VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri May 29 2009 - 13:07:26 CDT

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/      Fax: 217-244-6078