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At least 613 records · Page 34

Parallel derivative-free optimization for simulation-based design of behind-the-meter energy systems

In this work, the integrated design and dispatch of behind-the-meter or distributed resources (e.g. stationary battery storage and solar PV generation) is considered. A simulation-based framework is employed, generating high-fidelity results with closed-loop predictive control at a fine resolution, at the expense of high computational cost (several minutes to a few hours per design point). To address this challenge, parallel derivative-free design methods are considered. Four methods are compared, including state-of-the-art surrogate-based methods (Radial-Basis Functions and Gaussian processes) and sampling strategies, an evolutionary-based method, and a simple sequential grid refinement method. As a case study, two types of design problem with increasing complexity are considered, namely, the design of behind-the-meter resources (three design variables) and the inclusion of grid capacity (four design variables). The second yields a constrained design problem for which violations can only be determined after solving the computationally expensive simulation. For the three-dimensional case, all methods present a good performance, achieving a solution within 1% of the optimum after the first iteration, with the sequential grid refinement exhibiting the fastest convergence and achieving the best final objective value. This indicates that the parallel evaluation of multiple sampling points may be more important than the choice of method for small decision spaces. For the four-dimensional constrained case, the Genetic Algorithm presents the best tradeoff between performance and computational effort, while the rough objective function terrain generated by constraint violation penalties reduces the performance of surrogate-based methods. Contour plots with flat regions indicate flexibility in the optimal design and highlight the importance of characterizing the solution space.

24 POWER TRANSMISSION AND DISTRIBUTION↗

Neuromorphic Graph Algorithms: Extracting Longest Shortest Paths and Minimum Spanning Trees

Neuromorphic computing is poised to become a promising computing paradigm in the post Moore's law era due to its extremely low power usage and inherent parallelism. Traditionally speaking, a majority of the use cases for neuromorphic systems have been in the field of machine learning. In order to expand their usability, it is imperative that neuromorphic systems be used for non-machine learning tasks as well. The structural aspects of neuromorphic systems (i.e., neurons and synapses) are similar to those of graphs (i.e., nodes and edges), However, it is not obvious how graph algorithms would translate to their neuromorphic counterparts. In this work, we propose a preprocessing technique that introduces fractional offsets on the synaptic delays of neuromorphic graphs in order to break ties. This technique, in turn, enables two graph algorithms: longest shortest path extraction and minimum spanning trees.

Kay, Bill↗

The fusion code XGC: Enabling kinetic study of multi-scale edge turbulent transport in ITER [Book Chapter]

The XGC fusion gyrokinetic code combines state-of-the-art, portable computational and algorithmic technologies to enable complicated multiscale simulations of turbulence and transport dynamics in ITER edge plasma on the largest US open-science computer, the CRAY XK7 Titan, at its maximal heterogeneous capability, which have not been possible before due to a factor of over 10 shortage in the time-to-solution for less than 5 days of wall-clock time for one physics case. Frontier techniques such as nested OpenMP parallelism, adaptive parallel I/O, staging I/O and data reduction using dynamic and asynchronous applications interactions, dynamic repartitioning for balancing computational work in pushing particles and in grid related work, scalable and accurate discretization algorithms for non-linear Coulomb collisions, and communication-avoiding subcycling technology for pushing particles on both CPUs and GPUs are also utilized to dramatically improve the scalability and time-to-solution, hence enabling the difficult kinetic ITER edge simulation on a present-day leadership class computer.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

RMC - A Monte Carlo code for reactor physics analysis

A new Monte Carlo neutron transport code RMC has been being developed by Department of Engineering Physics, Tsinghua University, Beijing as a tool for reactor physics analysis on high-performance computing platforms. To meet the requirements of reactor analysis, RMC now has such functions as criticality calculation, fixed-source calculation, burnup calculation and kinetics simulations. Some techniques for geometry treatment, new burnup algorithm, source convergence acceleration, massive tally and parallel calculation, and temperature dependent cross sections processing are researched and implemented in RMC to improve the efficiency. Validation results of criticality calculation, burnup calculation, source convergence acceleration, tallies performance and parallel performance shown in this paper prove the capabilities of RMC in dealing with reactor analysis problems with good performances. (authors)

