FYI: If you are planning to run single-node, you don't need MPI. Just compile with default settings and you'll get a thread-parallel version that supports MPI parallelization within mdrun based on multi-threading (using the library thread-MPI). In practice his means that: $ mdrun -nt 2 will use two CPU cores and if you omit the -nt option it will use all cores available.
-- Szilárd On Sat, Nov 10, 2012 at 11:48 AM, Bahar Mehrpuyan <baharmehrpu...@yahoo.com>wrote: > hi gmx users > > I installed gromacs 4.5.5 on my Ubuntu system , and every thing was OK, > but when i try to run mpirun, the following error appears: > $ mpirun -np 2 mdrun -v -deffnm md_0_1 > mpiexec_bahar-laptop: cannot connect to local mpd > (/tmp/mpd2.console_bahar); possible causes: > 1. no mpd is running on this host > 2. an mpd is running but was started without a "console" (-n option) > In case 1, you can start an mpd on this host with: > mpd & > and you will be able to run jobs just on this host. > > > > > here is the detailed description of installing: > > 1) installing openmpi-1.4.1 from package manager > > 2)fftw3 > ./configure --prefix=/home/bahar/program --enable-threads --enable-float > --enable-sse > make > > make istall > > 3)gromacs > exportCPPFLAGS="-I/home/bahar/program/include" > > export LDFLAGS="-L/home/bahar/program/lib" > > ./configure --prefix=/home/bahar/4-5-5 --enable-mpi > make > make mdrun > make install > make install-mdrun > > Any suggestion would be greatly appreciated. > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
