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

[Mark Abraham]

On 9/03/2010 3:42 PM, Sarath Kumar wrote:
>     Message: 1
>     Date: 8 Mar 2010 11:49:40 -0000
>     From: "sarbani chattopadhyay" <sarbani_c84 at rediffmail.com
>     <mailto:sarbani_c84 at rediffmail.com>>
>     Subject: [gmx-users] mdrun_d not running in parallel
>     To: <gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>>
>     Message-ID:
>     <20100308114940.35527.qmail at f5mail-236-242.rediffmail.com
>     <mailto: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.

That configure flag is not relevant unless you are compiling FFTW 2.x to 
link to GROMACS, though FFTW does plan to re-introduce such 
functionality in the future.

Mark