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NAMD Scaling on Jaguar XT5
The NAMD molecular dynamics program excels at simulating, in atomic detail, the complex molecular machinery of living cells. NAMD now enables hundred-million-atom simulations using the full capabilities of the nation's fastest supercomputers due to parallel programming innovations reported in a paper at the SC11 supercomputing conference. While parallel supercomputers have massive amounts of memory in aggregate, any part of the machine can directly access only a small fraction. To fit the molecular blueprint of cellular structures such as the chromatophore in the memory of such machines, a compressed data format was developed that exploits the repetitive nature of proteins, nucleic acids, lipid membranes, and solvent. This format requires only a small amount of data to be copied to all parts of the supercomputer, while the remainder is read from disks in parallel and distributed across the machine. Simulation output and the balancing of work loads are similarly distributed. The Charm++ parallel programming system, on which NAMD is built, was also extended to allow the molecular structure and other data to be shared among the increasing number of cores in modern processors. A hundred-million-atom simulation can now run on supercomputers with only 2 gigabytes of memory per node, such as the IBM BlueGene/P. The enhancements are available to computational biologists world-wide in special memory-optimized versions of NAMD 2.8.