[gmx-users] mdrun with mpi runs slow
feenstra at chem.vu.nl
Thu Nov 27 10:40:05 CET 2003
Dennis Kühl wrote:
> I'm running gromacs on a cluster with 20 nodes, but mdrun only get's
> less than 5% of the cpu's (each node has two cpu's). The line in 'top'
> looks like this:
> 29025 kuehl 20 0 4600 4484 1640 S 3.1 0.2 0:13 mdrun
> Usually there are other applications on that cluster, they get all the
> available cpu time. But even when there are no other running apps
> doesn't work fast. Some collegues of mine think that the processes are
> waiting for something different than cpu-time (e.g. I/O).
> Has anyone an idea?
Yes - Communication. It may also be that your mpi is not configured
optimally for Gromacs. Search the archives, it has come up often enough.
> grompp -f grompp.mdp -p topol.top -c conf.gro -o testlauf.tpr -np 15
How many atoms are in your system? 15 CPU's is a large number, which is
only efficient for *huge* numbers of atoms (think order of millions!).
Even then, scaling of Gromacs above 8CPU's on the average Linux cluster
isn't what we would like it to be...
| | |
| _ _ ___,| K. Anton Feenstra |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
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| | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/ |
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