Charge and force on a conductive sphere between two parallel electrodes: A Stokesian dynamics approach
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catalysis (homogeneous), solar (photovoltaic), bio↗
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Nonlinear parallel momentum transport in strong electrostatic turbulence
Most existing theoretical studies of momentum transport focus on calculating the Reynolds stress based on quasilinear theory, without considering the nonlinear momentum flux-〈v{sup ~}{sub r}n{sup ~}u{sup ~}{sub ∥}〉. However, a recent experiment on TORPEX found that the nonlinear toroidal momentum flux induced by blobs makes a significant contribution as compared to the Reynolds stress [Labit et al., Phys. Plasmas 18, 032308 (2011)]. In this work, the nonlinear parallel momentum flux in strong electrostatic turbulence is calculated by using a three dimensional Hasegawa-Mima equation, which is relevant for tokamak edge turbulence. It is shown that the nonlinear diffusivity is smaller than the quasilinear diffusivity from Reynolds stress. However, the leading order nonlinear residual stress can be comparable to the quasilinear residual stress, and so may be important to intrinsic rotation in tokamak edge plasmas. A key difference from the quasilinear residual stress is that parallel fluctuation spectrum asymmetry is not required for nonlinear residual stress.
70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
Non-equilibrium reaction and relaxation dynamics in a strongly interacting explicit solvent: F + CD{sub 3}CN treated with a parallel multi-state EVB model
We describe a parallelized linear-scaling computational framework developed to implement arbitrarily large multi-state empirical valence bond (MS-EVB) calculations within CHARMM and TINKER. Forces are obtained using the Hellmann-Feynman relationship, giving continuous gradients, and good energy conservation. Utilizing multi-dimensional Gaussian coupling elements fit to explicitly correlated coupled cluster theory, we built a 64-state MS-EVB model designed to study the F + CD{sub 3}CN → DF + CD{sub 2}CN reaction in CD{sub 3}CN solvent (recently reported in Dunning et al. [Science 347(6221), 530 (2015)]). This approach allows us to build a reactive potential energy surface whose balanced accuracy and efficiency considerably surpass what we could achieve otherwise. We ran molecular dynamics simulations to examine a range of observables which follow in the wake of the reactive event: energy deposition in the nascent reaction products, vibrational relaxation rates of excited DF in CD{sub 3}CN solvent, equilibrium power spectra of DF in CD{sub 3}CN, and time dependent spectral shifts associated with relaxation of the nascent DF. Many of our results are in good agreement with time-resolved experimental observations, providing evidence for the accuracy of our MS-EVB framework in treating both the solute and solute/solvent interactions. The simulations provide additional insight into the dynamics at sub-picosecond time scales that are difficult to resolve experimentally. In particular, the simulations show that (immediately following deuterium abstraction) the nascent DF finds itself in a non-equilibrium regime in two different respects: (1) it is highly vibrationally excited, with ∼23 kcal mol{sup −1} localized in the stretch and (2) its post-reaction solvation environment, in which it is not yet hydrogen-bonded to CD{sub 3}CN solvent molecules, is intermediate between the non-interacting gas-phase limit and the solution-phase equilibrium limit. Vibrational relaxation of the nascent DF results in a spectral blue shift, while relaxation of the post-reaction solvation environment results in a red shift. These two competing effects mean that the post-reaction relaxation profile is distinct from what is observed when Franck-Condon vibrational excitation of DF occurs within a microsolvation environment initially at equilibrium. Our conclusions, along with the theoretical and parallel software framework presented in this paper, should be more broadly applicable to a range of complex reactive systems.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Electron parallel closures for various ion charge numbers
Electron parallel closures for the ion charge number Z = 1 [J.-Y. Ji and E. D. Held, Phys. Plasmas 21, 122116 (2014)] are extended for 1 ≤ Z ≤ 10. Parameters are then computed for various Z with the same form of the Z = 1 kernels adopted. The parameters are smoothly varying in Z and hence can be used to interpolate parameters and closures for noninteger, effective ion charge numbers.
