[gmx-users] Gromacs setup on dual core machine

[Ricardo Soares]

Kpiwara De X-nelo wrote:
> Hello
> You'll need FFTW (fftw.org <http://fftw.org>) LAM/MPI (lam-mpi.org 
> <http://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
>
> then
>
> 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 <mailto:gondo at ibb.unesp.br>
> +55 (14) 3811-6254
Hello Matheus, you sure did help!
But that way I'd need to uninstall gromacs and reinstall. Is there a way 
to include the LAM/MPI package in an already installed instance of 
Gromacs? If not, how do I uninstal it?

Thanks again!

-- 
___________________________________________________________

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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