[gmx-users] Gromacs setup on dual core machine

Kpiwara De X-nelo kpiwara at gmail.com
Tue Mar 11 03:02:59 CET 2008

You'll need FFTW (fftw.org) LAM/MPI (lam-mpi.org) and gromacs sources
Download the 3 packages
start with the Lam/MPI (configure , make ,  make install)
Then fftw (the 2.1.5 version is needed, the 3.2 supports it but is still
unstable) (configure --enable-mpi, make, make install)
Then, finally, the GROMACS (configure --with-fft=fftw2 --enable-mpi , make ,
make install)

It should be running
as a non root user type lamboot
It should start the lam/mpi

run your simulations as usual just changing these
grompp -v -f xx -o xx -c xx -p xx -np #

the -np generate statusfile for # nodes


mpirun c0 C mdrun -v -s xx -o xx -e xx -c xx -g x -np # log >& xx

Number of nodes (#) , must be the same as used for grompp

the mpirun c0 C tells it to run on the maximun available nodes.

Hope I helped.

Matheus Fazian Ige Gondo
Departamento de Física e Biofísica
Instituto de Biociências
Unesp - Botucatu - SP
gondo at ibb.unesp.br
+55 (14) 3811-6254

On Thu, Mar 6, 2008 at 5:35 PM, Ricardo Soares <rsoares at fcfrp.usp.br> wrote:
> Hi everybody,
>  I think this may sound rather trivial for most users, but I intend to
>  install gromacs 3.3.1 on a dual core machine and I want to be sure what
>  to do. Could anyone indicate me some online tutorial to do so (as well
>  some simulation examples)? Is this considered parallelization (within
>  one computer)? Simply compiling mdrun with MPI works?
>  Thanks in advance.
>  --
>  ___________________________________________________________
>  Ricardo Oliveira dos Santos Soares
>  Post-graduation Student in Biological Physics
>  University of Sao Paulo - USP
>  Faculty of Farmaceutical Sciences of Ribeirao Preto - FCFRP
>  Phone: 55 (16) 3602-4840
>  Curriculum Lattes - http://lattes.cnpq.br/0777038258459931
>  ___________________________________________________________
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