Modern Concurrency Abstractions for C
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The Effect of Compression and Expansion on Stochastic Reaction Networks
IMT School for Advanced Studies, Lucca Lucca, Italy The Effect of Compression and Expansion on Stochastic Reaction Networks PhD Program in Institutions, Markets and Technologies Curriculum in Computer Science and Systems Engineering (CSSE) XXXI Cycle By Tabea Waizmann 2021 The dissertation of Tabea Waizmann is approved. Program Coordinator: Prof. Rocco De Nicola, IMT Lucca Supervisor: Prof. Mirco Tribastone, IMT Lucca The dissertation of Tabea Waizmann has been reviewed by: Dr. Catia Trubiani, Gran Sasso Science Institute Prof. Michele Loreti, University of Camerino IMT School for Advanced Studies, Lucca 2021 To everyone who believed in me. Contents List of Figures ix List of Tables xi Acknowledgements xiii Vita and Publications xv Abstract xviii 1 Introduction 1 2 Background 6 2.1 Multisets . .6 2.2 Reaction Networks . .7 2.3 Ordinary Lumpability . 11 2.4 Layered Queuing Networks . 12 2.5 PEPA . 16 3 Coarse graining mass-action stochastic reaction networks by species equivalence 19 3.1 Species Equivalence . 20 3.1.1 Species equivalence as a generalization of Markov chain ordinary lumpability . 27 3.1.2 Characterization of SE for mass-action networks . 27 3.1.3 Computation of the maximal SE and reduced net- work . 28 vii 3.2 Applications . 31 3.2.1 Computational systems biology . 31 3.2.2 Epidemic processes in networks . 33 3.3 Discussion . 36 4 DiffLQN: Differential Equation Analysis of Layered Queuing Networks 37 4.1 DiffLQN .............................. 38 4.1.1 Architecture . 38 4.1.2 Capabilities . 38 4.1.3 Syntax . 39 4.2 Case Study: Client-Server dynamics . 41 4.3 Discussion . -
Introduction to Multi-Threading and Vectorization Matti Kortelainen Larsoft Workshop 2019 25 June 2019 Outline
Introduction to multi-threading and vectorization Matti Kortelainen LArSoft Workshop 2019 25 June 2019 Outline Broad introductory overview: • Why multithread? • What is a thread? • Some threading models – std::thread – OpenMP (fork-join) – Intel Threading Building Blocks (TBB) (tasks) • Race condition, critical region, mutual exclusion, deadlock • Vectorization (SIMD) 2 6/25/19 Matti Kortelainen | Introduction to multi-threading and vectorization Motivations for multithreading Image courtesy of K. Rupp 3 6/25/19 Matti Kortelainen | Introduction to multi-threading and vectorization Motivations for multithreading • One process on a node: speedups from parallelizing parts of the programs – Any problem can get speedup if the threads can cooperate on • same core (sharing L1 cache) • L2 cache (may be shared among small number of cores) • Fully loaded node: save memory and other resources – Threads can share objects -> N threads can use significantly less memory than N processes • If smallest chunk of data is so big that only one fits in memory at a time, is there any other option? 4 6/25/19 Matti Kortelainen | Introduction to multi-threading and vectorization What is a (software) thread? (in POSIX/Linux) • “Smallest sequence of programmed instructions that can be managed independently by a scheduler” [Wikipedia] • A thread has its own – Program counter – Registers – Stack – Thread-local memory (better to avoid in general) • Threads of a process share everything else, e.g. – Program code, constants – Heap memory – Network connections – File handles -
CSC 553 Operating Systems Multiple Processes
CSC 553 Operating Systems Lecture 4 - Concurrency: Mutual Exclusion and Synchronization Multiple Processes • Operating System design is concerned with the management of processes and threads: • Multiprogramming • Multiprocessing • Distributed Processing Concurrency Arises in Three Different Contexts: • Multiple Applications – invented to allow processing time to be shared among active applications • Structured Applications – extension of modular design and structured programming • Operating System Structure – OS themselves implemented as a set of processes or threads Key Terms Related to Concurrency Principles of Concurrency • Interleaving and overlapping • can be viewed as examples of concurrent processing • both present the same problems • Uniprocessor – the relative speed of execution of processes cannot be predicted • depends on activities of other processes • the way the OS handles interrupts • scheduling policies of the OS Difficulties of Concurrency • Sharing of global resources • Difficult for the OS to manage the allocation of resources optimally • Difficult to locate programming errors as results are not deterministic and reproducible Race Condition • Occurs when multiple processes or threads read and write data items • The final result depends on the order of execution – the “loser” of the race is the process that updates last and will determine the final value of the variable Operating System Concerns • Design and management issues raised by the existence of concurrency: • The OS must: – be able to keep track of various processes -
Type Checking Physical Frames of Reference for Robotic Systems
