[gmx-users] problem compiling gromacs 5.1

[Mark Abraham]

Hi,

On Sat, Oct 24, 2015 at 8:22 PM Ana Marija <sokovic.anamarija at gmail.com>
wrote:

> so I managed to install gromacs via:
>
> #in ams at login1:/lustre/beagle2/ams/new/gromacs/gromacs-5.1/build>
>
> cmake .. -DFFTWF_INCLUDE_DIR=/opt/fftw/3.3.4.0/abudhabi/include
> -DFFTWF_LIBRARY=/opt/fftw/3.3.4.0/abudhabi/lib/libfftw3f.a
> -DMPI_LIBRARY="/opt/cray/mpt/7.0.5/gni/mpich2-gnu/49/lib/libmpich.a;/opt/cray/mpt/7.0.5/gni/mpich2-gnu/49/lib/libfmpich_gnu_49.a;/opt/cray/mpt/7.0.5/gni/mpich2-gnu/49/lib/libmpl.a;/opt/cray/pmi/default/lib64/libpmi.a;/opt/cray/rca/default/lib64/librca.a;/opt/gcc/4.9.2/snos/lib64/libgfortran.a;/opt/gcc/4.9.2/snos/lib64/libstdc++.a;/opt/cray/alps/default/lib64/libalpslli.a;/opt/cray/alps/default/lib64/libalpsutil.a;/opt/gcc/4.9.2/snos/lib64/libgomp.a;/opt/gcc/4.9.2/snos/lib64/libquadmath.a;/opt/cray/ugni/default/lib64/libugni.a;/opt/cray/udreg/default/lib64/libudreg.a;/opt/cray/xpmem/default/lib64/libxpmem.a;/opt/cray/wlm_detect/default/lib64/libwlm_detect.a;/lib64/libdl.so.2"
> -DMPI_INCLUDE_PATH="/opt/cray/mpt/7.0.5/gni/mpich2-gnu/49/include"
> -DCMAKE_CXX_COMPILER=CC -DCMAKE_C_COMPILER=cc -DGMX_FORCE_CXX=ON
> -DGMX_DOUBLE=OFF -DGMX_PREFER_STATIC_LIBS=ON -DGMX_GPU=OFF -DGMX_MPI=ON
> -DCMAKE_INSTALL_PREFIX=/lustre/beagle2/ams/new/gromacs/ginstall
> -DGMX_X11=OFF -DGMX_BLAS_USER=/lustre/beagle2/ams/new/gromacs/lib/libblas.a
> -DGMX_LAPACK_USER=/lustre/beagle2/ams/new/gromacs/lib/liblapack.a
> -DCMAKE_SKIP_RPATH=ON -DGMX_BUILD_SHARED_EXE=OFF -DSPHINX_EXECUTABLE=OFF
>
> on the and of the installation it was reported that:
> GMX_FORCE_CXX
>  MPI_LIBRARY
>
> flags were not used. What I am worried about is MPI_LIBRARY flag. Does
> this means that gromacs just found on it's own MPI libraries or?
>

What's more likely? That I said earlier that the point of the modules you
loaded is that you are using the magic wrapper compilers Cray provides to
handle MPI for you, or that I'm wrong about that *and* about my assertion
that MPI_LIBRARY was useless? :-)

Not needing to know about such garbage is why you should be asking your
system administators to do these infrastructure things for you...

Mark