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

Reconstructing householder vectors from Tall-Skinny QR

The Tall-Skinny QR (TSQR) algorithm is more communication efficient than the standard Householder algorithm for QR decomposition of matrices with many more rows than columns. However, TSQR produces a different representation of the orthogonal factor and therefore requires more software development to support the new representation. Further, implicitly applying the orthogonal factor to the trailing matrix in the context of factoring a square matrix is more complicated and costly than with the Householder representation. We show how to perform TSQR and then reconstruct the Householder vector representation with the same asymptotic communication efficiency and little extra computational cost. We demonstrate the high performance and numerical stability of this algorithm both theoretically and empirically. The new Householder reconstruction algorithm allows us to design more efficient parallel QR algorithms, with significantly lower latency cost compared to Householder QR and lower bandwidth and latency costs compared with Communication-Avoiding QR (CAQR) algorithm. Experiments on supercomputers demonstrate the benefits of the communication cost improvements: in particular, our experiments show substantial improvements over tuned library implementations for tall-and-skinny matrices. Furthermore, we also provide algorithmic improvements to the Householder QR and CAQR algorithms, and we investigate several alternatives to the Householder reconstruction algorithm that sacrifice guarantees on numerical stability in some cases in order to obtain higher performance.

97 MATHEMATICS AND COMPUTING↗

Parallelized domain decomposition for multi-dimensional Lagrangian random walk mass-transfer particle tracking schemes

Lagrangian particle tracking schemes allow a wide range of flow and transport processes to be simulated accurately, but a major challenge is numerically implementing the inter-particle interactions in an efficient manner. This article develops a multi-dimensional, parallelized domain decomposition (DDC) strategy for mass-transfer particle tracking (MTPT) methods in which particles exchange mass dynamically. We show that this can be efficiently parallelized by employing large numbers of CPU cores to accelerate run times. In order to validate the approach and our theoretical predictions we focus our efforts on a well-known benchmark problem with pure diffusion, where analytical solutions in any number of dimensions are well established. In this work, we investigate different procedures for “tiling” the domain in two and three dimensions (2-D and 3-D), as this type of formal DDC construction is currently limited to 1-D. An optimal tiling is prescribed based on physical problem parameters and the number of available CPU cores, as each tiling provides distinct results in both accuracy and run time. We further extend the most efficient technique to 3-D for comparison, leading to an analytical discussion of the effect of dimensionality on strategies for implementing DDC schemes. Increasing computational resources (cores) within the DDC method produces a trade-off between inter-node communication and on-node work. For an optimally subdivided diffusion problem, the 2-D parallelized algorithm achieves nearly perfect linear speedup in comparison with the serial run-up to around 2700 cores, reducing a 5 h simulation to 8 s, while the 3-D algorithm maintains appreciable speedup up to 1700 cores.

97 MATHEMATICS AND COMPUTING↗

Frameworks, Algorithms, and Scalable Technologies for Mathematics (FASTMath) SciDAC Institute

The FASTMath SciDAC Institute addressed two key challenges that application scientists faced at the beginning of SciDAC-3. First, FASTMath helped them continue to improve the quality of their simulations by increasing accuracy and reliability of both their software and algorithms. Second, FASTMath helped them adapt their computations to make effective use of high-end computing facilities acquired by DOE over the past five years. This required the development of new mathematical algorithms that were appropriate for the physics problems being solved, implementations that scaled to million-way parallelism, and software that effectively leveraged both distributed memory and on-node parallelism. The Rensselaer Polytechnic Institute team’s efforts focused on the unstructured mesh technologies developed by FASTMath.

97 MATHEMATICS AND COMPUTING↗

Computer Science Research Needs for Parallel Discrete Event Simulation (PDES)

