The tremendous advance in computer technology in the past decade has made it possible to achieve the performance of a supercomputer on a very small budget. We have built a multi-CPU cluster of Pentium PC capable of parallel computations using the Message Passing Interface (MPI). We will discuss the configuration, performance, and application of the cluster to our work in physics.
With the advent of multi-core processors and their fast expansion, it is quite clear that {\em parallel computing} is now a genuine requirement in Computer Science and Engineering (and related) curriculum. In addition to the pervasiveness of parallel computing devices, we should take into account the fact that there are lot of existing softwares that are implemented in the sequential mode, and thus need to be adapted for a parallel execution. Therefore, it is required to the programmer to be able to design parallel programs and also to have some skills in moving from a given sequential code to…
In competitive parallel computing, the identical copies of a code in a phase of a sequential program are assigned to processor cores and the result of the fastest core is adopted. In the literature, it is reported that a superlinear speedup can be achieved if there is an enough fluctuation among the execution times consumed by the cores. Competitive parallel computing is a promising approach to use a huge amount of cores effectively. However, there is few theoretical studies on speedups which can be achieved by competitive parallel computing at present. In this paper, we present a behavioral m…
Quantum computing represents a paradigm shift for computation requiring an entirely new computer architecture. However, there is much that can be learned from traditional classical computer engineering. In this paper, we describe the Parallel Research Kernels (PRK), a tool that was very useful for designing classical parallel computing systems. The PRK are simple kernels written to expose bottlenecks that limit classical parallel computing performance. We hypothesize that an analogous tool for quantum computing, Quantum Research Kernels (QRK), may similarly aid the co-design of software and ha…
Serverless computing is increasingly being used for parallel computing, which have traditionally been implemented as stateful applications. Executing complex, burst-parallel, directed acyclic graph (DAG) jobs poses a major challenge for serverless execution frameworks, which will need to rapidly scale and schedule tasks at high throughput, while minimizing data movement across tasks. We demonstrate that, for serverless parallel computations, decentralized scheduling enables scheduling to be distributed across Lambda executors that can schedule tasks in parallel, and brings multiple benefits, i…
Game-theoretical approach to the analysis of parallel algorithms is proposed. The approach is based on presentation of the parallel computing as a congestion game. In the game processes compete for resources such as core of a central processing unit and a communication subsystem. There are players, resources and payoffs (time delays) of players which depend on resources usage. Comparative analysis of various optimality principles in the proposed model may be performed.
We present a highly scalable Monte Carlo (MC) three-dimensional photon transport simulation platform designed for heterogeneous computing systems. Through the development of a massively parallel MC algorithm using the Open Computing Language (OpenCL) framework, this research extends our existing graphics processing unit (GPU)-accelerated MC technique to a highly scalable vendor-independent heterogeneous computing environment, achieving significantly improved performance and software portability. A number of parallel computing techniques are investigated to achieve portable performance over a w…
The author's research of topologies of parallel computing systems and the tasks solved with them, including the corresponding tools of their modeling, is summarized in the present paper. The original topological model of such systems is presented based on the modified Amdahl law. It allowed formalizing the dependence of the necessary number of processors and the maximal distance between information-adjacent vertices in a graph on the directive values of acceleration or efficiency. The dependences of these values on the system interconnection topology and on the information graph of the paralle…
Performance Analysis of Embarassingly Parallel Application on Cluster Computer Environment: A Case Study of Virtual Screening with Autodock Vina 1.1 on Hastinapura Cluster
Aspects of compatibility of topologies of parallel computing systems and tasks are investigated. The introduction of appropriate indexes based on the original topological model of parallel computations and on the nontraditional description of a graph by its projections is proposed and elucidated. On the example of hypercubic computing system (CS) and tasks with ring and star information topologies, we demonstrate determining the indexes and their use in a comparative analysis of the applicability of interconnect with a given topology for solving tasks with the same and different types of infor…
While modern parallel computing systems offer high performance, utilizing these powerful computing resources to the highest possible extent demands advanced knowledge of various hardware architectures and parallel programming models. Furthermore, optimized software execution on parallel computing systems demands consideration of many parameters at compile-time and run-time. Determining the optimal set of parameters in a given execution context is a complex task, and therefore to address this issue researchers have proposed different approaches that use heuristic search or machine learning. In …
Many important computational problems require utilization of high performance computing (HPC) systems that consist of multi-level structures combining higher and higher numbers of devices with various characteristics. Utilizing full power of such systems requires programming parallel applications that are hybrid in two meanings: they can utilize parallelism on multiple levels at the same time and combine together programming interfaces specific for various types of computing devices. The main goal of parallel processing is increasing the processing performance, and therefore decreasing the app…
