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Multiscale biomolecular simulations in the exascale era

The complexity of biological systems and processes, spanning molecular to macroscopic scales, necessitates the use of multiscale simulations to get a comprehensive understanding. lar dynamics (MD) simulations are crucial for capturing processes beyond the ...

Current Biology Ltd2024

AiiDA 1.0, a scalable computational infrastructure for automated reproducible workflows and data provenance

Nicola Marzari, Giovanni Pizzi, Nicolas Frank Mounet, Martin Uhrin, Andrea Cepellotti, Boris Kozinsky, Fernando Gargiulo, Christoph Leopold Talirz, Leonid Kahle, Aliaksandr Yakutovich, Sebastiaan Philippe Huber, Snehal Pramod Kumbhar, Andrius Merkys, Conrad Johnston, Casper Welzel Andersen, Spyros Zoupanos, Elsa Passaro, Carl Simon Adorf, Francisco Fernando Ramirez

The ever-growing availability of computing power and the sustained development of advanced computational methods have contributed much to recent scientific progress. These developments present new challenges driven by the sheer amount of calculations and d ...

2020

Application of the Denovo Discrete Ordinates Radiation Transport Code to Large-Scale Fusion Neutronics

Olivier Sauter, Ambrogio Fasoli, Basil Duval, Stefano Coda, Martinus Gijs, Jonathan Graves, Yves Martin, Duccio Testa, Patrick Blanchard, Bruno Emanuel Ferreira De Sousa Correia, Alessandro Pau, Pierre-Thomas Paul Brun, Cristian Sommariva, Henri Weisen, Richard Pitts, Sun Hee Kim, Yann Camenen, Jan Horacek, Javier García Hernández, Marco Wischmeier, Mikhail Maslov, Nicola Vianello, Miguel Fernández Ruiz, Federico Nespoli, Antonio José Pereira de Figueiredo, Liang Yao, Yao Zhou, David Pfefferlé, Dalziel Joseph Wilson, Robin Humphry-Baker, Davide Galassi, José Pedro Rebelo Ferreira Marques, Ana Francisca Leal Silva Soares, Jonathan Marc Philippe Faustin, Daniel Scott Alessi, Arnout Lodewijk M Beckers, Julio Rodriguez, Hamish William Patten, Jonnathan Cesar Hidalgo Acosta, , , , , , , , ,

A portable platform for accelerated PIC codes and its application to GPUs using OpenACC

Laurent Villard, Stephan Brunner, Emmanuel Lanti, Trach-Minh Tran, Claudio Gheller

We present a portable platform, called PIC_ENGINE, for accelerating Particle-In-Cell (PIC) codes on heterogeneous many-core architectures such as Graphic Processing Units (GPUs). The aim of this development is efficient simulations on future exascale syste ...

Elsevier Science Bv2016

Shared Frontend for Manycore Server Processors

Ilknur Cansu Kaynak

Instruction-supplymechanisms, namely the branch predictors and instruction prefetchers, exploit recurring control flow in an application to predict the applicationâ s future control flow and provide the core with a useful instruction stream to execute in ...

EPFL2015

Memory Systems and Interconnects for Scale-Out Servers

Stavros Volos

The information revolution of the last decade has been fueled by the digitization of almost all human activities through a wide range of Internet services. The backbone of this information age are scale-out datacenters that need to collect, store, and proc ...

EPFL2015

Transactions Chasing Scalability and Instruction Locality on Multicores

Pinar Tözün

For several decades, online transaction processing (OLTP) has been one of the main server applications that drives innovations in the data management ecosystem, and in turn the database and computer architecture communities. Recent hardware trends oblige s ...

EPFL2014

Low Power and Scalable Many-Core Architecture for Big-Data Stream Computing

David Atienza Alonso, Martino Ruggiero, Karim Kanoun

In the last years the process of examining large amounts of different types of data, or Big-Data, in an effort to uncover hidden patterns or unknown correlations has become a major need in our society. In this context, stream mining applications are now wi ...

IEEE Press2014

SPBC: Leveraging the Characteristics of MPI HPC Applications for Scalable Checkpointing

André Schiper, Thomas Ropars

The high failure rate expected for future supercomputers requires the design of new fault tolerant solutions. Most checkpointing protocols are designed to work with any message-passing application but suffer from scalability issues at extreme scale. We tak ...

2013

SIMinG-1k: A thousand-core simulator running on general-purpose graphical processing units

David Atienza Alonso, Luca Benini, Martino Ruggiero, Shivani Raghav

This paper introduces SIMinG-1k-a manycore simulator infrastructure. SIMinG-1k is a graphics processing unit accelerated, parallel simulator for design-space exploration of large-scale manycore systems. It features an optimal trade-off between modeling acc ...

Wiley-Blackwell2013

Computational performance of a parallelized three-dimensional high-order spectral element toolbox

Michel Deville, Roland Bouffanais, Jonas Marcel Lätt, Christoph Bosshard

In this paper, a comprehensive performance review of an MPI-based high-order three-dimensional spectral element method C++ toolbox is presented. The focus is put on the performance evaluation of several aspects with a particular emphasis on the parallel ef ...

2011

Attaining Single-Chip, High-Performance Computing Through 3D Systems with Active Cooling

David Atienza Alonso, Mohamed Mostafa Sabry Aly, Ayse Kivilcim Coskun, Jie Meng

Three-dimensional (3D) stacking is an attractive method for designing large manycore chips as it provides high transistor integration densities, improves manufacturing yield due to smaller chip area, reduces wirelength and capacitance, and enables heteroge ...

Institute of Electrical and Electronics Engineers2011

PaxosInside

Rachid Guerraoui, Maysam Yabandeh

Amodernmanycore architecture can be viewed as a distributed system with explicit message passing to communicate between cores. Ensuring the consistency of shared state replicated over several cores is the key to the well functioning of such a system. Yet, ...

2010

Computational Performance of a Parallelized Three-Dimensional High-Order Spectral Element Toolbox

Michel Deville, Nicolas Fietier, Vincent Keller, Roland Bouffanais, Christoph Bosshard, Jonas Marcel Lätt, Sohrab Jairo Kehtari, Christian Clémençon

In this paper, a comprehensive performance review of all MPI-based high-order three-dimensional spectral element method C++ toolbox is presented. The focus is put on the performance evaluation of aspects with a particular emphasis on the parallel efficienc ...

Springer-Verlag New York, Ms Ingrid Cunningham, 175 Fifth Ave, New York, Ny 10010 Usa2009

Shore-MT: A Scalable Storage Manager for the Multicore Era

Anastasia Ailamaki, Babak Falsafi, Frederick Ryan Johnson, Ippokratis Pandis

Database storage managers have long been able to efficiently handle multiple concurrent requests. Until recently, however, a computer contained only a few single-core CPUs, and therefore only a few transactions could simultaneously access the storage manag ...

ACM2009

Optimal application-oriented resource brokering in a high performance computing grid

Vincent Keller

In the world of High Performance Computing (newly renamed "High Productivity Computing"), where the race for performance is on, where the hunt for the last Flop rages and where the developers swear by the Cult of Power, the different applications have diff ...

EPFL2008

Can a Helmholtz solver run on a cluster?

Marc Anthony David Habisreutinger, Emmanuel Leriche, Vincent Keller

Our vectorized Helmholtz solver runs at 85% efficiency on a NEC SX-5. The most time-consuming parts have been ported on SMP, NUMA, and cluster architectures. It is shown that an OpenMP version can deliver similar performance when running it on a 16 process ...

IEEE2006