[gmx-users] Gromacs setup on dual core machine

[Diego Enry]

Ricardo, you don't need to uninstall anithing. To run mpi jobs you
only need, mdrun_mpi.

./configure  (with your options)
make mdrun
make install-mdrun

done.

On Tue, Mar 11, 2008 at 1:55 PM, Ricardo Soares <rsoares at fcfrp.usp.br> wrote:
>
>  Kpiwara De X-nelo wrote:
> Hello
>  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
>
>  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
>  +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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-- 
Diego Enry B. Gomes
Laboratório de Modelagem e Dinamica Molecular
Universidade Federal do Rio de Janeiro - Brasil.