A cooperative conjugate gradient method for linear systems permitting multithread implementation of low complexity

This paper proposes a generalization of the conjugate gradient (CG) method used to solve the equation $Ax=b$ for a symmetric positive definite matrix $A$ of large size $n$. The generalization consists of permitting the scalar control parameters (= stepsizes in gradient and conjugate gradient directions) to be replaced by matrices, so that multiple descent and conjugate directions are updated simultaneously. Implementation involves the use of multiple agents or threads and is referred to as cooperative CG (cCG), in which the cooperation between agents resides in the fact that the calculation of each entry of the control parameter matrix now involves information that comes from the other agents. For a sufficiently large dimension $n$, the use of an optimal number of cores gives the result that the multithread implementation has worst case complexity $O(n^{2+1/3})$ in exact arithmetic. Numerical experiments, that illustrate the interest of theoretical results, are carried out on a multicore computer.Comment: Expanded version of manuscript submitted to the IEEE-CDC 2012 (Conference on Decision and Control

A load-sharing architecture for high performance optimistic simulations on multi-core machines

In Parallel Discrete Event Simulation (PDES), the simulation model is partitioned into a set of distinct Logical Processes (LPs) which are allowed to concurrently execute simulation events. In this work we present an innovative approach to load-sharing on multi-core/multiprocessor machines, targeted at the optimistic PDES paradigm, where LPs are speculatively allowed to process simulation events with no preventive verification of causal consistency, and actual consistency violations (if any) are recovered via rollback techniques. In our approach, each simulation kernel instance, in charge of hosting and executing a specific set of LPs, runs a set of worker threads, which can be dynamically activated/deactivated on the basis of a distributed algorithm. The latter relies in turn on an analytical model that provides indications on how to reassign processor/core usage across the kernels in order to handle the simulation workload as efficiently as possible. We also present a real implementation of our load-sharing architecture within the ROme OpTimistic Simulator (ROOT-Sim), namely an open-source C-based simulation platform implemented according to the PDES paradigm and the optimistic synchronization approach. Experimental results for an assessment of the validity of our proposal are presented as well

Parallel detrended fluctuation analysis for fast event detection on massive PMU data

("(c) 2015 IEEE. Personal use of this material is permitted. Permission from IEEE must be obtained for all other users, including reprinting/ republishing this material for advertising or promotional purposes, creating new collective works for resale or redistribution to servers or lists, or reuse of any copyrighted components of this work in other works.")Phasor measurement units (PMUs) are being rapidly deployed in power grids due to their high sampling rates and synchronized measurements. The devices high data reporting rates present major computational challenges in the requirement to process potentially massive volumes of data, in addition to new issues surrounding data storage. Fast algorithms capable of processing massive volumes of data are now required in the field of power systems. This paper presents a novel parallel detrended fluctuation analysis (PDFA) approach for fast event detection on massive volumes of PMU data, taking advantage of a cluster computing platform. The PDFA algorithm is evaluated using data from installed PMUs on the transmission system of Great Britain from the aspects of speedup, scalability, and accuracy. The speedup of the PDFA in computation is initially analyzed through Amdahl's Law. A revision to the law is then proposed, suggesting enhancements to its capability to analyze the performance gain in computation when parallelizing data intensive applications in a cluster computing environment

