> > Dear users
> > my gromacs is 3.3.3 my cpus are intel core2quad 2.4
> GHz and my mpi is
> > LAM 7.0.6
> > I can get the cpu usage of 4 cores on one node but
> when I run on 2
> > node the cpu usage of cores is low
> > I have installed gromacs with these instructions
> > Compile LAM 7
> > ./configure --prefix=/usr/local/share/lam7
> --enable-static
> > make |tee make.log
> > make install
> > make clean
> >
> > Compile fftw
> >
> > export MPI_HOME=/usr/local/share/lam7
> > export LAMHOME=/usr/local/share/lam7
> > export PATH=/usr/local/share/lam7/bin:$PATH
> > ./configure --prefix=/usr/local/share/fftw3
> --enable-mpi
> > make |tee make.log
> > make install
> > make distclean
> >
> > Compile Gromacs
> >
> > export MPI_HOME=/usr/local/share/lam7
> > export LAMHOME=/usr/local/share/lam7
> > export PATH=/usr/local/share/lam7/bin:$PATH
> >
> > ./configure --prefix=/usr/local/share/gromacs_333
> > --exec-prefix=/usr/local/share/gromacs_333
> --program-prefix=""
> > --program-suffix="" --enable-static
> --enable-mpi --disable-float
> > make |tee make.log
> > make install
> > make distclean
> >
> > lamboot -v lamhosts
> >
> >
> > Run Gromacs on 2 machine (each machine has 1
> core2quad)
> >
> > /usr/local/share/gromacs_333/bin/grompp -f md.mdp -po
> mdout.mdp -c
> > md.gro -r md_out.gro -n md.ndx -p md.top -o topol.tpr
> -np 2
> >
> > mpirun -np 2 /usr/local/share/gromacs_333/bin/mdrun
> -np 2-f topol.tpr
> > -o md.trr -c md_out.gro -e md.edr -g md.log &
> > I also test with -np 8 but my cpu usage is low and the
> speed is less
> > than single run!!!
> > thank you in your advance
> >
> >
>
> --
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