Graph clustering has many important applications in computing, but due to growing sizes of graphs, even traditionally fast clustering methods such as spectral partitioning can be computationally expensive for real-world graphs of interest. Motivated partly by this, so-called local algorithms for graph clustering have received significant interest due to the fact that they can find good clusters in a graph with work proportional to the size of the cluster rather than that of the entire graph. This feature has proven to be crucial in making such graph clustering and many of its downstream applic…
In practice, standard scheduling of parallel computing jobs almost always leaves significant portions of the available hardware unused, even with many jobs still waiting in the queue. The simple reason is that the resource requests of these waiting jobs are fixed and do not match the available, unused resources. However, with alternative but existing and well-established techniques it is possible to achieve a fully automated, adaptive parallelism that does not need pre-set, fixed resources. Here, we demonstrate that such an adaptively parallel program can indeed fill in all such scheduling gap…
Boston University（波士顿大学）；Ryerson University（瑞尔森大学）
Recent advances in computer architecture and networking opened the opportunity for parallelizing the clustering algorithms. This divide-and-conquer strategy often results in better results to centralized clustering with a much-improved time performance. This paper reviews key parallel clustering and provides insight into their strategy. The review brings together disparate attempts in parallel clustering to provide a comprehensive account of advances in this emerging field
Mass spectrometry, commonly used for protein identification, generates a massive number of spectra that need to be matched against a large database. In reality, most of them remain unidentified or mismatched due to unexpected post-translational modifications. Open modification search (OMS) has been proposed as a strategy to improve the identification rate by considering every possible change in spectra, but it expands the search space exponentially. In this work, we propose HyperOMS, which redesigns OMS based on hyperdimensional computing to cope with such challenges. Unlike existing algorithm…
Given all pairwise weights (distances) among a set of objects, filtered graphs provide a sparse representation by only keeping an important subset of weights. Such graphs can be passed to graph clustering algorithms to generate hierarchical clusters. In particular, the directed bubble hierarchical tree (DBHT) algorithm on filtered graphs has been shown to produce good hierarchical clusters for time series data. We propose a new parallel algorithm for constructing triangulated maximally filtered graphs (TMFG), which produces valid inputs for DBHT, and a scalable parallel algorithm for generatin…
This paper presents our solution for optimization task of the 3rd ACM-China IPCC. By the complexity analysis, we identified three time-consuming subroutines of original algorithm: marking edges, computing pseudo inverse and sorting edges. These subroutines becomes the main performance bottleneck owing to their super-linear time complexity. To address this, we proposed LGRASS, a linear graph spectral sparsification algorithm to run in strictly linear time. LGRASS takes advantage of spanning tree properties and efficient algorithms to optimize bottleneck subroutines. Furthermore, we crafted a pa…
Many organisations have a large network of connected computers, which at times may be idle. These could be used to run larger data processing problems were it not for the difficulty of organising and managing the deployment of such applications. ClusterBuilder is designed to make this task much simpler. ClusterBuilder uses its own Domain Specific Language (DSL) to describe the processing required that removes the need for a deep understanding of parallel programming techniques. The application uses extant sequential data objects which are then invoked in a parallel manner. ClusterBuilder uses …
This paper examines a new parallel computation model called bulk synchronous farm (BSF) that focuses on estimating the scalability of compute-intensive iterative algorithms aimed at cluster computing systems. In the BSF model, a computer is a set of processor nodes connected by a network and organized according to the master/slave paradigm. A cost metric of the BSF model is presented. This cost metric requires the algorithm to be represented in the form of operations on lists. This allows us to derive an equation that predicts the scalability boundary of a parallel program: the maximum number …
Current high-performance computer systems used for scientific computing typically combine shared memory computational nodes in a distributed memory environment. Extracting high performance from these complex systems requires tailored approaches. Task based parallel programming has been successful both in simplifying the programming and in exploiting the available hardware parallelism for shared memory systems. In this paper we focus on how to extend task parallel programming to distributed memory systems. We use a hierarchical decomposition of tasks and data in order to accommodate the differe…
This article describes a method for creating applications for cluster computing systems using the parallel BSF skeleton based on the original BSF (Bulk Synchronous Farm) model of parallel computations developed by the author earlier. This model uses the master/slave paradigm. The main advantage of the BSF model is that it allows to estimate the scalability of a parallel algorithm before its implementation. Another important feature of the BSF model is the representation of problem data in the form of lists that greatly simplifies the logic of building applications. The BSF skeleton is designed…
Parallel Collaborative ADMM Privacy Computing and Adaptive GPU Acceleration for Distributed Edge Networks
College of Cyber Security, Jinan University（暨南大学网络空间安全学院）；Department of Electrical and Computer Engineering, Western University（韦仕敦大学电气与计算机工程系）；School of Computer Science, Guangzhou University（广州大学计算机科学与工程学院）
Modern switches have packet processing capacity of up to multi-tera bits per second, and they are also becoming more and more programmable. We seek to understand whether the programmability can translate packet processing capacity to computational power for parallel computing applications. In this paper, we first develop a simple mathematical model to understand the costs and overheads of data plane computation. Then we validate the the performance benefits of offloading computation to network. Using experiments on real data center network, we finnd that offloading computation to the data plan…
