ArticleHigh performance computing : 31st International Conference, ISC High Performance 2016, Frankfurt, Germany, June 19-23, 2016, Proceedings. ISC High Performance (Conference) (31st : 2016 : Frankfurt, Germany)2016
Early Experiences Porting the NAMD and VMD Molecular Simulation and Analysis Software to GPU-Accelerated OpenPOWER Platforms.
Article in High performance computing : 31st International Conference, ISC High Performance 2016, Frankfurt, Germany, June 19-23, 2016, Proceedings. ISC High Performance (Conference) (31st : 2016 : Frankfurt, Germany), 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed.
- From wireframes to immersive reality: a historical perspective on molecular visualization software.Briefings in bioinformatics · 2026Review
- Atomistic simulations of intact virus capsids: A computational challenge worth the scientific payoff.Current opinion in structural biology · 2025Review
- Review
- Revolutionizing Molecular Design for Innovative Therapeutic Applications through Artificial Intelligence.Molecules (Basel, Switzerland) · 2024Review
- VMD as a Platform for Interactive Small Molecule Preparation and Visualization in Quantum and Classical Simulations.Journal of chemical information and modeling · 2023Article
- Revealing the Impacts of Chemical Complexity on Submicrometer Sea Spray Aerosol Morphology.ACS central science · 2023Article
- Application Experiences on a GPU-Accelerated Arm-based HPC Testbed.The proceedings of International Conference on High Performance Computing in Asia-Pacific Region (HPC Asia 2023 Workshops) : 27 February to 2 March 2023, Singapore. International Conference/Exhibition on High-Performance Computing in th... · 2023Article
- #COVIDisAirborne: AI-enabled multiscale computational microscopy of delta SARS-CoV-2 in a respiratory aerosol.The international journal of high performance computing applications · 2023Article
- Review of Electrostatic Force Calculation Methods and Their Acceleration in Molecular Dynamics Packages Using Graphics Processors.ACS omega · 2022Review
- All-atom molecular dynamics simulations of the combined effects of different phospholipids and cholesterol content on electroporation.RSC advances · 2022Article
- Accelerators for Classical Molecular Dynamics Simulations of Biomolecules.Journal of chemical theory and computation · 2022Review
- Accelerating AutoDock Vina with GPUs.Molecules (Basel, Switzerland) · 2022Article
- Experiences Porting NAMD to the Data Parallel C++ Programming Model.International Workshop on OpenCL · 2022Article
- #COVIDisAirborne: AI-Enabled Multiscale Computational Microscopy of Delta SARS-CoV-2 in a Respiratory Aerosol.bioRxiv : the preprint server for biology · 2021Article
- Defining the Energetic Basis for a Conformational Switch Mediating Ligand-Independent Activation of Mutant Estrogen Receptors in Breast Cancer.Molecular cancer research : MCR · 2021Article
- AI-driven multiscale simulations illuminate mechanisms of SARS-CoV-2 spike dynamics.The international journal of high performance computing applications · 2021Article
- Accelerating AutoDock4 with GPUs and Gradient-Based Local Search.Journal of chemical theory and computation · 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
- Scalable Molecular Dynamics with NAMD on the Summit System.IBM journal of research and developmentArticle
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4 authors.
Funding
Abstract
All-atom molecular dynamics simulations of biomolecules provide a powerful tool for exploring the structure and dynamics of large protein complexes within realistic cellular environments. Unfortunately, such simulations are extremely demanding in terms of their computational requirements, and they present many challenges in terms of preparation, simulation methodology, and analysis and visualization of results. We describe our early experiences porting the popular molecular dynamics simulation program NAMD and the simulation preparation, analysis, and visualization tool VMD to GPU-accelerated OpenPOWER hardware platforms. We report our experiences with compiler-provided autovectorization and compare with hand-coded vector intrinsics for the POWER8 CPU. We explore the performance benefits obtained from unique POWER8 architectural features such as 8-way SMT and its value for particular molecular modeling tasks. Finally, we evaluate the performance of several GPU-accelerated molecular modeling kernels and relate them to other hardware platforms.
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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.