[gmx-developers] How to set up a Gromacs development/debugging environment?

[Oliver Beckstein]

Dear all,

I am debugging x2top.c from the 3.0.5 distribution under Red Hat 7.1
(it seg-faults when it is supposed to generate angles from the bond
list -- it probably gets confused by my nano tube pdb file with lots
of C-rings...).

Unfortunately I don't manage to run it properly in gdb (can't set
breakpoints, can't find the stack frame when it crashes etc.). 

I compiled it within src/kernel with

    $ make CFLAGS="-g -Wall -Wno-unused" CPPFLAGS="-DDEBUG" x2top

and an additional (due to libtool; mpicc invocation found in the x2top
LT-script) 

    $ mpicc -g -Wall -Wno-unused -o x2topX \
       toppush.o nm2type.o pdb2top.o gen_ad.o gen_dum.o pgutil.o \
       resall.o hackblock.o add_par.o topexcl.o toputil.o topdirs.o \
       x2top.o \
       ../mdlib/.libs/libmd_mpi.so \
       -lnsl -lnsl ../gmxlib/.libs/libgmx_mpi.so -lnsl \
       [...lots of -l, libraries etc snipped ...]

in order to create a runnable binary.

I used all other compiled libraries from the production-compilation
(--enable-mpi --enable-shared --without-x).



Now I am wondering how the Gromacs developers themselves are debugging
the code, especially within a libtoolised environment.

If anyone cares to enligthen me my debugging efforts my bear more
fruit (and of course I am happy to share any patches if I manage to
fix my problem).

Yours,
Oli 




-- 
Oliver Beckstein   *   oliver at bioch.ox.ac.uk
http://www.tfkp.physik.uni-erlangen.de/~oli/