[gmx-users] benchmark: buying a new cluster

[Chris Neale]

To some extent, it depends on your interconnect and the number of atoms in the simulations that you will be doing. If you are using gigabit ethernet, then you may not scale very well beyond 8 cores on these dual node quad cores and so there is an argument to be made for 10% faster. However, if you are using a faster interconnecting wire, then you could easily parallelize (infiniband et al scales 100% to 32 cpus with >300K atoms for my cutoffs) and there is then an argument for more cores. I would personally go for additional cores. 

Also, I have never been involved in the purchasing and so I don't know too much about bulk discounts, but you should at least consider spending half of your money now and saving half for an upgrade in 6 months when the prices will have come down. I suppose that depends on whether you expect to be at 100% utilization immediately or if there will be a ramping up period of your usage.

Chris.

--original message--

Hi all,
we are going to buy a new cluster and we are in doubt about the frequency to consider.
Basically, we have the possibility to buy either 18 nodes dual quad-core (18x8 cores) bearing
Intel-Xeon E5430 2.66 MHz and FSB 1333 MHz or 15 nodes dual quad-core (15x8 cores) bearing
Intel-Xeon E5462 2.8 MHz and FSB 1600 MHz. The latest seems to be **only** 10% faster then the first.
However, thinking to the new gromacs4, we are in doubt about the best solution. Is it better to have
a **nominal** 10% cpu faster or to have 24 further cores?

Thanks in advance for any welcome suggestion,

Regards

andrea