[gmx-users] Re: mdrun_d not running in parallel

[Sarath Kumar]

>
> Message: 1
> Date: 8 Mar 2010 11:49:40 -0000
> From: "sarbani chattopadhyay" <sarbani_c84 at rediffmail.com>
> Subject: [gmx-users] mdrun_d not running in parallel
> To: <gmx-users at gromacs.org>
> Message-ID: <20100308114940.35527.qmail at f5mail-236-242.rediffmail.com>
> Content-Type: text/plain; charset="utf-8"
> Hi ,
>    I had installed gromacs4.0.7 in double preicision in 64 bit Mac 10.6.1
> computer with 8
> dual core processors.
>
> 1) I installed the fftw-3.0.1 in the following way
>
> ( in the directory)
>        ./configure --enable float
>        sudo make sudo make install
>        make distclean
>      ./configure --enable-threads
>       make
>      make install
>
> 2) I installed gromacs as
>             ./configure --disable-float
>             sudo make
>             sudo make install
>
> 3) I installed lam-7.1.4 as
>   ./configure --prefix=/usr/local/lam --without-fc
>    sudo make
>  sudo make install
>
> After that I went back to the gromacs directory
>  and did
>     make clean
>    ./configure --enable-mpi --program-suffix=_mpi
>  make mdrun
>  sudo make install -mdrun
>
> In this way I couldn't get mdrun_mpi_d. However I read from the revision
> notes that grompp
> and mdrun can run in parallel by themselves.( "-np" option is not there in
> grompp_d)
>
>
> However when I give the commands
> grompp_d  -f em.mdp -c solvated.gro -o em.tpr -zero
> lamboot
> nohup mpirun -np 8 mdrun_d -v -s em.tpr -deffnm em &
>
> the md.log file says nnodes=1. the simulation is not running in parallel.
>
> Where have I gone wrong?
> Any suggestion will be of great help.
> Thanks in advance.
> Sarbani
>
> ---------------------------------------------------------------------------------------------------


Try
first installing the fftw with the option of --enable-mpi,
as u  did for gromacs.
then again install the gromacs with options same as before.

Sarath Kumar B,
Research Scholar,
Centre for Biotechnology,
Anna University.
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