Computational Physics on Graphics Processing Units

The use of graphics processing units for scientific computations is an emerging strategy that can significantly speed up various different algorithms. In this review, we discuss advances made in the field of computational physics, focusing on classical molecular dynamics, and on quantum simulations for electronic structure calculations using the density functional theory, wave function techniques, and quantum field theory.Comment: Proceedings of the 11th International Conference, PARA 2012, Helsinki, Finland, June 10-13, 201

FLY on Cray: Porting, Optimization and Performance Analysis of Cosmological Simulation Code FLY on Cray XE6 Architecture

In this whitepaper we report work that was done to investigate and improve the performance of a mixed MPI and OpenMP implementation of the FLY code for cosmological simulations on a PRACE Tier-0 system Hermit (Cray XE6)

Development of Grid e-Infrastructure in South-Eastern Europe

Over the period of 6 years and three phases, the SEE-GRID programme has established a strong regional human network in the area of distributed scientific computing and has set up a powerful regional Grid infrastructure. It attracted a number of user communities and applications from diverse fields from countries throughout the South-Eastern Europe. From the infrastructure point view, the first project phase has established a pilot Grid infrastructure with more than 20 resource centers in 11 countries. During the subsequent two phases of the project, the infrastructure has grown to currently 55 resource centers with more than 6600 CPUs and 750 TBs of disk storage, distributed in 16 participating countries. Inclusion of new resource centers to the existing infrastructure, as well as a support to new user communities, has demanded setup of regionally distributed core services, development of new monitoring and operational tools, and close collaboration of all partner institution in managing such a complex infrastructure. In this paper we give an overview of the development and current status of SEE-GRID regional infrastructure and describe its transition to the NGI-based Grid model in EGI, with the strong SEE regional collaboration.Comment: 22 pages, 12 figures, 4 table

COMP Superscalar, an interoperable programming framework

COMPSs is a programming framework that aims to facilitate the parallelization of existing applications written in Java, C/C++ and Python scripts. For that purpose, it offers a simple programming model based on sequential development in which the user is mainly responsible for identifying the functions to be executed as asynchronous parallel tasks and annotating them with annotations or standard Python decorators. A runtime system is in charge of exploiting the inherent concurrency of the code, automatically detecting and enforcing the data dependencies between tasks and spawning these tasks to the available resources, which can be nodes in a cluster, clouds or grids. In cloud environments, COMPSs provides scalability and elasticity features allowing the dynamic provision of resources.This work has been supported by the following institutions: the Spanish Government with grant SEV-2011-00067 of the Severo Ochoa Program and contract Computacion de Altas Prestaciones VI (TIN2012-34557); by the SGR programme (2014-SGR-1051) of the Catalan Government; by the project The Human Brain Project, funded by the European Commission under contract 604102; by the ASCETiC project funded by the European Commission under contract 610874; by the EUBrazilCloudConnect project funded by the European Commission under contract 614048; and by the Intel-BSC Exascale Lab collaboration.Peer ReviewedPostprint (published version

Scaling Coupled Climate Models to Exascale: OpenACC-enabled ECEarth3 Earth System Model

Climate change due to increasing anthropogenic greenhouse gases and land surface change is currently one of the most relevant environmental concerns. It threatens ecosystems and human societies. However, its impact on the economy and our living standards depends largely on our ability to anticipate its effects and take appropriate action. Earth System Models (ESMs), such as EC-Earth, can be used to provide society with information on the future climate. EC-Earth3 generates reliable predictions and projections of global climate change, which are a prerequisite to support the development of national adaptation and mitigation strategies. This project investigates methods to enhance the parallel capabilities of EC-Earth3 by offloading bottleneck routines to GPUs and Intel Xeon Phi coprocessors. To gain a full understanding of climate change at a regional scale will require EC-Earth3 to be run at a much higher spatial resolution (T3999 ~5km) than is currently feasible. It is envisaged that the work outlined in this project will provide climate scientists with valuable data for simulations planned for future exascale systems

Code Optimization and Scaling of the Astrophysics Software Gadget on Intel Xeon Phi

The whitepaper reports our investigation into the porting, optimization and subsequent performance of the astrophysics software package GADGET, on the Intel Xeon Phi. The GADGET code is intended for cosmological N-body/SPH simulations to solve a wide range of astrophysical tasks. The test cases within the project were simulations of galaxy systems. A performance analysis of the code was carried out and porting, tuning and scaling of the GADGET code were completed. As a result, the hybrid MPI/OpenMP parallelization of the code has been enabled and scalability tests on the Intel Xeon Phi processors, on the PRACE EURORA system are reported

Performance Analysis and Enabling of the RayBen Code for the Intel® MIC Architecture

The subject of this project is the analysis and enabling of the RayBen code, which implements a finite difference scheme for the simulation of turbulent Rayleigh-Bénard convection in a closed cylindrical cell, for the Intel® Xeon Phi coprocessor architecture. After a brief introduction to the physical background of the code, the integration of Rayben into the benchmarking environment JuBE is discussed. The structure of the code is analysed through its call graph. The most performance-critical routines were identified. A detailed analysis of the OpenMP parallelization revealed several race conditions which were eliminated. The code was ported to the JUROPA cluster at the Jülich Supercomputing as well as to the EURORA cluster at CINECA. The performance of the code is discussed using the results of pure MPI and hybrid MPI/OpenMP benchmarks. It is shown that RayBen is a memory-intensive application that highly benefits from the MPI parallelization. The offloading mechanism for the Intel® MIC architecture lowers considerably the performance while the use of binaries that run exclusively on the coprocessor show a satisfactory performance and a scalability which is comparable to the CPU

Survey and Analysis of Production Distributed Computing Infrastructures

This report has two objectives. First, we describe a set of the production distributed infrastructures currently available, so that the reader has a basic understanding of them. This includes explaining why each infrastructure was created and made available and how it has succeeded and failed. The set is not complete, but we believe it is representative. Second, we describe the infrastructures in terms of their use, which is a combination of how they were designed to be used and how users have found ways to use them. Applications are often designed and created with specific infrastructures in mind, with both an appreciation of the existing capabilities provided by those infrastructures and an anticipation of their future capabilities. Here, the infrastructures we discuss were often designed and created with specific applications in mind, or at least specific types of applications. The reader should understand how the interplay between the infrastructure providers and the users leads to such usages, which we call usage modalities. These usage modalities are really abstractions that exist between the infrastructures and the applications; they influence the infrastructures by representing the applications, and they influence the ap- plications by representing the infrastructures

Hybrid Use of OmpSs for a Shock Hydrodynamics Proxy Application

The LULESH proxy application models the behavior of the ALE3D multi-physics code with an explicit shock hydrodynamics problem, and is made in order to evaluate interactions between programming models and architectures, using a representative code significantly less complex than the application it models. As identified in the PRACE deliverable D7.2.1 [1], the OmpSs programming model specifically targets programming at the exascale, and this whitepaper investigates the effectiveness of its support for development on hybrid architectures