Accelerating scientific codes by performance and accuracy modeling

Scientific software is often driven by multiple parameters that affect both accuracy and performance. Since finding the optimal configuration of these parameters is a highly complex task, it extremely common that the software is used suboptimally. In a typical scenario, accuracy requirements are imposed, and attained through suboptimal performance. In this paper, we present a methodology for the automatic selection of parameters for simulation codes, and a corresponding prototype tool. To be amenable to our methodology, the target code must expose the parameters affecting accuracy and performance, and there must be formulas available for error bounds and computational complexity of the underlying methods. As a case study, we consider the particle-particle particle-mesh method (PPPM) from the LAMMPS suite for molecular dynamics, and use our tool to identify configurations of the input parameters that achieve a given accuracy in the shortest execution time. When compared with the configurations suggested by expert users, the parameters selected by our tool yield reductions in the time-to-solution ranging between 10% and 60%. In other words, for the typical scenario where a fixed number of core-hours are granted and simulations of a fixed number of timesteps are to be run, usage of our tool may allow up to twice as many simulations. While we develop our ideas using LAMMPS as computational framework and use the PPPM method for dispersion as case study, the methodology is general and valid for a range of software tools and methods

Accelerating moderately stiff chemical kinetics in reactive-flow simulations using GPUs

The chemical kinetics ODEs arising from operator-split reactive-flow simulations were solved on GPUs using explicit integration algorithms. Nonstiff chemical kinetics of a hydrogen oxidation mechanism (9 species and 38 irreversible reactions) were computed using the explicit fifth-order Runge-Kutta-Cash-Karp method, and the GPU-accelerated version performed faster than single- and six-core CPU versions by factors of 126 and 25, respectively, for 524,288 ODEs. Moderately stiff kinetics, represented with mechanisms for hydrogen/carbon-monoxide (13 species and 54 irreversible reactions) and methane (53 species and 634 irreversible reactions) oxidation, were computed using the stabilized explicit second-order Runge-Kutta-Chebyshev (RKC) algorithm. The GPU-based RKC implementation demonstrated an increase in performance of nearly 59 and 10 times, for problem sizes consisting of 262,144 ODEs and larger, than the single- and six-core CPU-based RKC algorithms using the hydrogen/carbon-monoxide mechanism. With the methane mechanism, RKC-GPU performed more than 65 and 11 times faster, for problem sizes consisting of 131,072 ODEs and larger, than the single- and six-core RKC-CPU versions, and up to 57 times faster than the six-core CPU-based implicit VODE algorithm on 65,536 ODEs. In the presence of more severe stiffness, such as ethylene oxidation (111 species and 1566 irreversible reactions), RKC-GPU performed more than 17 times faster than RKC-CPU on six cores for 32,768 ODEs and larger, and at best 4.5 times faster than VODE on six CPU cores for 65,536 ODEs. With a larger time step size, RKC-GPU performed at best 2.5 times slower than six-core VODE for 8192 ODEs and larger. Therefore, the need for developing new strategies for integrating stiff chemistry on GPUs was discussed.Comment: 27 pages, LaTeX; corrected typos in Appendix equations A.10 and A.1

Performance Comparison of a Vertical Axis Wind Turbine using Commercial and Open Source Computational Fluid Dynamics based Codes

Computational Fluid Dynamics (CFD) is a very effective tool to analyse the flow characteristics within and around different mechanical artifacts such as automotive vehicles, turbomachines etc. CFD based analysis provides beneficial information about the flow behavior within a component, hence reducing the costs involved in the design process of that component. This has led the research-ers to develop an Open Source CFD code, commonly known as Open Field Opera-tion and Manipulation, or OpenFOAM. The development of OpenFOAM has made scientific research in the field of fluid dynamics available for almost no cost. Designers who rely on commercial CFD packages are hesitant on using Open Source CFD codes because of accuracy. They need to be convinced by proving its simulation capability as compared to any commercial CFD package. Hence, this study investigate the flow phenomenon in the vicinity of a Vertical Axis Wind Turbine (VAWT), using such open source code combinations that yields reasona-bly accurate results, which can be compared against any commercial CFD code

Automatic surrogate model type selection during the optimization of expensive black-box problems

The use of Surrogate Based Optimization (SBO) has become commonplace for optimizing expensive black-box simulation codes. A popular SBO method is the Efficient Global Optimization (EGO) approach. However, the performance of SBO methods critically depends on the quality of the guiding surrogate. In EGO the surrogate type is usually fixed to Kriging even though this may not be optimal for all problems. In this paper the authors propose to extend the well-known EGO method with an automatic surrogate model type selection framework that is able to dynamically select the best model type (including hybrid ensembles) depending on the data available so far. Hence, the expected improvement criterion will always be based on the best approximation available at each step of the optimization process. The approach is demonstrated on a structural optimization problem, i.e., reducing the stress on a truss-like structure. Results show that the proposed algorithm consequently finds better optimums than traditional kriging-based infill optimization