Performance characterization and acceleration of genome-mapping tools on HPC environments

Nowadays, the efficient analysis and exploitation of genomic information is paramount to future advancements in the healthcare sector, such as better diagnosis techniques and the development of improved disease treatments. In the past decades, the exponential increase in the biological data production has fostered the development of more efficient genomic pipelines. For that, modern genome analysis requires better and more scalable algorithms, and improved high-performance implementations that can exploit current hardware accelerators. For most genome analysis pipelines, sequence mapping is one of the most computationally intensive and time-consuming processing stages. The ultimate goal of this work is to propose techniques to accelerate read mapping, leveraging novel algorithms and hardware vector extensions. In this thesis, we present a thorough performance characterization of the most widely-used genome-mapping tools and propose acceleration techniques that can effectively improve the performance of these tools. To that end, first, we identify the most time-consuming kernels, their performance bottlenecks, and the underlying causes of inefficiency. Afterwards, we design and implement an accelerated version of one of the most time-consuming steps: pairwise sequence alignment. For that, we propose to replace the classical dynamic-programming algorithm, used within these tools, with the recently proposed wavefront alignment algorithm (WFA). Moreover, we design and implement the first fully-vectorized version of the WFA, leveraging Intel's AVX2 and AVX-512 instructions, to further accelerate sequence-to-sequence alignment. As a result, we demonstrate that our vectorized WFA implementation outperforms the original scalar WFA implementation between 1.1x-2.4x. In turn, this renders speedups from 2.4x up to 826.7x compared to the most widely-used alignment algorithm, KSW2 (used within Minimap2 and Bwa-Mem2). We conclude that these tools can be significantly accelerated by selecting better algorithms (like the WFA) and leveraging fine-tuned implementations that can exploit hardware resources available in current high performance computing (HPC) processors

