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Sun Blade NAMD Benchmarks

sunSun, via their BestPerf blog site, has released a series of NAMD benchmarks from their 6048/X6275 series blade servers.  The benchmarks feature 12 blade servers running the popular parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems.  They wanted to especially note the performance over the IBM BlueGene/L.  From the post:

.: The cluster of 12 Sun Blade X6275 server modules was 4.7x faster than 256 processor configuration of the IBM BlueGene/L

.: The cluster of 12 Sun Blade X6275 server modules exhibited excellent scalability for NAMD molecular dynamics simulation, up to 10.4x speedup for 12 blades relative to 1 blade

.: For largest molecule considered, the cluster of 12 Sun Blade X6275 server modules achieved a throughput of 0.094 seconds per simulation step

The systems consisted of two Intel Nehalem’s of the 2.93GHz flavor nad 24GB of memory each.  The software config consisted of SUSE Linux Enterprise Server 10 SP2 [kernel 2.6.16.60-0.31_lustre.1.8.0.1-sm], Scali MPI 5.6.6 and GNU compilers [ gcc 4.1.2 (1/15/2007), gfortran 4.1.2 (1/15/2007)].  They go into a fair amount of detail on which benchmarks were run and how.

See the full writeup here.

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