Programming Clojure Second Edition
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The Machine That Builds Itself: How the Strengths of Lisp Family
Khomtchouk et al. OPINION NOTE The Machine that Builds Itself: How the Strengths of Lisp Family Languages Facilitate Building Complex and Flexible Bioinformatic Models Bohdan B. Khomtchouk1*, Edmund Weitz2 and Claes Wahlestedt1 *Correspondence: [email protected] Abstract 1Center for Therapeutic Innovation and Department of We address the need for expanding the presence of the Lisp family of Psychiatry and Behavioral programming languages in bioinformatics and computational biology research. Sciences, University of Miami Languages of this family, like Common Lisp, Scheme, or Clojure, facilitate the Miller School of Medicine, 1120 NW 14th ST, Miami, FL, USA creation of powerful and flexible software models that are required for complex 33136 and rapidly evolving domains like biology. We will point out several important key Full list of author information is features that distinguish languages of the Lisp family from other programming available at the end of the article languages and we will explain how these features can aid researchers in becoming more productive and creating better code. We will also show how these features make these languages ideal tools for artificial intelligence and machine learning applications. We will specifically stress the advantages of domain-specific languages (DSL): languages which are specialized to a particular area and thus not only facilitate easier research problem formulation, but also aid in the establishment of standards and best programming practices as applied to the specific research field at hand. DSLs are particularly easy to build in Common Lisp, the most comprehensive Lisp dialect, which is commonly referred to as the “programmable programming language.” We are convinced that Lisp grants programmers unprecedented power to build increasingly sophisticated artificial intelligence systems that may ultimately transform machine learning and AI research in bioinformatics and computational biology. -
Lecture 4 Resource Protection and Thread Safety
Concurrency and Correctness – Resource Protection and TS Lecture 4 Resource Protection and Thread Safety 1 Danilo Piparo – CERN, EP-SFT Concurrency and Correctness – Resource Protection and TS This Lecture The Goals: 1) Understand the problem of contention of resources within a parallel application 2) Become familiar with the design principles and techniques to cope with it 3) Appreciate the advantage of non-blocking techniques The outline: § Threads and data races: synchronisation issues § Useful design principles § Replication, atomics, transactions and locks § Higher level concrete solutions 2 Danilo Piparo – CERN, EP-SFT Concurrency and Correctness – Resource Protection and TS Threads and Data Races: Synchronisation Issues 3 Danilo Piparo – CERN, EP-SFT Concurrency and Correctness – Resource Protection and TS The Problem § Fastest way to share data: access the same memory region § One of the advantages of threads § Parallel memory access: delicate issue - race conditions § I.e. behaviour of the system depends on the sequence of events which are intrinsically asynchronous § Consequences, in order of increasing severity § Catastrophic terminations: segfaults, crashes § Non-reproducible, intermittent bugs § Apparently sane execution but data corruption: e.g. wrong value of a variable or of a result Operative definition: An entity which cannot run w/o issues linked to parallel execution is said to be thread-unsafe (the contrary is thread-safe) 4 Danilo Piparo – CERN, EP-SFT Concurrency and Correctness – Resource Protection and TS To Be Precise: Data Race Standard language rules, §1.10/4 and /21: • Two expression evaluations conflict if one of them modifies a memory location (1.7) and the other one accesses or modifies the same memory location. -
An Evaluation of Go and Clojure
An evaluation of Go and Clojure A thesis submitted in partial satisfaction of the requirements for the degree Bachelors of Science in Computer Science Fall 2010 Robert Stimpfling Department of Computer Science University of Colorado, Boulder Advisor: Kenneth M. Anderson, PhD Department of Computer Science University of Colorado, Boulder 1. Introduction Concurrent programming languages are not new, but they have been getting a lot of attention more recently due to their potential with multiple processors. Processors have gone from growing exponentially in terms of speed, to growing in terms of quantity. This means processes that are completely serial in execution will soon be seeing a plateau in performance gains since they can only rely on one processor. A popular approach to using these extra processors is to make programs multi-threaded. The threads can execute in parallel and use shared memory to speed up execution times. These multithreaded processes can significantly speed up performance, as long as the number of dependencies remains low. Amdahl‘s law states that these performance gains can only be relative to the amount of processing that can be parallelized [1]. However, the performance gains are significant enough to be looked into. These gains not only come from the processing being divvied up into sections that run in parallel, but from the inherent gains from sharing memory and data structures. Passing new threads a copy of a data structure can be demanding on the processor because it requires the processor to delve into memory and make an exact copy in a new location in memory. Indeed some studies have shown that the problem with optimizing concurrent threads is not in utilizing the processors optimally, but in the need for technical improvements in memory performance [2]. -
