[gmx-users] Tipps for compiling gromacs 5 on BlueGene/Q

[Soren Wacker]

Hi,

I try to compile gromacs 5 on a BlueGene/Q. 
The non-mpi version works fine with letting gromacs build its own fftw libaries.
With mpi the generated file mdrun_mpi seems to be corrupt. 
Running it from both the login nodes and the cluster nodes gives:

>mdrun_mpi 
/bgsys/source/srcV1R2M2.15270/comm/sys/buildtools/pami/common/bgq/BgqPersonality.h:102: 
/bgsys/source/srcV1R2M2.15270/comm/sys/buildtools/pami/common/bgq/BgqPersonality.h<102>
Aborted (core dumped)

I would appreciate some help.

In the following, I show my build script. 
Is there anything wrong?

module purge
module load cmake/2.8.12.1
module load mpich2 



export FFLAGS='-O3 -qarch=qp -qtune=qp -qmaxmem=-1 '   #it was recommended to set this flags from the BGQ user guide
export CFLAGS='-O3 -qarch=qp -qtune=qp -qmaxmem=-1 '

cd ${BUILD_DIR}

cmake ${SOURCE_DIR} \
 -DCMAKE_C_COMPILER=mpicc \
 -DCMAKE_CXX_COMPILER=mpicxx \
 -DCMAKE_INSTALL_PREFIX=${INSTALL_DIR} \
 -DCMAKE_TOOLCHAIN_FILE=PATH/TO/BlueGeneQ-static-XL-CXX.cmake \
 -DGMX_BUILD_OWN_FFTW=ON \
 -DGMX_DEFAULT_SUFFIX=ON \
 -DGMX_MPI=ON \
 -DGMX_BUILD_MDRUN_ONLY=ON \
 -DGMX_RELAXED_DOUBLE_PRECISION=ON

make -j `nproc`
make install



As I said, this produces a corrupt mdrun_mpi file.
Thanks 
Soren