Vectorization system for unstructured codes with a Data-parallel Compiler IR

With Dennard Scaling coming to an end, Single Instruction Multiple Data (SIMD) offers itself as a way to improve the compute throughput of CPUs. One fundamental technique in SIMD code generators is the vectorization of data-parallel code regions. This has applications in outer-loop vectorization, whole-function vectorization and vectorization of explicitly data-parallel languages. This thesis makes contributions to the reliable vectorization of data-parallel code regions with unstructured, reducible control flow. Reducibility is the case in practice where all control-flow loops have exactly one entry point. We present P-LLVM, a novel, full-featured, intermediate representation for vectorizers that provides a semantics for the code region at every stage of the vectorization pipeline. Partial control-flow linearization is a novel partial if-conversion scheme, an essential technique to vectorize divergent control flow. Different to prior techniques, partial linearization has linear running time, does not insert additional branches or blocks and gives proved guarantees on the control flow retained. Divergence of control induces value divergence at join points in the control-flow graph (CFG). We present a novel control-divergence analysis for directed acyclic graphs with optimal running time and prove that it is correct and precise under common static assumptions. We extend this technique to obtain a quadratic-time, control-divergence analysis for arbitrary reducible CFGs. For this analysis, we show on a range of realistic examples how earlier approaches are either less precise or incorrect. We present a feature-complete divergence analysis for P-LLVM programs. The analysis is the first to analyze stack-allocated objects in an unstructured control setting. Finally, we generalize single-dimensional vectorization of outer loops to multi-dimensional tensorization of loop nests. SIMD targets benefit from tensorization through more opportunities for re-use of loaded values and more efficient memory access behavior. The techniques were implemented in the Region Vectorizer (RV) for vectorization and TensorRV for loop-nest tensorization. Our evaluation validates that the general-purpose RV vectorization system matches the performance of more specialized approaches. RV performs on par with the ISPC compiler, which only supports its structured domain-specific language, on a range of tree traversal codes with complex control flow. RV is able to outperform the loop vectorizers of state-of-the-art compilers, as we show for the SPEC2017 nab_s benchmark and the XSBench proxy application.Mit dem Ausreizen des Dennard Scalings erreichen die gewohnten Zuwächse in der skalaren Rechenleistung zusehends ihr Ende. Moderne Prozessoren setzen verstärkt auf parallele Berechnung, um den Rechendurchsatz zu erhöhen. Hierbei spielen SIMD Instruktionen (Single Instruction Multiple Data), die eine Operation gleichzeitig auf mehrere Eingaben anwenden, eine zentrale Rolle. Eine fundamentale Technik, um SIMD Programmcode zu erzeugen, ist der Einsatz datenparalleler Vektorisierung. Diese unterliegt populären Verfahren, wie der Vektorisierung äußerer Schleifen, der Vektorisierung gesamter Funktionen bis hin zu explizit datenparallelen Programmiersprachen. Der Beitrag der vorliegenden Arbeit besteht darin, ein zuverlässiges Vektorisierungssystem für datenparallelen Code mit reduziblem Steuerfluss zu entwickeln. Diese Anforderung ist für alle Steuerflussgraphen erfüllt, deren Schleifen nur einen Eingang haben, was in der Praxis der Fall ist. Wir präsentieren P-LLVM, eine ausdrucksstarke Zwischendarstellung für Vektorisierer, welche dem Programm in jedem Stadium der Transformation von datenparallelem Code zu SIMD Code eine definierte Semantik verleiht. Partielle Steuerfluss-Linearisierung ist ein neuer Algorithmus zur If-Conversion, welcher Sprünge erhalten kann. Anders als existierende Verfahren hat Partielle Linearisierung eine lineare Laufzeit und fügt keine neuen Sprünge oder Blöcke ein. Wir zeigen Kriterien, unter denen der Algorithmus Steuerfluss erhält, und beweisen diese. Steuerflussdivergenz induziert Divergenz an Punkten zusammenfließenden Steuerflusses. Wir stellen eine neue Steuerflussdivergenzanalyse für azyklische Graphen mit optimaler Laufzeit vor und beweisen deren Korrektheit und Präzision. Wir verallgemeinern die Technik zu einem Algorithmus mit quadratischer Laufzeit für beliebiege, reduzible Steuerflussgraphen. Eine Studie auf realistischen Beispielgraphen zeigt, dass vergleichbare Techniken entweder weniger präsize sind oder falsche Ergebnisse liefern. Ebenfalls präsentieren wir eine Divergenzanalyse für P-LLVM Programme. Diese Analyse ist die erste Divergenzanalyse, welche Divergenz in stapelallokierten Objekten unter unstrukturiertem Steuerfluss analysiert. Schließlich generalisieren wir die eindimensionale Vektorisierung von äußeren Schleifen zur multidimensionalen Tensorisierung von Schleifennestern. Tensorisierung eröffnet für SIMD Prozessoren mehr Möglichkeiten, bereits geladene Werte wiederzuverwenden und das Speicherzugriffsverhalten des Programms zu optimieren, als dies mit Vektorisierung der Fall ist. Die vorgestellten Techniken wurden in den Region Vectorizer (RV) für Vektorisierung und TensorRV für die Tensorisierung von Schleifennestern implementiert. Wir zeigen auf einer Reihe von steuerflusslastigen Programmen für die Traversierung von Baumdatenstrukturen, dass RV das gleiche Niveau erreicht wie der ISPC Compiler, welcher nur seine strukturierte Eingabesprache verarbeiten kann. RV kann schnellere SIMD-Programme erzeugen als die Schleifenvektorisierer in aktuellen Industriecompilern. Dies demonstrieren wir mit dem nab_s benchmark aus der SPEC2017 Benchmarksuite und der XSBench Proxy-Anwendung

Efficient Algorithms for Large-Scale Image Analysis

This work develops highly efficient algorithms for analyzing large images. Applications include object-based change detection and screening. The algorithms are 10-100 times as fast as existing software, sometimes even outperforming FGPA/GPU hardware, because they are designed to suit the computer architecture. This thesis describes the implementation details and the underlying algorithm engineering methodology, so that both may also be applied to other applications

Analysis and parameter prediction of compiler transformation for graphics processors

In the last decade graphics processors (GPUs) have been extensively used to solve computationally intensive problems. A variety of GPU architectures by different hardware manufacturers have been shipped in a few years. OpenCL has been introduced as the standard cross-vendor programming framework for GPU computing. Writing and optimising OpenCL applications is a challenging task, the programmer has to take care of several low level details. This is even harder when the goal is to improve performance on a wide range of devices: OpenCL does not guarantee performance portability. In this thesis we focus on the analysis and the portability of compiler optimisations. We describe the implementation of a portable compiler transformation: thread-coarsening. The transformation increases the amount of work carried out by a single thread running on the GPU. The goal is to reduce the amount of redundant instructions executed by the parallel application. The first contribution is a technique to analyse performance improvements and degradations given by the compiler transformation, we study the changes of hardware performance counters when applying coarsening. In this way we identify the root causes of execution time variations due to coarsening. As second contribution, we study the relative performance of coarsening over multiple input sizes. We show that the speedups given by coarsening are stable for problem sizes larger than a threshold that we call saturation point. We exploit the existence of the saturation point to speedup iterative compilation. The last contribution of the work is the development of a machine learning technique that automatically selects a coarsening configuration that improves performance. The technique is based on an iterative model built using a neural network. The network is trained once for a GPU model and used for several programs. To prove the flexibility of our techniques, all our experiments have been deployed on multiple GPU models by different vendors

