Catalogue Search | MBRL
هل أنت متأكد أنك تريد إزالة الكتاب من الرف؟
{{itemTitle}}
719
نتائج ل
"Parallel programs (Computer programs)"
صنف حسب:
Using OpenCL
In 2011 many computer users were exploring the opportunities and the benefits of the massive parallelism offered by heterogeneous computing. In 2000 the Khronos Group, a not-for-profit industry consortium, was founded to create standard open APIs for parallel computing, graphics and dynamic media. Among them has been OpenCL, an open system for programming heterogeneous computers with components made by multiple manufacturers. This publication explains how heterogeneous computers work and how to program them using OpenCL. It also describes how to combine OpenCL with OpenGL for displaying graphical effects in real time. Chapter 1 describes briefly two older de facto standard and highly successful parallel programming systems: MPI and OpenMP. Collectively, the MPI, OpenMP, and OpenCL systems cover programming of all major parallel architectures: clusters, shared-memory computers, and the newest heterogeneous computers. Chapter 2, the technical core of the book, deals with OpenCL fundamentals: programming, hardware, and the interaction between them. Chapter 3 adds important information about such advanced issues as double-versus-single arithmetic precision, efficiency, memory use, and debugging. Chapters 2 and 3 contain several examples of code and one case study on genetic algorithms. These examples are related to linear algebra operations, which are very common in scientific, industrial, and business applications. Most of the book's examples can be found on the enclosed CD, which also contains basic projects for Visual Studio, MinGW, and GCC. This supplementary material will assist the reader in getting a quick start on OpenCL projects.
eBook
CUDA programming : a developer's guide to parallel computing with GPUs
If you need to learn CUDA but don't have experience with parallel computing, CUDA Programming: A Developer's Introduction offers a detailed guide to CUDA with a grounding in parallel fundamentals.It starts by introducing CUDA and bringing you up to speed on GPU parallelism and hardware, then delving into CUDA installation.
eBook
Selenium WebDriver Quick Start Guide
Selenium WebDriver is a platform-independent API for automating testing of both browser and mobile applications. It is also a core technology in many other browser automation tools, APIs and frameworks. This book will guide you through the WebDriver APIs that are used in automation tests.
eBook
Equivalent-accuracy accelerated neural-network training using analogue memory
Neural-network training can be slow and energy intensive, owing to the need to transfer the weight data for the network between conventional digital memory chips and processor chips. Analogue non-volatile memory can accelerate the neural-network training algorithm known as backpropagation by performing parallelized multiply–accumulate operations in the analogue domain at the location of the weight data. However, the classification accuracies of such in situ training using non-volatile-memory hardware have generally been less than those of software-based training, owing to insufficient dynamic range and excessive weight-update asymmetry. Here we demonstrate mixed hardware–software neural-network implementations that involve up to 204,900 synapses and that combine long-term storage in phase-change memory, near-linear updates of volatile capacitors and weight-data transfer with ‘polarity inversion’ to cancel out inherent device-to-device variations. We achieve generalization accuracies (on previously unseen data) equivalent to those of software-based training on various commonly used machine-learning test datasets (MNIST, MNIST-backrand, CIFAR-10 and CIFAR-100). The computational energy efficiency of 28,065 billion operations per second per watt and throughput per area of 3.6 trillion operations per second per square millimetre that we calculate for our implementation exceed those of today’s graphical processing units by two orders of magnitude. This work provides a path towards hardware accelerators that are both fast and energy efficient, particularly on fully connected neural-network layers.
Analogue-memory-based neural-network training using non-volatile-memory hardware augmented by circuit simulations achieves the same accuracy as software-based training but with much improved energy efficiency and speed.
Journal Article
HH-suite3 for fast remote homology detection and deep protein annotation
Background
HH-suite is a widely used open source software suite for sensitive sequence similarity searches and protein fold recognition. It is based on pairwise alignment of profile Hidden Markov models (HMMs), which represent multiple sequence alignments of homologous proteins.