PhysFrame: Type Checking Physical Frames of Reference for Robotic Systems Sayali Kate Michael Chinn Hongjun Choi Purdue University University of Virginia Purdue University USA USA USA [email protected] [email protected] [email protected] Xiangyu Zhang Sebastian Elbaum Purdue University University of Virginia USA USA [email protected] [email protected] ABSTRACT Engineering (ESEC/FSE ’21), August 23–27, 2021, Athens, Greece. ACM, New A robotic system continuously measures its own motions and the ex- York, NY, USA, 16 pages. https://doi.org/10.1145/3468264.3468608 ternal world during operation. Such measurements are with respect to some frame of reference, i.e., a coordinate system. A nontrivial 1 INTRODUCTION robotic system has a large number of different frames and data Robotic systems have rapidly growing applications in our daily life, have to be translated back-and-forth from a frame to another. The enabled by the advances in many areas such as AI. Engineering onus is on the developers to get such translation right. However, such systems becomes increasingly important. Due to the unique this is very challenging and error-prone, evidenced by the large characteristics of such systems, e.g., the need of modeling the phys- number of questions and issues related to frame uses on developers’ ical world and satisfying the real time and resource constraints, forum. Since any state variable can be associated with some frame, robotic system engineering poses new challenges to developers. reference frames can be naturally modeled as variable types. We One of the prominent challenges is to properly use physical frames hence develop a novel type system that can automatically infer of reference. -
Dynamic Extension of Typed Functional Languages
Dynamic Extension of Typed Functional Languages Don Stewart PhD Dissertation School of Computer Science and Engineering University of New South Wales 2010 Supervisor: Assoc. Prof. Manuel M. T. Chakravarty Co-supervisor: Dr. Gabriele Keller Abstract We present a solution to the problem of dynamic extension in statically typed functional languages with type erasure. The presented solution re- tains the benefits of static checking, including type safety, aggressive op- timizations, and native code compilation of components, while allowing extensibility of programs at runtime. Our approach is based on a framework for dynamic extension in a stat- ically typed setting, combining dynamic linking, runtime type checking, first class modules and code hot swapping. We show that this framework is sufficient to allow a broad class of dynamic extension capabilities in any statically typed functional language with type erasure semantics. Uniquely, we employ the full compile-time type system to perform run- time type checking of dynamic components, and emphasize the use of na- tive code extension to ensure that the performance benefits of static typing are retained in a dynamic environment. We also develop the concept of fully dynamic software architectures, where the static core is minimal and all code is hot swappable. Benefits of the approach include hot swappable code and sophisticated application extension via embedded domain specific languages. We instantiate the concepts of the framework via a full implementation in the Haskell programming language: providing rich mechanisms for dy- namic linking, loading, hot swapping, and runtime type checking in Haskell for the first time. We demonstrate the feasibility of this architecture through a number of novel applications: an extensible text editor; a plugin-based network chat bot; a simulator for polymer chemistry; and xmonad, an ex- tensible window manager. -
Towards Gradually Typed Capabilities in the Pi-Calculus
Towards Gradually Typed Capabilities in the Pi-Calculus Matteo Cimini University of Massachusetts Lowell Lowell, MA, USA matteo [email protected] Gradual typing is an approach to integrating static and dynamic typing within the same language, and puts the programmer in control of which regions of code are type checked at compile-time and which are type checked at run-time. In this paper, we focus on the π-calculus equipped with types for the modeling of input-output capabilities of channels. We present our preliminary work towards a gradually typed version of this calculus. We present a type system, a cast insertion procedure that automatically inserts run-time checks, and an operational semantics of a π-calculus that handles casts on channels. Although we do not claim any theoretical results on our formulations, we demonstrate our calculus with an example and discuss our future plans. 1 Introduction This paper presents preliminary work on integrating dynamically typed features into a typed π-calculus. Pierce and Sangiorgi have defined a typed π-calculus in which channels can be assigned types that express input and output capabilities [16]. Channels can be declared to be input-only, output-only, or that can be used for both input and output operations. As a consequence, this type system can detect unintended or malicious channel misuses at compile-time. The static typing nature of the type system prevents the modeling of scenarios in which the input- output discipline of a channel is discovered at run-time. In these scenarios, such a discipline must be enforced with run-time type checks in the style of dynamic typing. -
Enhanced Debugging for Data Races in Parallel
