Multicore Scheduling of Real-Time Irregular Parallel Algorithms in Linux

Face à estagnação da tecnologia uniprocessador registada na passada década, aos principais fabricantes de microprocessadores encontraram na tecnologia multi-core a resposta `as crescentes necessidades de processamento do mercado. Durante anos, os desenvolvedores de software viram as suas aplicações acompanhar os ganhos de performance conferidos por cada nova geração de processadores sequenciais, mas `a medida que a capacidade de processamento escala em função do número de processadores, a computação sequencial tem de ser decomposta em várias partes concorrentes que possam executar em paralelo, para que possam utilizar as unidades de processamento adicionais e completar mais rapidamente. A programação paralela implica um paradigma completamente distinto da programação sequencial. Ao contrário dos computadores sequenciais tipificados no modelo de Von Neumann, a heterogeneidade de arquiteturas paralelas requer modelos de programação paralela que abstraiam os programadores dos detalhes da arquitectura e simplifiquem o desenvolvimento de aplicações concorrentes. Os modelos de programação paralela mais populares incitam os programadores a identificar instruções concorrentes na sua lógica de programação, e a especificá-las sob a forma de tarefas que possam ser atribuídas a processadores distintos para executarem em simultâneo. Estas tarefas são tipicamente lançadas durante a execução, e atribuídas aos processadores pelo motor de execução subjacente. Como os requisitos de processamento costumam ser variáveis, e não são conhecidos a priori, o mapeamento de tarefas para processadores tem de ser determinado dinamicamente, em resposta a alterações imprevisíveis dos requisitos de execução. `A medida que o volume da computação cresce, torna-se cada vez menos viável garantir as suas restrições temporais em plataformas uniprocessador. Enquanto os sistemas de tempo real se começam a adaptar ao paradigma de computação paralela, há uma crescente aposta em integrar execuções de tempo real com aplicações interativas no mesmo hardware, num mundo em que a tecnologia se torna cada vez mais pequena, leve, ubíqua, e portável. Esta integração requer soluções de escalonamento que simultaneamente garantam os requisitos temporais das tarefas de tempo real e mantenham um nível aceitável de QoS para as restantes execuções. Para tal, torna-se imperativo que as aplicações de tempo real paralelizem, de forma a minimizar os seus tempos de resposta e maximizar a utilização dos recursos de processamento. Isto introduz uma nova dimensão ao problema do escalonamento, que tem de responder de forma correcta a novos requisitos de execução imprevisíveis e rapidamente conjeturar o mapeamento de tarefas que melhor beneficie os critérios de performance do sistema. A técnica de escalonamento baseado em servidores permite reservar uma fração da capacidade de processamento para a execução de tarefas de tempo real, e assegurar que os efeitos de latência na sua execução não afectam as reservas estipuladas para outras execuções. No caso de tarefas escalonadas pelo tempo de execução máximo, ou tarefas com tempos de execução variáveis, torna-se provável que a largura de banda estipulada não seja consumida por completo. Para melhorar a utilização do sistema, os algoritmos de partilha de largura de banda (capacity-sharing) doam a capacidade não utilizada para a execução de outras tarefas, mantendo as garantias de isolamento entre servidores. Com eficiência comprovada em termos de espaço, tempo, e comunicação, o mecanismo de work-stealing tem vindo a ganhar popularidade como metodologia para o escalonamento de tarefas com paralelismo dinâmico e irregular. O algoritmo p-CSWS combina escalonamento baseado em servidores com capacity-sharing e work-stealing para cobrir as necessidades de escalonamento dos sistemas abertos de tempo real. Enquanto o escalonamento em servidores permite partilhar os recursos de processamento sem interferências a nível dos atrasos, uma nova política de work-stealing que opera sobre o mecanismo de capacity-sharing aplica uma exploração de paralelismo que melhora os tempos de resposta das aplicações e melhora a utilização do sistema. Esta tese propõe uma implementação do algoritmo p-CSWS para o Linux. Em concordância com a estrutura modular do escalonador do Linux, ´e definida uma nova classe de escalonamento que visa avaliar a aplicabilidade da heurística p-CSWS em circunstâncias reais. Ultrapassados os obstáculos intrínsecos `a programação da kernel do Linux, os extensos testes experimentais provam que o p-CSWS ´e mais do que um conceito teórico atrativo, e que a exploração heurística de paralelismo proposta pelo algoritmo beneficia os tempos de resposta das aplicações de tempo real, bem como a performance e eficiência da plataforma multiprocessador.

