[HTML][HTML] Scalable molecular dynamics on CPU and GPU architectures with NAMD
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 …
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 …
resources to explore the time-dependent dynamics of molecular systems. We use this …
[图书][B] Decision diagrams for optimization
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 …
discrete optimization technology. It shows how decision diagrams implement the five main …
A Survey of Storage Systems in the RDMA era
Remote Direct Memory Access (RDMA) based network devices are increasingly being
deployed in modern data centers. RDMA brings significant performance improvements over …
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 …
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 …
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
Modern interconnects offer remote direct memory access (RDMA) features. Yet, most
applications rely on explicit message passing for communications albeit their unwanted …
applications rely on explicit message passing for communications albeit their unwanted …
Evaluating HPC networks via simulation of parallel workloads
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 …
building interconnection networks in large-scale supercomputers: torus, fat-tree, and …
Performance and scalability of hierarchical hybrid multigrid solvers for Stokes systems
In many applications involving incompressible fluid flow, the Stokes system plays an
important role. Complex flow problems may require extremely fine resolutions, easily …
important role. Complex flow problems may require extremely fine resolutions, easily …
Scalable molecular dynamics with NAMD on the summit system
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 …
has been used to make breakthroughs in understanding the structure and dynamics of large …