Algorithmic developments of the kinetic activation-relaxation technique: Accessing long-time kinetics of larger and more complex systems
M Trochet, A Sauvé-Lacoursière… - The Journal of chemical …, 2017 - pubs.aip.org
In spite of the considerable computer speed increase of the last decades, long-time atomic
simulations remain a challenge and most molecular dynamical simulations are limited to 1 μ …
simulations remain a challenge and most molecular dynamical simulations are limited to 1 μ …
Scalable performance prediction of codes with memory hierarchy and pipelines
We present the Analytical Memory Model with Pipelines (AMMP) of the Performance
Prediction Toolkit (PPT). PPT-AMMP takes high-level source code and hardware …
Prediction Toolkit (PPT). PPT-AMMP takes high-level source code and hardware …
An analytical memory hierarchy model for performance prediction
As the US Department of Energy (DOE) invests in exascale computing, performance
modeling of physics codes on CPUs remain a challenge in computational co-design due to …
modeling of physics codes on CPUs remain a challenge in computational co-design due to …
Discovering mechanisms relevant for radiation damage evolution
The response of a material to irradiation is a consequence of the kinetic evolution of defects
produced during energetic damage events. Thus, accurate predictions of radiation damage …
produced during energetic damage events. Thus, accurate predictions of radiation damage …
A brief history of HPC simulation and future challenges
High-performance Computing (HPC) systems have gone through many changes during the
past two decades in their architectural design to satisfy the increasingly large-scale scientific …
past two decades in their architectural design to satisfy the increasingly large-scale scientific …
Machine learning–enabled scalable performance prediction of scientific codes
G Chennupati, N Santhi, P Romero… - ACM Transactions on …, 2021 - dl.acm.org
Hardware architectures become increasingly complex as the compute capabilities grow to
exascale. We present the Analytical Memory Model with Pipelines (AMMP) of the …
exascale. We present the Analytical Memory Model with Pipelines (AMMP) of the …
Resource allocation for task-level speculative scientific applications: A proof of concept using parallel trajectory splicing
A Garmon, V Ramakrishnaiah, D Perez - Parallel Computing, 2022 - Elsevier
The constant increase in parallelism available on large-scale distributed computers poses
major scalability challenges to many scientific applications. A common strategy to improve …
major scalability challenges to many scientific applications. A common strategy to improve …
Exploiting model uncertainty to improve the scalability of long-time simulations using Parallel Trajectory Splicing
A Garmon, D Perez - … and Simulation in Materials Science and …, 2020 - iopscience.iop.org
We consider parallel trajectory splicing (ParSplice), a specialized molecular dynamics
method that extends simulation timescales through a parallel-in-time strategy, enabling …
method that extends simulation timescales through a parallel-in-time strategy, enabling …
Recent advances in accelerated molecular dynamics methods: Theory and applications
D Perez, T Lelièvre - … Computational Chemistry, First …, 2023 - lanlexperts.elsevierpure.com
By providing fully spatio-temporally-resolved atomistic trajectories, Molecular Dynamics
(MD) simulations can reveal fundamental characteristics of the thermodynamics and kinetics …
(MD) simulations can reveal fundamental characteristics of the thermodynamics and kinetics …
Speculation and replication in temperature accelerated dynamics
Accelerated Molecular Dynamics (AMD) is a class of MD-based algorithms for the long-time
scale simulation of atomistic systems that are characterized by rare-event transitions …
scale simulation of atomistic systems that are characterized by rare-event transitions …