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
[EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]>
+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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