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

[Mark Abraham]

On Fri, Nov 9, 2012 at 3:29 PM, Christopher Neale <
chris.neale at mail.utoronto.ca> wrote:

> 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.
>

There's no code currently optimized for BlueGene/Q. The code currently
distributed with GROMACS predates BGQ. Whether there will be optimized
kernels for BGQ in 4.6 remains to be seen.

Mark


> 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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