L Fu - Dao: a novel programming language for bioinformatics

Motivation Example Features Concurrent Programming JIT ClangDao Future Dao: a novel programming language for bioinformatics Limin Fu UC San Diego BOSC 2012 July 14, 2012

Motivation Example Features Concurrent Programming JIT ClangDao FutureWhy a new language for bioinformatics? A simple fact: Programming languages commonly used in bioinformatics are designed before: multi-core machines started to become common; some important programming paradigms are widely accepted. Once a language has got a lot of backward compatibility to maintain, it becomes very hard to add new features or support new programming paradigms without introducing inconsistency!

Motivation Example Features Concurrent Programming JIT ClangDao FutureDao programming language (http://daovm.net) Key Features Optional typing with type inference and static type checking; Native support for concurrent programming; LLVM-based Just-In-Time (JIT) compiling; Simple C interfaces for easy embedding and extending; Clang-based tool for automatic wrapping of C/C++ libraries;

Motivation Example Features Concurrent Programming JIT ClangDao FutureA simple example Use thread task to compute the sum of squares: # Start a thread task and return a future value: fut = mt.start( $now )::{ sum2 = 0 for( i = 1 : 1000 ) sum2 += i * i return sum2 }

Motivation Example Features Concurrent Programming JIT ClangDao FutureA simple example Use thread task to compute the sum of squares: # Start a thread task and return a future value: fut = mt.start( $now )::{ sum2 = 0 for( i = 1 : 1000 ) sum2 += i * i return sum2 } Due to type inference, variable fut will be a future value with type, future<int> It is optional to write the type explicitly as the following, fut : future<int> = mt.start( $now )::{ ...

Motivation Example Features Concurrent Programming JIT ClangDao FutureA simple example Use thread task to compute the sum of squares: # Start a thread task and return a future value: fut = mt.start( $now )::{ sum2 = 0 for( i = 1 : 1000 ) sum2 += i * i return sum2 } mt built-in module for multi-threading; mt.start()::{} a code section method to start a thread task; The thread task will be executed in a different thread.

Motivation Example Features Concurrent Programming JIT ClangDao FutureA simple example Use thread task to compute the sum of squares: # Start a thread task and return a future value: fut = mt.start( $now )::{ sum2 = 0 for( i = 1 : 1000 ) sum2 += i * i return sum2 } An enum symbol to request immediate start of the thread task. (More or less a combination of C++ enum and Ruby symbol.)

Motivation Example Features Concurrent Programming JIT ClangDao FutureConcurrent programming: parallelized code section methods Parallelized code section methods The multi-threading module mt provides a number of parallelized code section methods: mt.iterate(): iterate on array, list, map, or a number of iteration; mt.map(): map items of array, list or map to produce new array or list; mt.apply(): apply new values to the items of array, list or map; mt.find(): ﬁnd the ﬁrst item that satisfy a condition; Example, ls = {1,2,3,4,5,6} # Parallel iteration: mt.iterate( times => 10 )::{ [index] io.writeln( index ) } mt.iterate( ls, threads => 2 )::{ [item] io.writeln( item ) } # Parallel mapping and value application: ls2 = mt.map( ls, 2 )::{ [it] it*it } # ls2 = {1,4,9,16,25,36} mt.apply( ls, 2 )::{ [it] it*it } # ls = {1,4,9,16,25,36}

Motivation Example Features Concurrent Programming JIT ClangDao FutureConcurrent programming: asynchronous classes Asynchronous classes Asynchronous classes produce asynchronous instances; Calling a method will automatically create a thread task; Thread tasks on the same instance are queued for execution. Example, class @Clustering { routine Run(){ DoKmeansClustering() } } cls = Clustering() job = cls.Run() while( 1 ){ DoSomethingElse(); if( job.wait( 0.1 ) ) break; # wait for 0.1 second }

Motivation Example Features Concurrent Programming JIT ClangDao FutureLLVM-based Just-In-Time (JIT) compiler Based on the Low Level Virtual Machine (LLVM); Emphasis on numeric computation; Compiles a subset of Dao virtual machine instructions;

Motivation Example Features Concurrent Programming JIT ClangDao FutureLLVM-based Just-In-Time (JIT) compiler Based on the Low Level Virtual Machine (LLVM); Emphasis on numeric computation; Compiles a subset of Dao virtual machine instructions; JIT Performance Test (time in seconds) Program Argument Dao Dao+JIT Speedup Python C (-O2) fannkuch 11 100.5 22.8 4.4X 339.3 4.8 mandelbrot 4000 40.0 5.1 7.8X 158.8 3.8 nbody 10000000 63.5 19.2 3.4X 333.4 2.4 spectral-norm 5000 98.0 7.6 12.8X 985.5 7.7 binary-trees 16 64.4 64.4 1.0X 22.3 5.5 Note: benchmark programs are taken from Computer Language Benchmarks Game http://shootout.alioth.debian.org

Motivation Example Features Concurrent Programming JIT ClangDao FutureClangDao: bringing C/C++ libraries to your ﬁnger tips Based on Clang (C Language Family Frontend for LLVM); Generate bindings directly from C/C++ header ﬁles; Support C/C++ functions, C structs, C callbacks, C++ classes and inheritance, C++ virtual functions, C++ templates (to some extent) etc.;

Motivation Example Features Concurrent Programming JIT ClangDao FutureClangDao: bringing C/C++ libraries to your ﬁnger tips List of bindings generated by ClangDao Scientiﬁc: DaoGSL GNU Science Library (GSL) DaoBamTools BamTools DaoGenomeTools GenomeTools DaoSVM LibSVM (Support Vector Machine) Visualization: DaoVTK Visualization Toolkit DaoMathGL MathGL 2D Graphics: DaoGraphicsMagick GraphicsMagick 3D Graphics: DaoOpenGL OpenGL DaoHorde3D Horde3D Engine DaoIrrlicht Irrlicht 3D Engine Multimedia: DaoSDL Simple DirectMedia Layer (SDL) DaoSFML Simple and Fast Multimedia Library GUI: DaoFLTK Fast Light Toolkit (FLTK) Miscellaneous: DaoXML libxml2 DaoBullet Bullet Physics Engine DaoGameKit GameKit Game Engine DaoGamePlay GamePlay Game Engine

Motivation Example Features Concurrent Programming JIT ClangDao FutureFuture development The development of Dao in the context of bioinformatics BioDao : future<Dao::Bioinformatics> = mt.start::{ DevelopDaoPackages( field => Bioinformatics ) } It should lead to an open source project named BioDao; This project will provide a large number of modules and packages for bioinformatics; It may start from screening candidate C/C++ bioinformatics libraries for automatic or semi-automatic binding; Suggestions for such libraries are highly welcome.

Motivation Example Features Concurrent Programming JIT ClangDao Future Thank you! Links and Contacts http://daovm.net https://github.com/daokoder daokoder@gmail.com l2fu@ucsd.edu

L Fu - Dao: a novel programming language for bioinformatics

by Jan Aerts on Jul 16, 2012

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