You will have to set the right environment variable for CFLAGS to get debug symbols:
cd gromacs_directory CFLAGS="-O0 -g3" ./configure might do the trick. you can use gdb to check whether there are debug symbols in an executable. Alex Inon Sharony schrieb: > > reply to: > http://lists.gromacs.org/pipermail/gmx-users/2009-September/045006.html > > > "... > My usual advice is to compile GROMACS with -g, get a graphical > debugger(Totalview, ddd, insight, whatever) and spend a day stepping > through ashort mdrun to get some understanding about what is really > happening. > You will find it simpler if you've set the environment > variableGMX_NB_GENERIC=1 so that the nonbonded kernels are more > transparent. > ..." > > > > > Dear Mark and other GMX users, > > I've been trying to compile GMX for debugging, as you suggested, and > itappears that I'm not doing it correctly. I've added the "-g" flag > onthe "make" command's "CFLAGS" variable, and the installation seemed > tohave completed successfully, however when I try to preform some > simpledebugging (suggested > byhttp://www.gromacs.org/Developer_Zone/Programming_Guide/Programmers%27s_Guide)I > get error messages. > I've included the commands I ran for the installation of gromacs > withdebugging enabled, and the debugging commands I issued and their > result. > > > > A. ********************* > fftw-3.2.2 installation: > ------------------------ > > ./configure > make > make install > > > B. ******************************************** > > gromacs-4.0.5 installation in double-precission > ----------------------------------------------- > > ./configure --disable-float > make CFLAGS=-g > make install > > > C. ***************** > > "cat /tmp/gdb_cmds": > -------------------- > > break _gmx_error > break do_force > run -v > > > D. ****************************** > > "gdb -x gdb_cmds /usr/bin/mdrun": > --------------------------------- > > GNU gdb 6.8-debian > Copyright (C) 2008 Free Software Foundation, Inc. > License GPLv3+: GNU GPL version 3 or later > <http://gnu.org/licenses/gpl.html> > This is free software: you are free to change and redistribute it. > There is NO WARRANTY, to the extent permitted by law. Type "show copying" > and "show warranty" for details. > This GDB was configured as "i486-linux-gnu"... > (no debugging symbols found) > Function "_gmx_error" not defined. > Make breakpoint pending on future shared library load? (y or [n]) > [answered N; input not > from terminal] > Function "do_force" not defined. > Make breakpoint pending on future shared library load? (y or [n]) > [answered N; input not > from terminal] > (no debugging symbols found) > (no debugging symbols found) > (no debugging symbols found) > (no debugging symbols found) > (no debugging symbols found) > (no debugging symbols found) > (no debugging symbols found) > (no debugging symbols found) > (no debugging symbols found) > (no debugging symbols found) > (no debugging symbols found) > (no debugging symbols found) > (no debugging symbols found) > [Thread debugging using libthread_db enabled] > (no debugging symbols found) > (no debugging symbols found) > (no debugging symbols found) > (no debugging symbols found) > (no debugging symbols found) > > -- > Inon Sharony > ינון שרוני > +972(3)6407634 > atto.TAU.ac.IL/~inonshar > Please consider your environmental responsibility before printing this > e-mail. > > ------------------------------------------------------------------------ > > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
