High level algorithmic auto-tuning for scientific applications

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 2012.Cataloged from PDF version of thesis.Includes bibliographical references (p. 102-107).In this thesis, we describe a new classification of auto-tuning methodologies spanning from low-level optimizations to high-level algorithmic tuning. This classification spectrum of auto-tuning methods encompasses the space of tuning parameters from low-level optimizations (such as block sizes, iteration ordering, vectorization, etc.) to high-level algorithmic choices (such as whether to use an iterative solver or a direct solver). We present and analyze four novel auto-tuning systems that incorporate several techniques that fall along a spectrum from the low-level to the high-level: i) a multiplatform, auto-tuning parallel code generation framework for generalized stencil loops, ii) an auto-tunable algorithm for solving dense triangular systems, iii) an auto-tunable multigrid solver for sparse linear systems, and iv) tuned statistical regression techniques for fine-tuning wind forecasts and resource estimations to assist in the integration of wind resources into the electrical grid. We also include a project assessment report for a wind turbine installation for the City of Cambridge to highlight an area of application (wind prediction and resource assessment) where these computational auto-tuning techniques could prove useful in the future.by Cy P. Chan.Ph.D

Development of an Unsteady Aeroelastic Solver for the Analysis of Modern Turbomachinery Designs

Developers of aircraft gas turbine engines continually strive for greater efficiency and higher thrust-to-weight ratio designs. To meet these goals, advanced designs generally feature thin, low aspect airfoils, which offer increased performance but are highly susceptible to flow-induced vibrations. As a result, High Cycle Fatigue (HCF) has become a universal problem throughout the gas turbine industry and unsteady aeroelastic computational models are needed to predict and prevent these problems in modern turbomachinery designs. This research presents the development of a 3D unsteady aeroelastic solver for turbomachinery applications. To accomplish this, a well established turbomachinery Computational Fluid Dynamics (CFD) code called Corsair is loosely coupled to the commercial Computational Structural Solver (CSD) Ansys® through the use of a Fluid Structure Interaction (FSI) module. Significant modifications are made to Corsair to handle the integration of the FSI module and improve overall performance. To properly account for fluid grid deformations dictated by the FSI module, temporal based coordinate transformation metrics are incorporated into Corsair. Wall functions with user specified surface roughness are also added to reduce fluid grid density requirements near solid surfaces. To increase overall performance and ease of future modifications to the source code, Corsair is rewritten in Fortran 90 with an emphasis on reducing memory usage and improving source code readability and structure. As part of this effort, the shared memory data structure of Corsair is replaced with a distributed model. Domain decomposition of individual grids in the radial direction is also incorporated into Corsair for additional parallelization, along with a utility to automate this process in an optimal manner based on user input. This additional parallelization helps offset the inability to use the fine grain mp-threads parallelization in the original code on non-distributed memory architectures such as the PC Beowulf cluster used for this research. Conversion routines and utilities are created to handle differences in grid formats between Corsair and the FSI module. The resulting aeroelastic solver is tested using two simplified configurations. First, the well understood case of a flexible cylinder in cross flow is studied with the natural frequency of the cylinder set to the shedding frequency of the Von Karman streets. The cylinder is self excited and thus demonstrates the correct exchange of energy between the fluid and structural models. The second test case is based on the fourth standard configuration and demonstrates the ability of the solver to predict the dominant vibrational modes of an aeroelastic turbomachinery blade. For this case, a single blade from the fourth standard configuration is subjected to a step function from zero loading to the converged flow solution loading in order to excite the structural modes of the blade. These modes are then compared to those obtained from an in vacuo Ansys® analysis with good agreement between the two

