[gmx-users] gromacs-4.0.5 parallel run in 8 cpu: slow speed

Jussi Lehtola jussi.lehtola at helsinki.fi
Thu Jun 11 08:41:22 CEST 2009

On Thu, 2009-06-11 at 14:35 +0800, Thamu wrote:
>         Hi
>         Recently I successfully installed the gromacs-4.0.5 mpi
>         version.
>         I could run in 8 cpu. but the speed is very slow. 
>         Total number of atoms in the system is 78424.
>         while running all 8 cpu showing 95-100% CPU.

That's normal for a system that atoms/cpu ratio.
What's your system and what mdp file are you using?
Jussi Lehtola, FM, Tohtorikoulutettava
Fysiikan laitos, Helsingin Yliopisto
jussi.lehtola at helsinki.fi, p. 191 50632
Mr. Jussi Lehtola, M. Sc., Doctoral Student
Department of Physics, University of Helsinki, Finland
jussi.lehtola at helsinki.fi

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