METADOCK: A parallel metaheuristic schema for virtual screening methods

Virtual screening through molecular docking can be translated into an optimization problem, which can be tackled with metaheuristic methods. The interaction between two chemical compounds (typically a protein, enzyme or receptor, and a small molecule, or ligand) is calculated by using highly computationally demanding scoring functions that are computed at several binding spots located throughout the protein surface. This paper introduces METADOCK, a novel molecular docking methodology based on parameterized and parallel metaheuristics and designed to leverage heterogeneous computers based on heterogeneous architectures. The application decides the optimization technique at running time by setting a configuration schema. Our proposed solution finds a good workload balance via dynamic assignment of jobs to heterogeneous resources which perform independent metaheuristic executions when computing different molecular interactions required by the scoring functions in use. A cooperative scheduling of jobs optimizes the quality of the solution and the overall performance of the simulation, so opening a new path for further developments of virtual screening methods on high-performance contemporary heterogeneous platforms.Ingeniería, Industria y Construcció

Speculative Segmented Sum for Sparse Matrix-Vector Multiplication on Heterogeneous Processors

Sparse matrix-vector multiplication (SpMV) is a central building block for scientific software and graph applications. Recently, heterogeneous processors composed of different types of cores attracted much attention because of their flexible core configuration and high energy efficiency. In this paper, we propose a compressed sparse row (CSR) format based SpMV algorithm utilizing both types of cores in a CPU-GPU heterogeneous processor. We first speculatively execute segmented sum operations on the GPU part of a heterogeneous processor and generate a possibly incorrect results. Then the CPU part of the same chip is triggered to re-arrange the predicted partial sums for a correct resulting vector. On three heterogeneous processors from Intel, AMD and nVidia, using 20 sparse matrices as a benchmark suite, the experimental results show that our method obtains significant performance improvement over the best existing CSR-based SpMV algorithms. The source code of this work is downloadable at https://github.com/bhSPARSE/Benchmark_SpMV_using_CSRComment: 22 pages, 8 figures, Published at Parallel Computing (PARCO

GPU acceleration of brain image proccessing

Durante los últimos años se ha venido demostrando el alto poder computacional que ofrecen las GPUs a la hora de resolver determinados problemas. Al mismo tiempo, existen campos en los que no es posible beneficiarse completamente de las mejoras conseguidas por los investigadores, debido principalmente a que los tiempos de ejecución de las aplicaciones llegan a ser extremadamente largos. Este es por ejemplo el caso del registro de imágenes en medicina. A pesar de que se han conseguido aceleraciones sobre el registro de imágenes, su uso en la práctica clínica es aún limitado. Entre otras cosas, esto se debe al rendimiento conseguido. Por lo tanto se plantea como objetivo de este proyecto, conseguir mejorar los tiempos de ejecución de una aplicación dedicada al resgitro de imágenes en medicina, con el fin de ayudar a aliviar este problema

Framework for Simulation of Heterogeneous MpSoC for Design Space Exploration

Due to the ever-growing requirements in high performance data computation, multiprocessor systems have been proposed to solve the bottlenecks in uniprocessor systems. Developing efficient multiprocessor systems requires effective exploration of design choices like application scheduling, mapping, and architecture design. Also, fault tolerance in multiprocessors needs to be addressed. With the advent of nanometer-process technology for chip manufacturing, realization of multiprocessors on SoC (MpSoC) is an active field of research. Developing efficient low power, fault-tolerant task scheduling, and mapping techniques for MpSoCs require optimized algorithms that consider the various scenarios inherent in multiprocessor environments. Therefore there exists a need to develop a simulation framework to explore and evaluate new algorithms on multiprocessor systems. This work proposes a modular framework for the exploration and evaluation of various design algorithms for MpSoC system. This work also proposes new multiprocessor task scheduling and mapping algorithms for MpSoCs. These algorithms are evaluated using the developed simulation framework. The paper also proposes a dynamic fault-tolerant (FT) scheduling and mapping algorithm for robust application processing. The proposed algorithms consider optimizing the power as one of the design constraints. The framework for a heterogeneous multiprocessor simulation was developed using SystemC/C++ language. Various design variations were implemented and evaluated using standard task graphs. Performance evaluation metrics are evaluated and discussed for various design scenarios

Dynamic Lifetime Reliability and Energy Management for Network-on-Chip based Chip Multiprocessors

