ATCOM: Automatically tuned collective communication system for SMP clusters.

Conventional implementations of collective communications are based on point-to-point communications, and their optimizations have been focused on efficiency of those communication algorithms. However, point-to-point communications are not the optimal choice for modern computing clusters of SMPs due to their two-level communication structure. In recent years, a few research efforts have investigated efficient collective communications for SMP clusters. This dissertation is focused on platform-independent algorithms and implementations in this area;There are two main approaches to implementing efficient collective communications for clusters of SMPs: using shared memory operations for intra-node communications, and over-lapping inter-node/intra-node communications. The former fully utilizes the hardware based shared memory of an SMP, and the latter takes advantage of the inherent hierarchy of the communications within a cluster of SMPs. Previous studies focused on clusters of SMP from certain vendors. However, the previously proposed methods are not portable to other systems. Because the performance optimization issue is very complicated and the developing process is very time consuming, it is highly desired to have self-tuning, platform-independent implementations. As proven in this dissertation, such an implementation can significantly outperform the other point-to-point based portable implementations and some platform-specific implementations;The dissertation describes in detail the architecture of the platform-independent implementation. There are four system components: shared memory-based collective communications, overlapping mechanisms for inter-node and intra-node communications, a prediction-based tuning module and a micro-benchmark based tuning module. Each component is carefully designed with the goal of automatic tuning in mind

Modeling Complex Material Systems Using Stochastic Reconstruction and Lattice Particle Simulation

abstract: In this dissertation, three complex material systems including a novel class of hyperuniform composite materials, cellularized collagen gel and low melting point alloy (LMPA) composite are investigated, using statistical pattern characterization, stochastic microstructure reconstruction and micromechanical analysis. In Chapter 1, an introduction of this report is provided, in which a brief review is made about these three material systems. In Chapter 2, detailed discussion of the statistical morphological descriptors and a stochastic optimization approach for microstructure reconstruction is presented. In Chapter 3, the lattice particle method for micromechanical analysis of complex heterogeneous materials is introduced. In Chapter 4, a new class of hyperuniform heterogeneous material with superior mechanical properties is investigated. In Chapter 5, a bio-material system, i.e., cellularized collagen gel is modeled using correlation functions and stochastic reconstruction to study the collective dynamic behavior of the embed tumor cells. In chapter 6, LMPA soft robotic system is generated by generalizing the correlation functions and the rigidity tunability of this smart composite is discussed. In Chapter 7, a future work plan is presented.Dissertation/ThesisDoctoral Dissertation Materials Science and Engineering 201

Low-overhead scheduling for improving performance of scientific applications

Application performance can degrade significantly due to node-local load imbalances during application execution on a large number of SMP nodes. These imbalances can arise from the machine, operating system, or the application itself. Although dynamic load balancing within a node can mitigate imbalances, such load balancing is challenging because of its impact to data movement and synchronization overhead. We developed a series of scheduling strategies that mitigate imbalances without incurring high overhead. Our strategies provide performance gains for various HPC codes, and perform better than widely known scheduling strategies such as OpenMP guided scheduling. Our developed scheme and methodology allows for scaling applications to next-generation clusters of SMPs with minimal application programmer intervention. We expect these techniques to be increasingly useful for future machines approaching exascale

A Survey on Compiler Autotuning using Machine Learning

Since the mid-1990s, researchers have been trying to use machine-learning based approaches to solve a number of different compiler optimization problems. These techniques primarily enhance the quality of the obtained results and, more importantly, make it feasible to tackle two main compiler optimization problems: optimization selection (choosing which optimizations to apply) and phase-ordering (choosing the order of applying optimizations). The compiler optimization space continues to grow due to the advancement of applications, increasing number of compiler optimizations, and new target architectures. Generic optimization passes in compilers cannot fully leverage newly introduced optimizations and, therefore, cannot keep up with the pace of increasing options. This survey summarizes and classifies the recent advances in using machine learning for the compiler optimization field, particularly on the two major problems of (1) selecting the best optimizations and (2) the phase-ordering of optimizations. The survey highlights the approaches taken so far, the obtained results, the fine-grain classification among different approaches and finally, the influential papers of the field.Comment: version 5.0 (updated on September 2018)- Preprint Version For our Accepted Journal @ ACM CSUR 2018 (42 pages) - This survey will be updated quarterly here (Send me your new published papers to be added in the subsequent version) History: Received November 2016; Revised August 2017; Revised February 2018; Accepted March 2018

