Scalable molecular dynamics with NAMD

JC Phillips, R Braun, W Wang… - Journal of …, 2005 - Wiley Online Library
NAMD is a parallel molecular dynamics code designed for high‐performance simulation of
large biomolecular systems. NAMD scales to hundreds of processors on high‐end parallel …

The case of the missing supercomputer performance: Achieving optimal performance on the 8,192 processors of ASCI Q

F Petrini, DJ Kerbyson, S Pakin - Proceedings of the 2003 ACM/IEEE …, 2003 - dl.acm.org
In this paper we describe how we improved the effective performance of ASCI Q, the world's
second-fastest supercomputer, to meet our expectations. Using an arsenal of performance …

Bigsim: A parallel simulator for performance prediction of extremely large parallel machines

G Zheng, G Kakulapati, LV Kalé - 18th International Parallel …, 2004 - ieeexplore.ieee.org
Summary form only given. We present a parallel simulator-BigSim-for predicting
performance of machines with a very large number of processors. The simulator provides …

Proactive fault tolerance in MPI applications via task migration

S Chakravorty, CL Mendes, LV Kalé - International Conference on High …, 2006 - Springer
Failures are likely to be more frequent in systems with thousands of processors. Therefore,
schemes for dealing with faults become increasingly important. In this paper, we present a …

[图书][B] Parallel science and engineering applications: The Charm++ approach

LV Kale, A Bhatele - 2016 - books.google.com
This book highlights the use of Charm++ in a wide variety of scientific and engineering
fields. It emphasizes the adaptivity, asynchrony, and message-driven execution of Charm++ …

Combing the communication hairball: Visualizing parallel execution traces using logical time

KE Isaacs, PT Bremer, I Jusufi… - IEEE transactions on …, 2014 - ieeexplore.ieee.org
With the continuous rise in complexity of modern supercomputers, optimizing the
performance of large-scale parallel programs is becoming increasingly challenging …

ParFUM: a parallel framework for unstructured meshes for scalable dynamic physics applications

OS Lawlor, S Chakravorty, TL Wilmarth… - Engineering with …, 2006 - Springer
Unstructured meshes are used in many engineering applications with irregular domains,
from elastic deformation problems to crack propagation to fluid flow. Because of their …

A comparative analysis of load balancing algorithms applied to a weather forecast model

ER Rodrigues, POA Navaux, J Panetta… - 2010 22nd …, 2010 - ieeexplore.ieee.org
Among the many reasons for load imbalance in weather forecasting models, the dynamic
imbalance caused by localized variations on the state of the atmosphere is the hardest one …

Evaluating similarity-based trace reduction techniques for scalable performance analysis

K Mohror, KL Karavanic - Proceedings of the conference on high …, 2009 - dl.acm.org
Event traces are required to correctly diagnose a number of performance problems that arise
on today's highly parallel systems. Unfortunately, the collection of event traces can produce …

[PDF][PDF] Proactive fault tolerance in large systems

S Chakravorty, C Mendes, LV Kale - HPCRI Workshop in conjunction with …, 2005 - Citeseer
High-performance systems with thousands of processors have been introduced in the recent
past, and systems with hundreds of thousands of processors should become available in the …