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.abra...@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.anamar...@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.abra...@gmail.com> wrote: >> >>> Hi, >>> >>> On Sat, Oct 24, 2015 at 8:22 PM Ana Marija <sokovic.anamar...@gmail.com> >>> wrote: >>> >>>> so I managed to install gromacs via: >>>> >>>> #in ams@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 >>> >> -- 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-requ...@gromacs.org.