In this dissertation, we study dynamic reliability management (DRM) and dynamic energy management (DEM) techniques for network-on-chip (NoC) based chip multiprocessors (CMPs). In the first part, the proposed DRM algorithm takes both the computational and the communication components of the CMP into consideration and combines thread migration and dynamic voltage and frequency scaling (DVFS) as the two primary techniques to change the CMP operation. The goal is to increase the lifetime reliability of the overall system to the desired target with minimal performance degradation. The simulation results on a variety of benchmarks on 16 and 64 core NoC based CMP architectures demonstrate that lifetime reliability can be improved by 100% for an average performance penalty of 7.7% and 8.7% for the two CMP architectures. In the second part of this dissertation, we first propose novel algorithms that employ Kalman filtering and long short term memory (LSTM) for workload prediction. These predictions are then used as the basis on which voltage/frequency (V/F) pairs are selected for each core by an effective dynamic voltage and frequency scaling algorithm whose objective is to reduce energy consumption but without degrading performance beyond the user set threshold. Secondly, we investigate the use of deep neural network (DNN) models for energy optimization under performance constraints in CMPs. The proposed algorithm is implemented in three phases. The first phase collects the training data by employing Kalman filtering for workload prediction and an efficient heuristic algorithm based on DVFS. The second phase represents the training process of the DNN model and in the last phase, the DNN model is used to directly identify V/F pairs that can achieve lower energy consumption without performance degradation beyond the acceptable threshold set by the user. Simulation results on 16 and 64 core NoC based architectures demonstrate that the proposed approach can achieve up to 55% energy reduction for 10% performance degradation constraints. Simulation experiments compare the proposed algorithm against existing approaches based on reinforcement learning and Kalman filtering and show that the proposed DNN technique provides average improvements in energy-delay-product (EDP) of 6.3% and 6% for the 16 core architecture and of 7.4% and 5.5% for the 64 core architecture

Distributed data mining in grid computing environments

The official published version of this article can be found at the link below.The computing-intensive data mining for inherently Internet-wide distributed data, referred to as Distributed Data Mining (DDM), calls for the support of a powerful Grid with an effective scheduling framework. DDM often shares the computing paradigm of local processing and global synthesizing. It involves every phase of Data Mining (DM) processes, which makes the workflow of DDM very complex and can be modelled only by a Directed Acyclic Graph (DAG) with multiple data entries. Motivated by the need for a practical solution of the Grid scheduling problem for the DDM workflow, this paper proposes a novel two-phase scheduling framework, including External Scheduling and Internal Scheduling, on a two-level Grid architecture (InterGrid, IntraGrid). Currently a DM IntraGrid, named DMGCE (Data Mining Grid Computing Environment), has been developed with a dynamic scheduling framework for competitive DAGs in a heterogeneous computing environment. This system is implemented in an established Multi-Agent System (MAS) environment, in which the reuse of existing DM algorithms is achieved by encapsulating them into agents. Practical classification problems from oil well logging analysis are used to measure the system performance. The detailed experiment procedure and result analysis are also discussed in this paper

Green Parallel Metaheuristics: Design, Implementation, and Evaluation

Fecha de lectura de Tesis Doctoral 14 mayo 2020Green parallel metaheuristics (GPM) is a new concept we want to introduce in this thesis. It is an idea inspired by two facts: (i) parallel metaheuristics could help as unique tools to solve optimization problems in energy savings applications and sustainability, and (ii) these algorithms themselves run on multiprocessors, clusters, and grids of computers and then consume energy, so they need an energy analysis study for their different implementations over multiprocessors. The context for this thesis is to make a modern and competitive effort to extend the capability of present intelligent search optimization techniques. Analyzing the different sequential and parallel metaheuristics considering its energy consumption requires a deep investigation of the numerical performance, the execution time for efficient future designing to these algorithms. We present a study of the speed-up of the different parallel implementations over a different number of computing units. Moreover, we analyze and compare the energy consumption and numerical performance of the sequential/parallel algorithms and their components: a jump in the efficiency of the algorithms that would probably have a wide impact on the domains involved.El Instituto Egipcio en Madrid, dependiente del Gobierno de Egipto

Workflow Scheduling Techniques and Algorithms in IaaS Cloud: A Survey

In the modern era, workflows are adopted as a powerful and attractive paradigm for expressing/solving a variety of applications like scientific, data intensive computing, and big data applications such as MapReduce and Hadoop. These complex applications are described using high-level representations in workflow methods. With the emerging model of cloud computing technology, scheduling in the cloud becomes the important research topic. Consequently, workflow scheduling problem has been studied extensively over the past few years, from homogeneous clusters, grids to the most recent paradigm, cloud computing. The challenges that need to be addressed lies in task-resource mapping, QoS requirements, resource provisioning, performance fluctuation, failure handling, resource scheduling, and data storage. This work focuses on the complete study of the resource provisioning and scheduling algorithms in cloud environment focusing on Infrastructure as a service (IaaS). We provided a comprehensive understanding of existing scheduling techniques and provided an insight into research challenges that will be a possible future direction to the researchers