Parallel Branch-and-Bound in Multi-core Multi-CPU Multi-GPU Heterogeneous Environments

International audienceWe investigate the design of parallel B&B in large scale heterogeneous compute environments where processing units can be composed of a mixture of multiple shared memory cores, multiple distributed CPUs and multiple GPUs devices. We describe two approaches addressing the critical issue of how to map B&B workload with the different levels of parallelism exposed by the target compute platform. We also contribute a throughout large scale experimental study which allows us to derive a comprehensive and fair analysis of the proposed approaches under different system configurations using up to 16 GPUs and up to 512 CPU-cores. Our results shed more light on the main challenges one has to face when tackling B&B algorithms while describing efficient techniques to address them. In particular, we are able to obtain linear speed-ups at moderate scales where adaptive load balancing among the heterogeneous compute resources is shown to have a significant impact on performance. At the largest scales, intra-node parallelism and hybrid decentralized load balancing is shown to have a crucial importance in order to alleviate locking issues among shared memory threads and to scale the distributed resources while optimizing communication costs and minimizing idle time

An Introduction to Programming for Bioscientists: A Python-based Primer

Computing has revolutionized the biological sciences over the past several decades, such that virtually all contemporary research in the biosciences utilizes computer programs. The computational advances have come on many fronts, spurred by fundamental developments in hardware, software, and algorithms. These advances have influenced, and even engendered, a phenomenal array of bioscience fields, including molecular evolution and bioinformatics; genome-, proteome-, transcriptome- and metabolome-wide experimental studies; structural genomics; and atomistic simulations of cellular-scale molecular assemblies as large as ribosomes and intact viruses. In short, much of post-genomic biology is increasingly becoming a form of computational biology. The ability to design and write computer programs is among the most indispensable skills that a modern researcher can cultivate. Python has become a popular programming language in the biosciences, largely because (i) its straightforward semantics and clean syntax make it a readily accessible first language; (ii) it is expressive and well-suited to object-oriented programming, as well as other modern paradigms; and (iii) the many available libraries and third-party toolkits extend the functionality of the core language into virtually every biological domain (sequence and structure analyses, phylogenomics, workflow management systems, etc.). This primer offers a basic introduction to coding, via Python, and it includes concrete examples and exercises to illustrate the language's usage and capabilities; the main text culminates with a final project in structural bioinformatics. A suite of Supplemental Chapters is also provided. Starting with basic concepts, such as that of a 'variable', the Chapters methodically advance the reader to the point of writing a graphical user interface to compute the Hamming distance between two DNA sequences.Comment: 65 pages total, including 45 pages text, 3 figures, 4 tables, numerous exercises, and 19 pages of Supporting Information; currently in press at PLOS Computational Biolog

The Reachability Problem for Petri Nets is Not Elementary

Petri nets, also known as vector addition systems, are a long established model of concurrency with extensive applications in modelling and analysis of hardware, software and database systems, as well as chemical, biological and business processes. The central algorithmic problem for Petri nets is reachability: whether from the given initial configuration there exists a sequence of valid execution steps that reaches the given final configuration. The complexity of the problem has remained unsettled since the 1960s, and it is one of the most prominent open questions in the theory of verification. Decidability was proved by Mayr in his seminal STOC 1981 work, and the currently best published upper bound is non-primitive recursive Ackermannian of Leroux and Schmitz from LICS 2019. We establish a non-elementary lower bound, i.e. that the reachability problem needs a tower of exponentials of time and space. Until this work, the best lower bound has been exponential space, due to Lipton in 1976. The new lower bound is a major breakthrough for several reasons. Firstly, it shows that the reachability problem is much harder than the coverability (i.e., state reachability) problem, which is also ubiquitous but has been known to be complete for exponential space since the late 1970s. Secondly, it implies that a plethora of problems from formal languages, logic, concurrent systems, process calculi and other areas, that are known to admit reductions from the Petri nets reachability problem, are also not elementary. Thirdly, it makes obsolete the currently best lower bounds for the reachability problems for two key extensions of Petri nets: with branching and with a pushdown stack.Comment: Final version of STOC'1

Local search methods for the discrete time/resource trade-off problem in project networks.

Abstract: In this paper we consider the discrete time/resource trade-off problem in project networks. Given a project network consisting of nodes (activities) and arcs (technological precedence relations specifying that an activity can only start when al of its predecessors have been completed), in which the duration of the activities is a discrete, on-increasing function of the amount of a single renewable resource committed to it, the discrete time/resource trade-off problem minimizes the project makespan subject to precedence constraints and a single renewable resource constraint. For each activity a work content is specified such that all execution modes (duration-resource pairs) for performing the activity are allowed as long as the product of the duration and the resource requirement is at least as large as the specified work content. We present a tabu search procedure which is based on subdividing the problem into a mode assignment phase and a resource-constrained project scheduling phase with fixed mode assignments. Extensive computational experience, including a comparison with other local search methods, is reported.Scheduling; Methods; Networks; Product; Assignment;

A Survey on Compiler Autotuning using Machine Learning

Since the mid-1990s, researchers have been trying to use machine-learning based approaches to solve a number of different compiler optimization problems. These techniques primarily enhance the quality of the obtained results and, more importantly, make it feasible to tackle two main compiler optimization problems: optimization selection (choosing which optimizations to apply) and phase-ordering (choosing the order of applying optimizations). The compiler optimization space continues to grow due to the advancement of applications, increasing number of compiler optimizations, and new target architectures. Generic optimization passes in compilers cannot fully leverage newly introduced optimizations and, therefore, cannot keep up with the pace of increasing options. This survey summarizes and classifies the recent advances in using machine learning for the compiler optimization field, particularly on the two major problems of (1) selecting the best optimizations and (2) the phase-ordering of optimizations. The survey highlights the approaches taken so far, the obtained results, the fine-grain classification among different approaches and finally, the influential papers of the field.Comment: version 5.0 (updated on September 2018)- Preprint Version For our Accepted Journal @ ACM CSUR 2018 (42 pages) - This survey will be updated quarterly here (Send me your new published papers to be added in the subsequent version) History: Received November 2016; Revised August 2017; Revised February 2018; Accepted March 2018

C++ Design Patterns for Low-latency Applications Including High-frequency Trading

This work aims to bridge the existing knowledge gap in the optimisation of latency-critical code, specifically focusing on high-frequency trading (HFT) systems. The research culminates in three main contributions: the creation of a Low-Latency Programming Repository, the optimisation of a market-neutral statistical arbitrage pairs trading strategy, and the implementation of the Disruptor pattern in C++. The repository serves as a practical guide and is enriched with rigorous statistical benchmarking, while the trading strategy optimisation led to substantial improvements in speed and profitability. The Disruptor pattern showcased significant performance enhancement over traditional queuing methods. Evaluation metrics include speed, cache utilisation, and statistical significance, among others. Techniques like Cache Warming and Constexpr showed the most significant gains in latency reduction. Future directions involve expanding the repository, testing the optimised trading algorithm in a live trading environment, and integrating the Disruptor pattern with the trading algorithm for comprehensive system benchmarking. The work is oriented towards academics and industry practitioners seeking to improve performance in latency-sensitive applications