Historically, scientific computing efforts have demonstrated the clear need for, and effective use of, supercomputing with traditional time-stepped simulations. Nevertheless, there are several areas in the mission spaces of the U.S. Department of Energy and other agencies waiting to tap advanced computing research using a different, discrete event style of modeling, simulation, and analysis. These span a wide spectrum of applications including energy grid resilience, urban planning and policy, transportation science, building technologies, emergency response and planning, environmental impact analysis, computational epidemiology, Internet communications, cyber security, and cyber-physical systems, to name only a few. Even within traditional scientific applications, the role of discrete event modes of execution is increasing in the form of new event-based mathematical solvers such as quantized state integration methods and discrete-continuous hybrid system solvers. Co-design of advanced supercomputing hardware systems is another area that exploits discrete event simulation at its core for effective analyses. Complex systems, entity behaviors and interconnections play a significant role in all these applications, which are mapped to large-scale models with discrete event formulations. To make advancements in all the aforementioned scientific areas, many technical aspects need to be more thoroughly studied and deeply understood in parallel discrete event simulation (PDES). The unique dynamics inherent in a discrete event modeling approach, by their very nature, intersect and influence the entire stack of the computing system, including (a) the unique nature of the instruction sets exercised in PDES workloads without a predominance of high-precision floating point operations, (b) virtual time-constrained multi-threaded execution of many logical processes per processor, (c) extremely variable and difficult to predict network traffic characteristics, (d) interfaces and inter-dependencies with machine learning and artificial intelligence codes at higher software layers, and (e) highly challenging load balancing needs, especially in effectively accounting for accelerated/extremely heterogeneous computing in current and future high-performance computing systems. Efficient and accurate parallel execution of PDES workloads is also dominated by challenges in dealing with their asynchronous concurrency fundamentally present at the model level. Conservative synchronization, optimistic/speculative synchronization, and their hybrid schemes open new questions in fundamental computer science with respect to reversibility of computation and prediction (lookahead) of behaviors inherent within model codes. On the implementation front, there are relatively few scalable, general-purpose parallel discrete event simulators in the world, and even fewer have been studied on emerging hardware platforms. To enable scientific advances using PDES, the research needs in computer science must also be pursued and met in the intersection of the algorithmic and hardware-aware aspects of scalable PDES engines. This report is aimed at capturing a computer science-oriented view of this important area of research in PDES, presenting a sample of important applications with their inherent discrete event technology elements. Needs are outlined in core areas of parallel discrete event research as well as cross-cutting directions in computer science research that positively impact scientific advancements across several important application areas. A selection of priority research opportunities in advanced computing for PDES is identified to serve as reference for key research topics and their order of importance for scientific advancements.

97 MATHEMATICS AND COMPUTING↗

HPC4Mobilty w/ UCB

The purpose of this project is to examine the energy impact of urban-scale traffic for the Los Angeles Basin by developing and implementing a scalable traffic assignment model. An energy optimization function will be posed and when integrated into the optimization code for travel assignment it can be mathematically proven to converge. The energy optimization function can then be compared to the typical travel time optimization that is traditionally used in traffic assignment models. The analysis will begin with static traffic assignment models with the routing for all origin and destinations computed in parallel on high performance computing facilities. Convergence of the numerical methods rely on the solution of convex programs (or extensions of these). This step will mostly consist of demonstrating the ability to parallelize the Frank Wolfe algorithm on various platforms. This work will contribute to LBNL’s efforts to develop new processes, analytical tools, program designs, and business models to advance the state of the art in next-generation sustainable transportation solutions.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

Parallel FETI‐DP algorithm for efficient simulation of large‐scale EM problems

Summary An efficient parallelization of the dual‐primal finite‐element tearing and interconnecting (FETI‐DP) algorithm is presented for large‐scale electromagnetic simulations. As a nonoverlapping domain decomposition method, the FETI‐DP algorithm formulates a global interface problem, whose iterative solution is accelerated with a solution of a global corner problem. To achieve a good load balance for parallel computation, the original computational domain is decomposed into subdomains with similar sizes and shapes. The subdomains are then distributed to processors based on their close proximity to minimize inter‐processor communication. The parallel generalized minimal residual method, enhanced with the iterative classical Gram‐Schmidt orthogonalization scheme to reduce global communication, is adopted to solve the global interface problem with a fast convergence rate. The global corner‐related coarse problem is solved iteratively with a parallel communication‐avoiding biconjugate gradient stabilized method to minimize global communication, and its convergence is accelerated by a diagonal preconditioner constructed from the coarse system matrix. To alleviate neighboring communication overhead, the non‐blocking communication approach is employed in both generalized minimal residual and communication‐avoiding biconjugate gradient stabilized iterative solutions. Three numerical examples are presented to demonstrate the accuracy, scalability, and capability of the proposed parallel FETI‐DP algorithm for electromagnetic modeling of general objects and antenna arrays. Copyright © 2016 John Wiley & Sons, Ltd.

