[gmx-users] mdrun with mpi runs slow

[Anton Feenstra]

Dennis Kühl wrote:

> Hi!
> 
> 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...


-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
|(   |   )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands   |
| \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610           |
|             | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/       |
|             | "If You See Me Getting High, Knock Me Down"           |
|             | (Red Hot Chili Peppers)                               |
|_____________|_______________________________________________________|