Clojure, Given the Pun on Closure, Representing Anything Specific
dynamic, functional programming for the JVM “It (the logo) was designed by my brother, Tom Hickey. “It I wanted to involve c (c#), l (lisp) and j (java). I don't think we ever really discussed the colors Once I came up with Clojure, given the pun on closure, representing anything specific. I always vaguely the available domains and vast emptiness of the thought of them as earth and sky.” - Rich Hickey googlespace, it was an easy decision..” - Rich Hickey Mark Volkmann [email protected] Functional Programming (FP) In the spirit of saying OO is is ... encapsulation, inheritance and polymorphism ... • Pure Functions • produce results that only depend on inputs, not any global state • do not have side effects such as Real applications need some changing global state, file I/O or database updates side effects, but they should be clearly identified and isolated. • First Class Functions • can be held in variables • can be passed to and returned from other functions • Higher Order Functions • functions that do one or both of these: • accept other functions as arguments and execute them zero or more times • return another function 2 ... FP is ... Closures • main use is to pass • special functions that retain access to variables a block of code that were in their scope when the closure was created to a function • Partial Application • ability to create new functions from existing ones that take fewer arguments • Currying • transforming a function of n arguments into a chain of n one argument functions • Continuations ability to save execution state and return to it later think browser • back button 3 .. -
Proceedings of the 8Th European Lisp Symposium Goldsmiths, University of London, April 20-21, 2015 Julian Padget (Ed.) Sponsors
Proceedings of the 8th European Lisp Symposium Goldsmiths, University of London, April 20-21, 2015 Julian Padget (ed.) Sponsors We gratefully acknowledge the support given to the 8th European Lisp Symposium by the following sponsors: WWWLISPWORKSCOM i Organization Programme Committee Julian Padget – University of Bath, UK (chair) Giuseppe Attardi — University of Pisa, Italy Sacha Chua — Toronto, Canada Stephen Eglen — University of Cambridge, UK Marc Feeley — University of Montreal, Canada Matthew Flatt — University of Utah, USA Rainer Joswig — Hamburg, Germany Nick Levine — RavenPack, Spain Henry Lieberman — MIT, USA Christian Queinnec — University Pierre et Marie Curie, Paris 6, France Robert Strandh — University of Bordeaux, France Edmund Weitz — University of Applied Sciences, Hamburg, Germany Local Organization Christophe Rhodes – Goldsmiths, University of London, UK (chair) Richard Lewis – Goldsmiths, University of London, UK Shivi Hotwani – Goldsmiths, University of London, UK Didier Verna – EPITA Research and Development Laboratory, France ii Contents Acknowledgments i Messages from the chairs v Invited contributions Quicklisp: On Beyond Beta 2 Zach Beane µKanren: Running the Little Things Backwards 3 Bodil Stokke Escaping the Heap 4 Ahmon Dancy Unwanted Memory Retention 5 Martin Cracauer Peer-reviewed papers Efficient Applicative Programming Environments for Computer Vision Applications 7 Benjamin Seppke and Leonie Dreschler-Fischer Keyboard? How quaint. Visual Dataflow Implemented in Lisp 15 Donald Fisk P2R: Implementation of -
Java Concurrency in Practice
Java Concurrency in practice Chapters: 1,2, 3 & 4 Bjørn Christian Sebak ([email protected]) Karianne Berg ([email protected]) INF329 – Spring 2007 Chapter 1 - Introduction Brief history of concurrency Before OS, a computer executed a single program from start to finnish But running a single program at a time is an inefficient use of computer hardware Therefore all modern OS run multiple programs (in seperate processes) Brief history of concurrency (2) Factors for running multiple processes: Resource utilization: While one program waits for I/O, why not let another program run and avoid wasting CPU cycles? Fairness: Multiple users/programs might have equal claim of the computers resources. Avoid having single large programs „hog“ the machine. Convenience: Often desirable to create smaller programs that perform a single task (and coordinate them), than to have one large program that do ALL the tasks What is a thread? A „lightweight process“ - each process can have many threads Threads allow multiple streams of program flow to coexits in a single process. While a thread share process-wide resources like memory and files with other threads, they all have their own program counter, stack and local variables Benefits of threads 1) Exploiting multiple processors 2) Simplicity of modeling 3) Simplified handling of asynchronous events 4) More responsive user interfaces Benefits of threads (2) Exploiting multiple processors The processor industry is currently focusing on increasing number of cores on a single CPU rather than increasing clock speed. Well-designed programs with multiple threads can execute simultaneously on multiple processors, increasing resource utilization. -
