scholarly journals Controllers: An abstraction to ease the use of hardware accelerators

2017 ◽  
Vol 32 (6) ◽  
pp. 838-853 ◽  
Author(s):  
Ana Moreton–Fernandez ◽  
Hector Ortega–Arranz ◽  
Arturo Gonzalez–Escribano
Keyword(s):  
Graphics Processing Units ◽  
High Performance ◽  
Abstract Entity ◽  
Hardware Accelerators ◽  
Processing Unit ◽  
Central Processing ◽  
Computing Platforms ◽  
Graphics Processing ◽  
Performance Computing ◽  
Selection Of

Nowadays the use of hardware accelerators, such as the graphics processing units or XeonPhi coprocessors, is key in solving computationally costly problems that require high performance computing. However, programming solutions for an efficient deployment for these kind of devices is a very complex task that relies on the manual management of memory transfers and configuration parameters. The programmer has to carry out a deep study of the particular data that needs to be computed at each moment, across different computing platforms, also considering architectural details. We introduce the controller concept as an abstract entity that allows the programmer to easily manage the communications and kernel launching details on hardware accelerators in a transparent way. This model also provides the possibility of defining and launching central processing unit kernels in multi-core processors with the same abstraction and methodology used for the accelerators. It internally combines different native programming models and technologies to exploit the potential of each kind of device. Additionally, the model also allows the programmer to simplify the proper selection of values for several configuration parameters that can be selected when a kernel is launched. This is done through a qualitative characterization process of the kernel code to be executed. Finally, we present the implementation of the controller model in a prototype library, together with its application in several case studies. Its use has led to reductions in the development and porting costs, with significantly low overheads in the execution times when compared to manually programmed and optimized solutions which directly use CUDA and OpenMP.

scholarly journals High-performance computing in water resources hydrodynamics

2020 ◽  
Vol 22 (5) ◽  
pp. 1217-1235 ◽  
Author(s):  
M. Morales-Hernández ◽  
M. B. Sharif ◽  
S. Gangrade ◽  
T. T. Dullo ◽  
S.-C. Kao ◽  
...  
Keyword(s):  
Water Resources ◽  
High Performance Computing ◽  
Graphics Processing Units ◽  
High Performance ◽  
Large Scale ◽  
Test Case ◽  
Processing Unit ◽  
Central Processing ◽  
Graphics Processing ◽  
Performance Computing

Abstract This work presents a vision of future water resources hydrodynamics codes that can fully utilize the strengths of modern high-performance computing (HPC). The advances to computing power, formerly driven by the improvement of central processing unit processors, now focus on parallel computing and, in particular, the use of graphics processing units (GPUs). However, this shift to a parallel framework requires refactoring the code to make efficient use of the data as well as changing even the nature of the algorithm that solves the system of equations. These concepts along with other features such as the precision for the computations, dry regions management, and input/output data are analyzed in this paper. A 2D multi-GPU flood code applied to a large-scale test case is used to corroborate our statements and ascertain the new challenges for the next-generation parallel water resources codes.

scholarly journals The VOLNA-OP2 tsunami code (version 1.5)

2018 ◽  
Vol 11 (11) ◽  
pp. 4621-4635 ◽  
Author(s):  
Istvan Z. Reguly ◽  
Daniel Giles ◽  
Devaraj Gopinathan ◽  
Laure Quivy ◽  
Joakim H. Beck ◽  
...  
Keyword(s):  
Graphics Processing Units ◽  
High Performance ◽  
Shallow Water Equation ◽  
Xeon Phi ◽  
Intel Xeon Phi ◽  
Central Processing ◽  
Domain Specific ◽  
Computing Platforms ◽  
Graphics Processing ◽  
Intel Xeon