Performance analysis and tuning in multicore environments

Performance analysis is the task of monitor the behavior of a program execution. The main goal is to find out the possible adjustments that might be done in order improve the performance. To be able to get that improvement it is necessary to find the different causes of overhead. Nowadays we are already in the multicore era, but there is a gap between the level of development of the two main divisions of multicore technology (hardware and software). When we talk about multicore we are also speaking of shared memory systems, on this master thesis we talk about the issues involved on the performance analysis and tuning of applications running specifically in a shared Memory system. We move one step ahead to take the performance analysis to another level by analyzing the applications structure and patterns. We also present some tools specifically addressed to the performance analysis of OpenMP multithread application. At the end we present the results of some experiments performed with a set of OpenMP scientific application.Análisis de rendimiento es el área de estudio encargada de monitorizar el comportamiento de la ejecución de programas informáticos. El principal objetivo es encontrar los posibles ajustes que serán necesarios para mejorar el rendimiento. Para poder obtener esa mejora es necesario encontrar las principales causas de overhead. Actualmente estamos sumergidos en la era multicore, pero existe una brecha entre el nivel de desarrollo de sus dos principales divisiones (hardware y software). Cuando hablamos de multicore también estamos hablando de sistemas de memoria compartida. Nosotros damos un paso más al abordar el análisis de rendimiento a otro nivel por medio del estudio de la estructura de las aplicaciones y sus patrones. También presentamos herramientas de análisis de aplicaciones que son específicas para el análisis de rendimiento de aplicaciones paralelas desarrolladas con OpenMP. Al final presentamos los resultados de algunos experimentos realizados con un grupo de aplicaciones científicas desarrolladas bajo este modelo de programación.L'Anàlisi de rendiment és l'àrea d'estudi encarregada de monitorar el comportament de l'execució de programes informàtics. El principal objectiu és trobar els possibles ajustaments que seran necessaris per a millorar el rendiment. Per a poder obtenir aquesta millora és necessari trobar les principals causes de l'overhead (excessos de computació no productiva). Actualment estem immersos en l'era multicore, però existeix una rasa entre el nivell de desenvolupament de les seves dues principals divisions (maquinari i programari). Quan parlam de multicore, també estem parlant de sistemes de memòria compartida. Nosaltres donem un pas més per a abordar l'anàlisi de rendiment en un altre nivell per mitjà de l'estudi de l'estructura de les aplicacions i els seus patrons. També presentem eines d'anàlisis d'aplicacions que són específiques per a l'anàlisi de rendiment d'aplicacions paral·leles desenvolupades amb OpenMP. Al final, presentem els resultats d'alguns experiments realitzats amb un grup d'aplicacions científiques desenvolupades sota aquest model de programació

A Parallel Mesh-Adaptive Framework for Hyperbolic Conservation Laws

We report on the development of a computational framework for the parallel, mesh-adaptive solution of systems of hyperbolic conservation laws like the time-dependent Euler equations in compressible gas dynamics or Magneto-Hydrodynamics (MHD) and similar models in plasma physics. Local mesh refinement is realized by the recursive bisection of grid blocks along each spatial dimension, implemented numerical schemes include standard finite-differences as well as shock-capturing central schemes, both in connection with Runge-Kutta type integrators. Parallel execution is achieved through a configurable hybrid of POSIX-multi-threading and MPI-distribution with dynamic load balancing. One- two- and three-dimensional test computations for the Euler equations have been carried out and show good parallel scaling behavior. The Racoon framework is currently used to study the formation of singularities in plasmas and fluids.Comment: late submissio

PARALLEL COMPUTING ALGORITHMS FOR TANDEM

Tandem mass spectrometry, also known as MS/MS, is an analytical technique to measure the mass-to-charge ratio of charged ions and widely used in genomics, proteomics and metabolomics areas. There are two types of automatic ways to interpret tandem mass spectra: de novo methods and database searching methods. Both of them need to use massive computational resources and complicated comparison algorithms. The real-time peptide-spectrum matching (RT-PSM) algorithm is a database searching method to interpret tandem mass spectra with strict time constraints. Restricted by the hardware and architecture of an individual workstation the RT-PSM algorithm has to sacrifice the level of accuracy in order to provide prerequisite processing speed. The peptide-spectrum similarity scoring module is the most time-consuming part out of four modules in the RT-PSM algorithm, which is also the core of the algorithm. In this study, a multi-core computing algorithm is developed for individual workstations. Moreover, a distributed computing algorithm is designed for a cluster. The improved algorithms can achieve the speed requirement of RT-PSM without sacrificing the accuracy. With some expansion, this distributed computing algorithm can also support different PSM algorithms. Simulation results show that compared with the original RT-PSM, the parallelization version achieves 25 to 34 times speed-up based on different individual workstations. A cluster with 240 CPU cores could accelerate the similarity score module 210 times compare with the single-thread similarity score module and the whole peptide identification process 85 times compare with the single-thread peptide identification process

A Graph Grammar to Transform a Dataflow Graph into a Multithread Graph and its Application in Task Scheduling

The scheduling of tasks in a parallel program is an NP-complete problem, where scheduling tasks over multiple processing units requires an effective strategy to maximize the exploitation of the parallel hardware. Several studies focus on the scheduling of parallel programs described into DAGs (Directed Acyclic Graphs). However, this representation does not describe a multithreaded program suitably. This paper shows the structure and semantics of a DCG, an abstraction which describes a multithreaded program, and proposes standards to map structures found in DAGs into segments of a DCG. A graph grammar has been developed to perform the proposed transformation and case studies using DAGs found in the literature validate the transformation process. Besides the automatic translation and precise definition of the mapping, the use of a formal language also allowed the verification of the existence and uniqueness of the out coming model.