Towards Automatic and Adaptive Optimizations of MPI Collective Operations

Message passing is one of the most commonly used paradigms of parallel programming. Message Passing Interface, MPI, is a standard used in scientific and high-performance computing. Collective operations are a subset of MPI standard that deals with processes synchronization, data exchange and computation among a group of processes. The collective operations are commonly used and can be application performance bottleneck. The performance of collective operations depends on many factors, some of which are the input parameters (e.g., communicator and message size); system characteristics (e.g., interconnect type); the application computation and communication pattern; and internal algorithm parameters (e.g., internal segment size). We refer to an algorithm and its internal parameters as a method. The goal of this dissertation is a performance improvement of MPI collective operations and applications that use them. In our framework, during a collective call, a system-specific decision function is invoked to select the most appropriate method for the particular collective instance. This dissertation focuses on automatic techniques for system-specific decision function generation. Our approach takes the following steps: first, we collect method performance information on the system of interest; second, we analyze this information using parallel communication models, graphical encoding methods, and decision trees; third, based on the previous step, we automatically generate the system-specific decision function to be used at run-time. In situation when a detailed performance measurement is not feasible, method performance models can be used to supplement the measured method performance information. We build and evaluate parallel communication models of 35 different collective algorithms. These models are built on top of the three commonly used point-to-point communication models, Hockney, LogGP, and PLogP.We use the method performance information on a system to build quadtrees and C4.5 decision trees of variable sizes and accuracies. The collective method selection functions are then generated automatically from these trees. Our experiments show that quadtrees of three or four levels are often enough to approximate experimentally optimal decision with a small mean performance penalty (less than 10%). The C4.5 decision trees are even more accurate (with mean performance penalty of less than 5%). The size and accuracy of C4.5 decision trees can be further improved with use of appropriate composite attributes (such as “total message size”, or “even communicator size”.) Finally, we apply these techniques to tune the collective operations on the Grig cluster at the University of Tennessee and to improve an application performance on the Cray XT4 system at Oak Ridge National Laboratory. The tuned collective is able to achieve more than 40% mean performance improvement over the native broadcast implementation. Using the platform-specific reduce on Cray XT4 lead to 10% improvement in the overall application performance. Our results show that the methods we explored are both applicable and effective for the system-specific optimizations of collective operations and are a right step toward automatically tunable, adaptive, MPI collectives

Autotuning wavefront patterns for heterogeneous architectures

Manual tuning of applications for heterogeneous parallel systems is tedious and complex. Optimizations are often not portable, and the whole process must be repeated when moving to a new system, or sometimes even to a different problem size. Pattern based parallel programming models were originally designed to provide programmers with an abstract layer, hiding tedious parallel boilerplate code, and allowing a focus on only application specific issues. However, the constrained algorithmic model associated with each pattern also enables the creation of pattern-specific optimization strategies. These can capture more complex variations than would be accessible by analysis of equivalent unstructured source code. These variations create complex optimization spaces. Machine learning offers well established techniques for exploring such spaces. In this thesis we use machine learning to create autotuning strategies for heterogeneous parallel implementations of applications which follow the wavefront pattern. In a wavefront, computation starts from one corner of the problem grid and proceeds diagonally like a wave to the opposite corner in either two or three dimensions. Our framework partitions and optimizes the work created by these applications across systems comprising multicore CPUs and multiple GPU accelerators. The tuning opportunities for a wavefront include controlling the amount of computation to be offloaded onto GPU accelerators, choosing the number of CPU and GPU threads to process tasks, tiling for both CPU and GPU memory structures, and trading redundant halo computation against communication for multiple GPUs. Our exhaustive search of the problem space shows that these parameters are very sensitive to the combination of architecture, wavefront instance and problem size. We design and investigate a family of autotuning strategies, targeting single and multiple CPU + GPU systems, and both two and three dimensional wavefront instances. These yield an average of 87% of the performance found by offline exhaustive search, with up to 99% in some cases

Predictive analysis and optimisation of pipelined wavefront applications using reusable analytic models

Pipelined wavefront computations are an ubiquitous class of high performance parallel algorithms used for the solution of many scientific and engineering applications. In order to aid the design and optimisation of these applications, and to ensure that during procurement platforms are chosen best suited to these codes, there has been considerable research in analysing and evaluating their operational performance. Wavefront codes exhibit complex computation, communication, synchronisation patterns, and as a result there exist a large variety of such codes and possible optimisations. The problem is compounded by each new generation of high performance computing system, which has often introduced a previously unexplored architectural trait, requiring previous performance models to be rewritten and reevaluated. In this thesis, we address the performance modelling and optimisation of this class of application, as a whole. This differs from previous studies in which bespoke models are applied to specific applications. The analytic performance models are generalised and reusable, and we demonstrate their application to the predictive analysis and optimisation of pipelined wavefront computations running on modern high performance computing systems. The performance model is based on the LogGP parameterisation, and uses a small number of input parameters to specify the particular behaviour of most wavefront codes. The new parameters and model equations capture the key structural and behavioural differences among different wavefront application codes, providing a succinct summary of the operations for each application and insights into alternative wavefront application design. The models are applied to three industry-strength wavefront codes and are validated on several systems including a Cray XT3/XT4 and an InfiniBand commodity cluster. Model predictions show high quantitative accuracy (less than 20% error) for all high performance configurations and excellent qualitative accuracy. The thesis presents applications, projections and insights for optimisations using the model, which show the utility of reusable analytic models for performance engineering of high performance computing codes. In particular, we demonstrate the use of the model for: (1) evaluating application configuration and resulting performance; (2) evaluating hardware platform issues including platform sizing, configuration; (3) exploring hardware platform design alternatives and system procurement and, (4) considering possible code and algorithmic optimisations