[gmx-users] BGQ compilation with verlet kernels: #include file "kernel_impl.h" not found.

Mark Abraham mark.j.abraham at gmail.com
Wed Sep 18 17:39:50 CEST 2013

Thanks for the follow up.

The take-home lesson is that building for BlueGene/Q is unlike
building for the usual homogenous x86 cluster. You still need an MPI
and non-MPI build, but the latter should be targeted at the front end
(Linux on PowerPC, usually), unless/until GROMACS tools acquire MPI
functionality useful on a BlueGene/Q scale.


On Wed, Sep 18, 2013 at 2:07 AM, Christopher Neale
<chris.neale at mail.utoronto.ca> wrote:
> Indeed, it works just fine when I compile with mpi. I never thought to check that. My usual procedure is
> to compile the whole package without mpi and then to compile mdrun with mpi. Thanks for the help Mark.
> Here is the compilation script that worked for me.
> module purge
> module load vacpp/12.1 xlf/14.1 mpich2/xl
> module load cmake/2.8.8
> module load fftw/3.3.2
> export FFTW_LOCATION=/scinet/bgq/Libraries/fftw-3.3.2
> cmake ../source/ \
>       -DCMAKE_TOOLCHAIN_FILE=BlueGeneQ-static-XL-C \
>       -DCMAKE_INSTALL_PREFIX=$(pwd) \
>       -DGMX_X11=OFF \
>       -DGMX_MPI=ON \
> make -j 16
> make install
> --
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