Mixing R with Other Languages JOHN D
Mixing R with other languages JOHN D. COOK, PHD SINGULAR VALUE CONSULTING Why R? Libraries, libraries, libraries De facto standard for statistical research Nice language, as far as statistical languages go “Quirky, flawed, and an enormous success.” Why mix languages? Improve performance of R code Execution speed (e.g. loops) Memory management Raid R’s libraries How to optimize R Vectorize Rewrite not using R A few R quirks Everything is a vector Everything can be null or NA Unit-offset vectors Zero index legal but strange Negative indices remove elements Matrices filled by column by default $ acts like dot, dot not special C package interface Must manage low-level details of R object model and memory Requires Rtools on Windows Lots of macros like REALSXP, PROTECT, and UNPROTECT Use C++ (Rcpp) instead “I do not recommend using C for writing new high-performance code. Instead write C++ with Rcpp.” – Hadley Wickham Rcpp The most widely used extension method for R Call C, C++, or Fortran from R Companion project RInside to call R from C++ Extensive support even for advanced C++ Create R packages or inline code http://rcpp.org Dirk Eddelbuettel’s book Simple Rcpp example library(Rcpp) cppFunction('int add(int x, int y, int z) { int sum = x + y + z; return sum; }') add(1, 2, 3) .NET RDCOM http://sunsite.univie.ac.at/rcom/ F# type provider for R http://bluemountaincapital.github.io/FSharpRProvider/ R.NET https://rdotnet.codeplex.com/ SQL Server 2016 execute sp_execute_external_script @language = N'R' , @script = -
Common Lisp Alan Dipert, [email protected] Orange Combinator 2018-12-17 Lisp History
Old-School FP Common Lisp Alan Dipert, [email protected] Orange Combinator 2018-12-17 Lisp History Invented by John McCarthy at MIT in 1958 Inspired by Alonzo Church’s lambda calculus Described in 1960 paper, Recursive Functions of Symbolic Expressions and Their Computation by Machine, Part I Shows a Turing-complete language for algorithms and defines it in terms of an eval function written in itself Implemented by Steve Russell around 1960 A student of McCarthy’s, Russell saw McCarthy’s paper on his desk, read it, and implemented the eval function in machine code. The result was a Lisp interpreter. Language represented with its own data structures: homoiconicity Lambda Calculus Lisp (λx.M) (lambda (x) M…) Lambda abstraction Anonymous function M is any lambda term M… is zero or more expressions β-reduction Evaluation ((λx.M) E) → (M[x:=E]) ((lambda (x) M…) E) → (M[x:=E]) Relationship to AI Associated with Artificial Intelligence (AI) research since its invention at the MIT AI Lab by McCarthy in 1958 First symbolic programming language As opposed to numeric like Fortran (1957) Objects and operations upon them not necessarily numeric Logical Set-theoretic First garbage-collected language Memory reclaimed automatically when possible Really they just needed a decent scripting language to iterate quickly with Today, most programming is “symbolic”! Classic Lisp: member* (defun member* (x xs) (if xs (if (eql (car xs) x) xs (member* x (cdr xs))))) (member* 2 ‘(1 2 3)) → ‘(2 3) defun: defines a function in the current -
A History of Clojure
A History of Clojure RICH HICKEY, Cognitect, Inc., USA Shepherd: Mira Mezini, Technische Universität Darmstadt, Germany Clojure was designed to be a general-purpose, practical functional language, suitable for use by professionals wherever its host language, e.g., Java, would be. Initially designed in 2005 and released in 2007, Clojure is a dialect of Lisp, but is not a direct descendant of any prior Lisp. It complements programming with pure functions of immutable data with concurrency-safe state management constructs that support writing correct multithreaded programs without the complexity of mutex locks. Clojure is intentionally hosted, in that it compiles to and runs on the runtime of another language, such as the JVM. This is more than an implementation strategy; numerous features ensure that programs written in Clojure can leverage and interoperate with the libraries of the host language directly and efficiently. In spite of combining two (at the time) rather unpopular ideas, functional programming and Lisp, Clojure has since seen adoption in industries as diverse as finance, climate science, retail, databases, analytics, publishing, healthcare, advertising and genomics, and by consultancies and startups worldwide, much to the career-altering surprise of its author. Most of the ideas in Clojure were not novel, but their combination puts Clojure in a unique spot in language design (functional, hosted, Lisp). This paper recounts the motivation behind the initial development of Clojure and the rationale for various design decisions and language constructs. It then covers its evolution subsequent to release and adoption. CCS Concepts: • Software and its engineering ! General programming languages; • Social and pro- fessional topics ! History of programming languages. -
C/C++ Thread Safety Analysis
