Steven J. Plimpton

Bio: Steven J. Plimpton is an academic researcher from Sandia National Laboratories. The author has contributed to research in topics: Parallel algorithm & Direct simulation Monte Carlo. The author has an hindex of 44, co-authored 128 publications receiving 62532 citations.

Maintaining connected components for infinite graph streams

Abstract: We present an algorithm to maintain the connected components of a graph that arrives as an infinite stream of edges. We formalize the algorithm on X-stream, a new parallel theoretical computational model for infinite streams. Connectivity-related queries, including component spanning trees, are supported with some latency, returning the state of the graph at the time of the query. Because an infinite stream may eventually exceed the storage limits of any number of finite-memory processors, we assume an aging command or daemon where "uninteresting" edges are removed when the system nears capacity. Following an aging command the system will block queries until its data structures are repaired, but edges will continue to be accepted from the stream, never dropped. The algorithm will not fail unless a model-specific constant fraction of the aggregate memory across all processors is full. In normal operation, it will not fail unless aggregate memory is completely full.Unlike previous theoretical streaming models designed for finite graphs that assume a single shared memory machine or require arbitrary-size intemediate files, X-stream distributes a graph over a ring network of finite-memory processors. Though the model is synchronous and reminiscent of systolic algorithms, our implementation uses an asynchronous message-passing system. We argue the correctness of our X-stream connected components algorithm, and give preliminary experimental results on synthetic and real graph streams.

Increasing molecular dynamics simulation rates with an 8-fold increase in electrical power efficiency

Abstract: Electrical power efficiency is a primary concern in designing modern HPC systems. Common strategies to improve CPU power efficiency rely on increased parallelism within a processor that is enabled both by an increase in the vector capabilities within the core and also the number of cores within a processor. Although many-core processors have been available for some time, achieving power-efficient performance has been challenging due to the offload model. Here, we evaluate performance of the molecular dynamics code LAMMPS on two new Intel® processors including the second generation many-core Intel® Xeon Phi™ processor that is available as a bootable CPU. We describe our approach to measure power consumption out-of-band and software optimizations necessary to achieve energy efficiency. We analyze benefits from Intel® Advanced Vector Extensions 512 instructions and demonstrate increased simulations rates with over 9X the CPU+DRAM power efficiency when compared to the unoptimized code on previous generation processors.

Validation simulations of the DSMC code SPARTA

Abstract: The Direct Simulation Monte Carlo (DSMC) method has been used for over 50 years to simulate rarified gas flows for a wide range of applications where continuum assumptions fail. Extensive efforts to validate and verify the DSMC method are essential to establishing confidence in the technique and to promoting its broader application. Here, validation results for two cases are presented using a recently developed, open-source DSMC code called SPARTA.

The diffusion of simple penetrants in tangent site polymer melts

Abstract: The diffuse behavior of penetrants in simple polymer melts was investigated by molecular dynamics simulation. For the case where the polymer melt consisted of pearl-necklace chains, the diffusive behavior of the loose pearl penetrants was seen to be qualitatively different than would be expected in realistic models of polymer melts. In particular, there was little or no “non-Fickian” region; the variation of the diffusion coefficient with the penetrant diameter was what one would expect for diffusion through small molecular liquids; and, finally, the long time tail of the velocity autocorrelation displayed a “−3/2” power law form, also as in the small molecular liquid case. When the chains’ backbone motion was further constrained by the introduction of a bond angle potential, the qualitative nature of the penetrant diffusion became more “polymer-like.” A non-Fickian region developed; the diffusion coefficient varied more rapidly with penetrant diameter; and the velocity autocorrelation function developed a “−5/2” power law tail.

Direct Simulation Monte Carlo Investigation of Hydrodynamic Instabilities in Gases.

Abstract: The Rayleigh-Taylor instability (RTI) is investigated using the Direct Simulation Monte Carlo (DSMC) method of molecular gas dynamics. Here, two-dimensional and three-dimensional DSMC RTI simulations are performed to quantify the growth of flat and single-mode-perturbed interfaces between two atmospheric-pressure monatomic gases. The DSMC simulations reproduce all qualitative features of the RTI and are in reasonable quantitative agreement with existing theoretical and empirical models in the linear, nonlinear, and self-similar regimes. At late times, the instability is seen to exhibit a self-similar behavior, in agreement with experimental observations. For the conditions simulated, diffusion can influence the initial instability growth significantly.

Fast parallel algorithms for short-range molecular dynamics

Abstract: Three parallel algorithms for classical molecular dynamics are presented. The first assigns each processor a fixed subset of atoms; the second assigns each a fixed subset of inter-atomic forces to compute; the third assigns each a fixed spatial region. The algorithms are suitable for molecular dynamics models which can be difficult to parallelize efficiently—those with short-range forces where the neighbors of each atom change rapidly. They can be implemented on any distributed-memory parallel machine which allows for message-passing of data between independently executing processors. The algorithms are tested on a standard Lennard-Jones benchmark problem for system sizes ranging from 500 to 100,000,000 atoms on several parallel supercomputers--the nCUBE 2, Intel iPSC/860 and Paragon, and Cray T3D. Comparing the results to the fastest reported vectorized Cray Y-MP and C90 algorithm shows that the current generation of parallel machines is competitive with conventional vector supercomputers even for small problems. For large problems, the spatial algorithm achieves parallel efficiencies of 90% and a 1840-node Intel Paragon performs up to 165 faster than a single Cray C9O processor. Trade-offs between the three algorithms and guidelines for adapting them to more complex molecular dynamics simulations are also discussed.

疟原虫var基因转换速率变化导致抗原变异[英]／Paul H, Robert P, Christodoulou Z, et al//Proc Natl Acad Sci U S A

Abstract: 抗原变异可使得多种致病微生物易于逃避宿主免疫应答。表达在感染红细胞表面的恶性疟原虫红细胞表面蛋白1（PfPMP1）与感染红细胞、内皮细胞、树突状细胞以及胎盘的单个或多个受体作用，在黏附及免疫逃避中起关键的作用。每个单倍体基因组var基因家族编码约60种成员，通过启动转录不同的var基因变异体为抗原变异提供了分子基础。