PARALLEL ALGORITHMS FOR MAXIMAL CLIQUES IN CIRCLE GRAPHS AND UNRESTRICTED DEPTH SEARCH

We present parallel algorithms on the BSP/CGM model, with p processors, to count and generate all the maximal cliques of a circle graph with n vertices and m edges. To count the number of all the maximal cliques, without actually generating them, our algorithm requires O(log p) communication rounds with O(nm/p) local computation time. We also present an algorithm to generate the first maximal clique in O(log p) communication rounds with O(nm/p) local computation, and to generate each one of the subsequent maximal cliques this algorithm requires O(log p) communication rounds with O(m/p) local computation. The maximal cliques generation algorithm is based on generating all maximal paths in a directed acyclic graph, and we present an algorithm for this problem that uses O(log p) communication rounds with O(m/p) local computation for each maximal path. We also show that the presented algorithms can be extended to the CREW PRAM model.

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.

Parallel algorithms for network routing problems and recurrences /

"Grant no. US NSF MCS75-21758."

Energy consumption of parallel algorithms for solving linear systems on HPC architecture

Modern High-Performance Computing HPC systems are gradually increasing in size and complexity due to the correspondent demand of larger simulations requiring more complicated tasks and higher accuracy. However, as side effects of the Dennard’s scaling approaching its ultimate power limit, the efficiency of software plays also an important role in increasing the overall performance of a computation. Tools to measure application performance in these increasingly complex environments provide insights into the intricate ways in which software and hardware interact. The monitoring of the power consumption in order to save energy is possible through processors interfaces like Intel Running Average Power Limit RAPL. Given the low level of these interfaces, they are often paired with an application-level tool like Performance Application Programming Interface PAPI. Since several problems in many heterogeneous fields can be represented as a complex linear system, an optimized and scalable linear system solver algorithm can decrease significantly the time spent to compute its resolution. One of the most widely used algorithms deployed for the resolution of large simulation is the Gaussian Elimination, which has its most popular implementation for HPC systems in the Scalable Linear Algebra PACKage ScaLAPACK library. However, another relevant algorithm, which is increasing in popularity in the academic field, is the Inhibition Method. This thesis compares the energy consumption of the Inhibition Method and Gaussian Elimination from ScaLAPACK to profile their execution during the resolution of linear systems above the HPC architecture offered by CINECA. Moreover, it also collates the energy and power values for different ranks, nodes, and sockets configurations. The monitoring tools employed to track the energy consumption of these algorithms are PAPI and RAPL, that will be integrated with the parallel execution of the algorithms managed with the Message Passing Interface MPI.

Parallel relaxed and extrapolated algorithms for computing PageRank

In this paper, parallel Relaxed and Extrapolated algorithms based on the Power method for accelerating the PageRank computation are presented. Different parallel implementations of the Power method and the proposed variants are analyzed using different data distribution strategies. The reported experiments show the behavior and effectiveness of the designed algorithms for realistic test data using either OpenMP, MPI or an hybrid OpenMP/MPI approach to exploit the benefits of shared memory inside the nodes of current SMP supercomputers.

A many-core co-processor for embedded parallel computing on FPGA

Single processor architectures are unable to provide the required performance of high performance embedded systems. Parallel processing based on general-purpose processors can achieve these performances with a considerable increase of required resources. However, in many cases, simplified optimized parallel cores can be used instead of general-purpose processors achieving better performance at lower resource utilization. In this paper, we propose a configurable many-core architecture to serve as a co-processor for high-performance embedded computing on Field-Programmable Gate Arrays. The architecture consists of an array of configurable simple cores with support for floating-point operations interconnected with a configurable interconnection network. For each core it is possible to configure the size of the internal memory, the supported operations and number of interfacing ports. The architecture was tested in a ZYNQ-7020 FPGA in the execution of several parallel algorithms. The results show that the proposed many-core architecture achieves better performance than that achieved with a parallel generalpurpose processor and that up to 32 floating-point cores can be implemented in a ZYNQ-7020 SoC FPGA.

Parallel programming in biomedical signal processing

Dissertação para obtenção do Grau de Mestre em Engenharia Biomédica

A public transport bus assignment problem: parallel metaheuristics assessment

Combinatorial Optimization Problems occur in a wide variety of contexts and generally are NP-hard problems. At a corporate level solving this problems is of great importance since they contribute to the optimization of operational costs. In this thesis we propose to solve the Public Transport Bus Assignment problem considering an heterogeneous fleet and line exchanges, a variant of the Multi-Depot Vehicle Scheduling Problem in which additional constraints are enforced to model a real life scenario. The number of constraints involved and the large number of variables makes impracticable solving to optimality using complete search techniques. Therefore, we explore metaheuristics, that sacrifice optimality to produce solutions in feasible time. More concretely, we focus on the development of algorithms based on a sophisticated metaheuristic, Ant-Colony Optimization (ACO), which is based on a stochastic learning mechanism. For complex problems with a considerable number of constraints, sophisticated metaheuristics may fail to produce quality solutions in a reasonable amount of time. Thus, we developed parallel shared-memory (SM) synchronous ACO algorithms, however, synchronism originates the straggler problem. Therefore, we proposed three SM asynchronous algorithms that break the original algorithm semantics and differ on the degree of concurrency allowed while manipulating the learned information. Our results show that our sequential ACO algorithms produced better solutions than a Restarts metaheuristic, the ACO algorithms were able to learn and better solutions were achieved by increasing the amount of cooperation (number of search agents). Regarding parallel algorithms, our asynchronous ACO algorithms outperformed synchronous ones in terms of speedup and solution quality, achieving speedups of 17.6x. The cooperation scheme imposed by asynchronism also achieved a better learning rate than the original one.