C/C++ Thread Safety Analysis DeLesley Hutchins Aaron Ballman Dean Sutherland Google Inc. CERT/SEI Email: [email protected] Email: [email protected] Email: [email protected] Abstract—Writing multithreaded programs is hard. Static including MacOS, Linux, and Windows. The analysis is analysis tools can help developers by allowing threading policies currently implemented as a compiler warning. It has been to be formally specified and mechanically checked. They essen- deployed on a large scale at Google; all C++ code at Google is tially provide a static type system for threads, and can detect potential race conditions and deadlocks. now compiled with thread safety analysis enabled by default. This paper describes Clang Thread Safety Analysis, a tool II. OVERVIEW OF THE ANALYSIS which uses annotations to declare and enforce thread safety policies in C and C++ programs. Clang is a production-quality Thread safety analysis works very much like a type system C++ compiler which is available on most platforms, and the for multithreaded programs. It is based on theoretical work analysis can be enabled for any build with a simple warning on race-free type systems [3]. In addition to declaring the flag: −Wthread−safety. The analysis is deployed on a large scale at Google, where type of data ( int , float , etc.), the programmer may optionally it has provided sufficient value in practice to drive widespread declare how access to that data is controlled in a multithreaded voluntary adoption. Contrary to popular belief, the need for environment. annotations has not been a liability, and even confers some Clang thread safety analysis uses annotations to declare benefits with respect to software evolution and maintenance. -
Steps Towards Teaching the Clojure Programming Language in an Introductory CS Class
Overview of Clojure Technical challenges of teaching Clojure as the first language Approaches to teaching Clojure to beginners Conclusions Steps towards teaching the Clojure programming language in an introductory CS class Elena Machkasova, Stephen J Adams, Joe Einertson University of Minnesota, Morris Trends in Functional Programming in Education (TFPIE) 2013. 1 / 18 Overview of Clojure Technical challenges of teaching Clojure as the first language Approaches to teaching Clojure to beginners Conclusions Outline 1 Overview of Clojure 2 Technical challenges of teaching Clojure as the first language 3 Approaches to teaching Clojure to beginners 4 Conclusions 2 / 18 Overview of Clojure Technical challenges of teaching Clojure as the first language Approaches to teaching Clojure to beginners Conclusions What is Clojure? Clojure is a LISP. Developed by Rich Hickey, released in 2007, rapidly gaining popularity. Designed to support concurrency. Provides multiple immutable persistent data structures (lists, vectors, hash maps, sets, etc.). Runs on the JVM, fully integrated with Java. Provides REPL (Read Eval Print Loop). 3 / 18 Overview of Clojure Technical challenges of teaching Clojure as the first language Approaches to teaching Clojure to beginners Conclusions Why the popularity? Elegant. Efficient (fast bytecode, efficient implementation of data structures). Convenient and safe efficient multi-threading. Integrates with Java. 4 / 18 Overview of Clojure Technical challenges of teaching Clojure as the first language Approaches to teaching Clojure to beginners Conclusions Why Clojure in intro CS courses? It's a real-life language done well. Introduces multiple data structures; abstraction vs implementation. Can be used in later courses (concurrency, interoperability with Java, purely functional data structures). -
Efficient Scalable Thread-Safety-Violation Detection Finding Thousands of Concurrency Bugs During Testing
Efficient Scalable Thread-Safety-Violation Detection Finding thousands of concurrency bugs during testing Guangpu Li Shan Lu Madanlal Musuvathi University of Chicago University of Chicago Microsoft Research Suman Nath Rohan Padhye Microsoft Research University of California, Berkeley Abstract Keywords thread-safety violation; concurrency bugs; Concurrency bugs are hard to find, reproduce, and debug. debugging; reliability; scalability They often escape rigorous in-house testing, but result in ACM Reference Format: large-scale outages in production. Existing concurrency- Guangpu Li, Shan Lu, Madanlal Musuvathi, Suman Nath, bug detection techniques unfortunately cannot be part and Rohan Padhye. 2019. Efficient Scalable Thread-Safety- of industry’s integrated build and test environment due Violation Detection: Finding thousands of concurrency bugs to some open challenges: how to handle code developed during testing. In ACM SIGOPS 27th Symposium on Oper- by thousands of engineering teams that uses a wide ating Systems Principles (SOSP ’19), October 27–30, 2019, variety of synchronization mechanisms, how to report lit- Huntsville, ON, Canada. ACM, New York, NY, USA, 19 pages. https://doi.org/10.1145/3341301.3359638 tle/no false positives, and how to avoid excessive testing resource consumption. This paper presents TSVD, a thread-safety violation detector that addresses these challenges through a new design point in the domain of active testing. Unlike pre- 1 Introduction vious techniques that inject delays randomly or employ Concurrency bugs are hard to find, reproduce, and debug. expensive synchronization analysis, TSVD uses light- Race conditions can hide in rare thread interleavings weight monitoring of the calling behaviors of thread- that do not occur during testing but nevertheless show unsafe methods, not any synchronization operations, to up in production.