[gmx-users] gromacs-4.0.2, parallel performance in two quad core xeon machines

[Claus Valka]

Hello,

we have built a cluster with nodes that are comprised by the following: dual core Intel(R) Xeon(R) CPU E3110 @ 3.00GHz. The memory of each node has 16Gb of memory. The switch that we use is a dell power connect model. Each node has a Gigabyte ethernet card.

I tested the performance for a system of 7200 atoms in 4cores of one node, in 8 cores of one node and in 16 cores of two nodes. In one node the performance is getting better.
The problem I get is that moving from one node to two, the performance decreases dramatically (almost two days for a run that finishes in less than 3 hours!).

I have compiled gromacs with --enable-mpi option. I also have read previous archives from Mr Kurtzner, yet from what I saw is that they are focused on errors in gromacs 4 or on problems that previous versions of gromacs had. I get no errors, just low performance.

Is there any option that I must enable in order to succeed better performance in more than one nodes?  Or do you think according to your experience that the switch we use might be the problem? Or maybe should we have to activate anything from the nodes?

Thank you in advance,
Nikos




      
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