[gmx-users] problem with MPI

[Szilárd Páll]

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
<baharmehrpuyan at 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.
> --
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