[gmx-users] mdrun with mpi runs slow

Dennis Kühl kuehl at biochem.mpg.de
Wed Nov 26 09:47:01 CET 2003


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?

Here're my commands (there are only 15 nodes available):

grompp -f grompp.mdp -p topol.top -c conf.gro -o testlauf.tpr -np 15

lamboot ~/lamboot.startup

mpirun n0-14 mdrun -nice 0 -s testlauf.tpr -o testlauf.trr -v -c



PS: Gromacs runns with a different version of lam/mpi than the other
apps (I don't know the version numbers right now)

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