Properties and algorithms of the (n, k)-star graphs

The (n, k)-star interconnection network was proposed in 1995 as an attractive alternative to the n-star topology in parallel computation. The (n, k )-star has significant advantages over the n-star which itself was proposed as an attractive alternative to the popular hypercube. The major advantage of the (n, k )-star network is its scalability, which makes it more flexible than the n-star as an interconnection network. In this thesis, we will focus on finding graph theoretical properties of the (n, k )-star as well as developing parallel algorithms that run on this network. The basic topological properties of the (n, k )-star are first studied. These are useful since they can be used to develop efficient algorithms on this network. We then study the (n, k )-star network from algorithmic point of view. Specifically, we will investigate both fundamental and application algorithms for basic communication, prefix computation, and sorting, etc. A literature review of the state-of-the-art in relation to the (n, k )-star network as well as some open problems in this area are also provided.

Properties and algorithms of the (n, k)-arrangement graphs

The (n, k)-arrangement interconnection topology was first introduced in 1992. The (n, k )-arrangement graph is a class of generalized star graphs. Compared with the well known n-star, the (n, k )-arrangement graph is more flexible in degree and diameter. However, there are few algorithms designed for the (n, k)-arrangement graph up to present. In this thesis, we will focus on finding graph theoretical properties of the (n, k)- arrangement graph and developing parallel algorithms that run on this network. The topological properties of the arrangement graph are first studied. They include the cyclic properties. We then study the problems of communication: broadcasting and routing. Embedding problems are also studied later on. These are very useful to develop efficient algorithms on this network. We then study the (n, k )-arrangement network from the algorithmic point of view. Specifically, we will investigate both fundamental and application algorithms such as prefix sums computation, sorting, merging and basic geometry computation: finding convex hull on the (n, k )-arrangement graph. A literature review of the state-of-the-art in relation to the (n, k)-arrangement network is also provided, as well as some open problems in this area.

Properties and Algorithms of the KCube Graphs

The KCube interconnection topology was rst introduced in 2010. The KCube graph is a compound graph of a Kautz digraph and hypercubes. Compared with the at- tractive Kautz digraph and well known hypercube graph, the KCube graph could accommodate as many nodes as possible for a given indegree (and outdegree) and the diameter of interconnection networks. However, there are few algorithms designed for the KCube graph. In this thesis, we will concentrate on nding graph theoretical properties of the KCube graph and designing parallel algorithms that run on this network. We will explore several topological properties, such as bipartiteness, Hamiltonianicity, and symmetry property. These properties for the KCube graph are very useful to develop efficient algorithms on this network. We will then study the KCube network from the algorithmic point of view, and will give an improved routing algorithm. In addition, we will present two optimal broadcasting algorithms. They are fundamental algorithms to many applications. A literature review of the state of the art network designs in relation to the KCube network as well as some open problems in this field will also be given.

Performance results of running parallel applications on the InteGrade

The InteGrade middleware intends to exploit the idle time of computing resources in computer laboratories. In this work we investigate the performance of running parallel applications with communication among processors on the InteGrade grid. As costly communication on a grid can be prohibitive, we explore the so-called systolic or wavefront paradigm to design the parallel algorithms in which no global communication is used. To evaluate the InteGrade middleware we considered three parallel algorithms that solve the matrix chain product problem, the 0-1 Knapsack Problem, and the local sequence alignment problem, respectively. We show that these three applications running under the InteGrade middleware and MPI take slightly more time than the same applications running on a cluster with only LAM-MPI support. The results can be considered promising and the time difference between the two is not substantial. The overhead of the InteGrade middleware is acceptable, in view of the benefits obtained to facilitate the use of grid computing by the user. These benefits include job submission, checkpointing, security, job migration, etc. Copyright (C) 2009 John Wiley & Sons, Ltd.

Improvements in the score matrix calculation method using parallel score estimating algorithm

The increasing amount of sequences stored in genomic databases has become unfeasible to the sequential analysis. Then, the parallel computing brought its power to the Bioinformatics through parallel algorithms to align and analyze the sequences, providing improvements mainly in the running time of these algorithms. In many situations, the parallel strategy contributes to reducing the computational complexity of the big problems. This work shows some results obtained by an implementation of a parallel score estimating technique for the score matrix calculation stage, which is the first stage of a progressive multiple sequence alignment. The performance and quality of the parallel score estimating are compared with the results of a dynamic programming approach also implemented in parallel. This comparison shows a significant reduction of running time. Moreover, the quality of the final alignment, using the new strategy, is analyzed and compared with the quality of the approach with dynamic programming.