A SEISMOLOGIC STUDY OF THE NORTHERN MISSISSIPPI EMBAYMENT

Part 1: Crustal structure in the New Madrid Seismic Zone (NMSZ) is investigated through a detailed study of explosion data obtained from the Embayment Seismic Excitation Experiment. The data show a distinct anisotropy in distance attenuation for both P and S waves in the range from 0 to 200km distance. Waves that propagate northward from the 1,134kg Marked Tree, Arkansas, explosion attenuate quickly with distance until a range of about 100km from the source where high-amplitude, high-phase velocity critical reflections from the boundary between the middle crust and rift pillow structure produce high amplitude waves. Propagation southward from the 2,268kg Mooring, Tennessee blast shows less distance attenuation compared to northward propagation. Reflections from the middle crust-lower crust boundary occur but do not significantly increase in amplitude with distance and travel with slower apparent phase velocity than observed for the northward propagation data set. A smooth velocity model is developed using a stabilized Weichert-Herglotz travel time inversion using first arrival travel times. Then an inversion using the travel time of both direct and middle crustal reflected waves is developed to obtain a 2D inhomogeneous-layered isotropic crustal model. The result reveals that there is a significant southwest dip to the top of the middle crust interface in the vicinity of the NMSZ, consistent with previously inferred changes in the thickness of the rift pillow model. This 2D feature characterizes the local wave propagation along the Reelfoot Rift and demonstrates the need for an improvement of the current Central United States velocity model.Part 2: Obtaining reliable empirical Greens functions (EGFs) from ambient noise by seismic interferometry requires homogenously distributed noise sources. However, it is difficult to attain this condition since ambient noise data usually contains highly correlated signals from earthquakes or other transient sources from human activities. Removing these transient signals is one of the most essential steps in the whole data processing flow to obtain EGFs. We propose to use a denoising method based on the continuous wavelet transform to achieve this goal. The noise level is estimated in the wavelet domain for each scale by determing the 99% confidence level of the empirical probability density function of the noise wavelet coefficients. The correlated signals are then removed by an efficient soft thresholding method. The same denoising algorithm is also applied to remove the noise in the final stacked cross-correlogram. A complete data processing workflow is provided with the overall data processing procedure divided into four stages: (1) single station data preparation, (2) removal of earthquakes and other transient signals in the seismic record, (3) spectrum whitening, cross-correlation and temporal stacking, and (4) remove the noise in the stacked cross-correlogram to deliver the final EGF. The whole process is automated to make it accessible for large datasets. Synthetic data constructed with a recorded earthquake and recorded ambient noise is used to test the denoising method. We then apply the new processing workflow to data recorded by the USArray Transportable Array stations near the New Madrid Seismic Zone where many seismic events and transient signals are observed. We compare the EGFs calculated from our workflow with commonly used time domain normalization method and our results show improved signal-to-noise ratios. The new workflow can deliever reliable EGFs for further studies.Part 3: We incorporate seismic ambient noise data recorded by different temporary and permanent broadband stations around the northern Mississippi Embayment from 1990 to 2018 to develop a crustal shear wave velocity (Vs) model for this area with full waveform ambient noise tomography. Empirical Greens functions at periods between 8 and 40s for all the possible pairs of stations are extracted by using a new seismic ambient noise data processing flow based on the continuous wavelet transform. Synthetic waveforms are then calculated through a heterogeneous Earth model using a GPU-enabled collocated finite-difference code. The cross-correlation time shifts between the synthetic waveforms and the extracted empirical Greens functions are used to construct the velocity updated kernel by using the adjoint method. Starting from the Central United States Velocity Model, the shear wave velocity model is then iteratively updated with the Vs kernel calculated in each iteration. Checkerboard tests show that perturbations in the top 30km of the crust are well recovered but amplitude recovery ability gradually decreases for deeper structure. We find that velocity lows characterize the Reelfoot Rift Graben and Rough Creek Graben separated by a high velocity crust. High velocity anomalies are observed under the Ozark Uplift and Paducah Gravity Lineament. A low velocity area previously interpreted as the Missouri Batholith is observed between them. A massive high velocity body in the southeast Mississippi Embayment is observed and is explained by the faulting as well as partly mafic intrusion. The Ouachita-Appalachian Thrust Front is clearly observed with a thinner crustal layer underneath. The rift pillow is well observed in the final tomography model along the Reelfoot Rift in the lower crust. The final inverted velocity model is consistent with local geological features and can be used for other seismological studies such as earthquake source determination and earthquake hazard assessment

the plenoptic sensor

In this thesis, we will introduce the innovative concept of a plenoptic sensor that can determine the phase and amplitude distortion in a coherent beam, for example a laser beam that has propagated through the turbulent atmosphere.. The plenoptic sensor can be applied to situations involving strong or deep atmospheric turbulence. This can improve free space optical communications by maintaining optical links more intelligently and efficiently. Also, in directed energy applications, the plenoptic sensor and its fast reconstruction algorithm can give instantaneous instructions to an adaptive optics (AO) system to create intelligent corrections in directing a beam through atmospheric turbulence. The hardware structure of the plenoptic sensor uses an objective lens and a microlens array (MLA) to form a mini “Keplerian” telescope array that shares the common objective lens. In principle, the objective lens helps to detect the phase gradient of the distorted laser beam and the microlens array (MLA) helps to retrieve the geometry of the distorted beam in various gradient segments. The software layer of the plenoptic sensor is developed based on different applications. Intuitively, since the device maximizes the observation of the light field in front of the sensor, different algorithms can be developed, such as detecting the atmospheric turbulence effects as well as retrieving undistorted images of distant objects. Efficient 3D simulations on atmospheric turbulence based on geometric optics have been established to help us perform optimization on system design and verify the correctness of our algorithms. A number of experimental platforms have been built to implement the plenoptic sensor in various application concepts and show its improvements when compared with traditional wavefront sensors. As a result, the plenoptic sensor brings a revolution to the study of atmospheric turbulence and generates new approaches to handle turbulence effect better

