VMD-L Mailing List

From: David Tanner (dtanner_at_ks.uiuc.edu)
Date: Fri May 29 2009 - 13:30:24 CDT

Putting the link command after all the object files did fix the problem;
thankyou. I didn't know order mattered.

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 1:24 PM, John Stone <johns_at_ks.uiuc.edu> wrote:

>
> David,
> In the case below, you want to have the -lmolfile_plugin and -lm at
> the end of the g++ link command, _after_ all of the object files.
> You may also want to check that you're linking against the right
> libmolfile_plugin.a (e.g. 32-bit vs. 64-bit, etc).
>
> Cheers,
> John
>
> On Fri, May 29, 2009 at 01:18:28PM -0500, David Tanner wrote:
> > 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
> > >
>
> --
> 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
>