[gmx-users] Gromacs setup on dual core machine

[Jens Pohl]

Hello!

I have a similar problem with installing gromacs on a dual core machine. 
When I go through the procedure described by Matheus Fazian Ige Gondo a bit further down installing lam/mpi then fftw and finally gromacs everything seems to be working fine, but lam/mpi doesn't recognize the two cores and with mdrun there will be an fatal error. grompp and mdrun both were run with -np 2 and the output of mdrun says, that the file was made for two nodes but mdrun expected it to be for one node. 

With lamnodes there is only one node on cpu0 on localhost... What to do in this case?

Thanks in advance
Jens


>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
> ___________________________________________________________
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