James N. Glosli

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We report the computational advances that have enabled the first micron-scale simulation of a Kelvin-Helmholtz (KH) instability using molecular dynamics (MD). The advances are in three key areas for massively parallel computation such as on BlueGene/L (BG/L): fault tolerance, application kernel optimization, and highly efficient parallel I/O. In particular,(More)
With supercomputers anticipated to expand from thousands to millions of cores, one of the challenges facing scientists is how to effectively utilize this ever-increasing number. We report here an approach that creates a heterogeneous decomposition by partitioning effort according to the scaling properties of the component algorithms. We demonstrate our(More)
We investigate solidification in tantalum and uranium systems ranging in size from 64,000 to 524,288,000 atoms on the IBM BlueGene/L computer at LLNL. Using the newly developed ddcMD code, we achieve performance rates as high as 103 TFlops, with a performance of 101.7 TFlop sustained over a 7 hour run on 131,072 cpus. We demonstrate superb strong and weak(More)
We have developed the capability to rapidly simulate cardiac electrophysiological phenomena in a human heart discretised at a resolution comparable with the length of a cardiac myocyte. Previous scientific investigation has generally invoked simplified geometries or coarse-resolution hearts, with simulation duration limited to 10s of heartbeats. Using(More)
We have developed a highly efficient and scalable cardiac electrophysiology simulation capability that supports groundbreaking resolution and detail to elucidate the mechanisms of sudden cardiac death from arrhythmia. We can simulate thousands of heartbeats at a resolution of 0.1 mm, comparable to the size of cardiac cells, thereby enabling scientific(More)
Blue Gene/L represents a new way to build supercomputers, using a large number of low power processors, together with multiple integrated interconnection networks. Whether real applications can scale to tens of thousands of processors (on a machine like Blue Gene/L) has been an open question. In this paper, we describe early experience with several physics(More)
Although computer simulation has played a central role in the study of nucleation and growth since the earliest molecular dynamics simulations almost 50 years ago, confusion surrounding the effect of finite size on such simulations has limited their applicability. Modeling solidification in molten tantalum on the Blue Gene/L computer, we report here on the(More)
We have investigated the performance characteristics of hardware transactional memory (HTM) on the Blue Gene/Q computer in comparison with conventional concurrency control mechanisms, using a molecular dynamics application as an example. Benchmark tests, along with overhead-cost and scalability analysis, quantify relative performance advantages of HTM over(More)
We propose and analyze threading algorithms for hybrid MPI/OpenMP parallelization of a molecular-dynamics simulation, which are scalable on large multicore clusters. Two data-privatization thread scheduling algorithms via nucleation-growth allocation are introduced: (1) compact-volume allocation scheduling (CVAS); and (2) breadth-first allocation scheduling(More)