Zhang, Kedi↗

Exponential Runge-Kutta Parareal for non-diffusive equations

Parareal is a well-known parallel-in-time algorithm that combines a coarse and fine propagator within a parallel iteration. It allows for large-scale parallelism that leads to significantly reduced computational time compared to serial time-stepping methods. However, like many parallel-in-time methods it can fail to converge when applied to non-diffusive equations such as hyperbolic systems or dispersive nonlinear wave equations. Here, this paper explores the use of exponential integrators within the Parareal iteration. Exponential integrators are particularly interesting candidates for Parareal because of their ability to resolve fast-moving waves, even at the large stepsizes used by coarse propagators. This work begins with an introduction to exponential Parareal integrators followed by several motivating numerical experiments involving the nonlinear Schrödinger equation. These experiments are then analyzed using linear analysis that approximates the stability and convergence properties of the exponential Parareal iteration on nonlinear problems. The paper concludes with two additional numerical experiments involving the dispersive Kadomtsev-Petviashvili equation and the hyperbolic Vlasov-Poisson equation. These experiments demonstrate that exponential Parareal methods offer improved time-to-solution compared to serial exponential integrators when solving certain non-diffusive equations.

97 MATHEMATICS AND COMPUTING↗

GPU acceleration of Swendsen–Wang dynamics

When simulating a lattice system near its critical temperature, local algorithms for modeling the system’s evolution can introduce very large autocorrelation times into sampled data. Here, this critical slowing down places restrictions on the analysis that can be completed in a timely manner of the behavior of systems around the critical point. Because it is often desirable to study such systems around this point, a new algorithm must be introduced. Therefore, we turn to cluster algorithms, such as the Swendsen–Wang algorithm and the Wolff clustering algorithm. They incorporate global updates which generate new lattice configurations with little correlation to previous states, even near the critical point. We look to accelerate the rate at which these algorithm are capable of running by implementing and benchmarking a parallel implementation of each algorithm designed to run on GPUs under NVIDIA’s CUDA framework. A 17 and 90 fold increase in the computational rate was, respectively, experienced when measured against the equivalent algorithm implemented in serial code.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Computational Fluid Dynamics Using the Adaptive Wavelet-Collocation Method

Advancements to the adaptive wavelet-collocation method over the last decade have opened up a number of new possible areas for active research. Volume penalization techniques allow complex immersed boundary conditions to be used with high efficiency for both internal and external flows. Anisotropic methods make it possible to use body-fitted meshes while still taking advantage of the dynamic adaptability properties wavelet-based methods provide. The parallelization of the approach has made it possible to perform large high-resolution simulations of detonation initiation and fluid instabilities to uncover new physical insights that would otherwise be difficult to discover. Other developments include space-time adaptive methods and nonreflecting boundary conditions. This article summarizes the work performed using the adaptive wavelet-collocation method developed by Vasilyev and coworkers over the past decade.

42 ENGINEERING↗

Parallel and interacting stochastic approximation annealing algorithms for global optimisation

We present the parallel and interacting stochastic approximation annealing (PISAA) algorithm, a stochastic simulation procedure for global optimisation, that extends and improves the stochastic approximation annealing (SAA) by using population Monte Carlo ideas. The efficiency of standard SAA algorithm crucially depends on its selfadjusting mechanism which presents stability issues in high dimensional or rugged optimisation problems. The proposed algorithm involves simulating a population of SAA chains that interact each other in a manner that significantly improves the stability of the self-adjusting mechanism and the search for the global optimum in the sampling space, as well as it inherits SAA desired convergence properties when a square-root cooling schedule is used. It can be implemented in parallel computing environments in order to mitigate the computational overhead. As a result, PISAA can address complex optimisation problems that it would be difficult for SAA to satisfactory address. We demonstrate the good performance of the proposed algorithm on challenging applications including Bayesian network learning and protein folding. Our numerical comparisons suggest that PISAA outperforms the simulated annealing, stochastic approximation annealing, and annealing evolutionary stochastic approximation Monte Carlo.

Local trap↗

E4D_RT

Time-lapse ERT imaging for monitoring both natural and engineered subsurface processes has advanced rapidly over the past 15-20 years. However, imaging results generally required a significant amount of manual and computational effort, and therefore were not available while the process was occurring. Although the value of real-time imaging was recognized, several obstacles prevented it's implementation. E4D_RT addresses these obstacles by 1) providing specialized algorithms that negate the need for user intervention, thereby automating the time-lapse data processing steps, 2) linking field data collection systems with parallel supercomputing systems via wireless data transfer link, and 3) addressing the computational burdens by utilizing distributed memory supercomputing resources, thereby enabling rapid data processing and imaging results.

