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? also gmx_mpi is there: ams@login1:/lustre/beagle2/ams/new/gromacs/gromacs-5.1/build/bin> ls gmx_mpi template On Sat, Oct 24, 2015 at 11:39 AM, Mark Abraham <mark.j.abra...@gmail.com> wrote: > Hi, > > On Sat, Oct 24, 2015 at 6:32 PM Ana Marija <sokovic.anamar...@gmail.com> > wrote: > >> Hay Mark, >> >> is it -DSPHINX_EXECUTABLE=OFF >> > > They're equivalent - cmake regards both of them as equivalent to "not > found." > > >> also just curious would commenting out that 62 line in >> /lustre/beagle2/ams/new/gromacs/gromacs-5.1/docs/CMakeLists.txt >> solve the problem as well? >> > > Looks like it, but not touching the source code is generally a good > strategy. It's much easier to record a cmake command than to record how the > source code was patched. > > >> can you please tell me what other flags I need in cmake or you are saying >> that I just have some redundant stuff there? >> > > I can't tell what you need, that's between you, the machine, the sysadmins > and their docs. I've said you have a bunch of things that don't exist / > don't exist any more and that makes your life more complex than you want it > to be. > > Mark > > >> Ana >> >> On Sat, Oct 24, 2015 at 11:29 AM, Mark Abraham <mark.j.abra...@gmail.com> >> wrote: >> >>> Hi, >>> >>> That one's our fault, sorry :-( It'll be fixed in 5.1.1 out shortly, but >>> you can work around it by adding >>> >>> -DSPHINX_EXECUTABLE=no >>> >>> to your cmake call (which, by the way, still has a lot of stuff in it >>> that I've said you don't want to have) >>> >>> Mark >>> >>> On Sat, Oct 24, 2015 at 6:14 PM Ana Marija <sokovic.anamar...@gmail.com> >>> wrote: >>> >>>> HI, >>>> >>>> I tried to configure gromacs 5.1 via: >>>> >>>> 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_EXTERNAL_BLAS=OFF -DGMX_EXTERNAL_LAPACK=OFF >>>> >>>> >>>> But I am getting this error: >>>> -- Found PythonInterp: /usr/bin/python (found version "2.6.9") >>>> CMake Error at cmake/FindSphinx.cmake:52 (string): >>>> string sub-command REGEX, mode REPLACE needs at least 6 arguments >>>> total to >>>> command. >>>> Call Stack (most recent call first): >>>> docs/CMakeLists.txt:62 (find_package) >>>> >>>> line 62 in >>>> /lustre/beagle2/ams/new/gromacs/gromacs-5.1/docs/CMakeLists.txt >>>> looks like this: >>>> >>>> find_package(Sphinx 1.2.3 QUIET COMPONENTS pygments) >>>> >>>> can you please advise me on what to do? >>>> >>>> Thanks >>>> Ana >>>> -- >>>> 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. >>>> >>> >> -- 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.