[gmx-users] Gromacs scaling problem

[M.N. Manoj]

Dear friends,

We have observed the following scaling problem on our cluster:

Cluster config:
Nodes = 3, Processor = Xeon quad core 1.86 Ghz, 2 processors per node.
Network= gigabit

We have used the "dppc" system from gromacs website to benchmark this
cluster.
The following are the results, with gromacs 3.3.2  ( configured with MPICH2
)

1. With np 8, we get 1.29 ns/day ( all running on 1 node)
2. With np 12 we get 1.50 ns/day
3. With np 16 we get 1.433 ns/day
4. With np 24 we get 0.517 ns/day

We understand the scalability decreases with number of processors, but why
the ns/day comes down with higher job distribution?

Kindly advice whats going wrong...
Thanks in advance...

M.N. Manoj
CEO
Jigsaw Bio Solutions,
Bangalore - INDIA
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