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" \
LIBS="-lmass"
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?
Thanks,
Dejun
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