GPU-accelerated Parallel Solutions to the Quadratic Assignment Problem

The Quadratic Assignment Problem (QAP) is an important combinatorial optimization problem with applications in many areas including logistics and manufacturing. QAP is known to be NP-hard, a computationally challenging problem, which requires the use of sophisticated heuristics in finding acceptable solutions for most real-world data sets. In this paper, we present GPU-accelerated implementations of a 2opt and a tabu search algorithm for solving the QAP. For both algorithms, we extract parallelism at multiple levels and implement novel code optimization techniques that fully utilize the GPU hardware. On a series of experiments on the well-known QAPLIB data sets, our solutions, on average run an order-of-magnitude faster than previous implementations and deliver up to a factor of 63 speedup on specific instances. The quality of the solutions produced by our implementations of 2opt and tabu is within 1.03% and 0.15% of the best known values. The experimental results also provide key insight into the performance characteristics of accelerated QAP solvers. In particular, the results reveal that both algorithmic choice and the shape of the input data sets are key factors in finding efficient implementations.Comment: 25 pages, 9 figures; parts of this work appeared as short papers in XSEDE14 and XSEDE15 conferences. This version of the paper is a substantial extension of previous work with optimizations for newer GPU platforms and extended experimental result

A GPU-based Iterated Tabu Search for Solving the Quadratic 3-dimensional Assignment Problem

International audienceThe quadratic 3-dimensional assignment problem (Q3AP) is an extension of the well-known NP-hard quadratic assignment problem. It has been proved to be one of the most difficult combinatorial optimization problems. Local search (LS) algorithms are a class of heuristics which have been successfully applied to solve such hard optimization problem. These methods handle with a single solution iteratively improved by exploring its neighborhood in the solution space. In this paper, we propose an iterated tabu search for solving the Q3AP. The design of this algorithm is essentially based on a new large neighborhood structure. Indeed, in LS heuristics, designing operators to explore large promising regions of the search space may improve the quality of the obtained solutions. However, designing such neighborhood is at the expense of a highly computationally process. Therefore, the use of graphics processing units (GPUs) provides an efficient complementary way to speed up the search. The proposed GPU-based iterated tabu search has been experimented on 5 different Q3AP instances. The obtained results are convincing both in terms of efficiency, quality and robustness of the provided solutions at run time

Parallel Hybrid Evolutionary Algorithms on GPU

International audienceOver the last years, interest in hybrid metaheuristics has risen considerably in the field of optimization. Combinations of methods such as evolutionary algorithms and local searches have provided very powerful search algorithms. However, due to their complexity, the computational time of the solution search exploration remains exorbitant when large problem instances are to be solved. Therefore, the use of GPU-based parallel computing is required as a complementary way to speed up the search. This paper presents a new methodology to design and implement efficiently and effectively hybrid evolutionary algorithms on GPU accelerators. The methodology enables efficient mappings of the explored search space onto the GPU memory hierarchy. The experimental results show that the approach is very efficient especially for large problem instances

Parallel Local Search on GPU

www.lifl.fr/~luongLocal search algorithms are a class of algorithms to solve complex optimization problems in science and industry. Even if these metaheuristics allow to significantly reduce the computational time of the solution exploration space, the iterative process remains costly when very large problem instances are dealt with. As a solution, graphics processing units (GPUs) represent an efficient alternative for calculations instead of traditional CPU. This paper presents a new methodology to design and implement local search algorithms on GPU. Methods such as tabu search, hill climbing or iterated local search present similar concepts that can be parallelized on GPU and then a general cooperative model can be highlighted. In addition to single-solution based metaheuristics on GPU, this model can be extended with a hybrid multi-core and multi-GPU approach for multiple local search methods such as multistart. The conclusions from both GPU and multi-GPU experiments indicate significant speed-ups compared to CPU approaches

GPU-based Approaches for Multiobjective Local Search Algorithms. A Case Study: the Flowshop Scheduling Problem

International audienceMultiobjective local search algorithms are efficient methods to solve complex problems in science and industry. Even if these heuristics allow to significantly reduce the computational time of the solution search space exploration, this latter cost remains exorbitant when very large problem instances are to be solved. As a result, the use of GPU computing has been recently revealed as an efficient way to accelerate the search process. This paper presents a new methodology to design and implement efficiently GPU-based multiobjective local search algorithms. The experimental results show that the approach is promising especially for large problem instances

Computing Platforms for Big Biological Data Analytics: Perspectives and Challenges.

The last decade has witnessed an explosion in the amount of available biological sequence data, due to the rapid progress of high-throughput sequencing projects. However, the biological data amount is becoming so great that traditional data analysis platforms and methods can no longer meet the need to rapidly perform data analysis tasks in life sciences. As a result, both biologists and computer scientists are facing the challenge of gaining a profound insight into the deepest biological functions from big biological data. This in turn requires massive computational resources. Therefore, high performance computing (HPC) platforms are highly needed as well as efficient and scalable algorithms that can take advantage of these platforms. In this paper, we survey the state-of-the-art HPC platforms for big biological data analytics. We first list the characteristics of big biological data and popular computing platforms. Then we provide a taxonomy of different biological data analysis applications and a survey of the way they have been mapped onto various computing platforms. After that, we present a case study to compare the efficiency of different computing platforms for handling the classical biological sequence alignment problem. At last we discuss the open issues in big biological data analytics

