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

[Mark Abraham]

On Tue, Apr 7, 2015 at 6:45 PM, Soren Wacker <swacker at ucalgary.ca> wrote:

> 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.
>

That's nice, but the result is useless for running on BG/Q compute nodes.
co

> 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.
>

That looks like your MPI is mis-configured to get header files from a
source distribution, and these don't match what the compute nodes are using
at runtime, or such. /bgsys/drivers is the usual top-level directory for
such gear on BG/Q.


> In the following, I show my build script.
> Is there anything wrong?
>
> module purge
> module load cmake/2.8.12.1
> module load mpich2
>

You want to use IBM's compilers and MPI for the compute nodes, not stuff
lying around on the login machine, but you'll have to follow your local
documentation to find out how.

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 \
>

Obviously, you should refer to the real file...

 -DGMX_BUILD_OWN_FFTW=ON \
>

This is not likely to be the problem, but is fragile enough that I would
not do it. This convenience feature is intended for quick deployment of
GROMACS on personal machines. Million-dollar parallel HPC infrastructure
should have a system-wide install of FFTW, to which you should link.

Mark

 -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
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>