Hi we have fixed quite a few installation issues since beta2. Could you try to download the latest version from git? git clone git://git.gromacs.org/gromacs.git
Let us know if you still see the issue. If you don't have git you can download it from: https://github.com/gromacs/gromacs/archive/master.zip Roland On Mon, Mar 17, 2014 at 8:10 AM, jk <broodkil...@gmail.com> wrote: > Hello everyone, my name is Jacek and I am new to GROMACS :) I have recently > downloaded and tried to compile the second beta of GROMACS 5, and run into > some issues along the way, so I decided to ask around and see if I can find > some help. Basically, what I wanted to do was to compile a few different > variants of GROMACS 5 to see how they perform against each other. I was > interested in comparing single and double precision builds, CUDA vs no CUDA > and MPI vs no MPI, in various combinations. Eventually though, I have only > managed to succesfully compile a single-precision, CUDA-extended and > MPI-paralellized build, and none other. > > > Now to the details: > (1) Compiling with -DGMX_DOUBLE=OFF, -DGMX_MPI=OFF and -DGMX_GPU=OFF > terminates early with a fatal error of lacking MPI headers: > > [ 3%] Building C object > src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/calc_verletbuf.c.o > In file included from > > /media/sda4/soft/struct/gromacs-5.0-beta2/src/gromacs/legacyheaders/types/commrec.h:40:0, > from > > /media/sda4/soft/struct/gromacs-5.0-beta2/src/gromacs/legacyheaders/coulomb.h:43, > from > > /media/sda4/soft/struct/gromacs-5.0-beta2/src/gromacs/gmxpreprocess/calc_verletbuf.c:49: > > /media/sda4/soft/struct/gromacs-5.0-beta2/src/gromacs/legacyheaders/types/../../utility/gmxmpi.h:62:17: > fatal error: mpi.h: No such file or directory > compilation terminated. > make[2]: *** > [src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/calc_verletbuf.c.o] > Error 1 > make[1]: *** [src/gromacs/CMakeFiles/libgromacs.dir/all] Error 2 > make: *** [all] Error 2 > > (2) Compiling with -DGMX_DOUBLE=OFF, -DGMX_MPI=OFF and -DGMX_GPU=ON > terminates exactly the same, but after some CUDA stuff is compiled. > > (3) Compiling with -DGMX_DOUBLE=OFF, -DGMX_MPI=ON and -DGMX_GPU=OFF > terminates at link with a fatal error of lacking CUDA-specific objects: > > [ 92%] Building CXX object > share/template/CMakeFiles/template.dir/template.cpp.o > Linking CXX executable ../../bin/template > ../../lib/libgromacs_mpi.so.0.0.0: undefined reference to > `nbnxn_cuda_init_const' > (...some more undefined refs) > ../../lib/libgromacs_mpi.so.0.0.0: undefined reference to > `pick_compatible_gpus' > collect2: ld returned 1 exit status > make[2]: *** [bin/template] Error 1 > make[1]: *** [share/template/CMakeFiles/template.dir/all] Error 2 > make: *** [all] Error 2 > > (4) Compiling with -DGMX_DOUBLE=OFF, -DGMX_GPU=ON and -DGMX_MPI=ON works > fine, as mentioned before. > > (5) Compiling with -DGMX_DOUBLE=ON, -DGMX_MPI=OFF and -DGMX_GPU=OFF > terminates identically as (1) > > (6) Compiling with -DGMX_DOUBLE=ON, -DGMX_MPI=ON and -DGMX_GPU=OFF > terminates identically as (3) > > > Each recompilation attempt was made in a fresh direction, with all the > files > from a previous build removed, so as to avoid any conflicts. I can post > links to complete compilation logs to PasteBin, if necessary. On the > technical side of things, I am running a 64-bit Ubuntu 12.04 system on a > quad-core i7-860 CPU, with 16GB of RAM and a brand new GTX 780Ti gfx card > on > hand-compiled CUDA 5.5 (driver+toolkit). > Of the relevant libs, I have the latest FFTW-3.3.3 compiled nicely in > single > ('--enable-float --enable-shared --enable-sse2') and double precision > ('--enable-shared --enable-sse2') variants stored in separate folders, > which > I pass to Cmake through the -DFFTW(F)_LIBRARY parameter. I have OpenMPI > 1.4.3.2, MPICH2 and libboost 1.46.1, all from the offical Ubuntu repo. > > My guess is that the build system somehow disregards the flags sent to it > and wants MPI/CUDA files even when directly told to skip them. Any ideas on > how to fix/work around this? > > > -- > View this message in context: > http://gromacs.5086.x6.nabble.com/Compilation-issues-with-GROMACS-5-beta-2-tp5015221.html > Sent from the GROMACS Users Forum mailing list archive at Nabble.com. > -- > 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. > -- ORNL/UT Center for Molecular Biophysics cmb.ornl.gov 865-241-1537, ORNL PO BOX 2008 MS6309 -- 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.