Lock-free Parallel Dynamic Programming

We show a method for parallelizing top down dynamic programs in a straightforward way by a careful choice of a lock-free shared hash table implementation and randomization of the order in which the dynamic program computes its subproblems. This generic approach is applied to dynamic programs for knapsack, shortest paths, and RNA structure alignment, as well as to a state-of-the-art solution for minimizing the máximum number of open stacks. Experimental results are provided on three different modern multicore architectures which show that this parallelization is effective and reasonably scalable. In particular, we obtain over 10 times speedup for 32 threads on the open stacks problem.

Parallel Algorithms for FE-BE Coupling

When non linear physical systems of infinite extent are modelled, such as tunnels and perforations, it is necessary to simulate suitably the solution in the infinite as well as the non linearity. The finite element method (FEM) is a well known procedure for simulating the non linear behavior. However, the treatment of the infinite field with domain truncations is often questionable. On the other hand, the boundary element method (BEM) is suitable to simulate the infinite behavior without truncations. Because of this, by the combination of both methods, suitable use of the advantages of each one may be obtained. Several possibilities of FEM-BEM coupling and their performance in some practical cases are discussed in this paper. Parallelizable coupling algorithms based on domain decomposition are developed and compared with the most traditional coupling methods.

Automatic generation of portable multi-dimensionally decomposed parallel structured mesh software

Abstract not available

Suporte à computação paralela e distribuída em Java: API e comunicação entre nós cooperantes

Este trabalho é uma parte do tema global “Suporte à Computação Paralela e Distribuída em Java”, também tema da tese de Daniel Barciela no mestrado de Engenharia Informática do Instituto Superior de Engenharia do Porto. O seu objetivo principal consiste na definição/criação da interface com o programador, assim como também abrange a forma como os nós comunicam e cooperam entre si para a execução de determinadas tarefas, de modo a atingirem um único objetivo global. No âmbito desta dissertação foi realizado um estudo prévio relativamente aos modelos teóricos referentes à computação paralela, assim como também foram analisadas linguagens e frameworks que fornecem suporte a este mesmo tipo de computação. Este estudo teve como principal objetivo a análise da forma como estes modelos e linguagens permitem ao programador expressar o processamento paralelo no desenvolvimento das aplicações. Como resultado desta dissertação surgiu a framework denominada Distributed Parallel Framework for Java (DPF4j), cujo objetivo principal é fornecer aos programadores o suporte para o desenvolvimento de aplicações paralelas e distribuídas. Esta framework foi desenvolvida na linguagem Java. Esta dissertação contempla a parte referente à interface de programação e a toda a comunicação entre nós cooperantes da framework DPF4j. Por fim, foi demonstrado através dos testes realizados que a DPF4j, apesar de ser ainda um protótipo, já demonstra ter uma performance superior a outras frameworks e linguagens que possuem os mesmos objetivos.

Optimizing memory transactions for large-scale programs

Even though Software Transactional Memory (STM) is one of the most promising approaches to simplify concurrent programming, current STM implementations incur significant overheads that render them impractical for many real-sized programs. The key insight of this work is that we do not need to use the same costly barriers for all the memory managed by a real-sized application, if only a small fraction of the memory is under contention lightweight barriers may be used in this case. In this work, we propose a new solution based on an approach of adaptive object metadata (AOM) to promote the use of a fast path to access objects that are not under contention. We show that this approach is able to make the performance of an STM competitive with the best fine-grained lock-based approaches in some of the more challenging benchmarks. (C) 2015 Elsevier Inc. All rights reserved.

Flow updating: fault-tolerant aggregation for dynamic networks

Documento submetido para revisão pelos pares. A publicar em Journal of Parallel and Distributed Computing. ISSN 0743-7315

Efficient mining of discriminative molecular fragments

Frequent pattern discovery in structured data is receiving an increasing attention in many application areas of sciences. However, the computational complexity and the large amount of data to be explored often make the sequential algorithms unsuitable. In this context high performance distributed computing becomes a very interesting and promising approach. In this paper we present a parallel formulation of the frequent subgraph mining problem to discover interesting patterns in molecular compounds. The application is characterized by a highly irregular tree-structured computation. No estimation is available for task workloads, which show a power-law distribution in a wide range. The proposed approach allows dynamic resource aggregation and provides fault and latency tolerance. These features make the distributed application suitable for multi-domain heterogeneous environments, such as computational Grids. The distributed application has been evaluated on the well known National Cancer Institute’s HIV-screening dataset.

Supporting ad hoc collaborations in peer-to-peer networks

Traditionally, applications and tools supporting collaborative computing have been designed only with personal computers in mind and support a limited range of computing and network platforms. These applications are therefore not well equipped to deal with network heterogeneity and, in particular, do not cope well with dynamic network topologies. Progress in this area must be made if we are to fulfil the needs of users and support the diversity, mobility, and portability that are likely to characterise group work in future. This paper describes a groupware platform called Coco that is designed to support collaboration in a heterogeneous network environment. The work demonstrates that progress in the p development of a generic supporting groupware is achievable, even in the context of heterogeneous and dynamic networks. The work demonstrates the progress made in the development of an underlying communications infrastructure, building on peer-to-peer concept and topologies to improve scalability and robustness.