Development of Micro-Macro Continuum-Discontinuum Coupled Numerical Method

A micro-macro and continuum-discontinuum coupled model and corresponding computer codes are developed in this thesis for rock dynamics study. Firstly, a new micromechanical model for describing the elastic continuum based on the underlying microstructure of material is proposed. The model provides a more general description of material than linear elasticity. Then, a numerical model Distinct Lattice Spring Model (DLSM) is developed based on the RMIB theory. The new proposed model has the advantages of being meshless, and automatic continuum description through underlying discontinuum structure and directly using macroscopic elastic parameters. Following this, the multi-scale DLSM (m-DLSM) is proposed to combine DLSM and NMM. The proposed model uses a tri-layer structure and the macro model can be automatically released into micro model during calculation. Forth ward, the ability of DLSM on modeling dynamic failure is studied. A damage based micro constitutive law is developed. Relationships between the micro constitutive parameters and the macro mechanical parameters of material are provided. The micro parameters can directly be obtained from macro experimental results, i.e., tensile strength and fracture energy, through these equations. Moreover, the ability of DLSM on modeling wave propagation is enhanced and verified. Non-reflection boundary condition and methods to represent discontinuity in DLSM are developed. Finally, the parallelization of DLSM and 2D implicit DLSM are introduced. The main achievements of the whole PhD work and future research works are summarized and prospected in the conclusion part of the thesis

Nonlinear solid mechanics analysis using the parallel selective element-free Galerkin method

A variety of meshless methods have been developed in the last fifteen years with an intention to solve practical engineering problems, but are limited to small academic problems due to associated high computational cost as compared to the standard finite element methods (FEM). The main objective of this thesis is the development of an efficient and accurate algorithm based on meshless methods for the solution of problems involving both material and geometrical nonlinearities, which are of practical importance in many engineering applications, including geomechanics, metal forming and biomechanics. One of the most commonly used meshless methods, the element-free Galerkin method (EFGM) is used in this research, in which maximum entropy shape functions (max-ent) are used instead of the standard moving least squares shape functions, which provides direct imposition of the essential boundary conditions. Initially, theoretical background and corresponding computer implementations of the EFGM are described for linear and nonlinear problems. The Prandtl-Reuss constitutive model is used to model elasto-plasticity, both updated and total Lagrangian formulations are used to model finite deformation and consistent or algorithmic tangent is used to allow the quadratic rate of asymptotic convergence of the global Newton-Raphson algorithm. An adaptive strategy is developed for the EFGM for two- and three-dimensional nonlinear problems based on the Chung & Belytschko error estimation procedure, which was originally proposed for linear elastic problems. A new FE-EFGM coupling procedure based on max-ent shape functions is proposed for linear and geometrically nonlinear problems, in which there is no need of interface elements between the FE and EFG regions or any other special treatment, as required in the most previous research. The proposed coupling procedure is extended to become adaptive FE-EFGM coupling for two- and three-dimensional linear and nonlinear problems, in which the Zienkiewicz & Zhu error estimation procedure with the superconvergent patch recovery method for strains and stresses recovery are used in the FE region of the problem domain, while the Chung & Belytschko error estimation procedure is used in the EFG region of the problem domain. Parallel computer algorithms based on distributed memory parallel computer architecture are also developed for different numerical techniques proposed in this thesis. In the parallel program, the message passing interface library is used for inter-processor communication and open-source software packages, METIS and MUMPS are used for the automatic domain decomposition and solution of the final system of linear equations respectively. Separate numerical examples are presented for each algorithm to demonstrate its correct implementation and performance, and results are compared with the corresponding analytical or reference results

The exploitation of acoustic-to-seismic coupling for the determination of soil properties

Laboratory measurements of three predicted wave types (two compressional or P-waves and one shear S-wave) have been made in artificial soils. The Type-I P and S-wave are predicted to be most sensitive to the macroscopic elastic properties of the frame, whilst the Type II P-wave is predicted to be most sensitive to the hydrodynamic material properties. A loudspeaker source has been used for the preferential excitation of the Type II P-wave whilst preferential excitement of the Type-I P-wave has been accomplished using a mechanical shaker. Probe microphone measurements of the Type-II wave allowed the flow resistivity and tortuosity of the material to be determined using a rigid frame model, whilst deduction of elastic moduli has been made from signals received at buried geophones. It has been shown that microphone signals include Type-I P-wave energy in a high flow resistivity soil. Acoustically deduced soil properties are consistent with mechanically derived values. A systematic investigation of outdoor measurements of acoustic-to-seismic coupling ratio has been made. From the measurements, it has been found that the geophone-ground coupling has a great effect upon the measured coupling ratio. In-situ calibration methods have been developed to overcome this problem. whilst the novel use of a Laser Doppler Vibrometer has been proposed to provide a completely non-invasive method of measuring motion in soils. The measured coupling ratio has been compared with theoretical predictions, using a modified Bio-Sto11 formulation. The model can be used to predict values of flow resistivity, porosity, bulk and shear moduli and layer depths. Reasonable agreement has been obtained between the model and data. Procedures that exploit acoustic-to-seismic coupling data and models to determine soil properties have been developed and used to measure the soil properties of friable agricultural soils where more standard investigation techniques have proved unsuitable