[gmx-users] problem compiling gromacs 5.1

[Ana Marija]

HI,

I was able to compile gromacs 5.1 via:

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_INCLUDE_PATH="/opt/cray/mpt/7.0.5/gni/mpich2-gnu/49/include"
-DCMAKE_CXX_COMPILER=CC -DCMAKE_C_COMPILER=cc  -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

Thank you for all your help and patience with mine somewhat basic questions!

Cheers,
Ana


On Sat, Oct 24, 2015 at 9:31 PM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> Hi,
>
> The purpose of using a wrapper compiler is that it handles linking all the
> right stuff. MPI_LIBRARY was a thing from a cmake module we used only in
> Gromacs 4.5, before we removed it when we decided that wrapper compilers do
> a better job. So there's nothing that replaces it. That the recent
> installation guides make zero mention of linking MPI libraries is a big
> clue...
>
> Mark
>
> On Sat, 24 Oct 2015 22:05 Ana Marija <sokovic.anamarija at gmail.com> wrote:
>
>> 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/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
>>>
>>