[gmx-developers] problem about Gromacs CVS version 3.3.99_development_200800503 parallel efficiency

Yang Ye leafyoung at yahoo.com
Fri Jun 20 15:04:09 CEST 2008


This is related to the type of your network connection.

If it is just ethernet, such low CPU utilization is expected. Also, if
your system has a small number of atoms, the speed-up through parallel
is also small.

So, reduce the number of parallel, or wait for Gromacs 4, or change to a
better inter-node network (Infiniband, etc), sorted according to
required time, IMHO.

Yang Ye

xuji wrote:
> Hi all
> I have 3 nodes, and there're 8 CPUs in each node. I run a 24 processes
> mdrun on the three nodes. And I use MPICH2 environment. But the
> efficiency of the mdrun program is very low. The occupancy of each CPU
> is only about 10%. I don't know why. Can some one give me some help?
> Appricaite any help in advance!
> Best wishes!
> Ji Xu
> xuji at home.ipe.ac.cn <mailto:xuji at home.ipe.ac.cn>
> 2008-06-20
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