Proceedings of the 3rd Annual Conference on Aerospace Computational Control, volume 1

Conference topics included definition of tool requirements, advanced multibody component representation descriptions, model reduction, parallel computation, real time simulation, control design and analysis software, user interface issues, testing and verification, and applications to spacecraft, robotics, and aircraft

Customizing the Computation Capabilities of Microprocessors.

Designers of microprocessor-based systems must constantly improve performance and increase computational efficiency in their designs to create value. To this end, it is increasingly common to see computation accelerators in general-purpose processor designs. Computation accelerators collapse portions of an application's dataflow graph, reducing the critical path of computations, easing the burden on processor resources, and reducing energy consumption in systems. There are many problems associated with adding accelerators to microprocessors, though. Design of accelerators, architectural integration, and software support all present major challenges. This dissertation tackles these challenges in the context of accelerators targeting acyclic and cyclic patterns of computation. First, a technique to identify critical computation subgraphs within an application set is presented. This technique is hardware-cognizant and effectively generates a set of instruction set extensions given a domain of target applications. Next, several general-purpose accelerator structures are quantitatively designed using critical subgraph analysis for a broad application set. The next challenge is architectural integration of accelerators. Traditionally, software invokes accelerators by statically encoding new instructions into the application binary. This is incredibly costly, though, requiring many portions of hardware and software to be redesigned. This dissertation develops strategies to utilize accelerators, without changing the instruction set. In the proposed approach, the microarchitecture translates applications at run-time, replacing computation subgraphs with microcode to utilize accelerators. We explore the tradeoffs in performing difficult aspects of the translation at compile-time, while retaining run-time replacement. This culminates in a simple microarchitectural interface that supports a plug-and-play model for integrating accelerators into a pre-designed microprocessor. Software support is the last challenge in dealing with computation accelerators. The primary issue is difficulty in generating high-quality code utilizing accelerators. Hand-written assembly code is standard in industry, and if compiler support does exist, simple greedy algorithms are common. In this work, we investigate more thorough techniques for compiling for computation accelerators. Where greedy heuristics only explore one possible solution, the techniques in this dissertation explore the entire design space, when possible. Intelligent pruning methods ensure that compilation is both tractable and scalable.Ph.D.Computer Science & EngineeringUniversity of Michigan, Horace H. Rackham School of Graduate Studieshttp://deepblue.lib.umich.edu/bitstream/2027.42/57633/2/ntclark_1.pd

Analytical cost metrics: days of future past

2019 Summer.Includes bibliographical references.Future exascale high-performance computing (HPC) systems are expected to be increasingly heterogeneous, consisting of several multi-core CPUs and a large number of accelerators, special-purpose hardware that will increase the computing power of the system in a very energy-efficient way. Specialized, energy-efficient accelerators are also an important component in many diverse systems beyond HPC: gaming machines, general purpose workstations, tablets, phones and other media devices. With Moore's law driving the evolution of hardware platforms towards exascale, the dominant performance metric (time efficiency) has now expanded to also incorporate power/energy efficiency. This work builds analytical cost models for cost metrics such as time, energy, memory access, and silicon area. These models are used to predict the performance of applications, for performance tuning, and chip design. The idea is to work with domain specific accelerators where analytical cost models can be accurately used for performance optimization. The performance optimization problems are formulated as mathematical optimization problems. This work explores the analytical cost modeling and mathematical optimization approach in a few ways. For stencil applications and GPU architectures, the analytical cost models are developed for execution time as well as energy. The models are used for performance tuning over existing architectures, and are coupled with silicon area models of GPU architectures to generate highly efficient architecture configurations. For matrix chain products, analytical closed form solutions for off-chip data movement are built and used to minimize the total data movement cost of a minimum op count tree