Search results for "Distributed memory"
showing 10 items of 13 documents
MSAProbs-MPI: parallel multiple sequence aligner for distributed-memory systems
2016
This is a pre-copyedited, author-produced version of an article accepted for publication in Bioinformatics following peer review. The version of recordJorge González-Domínguez, Yongchao Liu, Juan Touriño, Bertil Schmidt; MSAProbs-MPI: parallel multiple sequence aligner for distributed-memory systems, Bioinformatics, Volume 32, Issue 24, 15 December 2016, Pages 3826–3828, https://doi.org/10.1093/bioinformatics/btw558is available online at: https://doi.org/10.1093/bioinformatics/btw558 [Abstracts] MSAProbs is a state-of-the-art protein multiple sequence alignment tool based on hidden Markov models. It can achieve high alignment accuracy at the expense of relatively long runtimes for large-sca…
Big Data in metagenomics: Apache Spark vs MPI.
2020
The progress of next-generation sequencing has lead to the availability of massive data sets used by a wide range of applications in biology and medicine. This has sparked significant interest in using modern Big Data technologies to process this large amount of information in distributed memory clusters of commodity hardware. Several approaches based on solutions such as Apache Hadoop or Apache Spark, have been proposed. These solutions allow developers to focus on the problem while the need to deal with low level details, such as data distribution schemes or communication patterns among processing nodes, can be ignored. However, performance and scalability are also of high importance when…
Moving Learning Machine Towards Fast Real-Time Applications: A High-Speed FPGA-based Implementation of the OS-ELM Training Algorithm
2018
Currently, there are some emerging online learning applications handling data streams in real-time. The On-line Sequential Extreme Learning Machine (OS-ELM) has been successfully used in real-time condition prediction applications because of its good generalization performance at an extreme learning speed, but the number of trainings by a second (training frequency) achieved in these continuous learning applications has to be further reduced. This paper proposes a performance-optimized implementation of the OS-ELM training algorithm when it is applied to real-time applications. In this case, the natural way of feeding the training of the neural network is one-by-one, i.e., training the neur…
Distributed Computing on Distributed Memory
2018
Distributed computation is formalized in several description languages for computation, as e.g. Unified Modeling Language (UML), Specification and Description Language (SDL), and Concurrent Abstract State Machines (CASM). All these languages focus on the distribution of computation, which is somewhat the same as concurrent computation. In addition, there is also the aspect of distribution of state, which is often neglected. Distribution of state is most commonly represented by communication between active agents. This paper argues that it is desirable to abstract from the communication and to consider abstract distributed state. This includes semantic handling of conflict resolution, e.g. i…
Memory Resource Management for Real-Time Systems
2007
Dynamic memory storage has been widely used for years in computer science. However, its use in real-time systems has not been considered as an important issue, and memory management has not receive much consideration, whereas today's real-time applications are often characterized by highly fluctuating memory requirements. In this paper we present an approach to dynamic memory management for real-time systems. In response to application behavior and requests, the underlying memory management system adjusts resources to meet changing demands and user needs. The architectural framework that realizes this approach allows adaptive allocation of memory resources to applications involving both per…
The differences between distributed shared memory caching and proxy caching
2000
The authors discuss the similarities in caching between the extensively studied distributed shared memory systems and the emerging proxy systems. They believe that several of the techniques used in distributed shared memory systems can be adapted and applied to proxy systems.
A Low Cost Solution for 2D Memory Access
2006
Many of the new coding tools in the H.264/AVC video coding standard are based on 2D processing resulting in row-wise and column-wise memory accesses starting from arbitrary memory locations. This paper proposes a low cost solution for efficient realization of these 2D block memory accesses on sub-word parallel processors. It is based on the use of simple register-based data permutation networks placed between the processor and memory. The data rearrangement capabilities of the networks can further be extended with more complex control schemes. With the proposed control schemes, the networks enable row and column accesses from arbitrary memory locations for blocks of data while maintaining f…
A mixed geometric-systolic approach to parallel molecular dynamics simulations
1995
We have developed a flexible and efficient method of performing molecular dynamics simulations on distributed memory parallel computers. The novel feature is to use simultaneously spatial partitioning and systolic loop approaches according to a strategy which, for a given simulation, adapts itself to the multiprocessor system, allowing to approach optimal performance. The method assures high efficiencies even in situations in which, due to the exceeding large number of processors, the usage of a pure spatial decomposition would be impossible. The algorithm provides as particular cases both the pure spatial partitioning and the pure systolic parallelization schemes, so that its adoption assu…
Analyzing the Energy Efficiency of the Memory Subsystem in Multicore Processors
2014
In this paper we analyze the energy overhead incurred when operating with data stored in different levels of the memory subsystem (cache levels and DDR chips) of current multicore architectures. Our approach builds upon servet, a portable framework for the memory characterization of multicore processors, extending this suite with a power-related test that, when applied to a platform equipped with a power measurement mechanism, provides information on the efficiency of memory energy usage. As additional contributions, i) we provide a complete experimental study of the impact that the CPU performance states (also known as P-states) exert on the memory energy efficiency of a collection of rece…
Unified Parallel C++
2018
Abstract Although MPI is commonly used for parallel programming on distributed-memory systems, Partitioned Global Address Space (PGAS) approaches are gaining attention for programming modern multi-core CPU clusters. They feature a hybrid memory abstraction: distributed memory is viewed as a shared memory that is partitioned among nodes in order to simplify programming. In this chapter you will learn about Unified Parallel C++ (UPC++), a library-based extension of C++ that gathers the advantages of both PGAS and Object Oriented paradigms. The examples included in this chapter will help you to understand the main features of PGAS languages and how they can simplify the task of programming par…