Abstract. In this paper, we present the VOLNA-OP2 tsunami model and implementation; a finite-volume non-linear shallow-water equation (NSWE) solver built on the OP2 domain-specific language (DSL) for unstructured mesh computations. VOLNA-OP2 is unique among tsunami solvers in its support for several high-performance computing platforms: central processing units (CPUs), the Intel Xeon Phi, and graphics processing units (GPUs). This is achieved in a way that the scientific code is kept separate from various parallel implementations, enabling easy maintainability. It has already been used in production for several years; here we discuss how it can be integrated into various workflows, such as a statistical emulator. The scalability of the code is demonstrated on three supercomputers, built with classical Xeon CPUs, the Intel Xeon Phi, and NVIDIA P100 GPUs. VOLNA-OP2 shows an ability to deliver productivity as well as performance and portability to its users across a number of platforms.

scholarly journals HYPERDOCK: Improving virtual screening through parallel hyperheuristics

2019 ◽  
Vol 34 (1) ◽  
pp. 30-41
Author(s):  
Baldomero Imbernón ◽  
Antonio Llanes ◽  
José-Matías Cutillas-Lozano ◽  
Domingo Giménez
Keyword(s):  
Virtual Screening ◽  
High Performance ◽  
Graphics Processing Unit ◽  
Processing Unit ◽  
Central Processing ◽  
Pharmacological Targets ◽  
Graphics Processing ◽  
Computational Systems ◽  
Performance Computing ◽  
Different Levels

Virtual screening (VS) methods aid clinical research by predicting the interaction of ligands with pharmacological targets. The computational requirements of VS, along with the size of the databases, propitiate the use of high-performance computing. METADOCK is a tool for the application of metaheuristics to VS in heterogeneous clusters of computers based on central processing unit (CPU) and graphics processing unit (GPU). HYPERDOCK represents a step forward; the exploration for satisfactory metaheuristics is systematically approached by means of hyperheuristics working on top of the metaheuristic schema of METADOCK. Multiple metaheuristics are explored, so the process is computationally demanding. HYPERDOCK exploits the parallelism of METADOCK and includes parallelism at its own level. The different levels of parallelism can be used to exploit the parallelism offered by computational systems composed of multicore CPU + multi-GPUs. The efficient exploitation of these systems enables HYPERDOCK to improve ligand–receptor binding.

scholarly journals A lightweight approach to performance portability with targetDP

2016 ◽  
Vol 32 (2) ◽  
pp. 288-301
Author(s):  
Alan Gray ◽  
Kevin Stratford
Keyword(s):  
Particle Physics ◽  
Message Passing ◽  
Graphics Processing Units ◽  
High Performance ◽  
Large Scale ◽  
Message Passing Interface ◽  
Graphics Processing Unit ◽  
Processing Unit ◽  
Performance Portability ◽  
Graphics Processing

Leading high performance computing systems achieve their status through use of highly parallel devices such as NVIDIA graphics processing units or Intel Xeon Phi many-core CPUs. The concept of performance portability across such architectures, as well as traditional CPUs, is vital for the application programmer. In this paper we describe targetDP, a lightweight abstraction layer which allows grid-based applications to target data parallel hardware in a platform agnostic manner. We demonstrate the effectiveness of our pragmatic approach by presenting performance results for a complex fluid application (with which the model was co-designed), plus separate lattice quantum chromodynamics particle physics code. For each application, a single source code base is seen to achieve portable performance, as assessed within the context of the Roofline model. TargetDP can be combined with Message Passing Interface (MPI) to allow use on systems containing multiple nodes: we demonstrate this through provision of scaling results on traditional and graphics processing unit-accelerated large scale supercomputers.

scholarly journals Big Data and IT Network Data Visualization

2018 ◽  
Vol 3 (1) ◽  
pp. 9-16 ◽  
Author(s):  
Lidong Wang
Keyword(s):  
Big Data ◽  
Network Analysis ◽  
Graphics Processing Units ◽  
Data Analytics ◽  
High Performance ◽  
Big Data Analytics ◽  
Network Visualization ◽  
Network Data ◽  
Graphics Processing ◽  
Performance Computing

Visualization with graphs is popular in the data analysis of Information Technology (IT) networks or computer networks. An IT network is often modelled as a graph with hosts being nodes and traffic being flows on many edges. General visualization methods are introduced in this paper. Applications and technology progress of visualization in IT network analysis and big data in IT network visualization are presented. The challenges of visualization and Big Data analytics in IT network visualization are also discussed. Big Data analytics with High Performance Computing (HPC) techniques, especially Graphics Processing Units (GPUs) helps accelerate IT network analysis and visualization.