ENHANCED DEBUGGING FOR DATA RACES IN PARALLEL PROGRAMS USING OPENMP A Thesis Presented to the Faculty of the Department of Computer Science University of Houston In Partial Fulfillment of the Requirements for the Degree Master of Science By Marcus W. Hervey December 2016 ENHANCED DEBUGGING FOR DATA RACES IN PARALLEL PROGRAMS USING OPENMP Marcus W. Hervey APPROVED: Dr. Edgar Gabriel, Chairman Dept. of Computer Science Dr. Shishir Shah Dept. of Computer Science Dr. Barbara Chapman Dept. of Computer Science, Stony Brook University Dean, College of Natural Sciences and Mathematics ii iii Acknowledgements A special thank you to Dr. Barbara Chapman, Ph.D., Dr. Edgar Gabriel, Ph.D., Dr. Shishir Shah, Ph.D., Dr. Lei Huang, Ph.D., Dr. Chunhua Liao, Ph.D., Dr. Laksano Adhianto, Ph.D., and Dr. Oscar Hernandez, Ph.D. for their guidance and support throughout this endeavor. I would also like to thank Van Bui, Deepak Eachempati, James LaGrone, and Cody Addison for their friendship and teamwork, without which this endeavor would have never been accomplished. I dedicate this thesis to my parents (Billy and Olivia Hervey) who have always chal- lenged me to be my best, and to my wife and kids for their love and sacrifice throughout this process. ”Our greatest weakness lies in giving up. The most certain way to succeed is always to try just one more time.” – Thomas Alva Edison iv ENHANCED DEBUGGING FOR DATA RACES IN PARALLEL PROGRAMS USING OPENMP An Abstract of a Thesis Presented to the Faculty of the Department of Computer Science University of Houston In Partial Fulfillment of the Requirements for the Degree Master of Science By Marcus W. -
Reconciling Real and Stochastic Time: the Need for Probabilistic Refinement
DOI 10.1007/s00165-012-0230-y The Author(s) © 2012. This article is published with open access at Springerlink.com Formal Aspects Formal Aspects of Computing (2012) 24: 497–518 of Computing Reconciling real and stochastic time: the need for probabilistic refinement J. Markovski1,P.R.D’Argenio2,J.C.M.Baeten1,3 and E. P. de Vink1,3 1 Eindhoven University of Technology, Eindhoven, The Netherlands. E-mail: [email protected] 2 FaMAF, Universidad Nacional de Cordoba,´ Cordoba,´ Argentina 3 Centrum Wiskunde & Informatica, Amsterdam, The Netherlands Abstract. We conservatively extend an ACP-style discrete-time process theory with discrete stochastic delays. The semantics of the timed delays relies on time additivity and time determinism, which are properties that enable us to merge subsequent timed delays and to impose their synchronous expiration. Stochastic delays, however, interact with respect to a so-called race condition that determines the set of delays that expire first, which is guided by an (implicit) probabilistic choice. The race condition precludes the property of time additivity as the merger of stochastic delays alters this probabilistic behavior. To this end, we resolve the race condition using conditionally-distributed unit delays. We give a sound and ground-complete axiomatization of the process the- ory comprising the standard set of ACP-style operators. In this generalized setting, the alternative composition is no longer associative, so we have to resort to special normal forms that explicitly resolve the underlying race condition. Our treatment succeeds in the initial challenge to conservatively extend standard time with stochastic time. However, the ‘dissection’ of the stochastic delays to conditionally-distributed unit delays comes at a price, as we can no longer relate the resolved race condition to the original stochastic delays. -
Introduction to the Literature on Programming Language Design Gary T
Computer Science Technical Reports Computer Science 7-1999 Introduction to the Literature On Programming Language Design Gary T. Leavens Iowa State University Follow this and additional works at: http://lib.dr.iastate.edu/cs_techreports Part of the Programming Languages and Compilers Commons Recommended Citation Leavens, Gary T., "Introduction to the Literature On Programming Language Design" (1999). Computer Science Technical Reports. 59. http://lib.dr.iastate.edu/cs_techreports/59 This Article is brought to you for free and open access by the Computer Science at Iowa State University Digital Repository. It has been accepted for inclusion in Computer Science Technical Reports by an authorized administrator of Iowa State University Digital Repository. For more information, please contact [email protected]. Introduction to the Literature On Programming Language Design Abstract This is an introduction to the literature on programming language design and related topics. It is intended to cite the most important work, and to provide a place for students to start a literature search. Keywords programming languages, semantics, type systems, polymorphism, type theory, data abstraction, functional programming, object-oriented programming, logic programming, declarative programming, parallel and distributed programming languages Disciplines Programming Languages and Compilers This article is available at Iowa State University Digital Repository: http://lib.dr.iastate.edu/cs_techreports/59 Intro duction to the Literature On Programming Language Design Gary T. Leavens TR 93-01c Jan. 1993, revised Jan. 1994, Feb. 1996, and July 1999 Keywords: programming languages, semantics, typ e systems, p olymorphism, typ e theory, data abstrac- tion, functional programming, ob ject-oriented programming, logic programming, declarative programming, parallel and distributed programming languages. -
