcc -I./inc -Ilib/lib_LINUX -Llib/lib_LINUX -m32 -Wall -o obj/getplugins.o
-c src/getplugins.c
g++ -I./inc -Ilib/lib_LINUX -Llib/lib_LINUX -m32 -Wall -o bin/psapd
-lmolfile_plugin -lm obj/main.o obj/configio.o obj/molfileapi.o obj/hash.o
obj/getplugins.o
obj/getplugins.o(.text+0x107): In function `init_plugins':
: undefined reference to `molfile_biomoccaplugin_init'
obj/getplugins.o(.text+0x10c): In function `init_plugins':
: undefined reference to `molfile_cpmdplugin_init'
obj/getplugins.o(.text+0x111): In function `init_plugins':
: undefined reference to `molfile_psfplugin_init'

Thank you,
David E. Tanner

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
David E. Tanner
Theoretical and Computational Biophysics Group
3159 Beckman Institute
University of Illinois at Urbana-Champaign
405 N. Mathews
Urbana, IL 61801
http://www.linkedin.com/in/davidetanner
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

On Fri, May 29, 2009 at 1:07 PM, John Stone <johns_at_ks.uiuc.edu> wrote:

>
> David,
> You need to link using "g++" and not "gcc", as several of the VMD
> molfile plugins are written in C++. If that's not convenient, you could
> try manually linking with -lstdc++, but I think doing the final link step
> with "g++" will be far simpler for you.
>
> Cheers,
> John
>
>
> On Fri, May 29, 2009 at 01:02:59PM -0500, David Tanner wrote:
> > I am trying to use molfile_plugin in a personal MD program.
> > Below is my errored output from my make file.
> > The first 5 compiles are individual object files.
> > The 6th is compiling the binary file which, as I understand it, needs to
> be
> > linked to libmolfile_plugin.a, which I have located in lib/lib_LINUX
> (along
> > with all the shared libraries built with libmolfile_plugin.a).
> > The init_plugins function of getplugins.c contains the pre-processor
> command
> > MOLFILE_INIT_ALL which brings up all the molfile_..._init.
> > I don't understand what's wrong with my linking; all the appropriate
> files
> > contain "#include libmolfile_plugin.h", and I have tried to link to the
> > static library libmolfile_plugin.a.
> >
> > gcc -I./inc -Ilib/lib_LINUX -Llib/lib_LINUX -m32 -Wall -o obj/main.o -c
> > src/Main.C
> > gcc -I./inc -Ilib/lib_LINUX -Llib/lib_LINUX -m32 -Wall -o obj/configio.o
> -c
> > src/ConfigIO.C
> > gcc -I./inc -Ilib/lib_LINUX -Llib/lib_LINUX -m32 -Wall -o
> obj/molfileapi.o
> > -c src/MolfileAPI.C
> > gcc -I./inc -Ilib/lib_LINUX -Llib/lib_LINUX -m32 -Wall -o obj/hash.o -c
> > src/hash.c
> > gcc -I./inc -Ilib/lib_LINUX -Llib/lib_LINUX -m32 -Wall -o
> obj/getplugins.o
> > -c src/getplugins.c
> > gcc -I./inc -Ilib/lib_LINUX -Llib/lib_LINUX -m32 -Wall -o bin/psapd
> > -lmolfile_plugin -lm obj/main.o obj/configio.o obj/molfileapi.o
> obj/hash.o
> > obj/getplugins.o
> > obj/main.o(.eh_frame+0x11): undefined reference to `__gxx_personality_v0'
> > obj/configio.o(.eh_frame+0x11): undefined reference to
> > `__gxx_personality_v0'
> > obj/getplugins.o(.text+0x107): In function `init_plugins':
> > : undefined reference to `molfile_biomoccaplugin_init'
> > obj/getplugins.o(.text+0x10c): In function `init_plugins':
> > : undefined reference to `molfile_cpmdplugin_init'
> > obj/getplugins.o(.text+0x111): In function `init_plugins':
> > : undefined reference to `molfile_psfplugin_init'
> > obj/getplugins.o(.text+0x116): In function `init_plugins':
> > : undefined reference to `molfile_pdbplugin_init'
> > ...
> >
> > Thank you,
> > David E. Tanner
> >
> > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> > David E. Tanner
> > Theoretical and Computational Biophysics Group
> > 3159 Beckman Institute
> > University of Illinois at Urbana-Champaign
> > 405 N. Mathews
> > Urbana, IL 61801
> > http://www.linkedin.com/in/davidetanner
> > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>
> --
> 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
>