[gmx-users] Gromacs setup on dual core machine

[Kpiwara De X-nelo]

Hello Ricardo

Did you install with the sources ? (make install) ?
Go to the folder where you ran this command and run "make uninstall"

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 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
> ___________________________________________________________
>
>
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20080311/b8c2ddf6/attachment.html>