[HTML][HTML] Scalable molecular dynamics on CPU and GPU architectures with NAMD

JC Phillips, DJ Hardy, JDC Maia, JE Stone… - The Journal of …, 2020 - pubs.aip.org
NAMD is a molecular dynamics program designed for high-performance simulations of very
large biological objects on CPU-and GPU-based architectures. NAMD offers scalable …

AI-driven multiscale simulations illuminate mechanisms of SARS-CoV-2 spike dynamics

L Casalino, AC Dommer, Z Gaieb… - … Journal of High …, 2021 - journals.sagepub.com
We develop a generalizable AI-driven workflow that leverages heterogeneous HPC
resources to explore the time-dependent dynamics of molecular systems. We use this …

[图书][B] Decision diagrams for optimization

D Bergman, AA Cire, WJ Van Hoeve, J Hooker - 2016 - Springer
This introductory chapter explains the motivation for developing decision diagrams as a new
discrete optimization technology. It shows how decision diagrams implement the five main …

A Survey of Storage Systems in the RDMA era

S Ma, T Ma, K Chen, Y Wu - IEEE Transactions on Parallel and …, 2022 - ieeexplore.ieee.org
Remote Direct Memory Access (RDMA) based network devices are increasingly being
deployed in modern data centers. RDMA brings significant performance improvements over …

Warp speed: executing time warp on 1,966,080 cores

PD Barnes Jr, CD Carothers, DR Jefferson… - Proceedings of the 1st …, 2013 - dl.acm.org
Time Warp is an optimistic synchronization protocol for parallel discrete event simulation that
coordinates the available parallelism through its rollback and antimessage mechanisms. In …

GASNet-EX: A high-performance, portable communication library for exascale

D Bonachea, PH Hargrove - … Workshop on Languages and Compilers for …, 2018 - Springer
Abstract Partitioned Global Address Space (PGAS) models, typified by languages such as
Unified Parallel C (UPC) and Co-Array Fortran, expose one-sided communication as a key …

Enabling highly-scalable remote memory access programming with MPI-3 one sided

R Gerstenberger, M Besta, T Hoefler - Proceedings of the International …, 2013 - dl.acm.org
Modern interconnects offer remote direct memory access (RDMA) features. Yet, most
applications rely on explicit message passing for communications albeit their unwanted …

Evaluating HPC networks via simulation of parallel workloads

N Jain, A Bhatele, S White, T Gamblin… - SC'16: Proceedings of …, 2016 - ieeexplore.ieee.org
This paper presents an evaluation and comparison of three topologies that are popular for
building interconnection networks in large-scale supercomputers: torus, fat-tree, and …

Performance and scalability of hierarchical hybrid multigrid solvers for Stokes systems

B Gmeiner, U Rüde, H Stengel, C Waluga… - SIAM Journal on …, 2015 - SIAM
In many applications involving incompressible fluid flow, the Stokes system plays an
important role. Complex flow problems may require extremely fine resolutions, easily …

Scalable molecular dynamics with NAMD on the summit system

B Acun, DJ Hardy, LV Kale, K Li… - IBM journal of …, 2018 - ieeexplore.ieee.org
NAnoscale Molecular Dynamics (NAMD) is a parallel molecular dynamics application that
has been used to make breakthroughs in understanding the structure and dynamics of large …