70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
Accelerating ring-polymer molecular dynamics with parallel-replica dynamics
Nuclear quantum effects are important for systems containing light elements, and the effects are more prominent in the low temperature regime where the dynamics also becomes sluggish. We show that parallel replica (ParRep) dynamics, an accelerated molecular dynamics approach for infrequent-event systems, can be effectively combined with ring-polymer molecular dynamics, a semiclassical trajectory approach that gives a good approximation to zero-point and tunneling effects in activated escape processes. The resulting RP-ParRep method is a powerful tool for reaching long time scales in complex infrequent-event systems where quantum dynamics are important. Two illustrative examples, symmetric Eckart barrier crossing and interstitial helium diffusion in Fe and Fe–Cr alloy, are presented to demonstrate the accuracy and long-time scale capability of this approach.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
A Parallel EM Algorithm for Model-Based Clustering Applied to the Exploration of Large Spatio-Temporal Data
We develop a parallel EM algorithm for multivariate Gaussian mixture models and use it to perform model-based clustering of a large climate data set. Three variants of the EM algorithm are reformulated in parallel and a new variant that is faster is presented. All are implemented using the single program, multiple data (SPMD) programming model, which is able to take advantage of the combined collective memory of large distributed computer architectures to process larger data sets. Displays of the estimated mixture model rather than the data allow us to explore multivariate relationships in a way that scales to arbitrary size data. We study the performance of our methodology on simulated data and apply our methodology to a high resolution climate dataset produced by the community atmosphere model (CAM5). This article has supplementary material online.
Chen, Wei-Chen↗
Automatic and Transparent Resource Contention Mitigation for Improving Large-Scale Parallel File System Performance
Proportional to the scale increases in HPC systems, many scientific applications are becoming increasingly data intensive, and parallel I/O has become one of the dominant factors impacting the large-scale HPC application performance. On a typical large-scale HPC system, we have observed that the lack of a global workload coordination coupled with the shared nature of storage systems cause load imbalance and resource contention over the end-to-end I/O paths resulting in severe performance degradation. I/O load imbalance on HPC systems is generally a self-inflicted wound and mostly occurs between the I/O paths and resources consumed by each individual job. In this paper, we introduce TAPP-IO, a dynamic, shared load balancing framework for mitigating resource contention. TAPP-IO extends our previous work and solves two major limitations: First, it transparently intercepts file creation calls during runtime to balance the workload over all available storage targets. The usage of TAPP-IO requires no application source code modifications and is independent from any I/O middleware. The framework can be applied to almost any HPC platform and is suitable for systems that lack a centralized file system resource manager. Second, the framework proposes a new placement strategy to support not only file-per-process I/O, but also single shared file I/O. This opens the door to a new class of scientific applications that can leverage the placement library for improved performance. We demonstrate the effectiveness of our integration on the Titan system at the Oak Ridge National Laboratory. Our experiments with a synthetic benchmark and real-world HPC workload show that, even in a noisy production environment, TAPP-IO can improve large-scale application performance significantly.
Neuwirth, Sarah↗
Dynamical regimes of vortex flow in type-II superconductors with parallel twin boundaries
We explore the dynamics of driven magnetic flux lines in disordered type-II superconductors in the presence of twin boundaries oriented parallel to the direction of the applied magnetic field, using a three-dimensional elastic line model simulated with Langevin molecular dynamics. The lines are driven perpendicular to the planes to model the effect of an electric current applied parallel to the planes and perpendicular to the magnetic field. A study of the long-time non-equilibrium steady states for varying sample orientation and thickness reveals a rich collection of dynamical regimes spanning the depinning crossover region that separates the pinned and moving-lattice states of vortex matter. We observe the emergence of a preferred direction for the ordering of the Abrikosov lattice in the free- owing vortex regime due to asymmetric pinning by the planar defects. Furthermore, we have performed novel direct measurements of flux line excitations such as half-loops and double kinks to aid the characterization of the topologically rich flux flow profile.