Source record↗

SU-C-BRC-06: OpenCL-Based Cross-Platform Monte Carlo Simulation Package for Carbon Ion Therapy

Purpose: Monte Carlo (MC) simulation is considered to be the most accurate method for calculation of absorbed dose and fundamental physical quantities related to biological effects in carbon ion therapy. Its long computation time impedes clinical and research applications. We have developed an MC package, goCMC, on parallel processing platforms, aiming at achieving accurate and efficient simulations for carbon therapy. Methods: goCMC was developed under OpenCL framework. It supported transport simulation in voxelized geometry with kinetic energy up to 450 MeV/u. Class II condensed history algorithm was employed for charged particle transport with stopping power computed via Bethe-Bloch equation. Secondary electrons were not transported with their energy locally deposited. Energy straggling and multiple scattering were modeled. Production of secondary charged particles from nuclear interactions was implemented based on cross section and yield data from Geant4. They were transported via the condensed history scheme. goCMC supported scoring various quantities of interest e.g. physical dose, particle fluence, spectrum, linear energy transfer, and positron emitting nuclei. Results: goCMC has been benchmarked against Geant4 with different phantoms and beam energies. For 100 MeV/u, 250 MeV/u and 400 MeV/u beams impinging to a water phantom, range difference was 0.03 mm, 0.20 mm and 0.53 mm, and mean dose difference was 0.47%, 0.72% and 0.79%, respectively. goCMC can run on various computing devices. Depending on the beam energy and voxel size, it took 20∼100 seconds to simulate 10{sup 7} carbons on an AMD Radeon GPU card. The corresponding CPU time for Geant4 with the same setup was 60∼100 hours. Conclusion: We have developed an OpenCL-based cross-platform carbon MC simulation package, goCMC. Its accuracy, efficiency and portability make goCMC attractive for research and clinical applications in carbon therapy.

60 APPLIED LIFE SCIENCES↗

Wasatch: An architecture-proof multiphysics development environment using a Domain Specific Language and graph theory

To address the coding and software challenges of modern hybrid architectures, we propose an approach to multiphysics code development for high-performance computing. This approach is based on using a Domain Specific Language (DSL) in tandem with a directed acyclic graph (DAG) representation of the problem to be solved that allows runtime algorithm generation. When coupled with a large-scale parallel framework, the result is a portable development framework capable of executing on hybrid platforms and handling the challenges of multiphysics applications. In addition, we share our experience developing a code in such an environment – an effort that spans an interdisciplinary team of engineers and computer scientists.

97 MATHEMATICS AND COMPUTING↗

Massively parallel and linear-scaling algorithm for second-order Moller–Plesset perturbation theory applied to the study of supramolecular wires

Here, we present a scalable cross-platform hybrid MPI/OpenMP/OpenACC implementation of the Divide–Expand–Consolidate (DEC) formalism with portable performance on heterogeneous HPC architectures. The Divide–Expand–Consolidate formalism is designed to reduce the steep computational scaling of conventional many-body methods employed in electronic structure theory to linear scaling, while providing a simple mechanism for controlling the error introduced by this approximation. Our massively parallel implementation of this general scheme has three levels of parallelism, being a hybrid of the loosely coupled task-based parallelization approach and the conventional MPI +X programming model, where X is either OpenMP or OpenACC. We demonstrate strong and weak scalability of this implementation on heterogeneous HPC systems, namely on the GPU-based Cray XK7 Titan supercomputer at the Oak Ridge National Laboratory. Using the “resolution of the identity second-order Moller–Plesset perturbation theory” (RI-MP2) as the physical model for simulating correlated electron motion, the linear-scaling DEC implementation is applied to 1-aza-adamantane-trione (AAT) supramolecular wires containing up to 40 monomers (2440 atoms, 6800 correlated electrons, 24 440 basis functions and 91 280 auxiliary functions). This represents the largest molecular system treated at the MP2 level of theory, demonstrating an efficient removal of the scaling wall pertinent to conventional quantum many-body methods.

97 MATHEMATICS AND COMPUTING↗