ArticleSC ... conference proceedings. SC (Conference : Supercomputing)
Mapping to Irregular Torus Topologies and Other Techniques for Petascale Biomolecular Simulation.
Article in SC ... conference proceedings. SC (Conference : Supercomputing). The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
What it found
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Who cites it
9 citing papers in PubMed.
- Atomistic simulations of intact virus capsids: A computational challenge worth the scientific payoff.Current opinion in structural biology · 2025Review
- AI-driven multiscale simulations illuminate mechanisms of SARS-CoV-2 spike dynamics.The international journal of high performance computing applications · 2021Article
- AI-Driven Multiscale Simulations Illuminate Mechanisms of SARS-CoV-2 Spike Dynamics.bioRxiv : the preprint server for biology · 2020Article
- Scalable molecular dynamics on CPU and GPU architectures with NAMD.The Journal of chemical physics · 2020Article
- Protein Structure Prediction and Design in a Biologically Realistic Implicit Membrane.Biophysical journal · 2020Article
- Physical properties of the HIV-1 capsid from all-atom molecular dynamics simulations.Nature communications · 2017Article
- Atomic Detail Visualization of Photosynthetic Membranes with GPU-Accelerated Ray Tracing.Parallel computing · 2016Article
- Molecular dynamics simulations of large macromolecular complexes.Current opinion in structural biology · 2015Review
- Scalable Molecular Dynamics with NAMD on the Summit System.IBM journal of research and developmentArticle
Corrections and comments
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Authors and funding
5 authors.
Funding
Abstract
Currently deployed petascale supercomputers typically use toroidal network topologies in three or more dimensions. While these networks perform well for topology-agnostic codes on a few thousand nodes, leadership machines with 20,000 nodes require topology awareness to avoid network contention for communication-intensive codes. Topology adaptation is complicated by irregular node allocation shapes and holes due to dedicated input/output nodes or hardware failure. In the context of the popular molecular dynamics program NAMD, we present methods for mapping a periodic 3-D grid of fixed-size spatial decomposition domains to 3-D Cray Gemini and 5-D IBM Blue Gene/Q toroidal networks to enable hundred-million atom full machine simulations, and to similarly partition node allocations into compact domains for smaller simulations using multiple-copy algorithms. Additional enabling techniques are discussed and performance is reported for NCSA Blue Waters, ORNL Titan, ANL Mira, TACC Stampede, and NERSC Edison.
Identifiers
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.