Results
We developed a single-instruction multiple-data (SIMD) vectorized implementation of the Viterbi algorithm for profile HMM alignment and introduced various other speed-ups. These accelerated the search methods HHsearch by a factor 4 and HHblits by a factor 2 over the previous version 2.0.16. HHblits3 is ∼10× faster than PSI-BLAST and ∼20× faster than HMMER3. Jobs to perform HHsearch and HHblits searches with many query profile HMMs can be parallelized over cores and over cluster servers using OpenMP and message passing interface (MPI). The free, open-source, GPLv3-licensed software is available at
https://github.com/soedinglab/hh-suite
.
Conclusion
The added functionalities and increased speed of HHsearch and HHblits should facilitate their use in large-scale protein structure and function prediction, e.g. in metagenomics and genomics projects.
Journal Article
SurvivalGWAS_SV: software for the analysis of genome-wide association studies of imputed genotypes with “time-to-event” outcomes
Background
Analysis of genome-wide association studies (GWAS) with “time to event” outcomes have become increasingly popular, predominantly in the context of pharmacogenetics, where the survival endpoint could be death, disease remission or the occurrence of an adverse drug reaction. However, methodology and software that can efficiently handle the scale and complexity of genetic data from GWAS with time to event outcomes has not been extensively developed.
Results
SurvivalGWAS_SV is an easy to use software implemented using C# and run on Linux, Mac OS X & Windows operating systems. SurvivalGWAS_SV is able to handle large scale genome-wide data, allowing for imputed genotypes by modelling time to event outcomes under a dosage model. Either a Cox proportional hazards or Weibull regression model is used for analysis. The software can adjust for multiple covariates and incorporate SNP-covariate interaction effects.
Conclusions
We introduce a new console application analysis tool for the analysis of GWAS with time to event outcomes. SurvivalGWAS_SV is compatible with high performance parallel computing clusters, thereby allowing efficient and effective analysis of large scale GWAS datasets, without incurring memory issues. With its particular relevance to pharmacogenetic GWAS, SurvivalGWAS_SV will aid in the identification of genetic biomarkers of patient response to treatment, with the ultimate goal of personalising therapeutic intervention for an array of diseases.
Journal Article
Designing Scientific Applications on GPUs
General purpose graphics processing units (GPGPUs) enable researchers in a variety of fields to benefit from the computational power of all the cores available inside graphics cards. This book shows you how to use GPUs for applications in diverse scientific fields, from physics and mathematics to computer science. The book explains the methods necessary for designing or porting your scientific application on GPUs and will improve your knowledge about image processing, numerical applications, methodology to design efficient applications, optimization methods, and much more.
eBook
CADP 2011: a toolbox for the construction and analysis of distributed processes
CADP (
Construction and Analysis of Distributed Processes
) is a comprehensive software toolbox that implements the results of concurrency theory. Started in the mid-1980s, CADP has been continuously developed by adding new tools and enhancing existing ones. Today, CADP benefits from a worldwide user community, both in academia and industry. This paper presents the latest release, CADP 2011, which is the result of a considerable development effort spanning the last five years. The paper first describes the theoretical principles and the modular architecture of CADP, which has inspired several other recent model checkers. The paper then reviews the main features of CADP 2011, including compilers for various formal specification languages, equivalence checkers, model checkers, compositional verification tools, performance evaluation tools, and parallel verification tools running on clusters and grids. Finally, the paper surveys some significant case studies.
Journal Article
The Golden Ticket
The P-NP problem is the most important open problem in computer science, if not all of mathematics.The Golden Ticketprovides a nontechnical introduction to P-NP, its rich history, and its algorithmic implications for everything we do with computers and beyond. In this informative and entertaining book, Lance Fortnow traces how the problem arose during the Cold War on both sides of the Iron Curtain, and gives examples of the problem from a variety of disciplines, including economics, physics, and biology. He explores problems that capture the full difficulty of the P-NP dilemma, from discovering the shortest route through all the rides at Disney World to finding large groups of friends on Facebook. But difficulty also has its advantages. Hard problems allow us to safely conduct electronic commerce and maintain privacy in our online lives.
The Golden Ticketexplores what we truly can and cannot achieve computationally, describing the benefits and unexpected challenges of the P-NP problem.
eBook