The HPC Advisory Council has published a new Best Practices presentation entitled NAMD Performance Benchmark and Profiling for the 12-core AMD Opteron 6174 (Magny-Cours) processors running at 2.2 GHz.
NAMD is a parallel molecular dynamics code designed for high-performance simulations of large biomolecular systems and scales to hundreds of processors on high-end parallel platforms. NAMD was developed by the joint collaboration of the Theoretical and Computational Biophysics Group (TCB) and the Parallel Programming Laboratory (PPL) at the University of Illinois at Urbana-Champaign, and is distributed free of charge with source code. The presentation provides information on NAMD performance capabilities and the effect of different HPC cluster components (HW and SW) on NAMD.