Lecture 18 18.1 Distributed and Concurrent Systems 18.2 Race
CMPSCI 691ST Systems Fall 2011 Lecture 18 Lecturer: Emery Berger Scribe: Sean Barker 18.1 Distributed and Concurrent Systems In this lecture we discussed two broad issues in concurrent systems: clocks and race detection. The first paper we read introduced the Lamport clock, which is a scalar providing a logical clock value for each process. Every time a process sends a message, it increments its clock value, and every time a process receives a message, it sets its clock value to the max of the current value and the message value. Clock values are used to provide a `happens-before' relationship, which provides a consistent partial ordering of events across processes. Lamport clocks were later extended to vector clocks, in which each of n processes maintains an array (or vector) of n clock values (one for each process) rather than just a single value as in Lamport clocks. Vector clocks are much more precise than Lamport clocks, since they can check whether intermediate events from anyone have occurred (by looking at the max across the entire vector), and have essentially replaced Lamport clocks today. Moreover, since distributed systems are already sending many messages, the cost of maintaining vector clocks is generally not a big deal. Clock synchronization is still a hard problem, however, because physical clock values will always have some amount of drift. The FastTrack paper we read leverages vector clocks to do race detection. 18.2 Race Detection Broadly speaking, a race condition occurs when at least two threads are accessing a variable, and one of them writes the value while another is reading. -
Breadth First Search Vectorization on the Intel Xeon Phi
Breadth First Search Vectorization on the Intel Xeon Phi Mireya Paredes Graham Riley Mikel Luján University of Manchester University of Manchester University of Manchester Oxford Road, M13 9PL Oxford Road, M13 9PL Oxford Road, M13 9PL Manchester, UK Manchester, UK Manchester, UK [email protected] [email protected] [email protected] ABSTRACT Today, scientific experiments in many domains, and large Breadth First Search (BFS) is a building block for graph organizations can generate huge amounts of data, e.g. social algorithms and has recently been used for large scale anal- networks, health-care records and bio-informatics applica- ysis of information in a variety of applications including so- tions [8]. Graphs seem to be a good match for important cial networks, graph databases and web searching. Due to and large dataset analysis as they can abstract real world its importance, a number of different parallel programming networks. To process large graphs, different techniques have models and architectures have been exploited to optimize been applied, including parallel programming. The main the BFS. However, due to the irregular memory access pat- challenge in the parallelization of graph processing is that terns and the unstructured nature of the large graphs, its large graphs are often unstructured and highly irregular and efficient parallelization is a challenge. The Xeon Phi is a this limits their scalability and performance when executing massively parallel architecture available as an off-the-shelf on off-the-shelf systems [18]. accelerator, which includes a powerful 512 bit vector unit The Breadth First Search (BFS) is a building block of with optimized scatter and gather functions. -
Rapid Prototyping of High-Performance Concurrent Java Applications
Rapid Prototyping of High-Performance Concurrent Java Applications K.J.R. Powell Master of Science School of Computer Science School of Informatics University of Edinburgh 2002 (Graduation date:December 2002) Abstract The design and implementation of concurrent applications is more challenging than that of sequential applications. The aim of this project is to address this challenge by producing an application which can generate skeleton Java systems from a high-level PEPA modelling language description. By automating the process of translating the design into a Java skeleton system, the result will maintain the performance and be- havioural characteristics of the model, providing a sound framework for completing the concurrent application. This method accelerates the process of initial implementation whilst ensuring the system characterisics remain true to the high-level model. i Acknowledgements Many thanks to my supervisor Stephen Gilmore for his excellent guidance and ideas. I’d also like to express my gratitude to L.L. for his assistance above and beyond the call of duty in the field of editing. ii Declaration I declare that this thesis was composed by myself, that the work contained herein is my own except where explicitly stated otherwise in the text, and that this work has not been submitted for any other degree or professional qualification except as specified. (K.J.R. Powell) iii Table of Contents 1 Introduction 1 1.1 Principal Goal . 1 1.2 PEPA and Java . 2 1.3 Project Objective . 2 2 Performance Evaluation Process Algebra 4 2.1 Overview of PEPA and its role in design . 4 2.2 The Syntax of PEPA .