[gmx-users] Problems compiling

Wed Oct 15 16:18:01 CEST 2003

Hi all,
    I'm trying to compile Gromacs on a oMosix cluster using the mpi option and looking at the web page procedures.
I'm working on a RH8 distro.
I've successfully installed with the rpm -Uvh option all the rpm packages suggested.
Then I've run ./configure  --enable-float --enable-shared --program-suffix=_mpi
Until this point all seems to work fine but after the "make"  command i receive these warnings and errors:

mpicc -DHAVE_CONFIG_H -I. -I. -I../../src -I/usr/X11R6/include -I../../include -DGMXLIBDIR=\"/usr/local/gromacs/share/top\" -O6 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -malign-double -funroll-all-loops -c csettle.c -MT csettle.lo -MD -MP -MF .deps/csettle.TPlo -fPIC -DPIC -o .libs/csettle.o

mpicc -DHAVE_CONFIG_H -I. -I. -I../../src -I/usr/X11R6/include -I../../include -DGMXLIBDIR=\"/usr/local/gromacs/share/top\" -O6 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -malign-double -funroll-all-loops -c csettle.c -MT csettle.lo -MD -MP -MF .deps/csettle.TPlo -o csettle.o >/dev/null 2>&1

/bin/sh ../../libtool --mode=link mpicc -O6 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -malign-double -funroll-all-loops -o libmd_mpi.la -rpath /usr/local/gromacs/i686-pc-linux-gnu/lib -version-info 2:0:0 calcmu.lo calcvir.lo constr.lo coupling.lo dummies.lo ebin.lo edsam.lo ewald.lo fftgrid.lo force.lo ghat.lo init.lo mdatom.lo mdebin.lo minimize.lo ns.lo nsb.lo nsgrid.lo pme.lo poisson.lo pppm.lo psgather.lo pull.lo pullinit.lo pullio.lo pullutil.lo pssolve.lo psspread.lo shakef.lo sim_util.lo splittop.lo tables.lo tgroup.lo update.lo vcm.lo wnblist.lo clincs.lo csettle.lo -L/usr/X11R6/lib -lnsl -lnsl -lsrfftw_mpi -lsfftw_mpi -lsrfftw -lsfftw -lm -lXm -lXt -lSM -lICE -lXext -lXp -lX11

libtool: link: warning: library `/usr/local/lib/libsrfftw_mpi.la' was moved.

libtool: link: warning: library `/usr/local/lib/libsfftw_mpi.la' was moved.

libtool: link: warning: library `/usr/local/lib/libsrfftw.la' was moved.

libtool: link: warning: library `/usr/local/lib/libsfftw.la' was moved.

libtool: link: warning: `/usr/local/lib/libfreetype.la' seems to be moved

mpicc -shared .libs/calcmu.o .libs/calcvir.o .libs/constr.o .libs/coupling.o .libs/dummies.o .libs/ebin.o .libs/edsam.o .libs/ewald.o .libs/fftgrid.o .libs/force.o .libs/ghat.o .libs/init.o .libs/mdatom.o .libs/mdebin.o .libs/minimize.o .libs/ns.o .libs/nsb.o .libs/nsgrid.o .libs/pme.o .libs/poisson.o .libs/pppm.o .libs/psgather.o .libs/pull.o .libs/pullinit.o .libs/pullio.o .libs/pullutil.o .libs/pssolve.o .libs/psspread.o .libs/shakef.o .libs/sim_util.o .libs/splittop.o .libs/tables.o .libs/tgroup.o .libs/update.o .libs/vcm.o .libs/wnblist.o .libs/clincs.o .libs/csettle.o -Wl,--rpath -Wl,/usr/local/lib -Wl,--rpath -Wl,/usr/X11R6/lib -Wl,--rpath -Wl,/usr/local/lib -Wl,--rpath -Wl,/usr/X11R6/lib -L/usr/local/lib -L/usr/lesstif/lib -L/usr/local/lib/mysql -L/usr/X11R6/lib -lnsl /usr/local/lib/libsrfftw_mpi.so /usr/local/lib/libsfftw_mpi.so /usr/local/lib/libsrfftw.so /usr/local/lib/libsfftw.so -lm /usr/X11R6/lib/libXm.so -lXt -lSM -lICE -lXext -lXp -lX11 -Wl,-soname -Wl,libmd_mpi.so.2 -o .libs/libmd_mpi.so.2.0.0

(cd .libs && rm -f libmd_mpi.so.2 && ln -s libmd_mpi.so.2.0.0 libmd_mpi.so.2)

(cd .libs && rm -f libmd_mpi.so && ln -s libmd_mpi.so.2.0.0 libmd_mpi.so)

ar cru .libs/libmd_mpi.a calcmu.o calcvir.o constr.o coupling.o dummies.o ebin.o edsam.o ewald.o fftgrid.o force.o ghat.o init.o mdatom.o mdebin.o minimize.o ns.o nsb.o nsgrid.o pme.o poisson.o pppm.o psgather.o pull.o pullinit.o pullio.o pullutil.o pssolve.o psspread.o shakef.o sim_util.o splittop.o tables.o tgroup.o update.o vcm.o wnblist.o clincs.o csettle.o

ranlib .libs/libmd_mpi.a

creating libmd_mpi.la

.....AND THEN......

mpicc -DHAVE_CONFIG_H -I. -I. -I../../src -I/usr/X11R6/include -I../../include -DGMXLIBDIR=\"/usr/local/gromacs/share/top\" -O6 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -malign-double -funroll-all-loops -c `test -f grompp.c || echo './'`grompp.c

/bin/sh ../../libtool --mode=link mpicc -O6 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -malign-double -funroll-all-loops -o grompp topio.o toppush.o topcat.o topshake.o convparm.o tomorse.o sorting.o splitter.o dum_parm.o readir.o add_par.o topexcl.o toputil.o topdirs.o grompp.o ../mdlib/libmd_mpi.la ../gmxlib/libgmx_mpi.la -L/usr/X11R6/lib -lnsl -lnsl -lsrfftw_mpi -lsfftw_mpi -lsrfftw -lsfftw -lm -lXm -lXt -lSM -lICE -lXext -lXp -lX11

mkdir .libs