75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
PapyrusKV: a high-performance parallel key-value store for distributed NVM architectures
This paper introduces PapyrusKV, a parallel embedded key-value store (KVS) for distributed high-performance computing (HPC) architectures that offer potentially massive pools of nonvolatile memory (NVM). PapyrusKV stores keys with their values in arbitrary byte arrays across multiple NVMs in a distributed system. PapyrusKV provides standard KVS operations such as put, get, and delete. More importantly, PapyrusKV provides advanced features for HPC such as dynamic consistency control, zero-copy workflow, and asynchronous checkpoint/restart. Beyond filesystems, PapyrusKV provides HPC programmers with a high-level interface to exploit distributed NVM in the system, and it transparently organizes data to achieve high performance. Also, it allows HPC applications to specialize PapyrusKV to meet their specific requirements. We empirically evaluate PapyrusKV on three HPC systems with real NVM devices: OLCF's Summitdev, TACC's Stampede, and NERSC's Cori. Our results show that PapyrusKV can offer high performance, scalability, and portability across these various distributed NVM architectures.
97 MATHEMATICS AND COMPUTING↗
Reaching bandwidth saturation using transparent injection parallelization
Although logically available, applications may not exploit enough instantaneous communication concurrency to maximize network utilization on HPC systems. This is exacerbated in hybrid programming models that combine single program multiple data with OpenMP or CUDA. We present the design of a “multi-threaded” runtime able to transparently increase the instantaneous network concurrency and to provide near saturation bandwidth, independent of the application configuration and dynamic behavior. The runtime offloads communication requests from application level tasks to multiple communication servers. The servers use system specific performance models to attain network saturation. Our techniques alleviate the need for spatial and temporal application level message concurrency optimizations. Experimental results show improved message throughput and bandwidth by as much as 150% for 4 KB messages on InfiniBand and by as much as 120% for 4 KB messages on Cray Aries. For more complex operations such as all-to-all collectives, we observe as much as 30% speedup. This translates into 23% speedup on 12,288 cores for a NAS FT implemented using FFTW. We observe as much as 76% speedup on 1500 cores for an already optimized UPC+OpenMP geometric multigrid application using hybrid parallelism. For the geometric multigrid GPU implementation, we observe as much as 44% speedup on 512 GPUs.
Chaimov, Nicholas↗
Parallel simulated annealing with embedded machine learning and multifidelity models for reactor core design
This paper presents extensions to a penalty-free, parallel simulated annealing (SA) algorithm for multi-constrained combinatorial optimization with the aim of embedding multi-fidelity physics models into the annealing procedure. The method uses a low-fidelity, quickly executing model for rapid design space exploration and a high-fidelity model for detailed constraint resolution and on-the-fly bias correction. Machine learning models updated within the annealing procedure were used to bridge the gap between the multi-fidelity models, which led to accurate rapid exploration and efficient detailed constraint resolution. A software implementation of the new multi-fidelity optimization methods, called ML-PSA, was demonstrated on a continuous multi-fidelity optimization problem and a constrained combinatorial PWR lattice design problem. These problems demonstrate some of the features, parallel performance characteristics, and extensible nature of the multi-fidelity SA methods. This paper shows that the developed software and procedure are a general optimization tool that can be applied to a wide variety of scientific and engineering design optimization applications. (authors)
22 GENERAL STUDIES OF NUCLEAR REACTORS↗
Data communications for a collective operation in a parallel active messaging interface of a parallel computer
Algorithm selection for data communications in a parallel active messaging interface (`PAMI`) of a parallel computer, the PAMI composed of data communications endpoints, each endpoint including specifications of a client, a context, and a task, endpoints coupled for data communications through the PAMI, including associating in the PAMI data communications algorithms and bit masks; receiving in an origin endpoint of the PAMI a collective instruction, the instruction specifying transmission of a data communications message from the origin endpoint to a target endpoint; constructing a bit mask for the received collective instruction; selecting, from among the associated algorithms and bit masks, a data communications algorithm in dependence upon the constructed bit mask; and executing the collective instruction, transmitting, according to the selected data communications algorithm from the origin endpoint to the target endpoint, the data communications message.
