[gmx-users] Problem building Gromacs-4.5.5 on BlueGene/Q

Christopher Neale chris.neale at mail.utoronto.ca
Fri Nov 9 15:29:47 CET 2012

Dear Dejun:

I don't know why --enable-bluegene gives you problems or what it is supposed to do. Was the BGQ even 
available when gromacs 4.5.5 came out? I doubt it.

In any event, here is how my colleague successfully ran configure:

./configure \
    --build=ppc64 \
    --prefix=${HOME}/exec/gromacs-4.5.5 \
    --disable-ppc-altivec \
    --with-fft=fftw3 \
    --without-x \
    --enable-all-static \
    CC="bgxlc_r"  CFLAGS="-O3 -qarch=auto -qtune=auto -q64 -qinfo=all" \
    CXX="bgxlC_r" CXXFLAGS="-O3 -qarch=auto -qtune=auto -q64 -qinfo=all" \
    F77="bgxlf_r" FFLAGS="-O3 -qnoprefetch -qarch=auto -qtune=auto -q64 -qinfo=all" \
    CPPFLAGS="-I/opt/ibmcmp/xlmass/bg/7.3/include -I${HOME}/zx_local/fftw-3.3.2/include" \
    LDFLAGS="-L/opt/ibmcmp/xlmass/bg/7.3/lib64 -L${HOME}/zx_local/fftw-3.3.2/lib" \
    LIBS="-lmass_64 -lm"

-- original message --

I'm trying to build the mdrun binary for the BGQ system with the following commands (current dir is /scratch/dlin13/gromacs/gromacs-4.5.5/backend) :

../configure --prefix=/scratch/dlin13/gromacs/gromacs-4.5.5/backend \
              --build=powerpc64-bgq-linux \
              --enable-bluegene \
              --with-fft=fftw3 \
              --enable-float \
              --enable-mpi \
              --enable-shared=no \
              --without-dlopen \
              --disable-threads \
              --program-suffix=_mpi_bg \
                CC="mpixlc" CFLAGS="-O3 -qarch=450d -qtune=450" \
                CXX="mpixlcxx" CXXFLAGS="-O3 -qarch=450d -qtune=450" \
                CPPFLAGS="-I/scratch/dlin13/fftw/fftw-3.3.2-mpi/include" \
                F77="mpixlf77" FFLAGS="-O3 -qarch=auto -qtune=auto" \
                LDFLAGS="-L/scratch/dlin13/fftw/fftw-3.3.2-mpi/lib" \

make mdrun

The build generate some errors in the middle:

../../../../../src/gmxlib/nonbonded/nb_kernel_bluegene/nb_kernel_gen_bluegene.h", line 259.13: 1506-1231 (S) The built-in function "__fpadd" is not valid for the target architecture.
make[3]: *** [nb_kernel010_bluegene.lo] Error 1
make[3]: Leaving directory `/scratch/dlin13/gromacs/gromacs-4.5.5/backend/src/gmxlib/nonbonded/nb_kernel_bluegene'
make[2]: *** [all-recursive] Error 1
make[2]: Leaving directory `/scratch/dlin13/gromacs/gromacs-4.5.5/backend/src/gmxlib/nonbonded'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/scratch/dlin13/gromacs/gromacs-4.5.5/backend/src/gmxlib'
(cd ./src/mdlib && make ; exit 0)

and it finally stop at:
:0  -L/scratch/dlin13/fftw/fftw-3.3.2-mpi/lib  -o libgmxpreprocess_mpi.la -rpath /scratch/dlin13/gromacs/gromacs-4.5.5/backend/lib add_par.lo compute_io.lo convparm.lo fflibutil.lo gen_ad.lo gen_vsite.lo genhydro.lo gpp_atomtype.lo gpp_bond_atomtype.lo h_db.lo hackblock.lo hizzie.lo pdb2top.lo pgutil.lo readir.lo readpull.lo resall.lo sorting.lo specbond.lo ter_db.lo tomorse.lo topdirs.lo topexcl.lo topio.lo toppush.lo topshake.lo toputil.lo tpbcmp.lo vsite_parm.lo xlate.lo ../mdlib/libmd_mpi.la -lnsl -lm -lmass
mkdir .libs
libtool: link: cannot find the library `../mdlib/libmd_mpi.la' or unhandled argument `../mdlib/libmd_mpi.la'
make[1]: *** [libgmxpreprocess_mpi.la] Error 1
make[1]: Leaving directory `/scratch/dlin13/gromacs/gromacs-4.5.5/backend/src/kernel'

But if I leave out the --enable-bluegene option and configure otherwise the same way as I showed, it works. Does anyone have any suggestion?


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