[gmx-users] Cluster recommendations

David McGiven davidmcgivenn at gmail.com
Thu Jan 15 17:35:30 CET 2015

Dear Gromacs Users,

We’ve got some funding to build a new cluster. It’s going to be used mainly
for gromacs simulations (80% of the time). We run molecular dynamics
simulations of transmembrane proteins inside a POPC lipid bilayer. In a
typical system we have ~100000 atoms, from which almost 1/3 correspond to
water molecules. We employ usual conditions with PME for electorstatics and
cutoffs for LJ interactions.

I would like to hear your advice on which kind of machines are the best
bang-for-the-buck for that kind of simulations. For instance :

- Intel or AMD ? My understanding is that Intel is faster but expensive,
and AMD is slower but cheaper. So at the end you almost get the same
performance-per-buck. Right ?

- Many CPUs/Cores x machine or less ? My understanding is that the more
cores x machine the lesser the costs. One machine is always cheaper to buy
and maintain than various. Plus maybe you can save the costs of Infiniband
if you use large core densities ?

- Should we invest in an Infiniband network to run jobs across multiple
nodes ? Will the kind of simulations we run benefit from multiple nodes ?

- Would we benefit from adding GPU’s to the cluster ? If so, which ones ?

We now have a cluster with 48 and 64 AMD Opteron cores x machine (4
processors x machine) and we run our gromacs simulations there. We don’t
use MPI because our jobs are mostly run in a single node. As I said, with
48 or 64 cores x simulation in a single machine. So far, we’re quite
satisfied with the performance we get.

Any advice will be greatly appreciated.

Best Regards,

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