SeisNoise.jl: Ambient Seismic Noise Cross Correlation on the CPU and GPU in Julia

2020 ◽  
Vol 92 (1) ◽  
pp. 517-527
Author(s):  
Timothy Clements ◽  
Marine A. Denolle
Keyword(s):  
Seismic Noise ◽  
High Performance ◽  
Cross Correlation ◽  
Graphic Processing Unit ◽  
Ambient Seismic Noise ◽  
Processing Unit ◽  
Central Processing ◽  
And Performance ◽  
Noise Cross Correlation ◽  
Performance Computing

Abstract We introduce SeisNoise.jl, a library for high-performance ambient seismic noise cross correlation, written entirely in the computing language Julia. Julia is a new language, with syntax and a learning curve similar to MATLAB (see Data and Resources), R, or Python and performance close to Fortran or C. SeisNoise.jl is compatible with high-performance computing resources, using both the central processing unit and the graphic processing unit. SeisNoise.jl is a modular toolbox, giving researchers common tools and data structures to design custom ambient seismic cross-correlation workflows in Julia.

scholarly journals PI-FLAME: A parallel immune system simulator using the FLAME graphic processing unit environment

SIMULATION ◽  
2016 ◽  
Vol 93 (1) ◽  
pp. 69-84 ◽  
Author(s):  
Shailesh Tamrakar ◽  
Paul Richmond ◽  
Roshan M D’Souza
Keyword(s):  
Immune System ◽  
Graphics Processing Units ◽  
Processing Unit ◽  
Human Immune System ◽  
Innate And Adaptive Immunity ◽  
Agent Based ◽  
Central Processing ◽  
Agent Simulation ◽  
Study Population ◽  
Graphics Processing

Agent-based models (ABMs) are increasingly being used to study population dynamics in complex systems, such as the human immune system. Previously, Folcik et al. (The basic immune simulator: an agent-based model to study the interactions between innate and adaptive immunity. Theor Biol Med Model 2007; 4: 39) developed a Basic Immune Simulator (BIS) and implemented it using the Recursive Porous Agent Simulation Toolkit (RePast) ABM simulation framework. However, frameworks such as RePast are designed to execute serially on central processing units and therefore cannot efficiently handle large model sizes. In this paper, we report on our implementation of the BIS using FLAME GPU, a parallel computing ABM simulator designed to execute on graphics processing units. To benchmark our implementation, we simulate the response of the immune system to a viral infection of generic tissue cells. We compared our results with those obtained from the original RePast implementation for statistical accuracy. We observe that our implementation has a 13× performance advantage over the original RePast implementation.

An Accelerated 3D Navier–Stokes Solver for Flows in Turbomachines

2010 ◽  
Vol 133 (2) ◽  
Author(s):  
Tobias Brandvik ◽  
Graham Pullan
Keyword(s):  
Graphics Processing Units ◽  
Three Dimensional ◽  
Navier Stokes ◽  
Linear Scaling ◽  
Test Case ◽  
Processing Unit ◽  
Central Processing ◽  
Order Of Magnitude ◽  
Graphics Processing ◽  
Good Agreement

A new three-dimensional Navier–Stokes solver for flows in turbomachines has been developed. The new solver is based on the latest version of the Denton codes but has been implemented to run on graphics processing units (GPUs) instead of the traditional central processing unit. The change in processor enables an order-of-magnitude reduction in run-time due to the higher performance of the GPU. The scaling results for a 16 node GPU cluster are also presented, showing almost linear scaling for typical turbomachinery cases. For validation purposes, a test case consisting of a three-stage turbine with complete hub and casing leakage paths is described. Good agreement is obtained with previously published experimental results. The simulation runs in less than 10 min on a cluster with four GPUs.

Sign in / Sign up

Export Citation Format

Share Document