[gmx-users] problems building gromacs 3.3 with mpi on MacOS X

[Jack Howarth]

    Hopefully this will clarify the problem. Below is the output for the
same linkage from a build of gromacs 3.2.1 on MacOS X which successfully
completes...

/bin/sh ../../libtool --mode=link mpicc  -O6 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -no-cpp-precomp -finline-limit=1000 -faltivec -funroll-all-loops -mcpu=7450 -mtune=970 -I/sw/include/libxml2 -I/sw/include  -L/sw/lib  -o libgmx_mpi.la -rpath /sw/lib -version-info 3:0:0 3dview.lo atomprop.lo block_tx.lo bondfree.lo calcgrid.lo calch.lo confio.lo copyrite.lo disre.lo do_fit.lo enxio.lo ewald_util.lo fatal.lo ffscanf.lo filenm.lo futil.lo gbutil.lo fnbf.lo gmxfio.lo ifunc.lo index.lo cinvsqrtdata.lo invblock.lo macros.lo orires.lo main.lo maths.lo matio.lo mshift.lo mvdata.lo mvxvf.lo names.lo network.lo nrama.lo nrjac.lo nrnb.lo pargs.lo pbc.lo pdbio.lo princ.lo rando.lo random.lo gmx_random.lo rbin.lo readinp.lo replace.lo rmpbc.lo shift_util.lo sortwater.lo smalloc.lo stat.lo statutil.lo strdb.lo string2.lo symtab.lo tpxio.lo trnio.lo trxio.lo txtdump.lo typedefs.lo viewit.lo wgms.lo wman.lo writeps.lo xdrd.lo xtcio.lo xvgr.lo detectcpu.lo libxdrf.lo vec.l
 o dihres.lo xmlio.lo innerc.lo inner_altivec.lo mgmx.lo widget.lo -L/usr/X11R6/lib -lsrfftw_mpi -lsfftw_mpi -lsrfftw -lsfftw -lm  -lXm -lXt  -lSM -lICE -lXext -lXp -lX11  -L/sw/lib -lxml2 -lz -lpthread -L/sw/lib -liconv -lm 
mpicc -dynamiclib -flat_namespace -undefined suppress -o .libs/libgmx_mpi.3.0.0.dylib  .libs/3dview.o .libs/atomprop.o .libs/block_tx.o .libs/bondfree.o .libs/calcgrid.o .libs/calch.o .libs/confio.o .libs/copyrite.o .libs/disre.o .libs/do_fit.o .libs/enxio.o .libs/ewald_util.o .libs/fatal.o .libs/ffscanf.o .libs/filenm.o .libs/futil.o .libs/gbutil.o .libs/fnbf.o .libs/gmxfio.o .libs/ifunc.o .libs/index.o .libs/cinvsqrtdata.o .libs/invblock.o .libs/macros.o .libs/orires.o .libs/main.o .libs/maths.o .libs/matio.o .libs/mshift.o .libs/mvdata.o .libs/mvxvf.o .libs/names.o .libs/network.o .libs/nrama.o .libs/nrjac.o .libs/nrnb.o .libs/pargs.o .libs/pbc.o .libs/pdbio.o .libs/princ.o .libs/rando.o .libs/random.o .libs/gmx_random.o .libs/rbin.o .libs/readinp.o .libs/replace.o .libs/rmpbc.o .libs/shift_util.o .libs/sortwater.o .libs/smalloc.o .libs/stat.o .libs/statutil.o .libs/strdb.o .libs/string2.o .libs/symtab.o .libs/tpxio.o .libs/trnio.o .libs/trxio.o .libs/txtdump.o .libs/typed
 efs.o .libs/viewit.o .libs/wgms.o .libs/wman.o .libs/writeps.o .libs/xdrd.o .libs/xtcio.o .libs/xvgr.o .libs/detectcpu.o .libs/libxdrf.o .libs/vec.o .libs/dihres.o .libs/xmlio.o .libs/innerc.o .libs/inner_altivec.o .libs/mgmx.o .libs/widget.o  -L/sw/lib -L/usr/X11R6/lib -lsrfftw_mpi -lsfftw_mpi -lsrfftw -lsfftw -lXm -lXt -lSM -lICE -lXext -lXp -lX11 -lxml2 -lz -lpthread -liconv -lm -lc -install_name  /sw/lib/libgmx_mpi.3.dylib -compatibility_version 4 -current_version 4.0

...and here is the same linkage from a build of gromacs 3.2.1 which fails (using
the same compilers and lam 7.0.6 but fftw3 instead of fftw)...