Nested parallelism for multi-core HPC systems using Java

Since its introduction in 1993, the Message Passing Interface (MPI) has become a de facto standard for writing High Performance Computing (HPC) applications on clusters and Massively Parallel Processors (MPPs). The recent emergence of multi-core processor systems presents a new challenge for established parallel programming paradigms, including those based on MPI. This paper presents a new Java messaging system called MPJ Express. Using this system, we exploit multiple levels of parallelism - messaging and threading - to improve application performance on multi-core processors. We refer to our approach as nested parallelism. This MPI-like Java library can support nested parallelism by using Java or Java OpenMP (JOMP) threads within an MPJ Express process. Practicality of this approach is assessed by porting to Java a massively parallel structure formation code from Cosmology called Gadget-2. We introduce nested parallelism in the Java version of the simulation code and report good speed-ups. To the best of our knowledge it is the first time this kind of hybrid parallelism is demonstrated in a high performance Java application. (C) 2009 Elsevier Inc. All rights reserved.

An oblivious shortest-path routing algorithm for fully connected cubic networks

Fully connected cubic networks (FCCNs) are a class of newly proposed hierarchical interconnection networks for multicomputer systems, which enjoy the strengths of constant node degree and good expandability. The shortest path routing in FCCNs is an open problem. In this paper, we present an oblivious routing algorithm for n-level FCCN with N = 8(n) nodes, and prove that this algorithm creates a shortest path from the source to the destination. At the costs of both an O(N)-parallel-step off-line preprocessing phase and a list of size N stored at each node, the proposed algorithm is carried out at each related node in O(n) time. In some cases the proposed algorithm is superior to the one proposed by Chang and Wang in terms of the length of the routing path. This justifies the utility of our routing strategy. (C) 2006 Elsevier Inc. All rights reserved.

Fault tolerant decentralised K-Means clustering for asynchronous large-scale networks

The K-Means algorithm for cluster analysis is one of the most influential and popular data mining methods. Its straightforward parallel formulation is well suited for distributed memory systems with reliable interconnection networks, such as massively parallel processors and clusters of workstations. However, in large-scale geographically distributed systems the straightforward parallel algorithm can be rendered useless by a single communication failure or high latency in communication paths. The lack of scalable and fault tolerant global communication and synchronisation methods in large-scale systems has hindered the adoption of the K-Means algorithm for applications in large networked systems such as wireless sensor networks, peer-to-peer systems and mobile ad hoc networks. This work proposes a fully distributed K-Means algorithm (EpidemicK-Means) which does not require global communication and is intrinsically fault tolerant. The proposed distributed K-Means algorithm provides a clustering solution which can approximate the solution of an ideal centralised algorithm over the aggregated data as closely as desired. A comparative performance analysis is carried out against the state of the art sampling methods and shows that the proposed method overcomes the limitations of the sampling-based approaches for skewed clusters distributions. The experimental analysis confirms that the proposed algorithm is very accurate and fault tolerant under unreliable network conditions (message loss and node failures) and is suitable for asynchronous networks of very large and extreme scale.

Fine-grained multi-phase array designs

Hybrid multiprocessor architectures which combine re-configurable computing and multiprocessors on a chip are being proposed to transcend the performance of standard multi-core parallel systems. Both fine-grained and coarse-grained parallel algorithm implementations are feasible in such hybrid frameworks. A compositional strategy for designing fine-grained multi-phase regular processor arrays to target hybrid architectures is presented in this paper. The method is based on deriving component designs using classical regular array techniques and composing the components into a unified global design. Effective designs with phase-changes and data routing at run-time are characteristics of these designs. In order to describe the data transfer between phases, the concept of communication domain is introduced so that the producer–consumer relationship arising from multi-phase computation can be treated in a unified way as a data routing phase. This technique is applied to derive new designs of multi-phase regular arrays with different dataflow between phases of computation.

Application execution management on the InteGrade opportunistic grid middleware

The InteGrade project is a multi-university effort to build a novel grid computing middleware based on the opportunistic use of resources belonging to user workstations. The InteGrade middleware currently enables the execution of sequential, bag-of-tasks, and parallel applications that follow the BSP or the MPI programming models. This article presents the lessons learned over the last five years of the InteGrade development and describes the solutions achieved concerning the support for robust application execution. The contributions cover the related fields of application scheduling, execution management, and fault tolerance. We present our solutions, describing their implementation principles and evaluation through the analysis of several experimental results. (C) 2010 Elsevier Inc. All rights reserved.

A transactional runtime system for the Cell/BE architecture

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Application of ontologies in peer-to-peer database with routing queries based on ant colony algorithm

A significant set of information stored in different databases around the world, can be shared through peer-topeer databases. With that, is obtained a large base of knowledge, without the need for large investments because they are used existing databases, as well as the infrastructure in place. However, the structural characteristics of peer-topeer, makes complex the process of finding such information. On the other side, these databases are often heterogeneous in their schemas, but semantically similar in their content. A good peer-to-peer databases systems should allow the user access information from databases scattered across the network and receive only the information really relate to your topic of interest. This paper proposes to use ontologies in peer-to-peer database queries to represent the semantics inherent to the data. The main contribution of this work is enable integration between heterogeneous databases, improve the performance of such queries and use the algorithm of optimization Ant Colony to solve the problem of locating information on peer-to-peer networks, which presents an improve of 18% in results. © 2011 IEEE.