[gmx-users] problem compiling gromacs 5.1

Ana Marija sokovic.anamarija at gmail.com
Sat Oct 24 22:05:28 CEST 2015

For 4.6.7 gromacs MPI_Library flag was necessary as well as for 4.5.5. What
I am asking here is not weather my admins are doing a good job,and also as
you know some things you just got with machine,and sometimes things are not
great,so you have to make a workaround. What I am asking here is what is
the function and is there is a function of mpi_Library flag in gromacs 5.1
and was that flag replaced with a different one in that version?
On Oct 24, 2015 2:07 PM, "Mark Abraham" <mark.j.abraham at gmail.com> wrote:

> 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/
>> -DFFTWF_LIBRARY=/opt/fftw/
>> -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_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
>> on the and of the installation it was reported that:
>> 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

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