We haven't seen any molecular dynamics benchmarks on the newest processors: AMD Opteron (Istanbul) 6-core or Intel Xeon (Nehalem) 4-core. To help us get a better understanding of the performance on MD code, I took a look at two of the most common MD codes out there: LAMMPS and GROMACS. My results are a little surprising!

In our last benchmark blog post we discussed the performance of HPL on the Xeon 5500 series vs. Opteron 2400 series.  We are continuing this head-to-head comparison of the latest and greatest processors with the STREAM benchmark.  Click below to read our in-depth analysis of memory bandwidth between platforms.

This year has brought big advances to the CPU industry with the arrival of the Intel Xeon 5500 series "Nehalem" and the AMD Opteron 2400 series "Istanbul". While many different benchmarks have been published comparing both systems, they all have seemed to fall a bit short in showing an accurate comparison of the two platforms.. The HPC industry standard for benchmarking is HPL or High Performance Linpack, on which the "Top 500" list is based. Many industry insiders look to the results of this benchmark as an insight into how their systems will perform.

Users of HPC systems are always on the lookout for more performance for their applications. Some users turn to FPGAs (Field Programmable Gate Arrays, essentially a reconfigurable processor) to accelerate their algorithms but this options is time consuming and expensive. HPC users often look to the off the shelf market and in doing so found some kindred spirits: gamers.