Optimisation massivement multi-tâche sur grappes de calcul hétérogènes – Application aux problèmes de permutation

Branch-and-Bound (B&B) is a frequently used tree-search exploratory method for the exact resolution of combinatorial optimization problems (COPs). However, in practice, only small problem instances can be solved on a sequential computer, as B&B generates often generates a huge amount of subproblems to be evaluated. In order to solve large COPs, we revisit the design and implementation of massively parallel B&B on top of large heterogeneous clusters, integrating multi-core CPUs, many-core processors and GPUs.For the efficient storage and management of subproblems an original data structure (IVM) dedicated to permutation problems is used. Because of the highly irregular and unpredictable shape of the B&B tree, dynamic load balancing between parallel exploration processes is one of the main issues addressed in this thesis. Based on a compact encoding of the search space in the form of intervals, work stealing strategies for multi-core and GPU are proposed, as well as hierarchical approaches for load balancing in distributed memory multi-CPU/multi-GPU systems. Three permutation problems, the Flowshop Scheduling Problem (FSP), the Quadratic Assignment Problem (QAP) and the n-Queens puzzle problem are used as test-cases.The resolution, in 9 hours, of a FSP instance with an estimated sequential execution time of 22 years demonstrates the scalability of the proposed algorithms on a cluster composed of 36 GPUs.L'algorithme Branch-and-Bound (B&B) est une méthode de recherche arborescente fréquemment utilisé pour la résolution exacte de problèmes d'optimisation combinatoire (POC). Néanmoins, seules des petites instances peuvent être effectivement résolues sur une machine séquentielle, le nombre de sous-problèmes à évaluer étant souvent très grand. Visant la resolution de POC de grande taille, nous réexaminons la conception et l'implémentation d'algorithmes B&B massivement parallèles sur de larges plateformes hétérogènes de calcul, intégrant des processeurs multi-coeurs, many-cores et et processeurs graphiques (GPUs). Pour une représentation compacte en mémoire des sous-problèmes une structure de données originale (IVM), dédiée aux problèmes de permutation est utilisée. En raison de la forte irrégularité de l'arbre de recherche, l'équilibrage de charge dynamique entre processus d'exploration parallèles occupe une place centrale dans cette thèse. Basés sur un encodage compact de l'espace de recherche sous forme d'intervalles, des stratégies de vol de tâches sont proposées pour processeurs multi-core et GPU, ainsi une approche hiérarchique pour l'équilibrage de charge dans les systèmes multi-GPU et multi-CPU à mémoire distribuée. Trois problèmes d'optimisation définis sur l'ensemble des permutations, le problème d'ordonnancement Flow-Shop (FSP), d'affectation quadratique (QAP) et le problème des n-dames sont utilisés comme cas d'étude. La resolution en 9 heures d'une instance du FSP dont le temps de résolution séquentiel est estimé à 22 ans demontre la capacité de passage à l'échelle des algorithmes proposés sur une grappe de calcul composé de 36 GPUs

GPU Computing for Parallel Local Search Metaheuristics

International audienceLocal search metaheuristics (LSMs) are efficient methods for solving complex problems in science and industry. They allow significantly to reduce the size of the search space to be explored and the search time. Nevertheless, the resolution time remains prohibitive when dealing with large problem instances. Therefore, the use of GPU-based massively parallel computing is a major complementary way to speed up the search. However, GPU computing for LSMs is rarely investigated in the literature. In this paper, we introduce a new guideline for the design and implementation of effective LSMs on GPU. Very efficient approaches are proposed for CPU-GPU data transfer optimization, thread control, mapping of neighboring solutions to GPU threads and memory management. These approaches have been experimented using four well-known combinatorial and continuous optimization problems and four GPU configurations. Compared to a CPU-based execution, accelerations up to x80 are reported for the large combinatorial problems and up to x240 for a continuous problem. Finally, extensive experiments demonstrate the strong potential of GPU-based LSMs compared to cluster or grid-based parallel architectures

Registration using Graphics Processor Unit

Data point set registration is an important operation in coordinate metrology. Registration is the operation by which sampled point clouds are aligned with a CAD model by a 4X4 homogeneous transformation (e.g., rotation and translation). This alignment permits validation of the produced artifact\u27s geometry. State-of-the-art metrology systems are now capable of generating thousands, if not millions, of data points during an inspection operation, resulting in increased computational power to fully utilize these larger data sets. The registration process is an iterative nonlinear optimization operation having an execution time directly related to the number of points processed and CAD model complexity. The objective function to be minimized by this optimization is the sum of the square distances between each point in the point cloud and the closest surface in the CAD model. A brute force approach to registration, which is often used, is to compute the minimum distance between each point and each surface in the CAD model. As point cloud sizes and CAD model complexity increase, this approach becomes intractable and inefficient. Highly efficient numerical and analytical gradient based algorithms exist and their goal is to convergence to an optimal solution in minimum time. This thesis presents a new approach to efficiently perform the registration process by employing readily available computer hardware, the graphical processor unit (GPU). The data point set registration time for the GPU shows a significant improvement (around 15-20 times) over typical CPU performance. Efficient GPU programming decreases the complexity of the steps and improves the rate of convergence of the existing algorithms. The experimental setup reveals the exponential increasing nature of the CPU and the linear performance of the GPU in various aspects of an algorithm. The importance of CPU in the GPU programming is highlighted. The future implementations disclose the possible extensions of a GPU for higher order and complex coordinate metrology algorithms