97 MATHEMATICS AND COMPUTING↗
Data communications in a parallel active messaging interface of a parallel computer
Algorithm selection for data communications in a parallel active messaging interface (`PAMI`) of a parallel computer, the PAMI composed of data communications endpoints, each endpoint including specifications of a client, a context, and a task, endpoints coupled for data communications through the PAMI, including associating in the PAMI data communications algorithms and ranges of message sizes so that each algorithm is associated with a separate range of message sizes; receiving in an origin endpoint of the PAMI a data communications instruction, the instruction specifying transmission of a data communications message from the origin endpoint to a target endpoint, the data communications message characterized by a message size; selecting, from among the associated algorithms and ranges, a data communications algorithm in dependence upon the message size; and transmitting, according to the selected data communications algorithm from the origin endpoint to the target endpoint, the data communications message.
97 MATHEMATICS AND COMPUTING↗
Fencing direct memory access data transfers in a parallel active messaging interface of a parallel computer
Fencing direct memory access (`DMA`) data transfers in a parallel active messaging interface (`PAMI`) of a parallel computer, the PAMI including data communications endpoints, each endpoint including specifications of a client, a context, and a task, the endpoints coupled for data communications through the PAMI and through DMA controllers operatively coupled to segments of shared random access memory through which the DMA controllers deliver data communications deterministically, including initiating execution through the PAMI of an ordered sequence of active DMA instructions for DMA data transfers between two endpoints, effecting deterministic DMA data transfers through a DMA controller and a segment of shared memory; and executing through the PAMI, with no FENCE accounting for DMA data transfers, an active FENCE instruction, the FENCE instruction completing execution only after completion of all DMA instructions initiated prior to execution of the FENCE instruction for DMA data transfers between the two endpoints.
97 MATHEMATICS AND COMPUTING↗
Fencing direct memory access data transfers in a parallel active messaging interface of a parallel computer
Fencing direct memory access (`DMA`) data transfers in a parallel active messaging interface (`PAMI`) of a parallel computer, the PAMI including data communications endpoints, each endpoint including specifications of a client, a context, and a task, the endpoints coupled for data communications through the PAMI and through DMA controllers operatively coupled to segments of shared random access memory through which the DMA controllers deliver data communications deterministically, including initiating execution through the PAMI of an ordered sequence of active DMA instructions for DMA data transfers between two endpoints, effecting deterministic DMA data transfers through a DMA controller and a segment of shared memory; and executing through the PAMI, with no FENCE accounting for DMA data transfers, an active FENCE instruction, the FENCE instruction completing execution only after completion of all DMA instructions initiated prior to execution of the FENCE instruction for DMA data transfers between the two endpoints.
97 MATHEMATICS AND COMPUTING↗
Fencing direct memory access data transfers in a parallel active messaging interface of a parallel computer
Fencing direct memory access (`DMA`) data transfers in a parallel active messaging interface (`PAMI`) of a parallel computer, the PAMI including data communications endpoints, each endpoint including specifications of a client, a context, and a task, the endpoints coupled for data communications through the PAMI and through DMA controllers operatively coupled to segments of shared random access memory through which the DMA controllers deliver data communications deterministically, including initiating execution through the PAMI of an ordered sequence of active DMA instructions for DMA data transfers between two endpoints, effecting deterministic DMA data transfers through a DMA controller and a segment of shared memory; and executing through the PAMI, with no FENCE accounting for DMA data transfers, an active FENCE instruction, the FENCE instruction completing execution only after completion of all DMA instructions initiated prior to execution of the FENCE instruction for DMA data transfers between the two endpoints.
97 MATHEMATICS AND COMPUTING↗