/bin/sh ../../libtool --mode=link --tag=CC mpicc  -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -no-cpp-precomp -faltivec -mcpu=7450 -mtune=970  -L/sw/lib  -o libgmx_mpi.la -rpath /sw/lib -version-info 4:0:0 3dview.lo atomprop.lo block_tx.lo bondfree.lo calcgrid.lo calch.lo confio.lo copyrite.lo disre.lo do_fit.lo enxio.lo ewald_util.lo fatal.lo ffscanf.lo filenm.lo futil.lo gbutil.lo gmxfio.lo ifunc.lo index.lo cinvsqrtdata.lo invblock.lo macros.lo orires.lo sparsematrix.lo main.lo maths.lo matio.lo mtxio.lo mshift.lo mvdata.lo mvxvf.lo names.lo network.lo nrama.lo nrjac.lo nrnb.lo pargs.lo pbc.lo pdbio.lo princ.lo rando.lo random.lo gmx_random.lo rbin.lo readinp.lo replace.lo rmpbc.lo shift_util.lo sortwater.lo smalloc.lo stat.lo statutil.lo strdb.lo string2.lo symtab.lo tpxio.lo trnio.lo trxio.lo txtdump.lo typedefs.lo viewit.lo wgms.lo wman.lo writeps.lo xtcio.lo xvgr.lo libxdrf.lo gmx_arpack.lo dihres.lo xmlio.lo tcontrol.lo mgmx.lo widget.lo nonbonded/li
 bnonbonded.la gmx_blas/libblas.la        gmx_lapack/liblapack.la -L/usr/X11R6/lib -lfftw3f -lm /System/Library/Frameworks/vecLib.framework/Versions/A/vecLib -lXm -lXt  -lSM -lICE -lXext -lXp -lX11  
mpicc -dynamiclib  -flat_namespace -undefined suppress -o .libs/libgmx_mpi.4.dylib  .libs/3dview.o .libs/atomprop.o .libs/block_tx.o .libs/bondfree.o .libs/calcgrid.o .libs/calch.o .libs/confio.o .libs/copyrite.o .libs/disre.o .libs/do_fit.o .libs/enxio.o .libs/ewald_util.o .libs/fatal.o .libs/ffscanf.o .libs/filenm.o .libs/futil.o .libs/gbutil.o .libs/gmxfio.o .libs/ifunc.o .libs/index.o .libs/cinvsqrtdata.o .libs/invblock.o .libs/macros.o .libs/orires.o .libs/sparsematrix.o .libs/main.o .libs/maths.o .libs/matio.o .libs/mtxio.o .libs/mshift.o .libs/mvdata.o .libs/mvxvf.o .libs/names.o .libs/network.o .libs/nrama.o .libs/nrjac.o .libs/nrnb.o .libs/pargs.o .libs/pbc.o .libs/pdbio.o .libs/princ.o .libs/rando.o .libs/random.o .libs/gmx_random.o .libs/rbin.o .libs/readinp.o .libs/replace.o .libs/rmpbc.o .libs/shift_util.o .libs/sortwater.o .libs/smalloc.o .libs/stat.o .libs/statutil.o .libs/strdb.o .libs/string2.o .libs/symtab.o .libs/tpxio.o .libs/trnio.o .libs/trxio.o .libs/tx
 tdump.o .libs/typedefs.o .libs/viewit.o .libs/wgms.o .libs/wman.o .libs/writeps.o .libs/xtcio.o .libs/xvgr.o .libs/libxdrf.o .libs/gmx_arpack.o .libs/dihres.o .libs/xmlio.o .libs/tcontrol.o .libs/mgmx.o .libs/widget.o -all_load  nonbonded/.libs/libnonbonded.a gmx_blas/.libs/libblas.a gmx_lapack/.libs/liblapack.a  /usr/X11R6/lib/libXt.dylib /usr/X11R6/lib/libX11.dylib /usr/X11R6/lib/libXp.dylib /usr/X11R6/lib/libXext.dylib /usr/X11R6/lib/libICE.dylib /usr/X11R6/lib/libSM.dylib /usr/X11R6/lib/libXmu.dylib -L/sw/lib -L/usr/X11R6/lib -lXmu /sw/lib/libfftw3f.dylib -lm /sw/lib/libXm.dylib -lXt -lSM -lICE -lXext -lXp -lX11 -mcpu=7450 -mtune=970 -install_name  /sw/lib/libgmx_mpi.4.dylib -compatibility_version 5 -current_version 5.0

Hopefully this problem can be patched around.
           Jack