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GROMACS is a widely used package for biomolecular simulation, and over the last two decades it has evolved from small-scale efficiency to advanced heterogeneous acceleration and multi-level parallelism targeting some of the largest…

Computational Engineering, Finance, and Science · Computer Science 2015-06-03 Páll Szilárd , Mark James Abraham , Carsten Kutzner , Berk Hess , Erik Lindahl

Particle-Mesh (PM) codes are still very useful tools for testing predictions of cosmological models in cases when extra high resolution is not very important. We release for public use a cosmological PM N-body code. We provide a complete…

Astrophysics · Physics 2007-05-23 Anatoly Klypin , Jon Holtzman

The field of astrophysics has long sought computational tools capable of harnessing the power of modern GPUs to simulate the complex dynamics of astrophysical phenomena. The Kratos Framework, a novel GPU-based simulation system designed to…

Instrumentation and Methods for Astrophysics · Physics 2025-03-04 Lile Wang

3D Gaussian Splatting (3DGS) has emerged as a leading neural rendering technique for high-fidelity view synthesis, prompting the development of dedicated 3DGS accelerators for resource-constrained platforms. The conventional decoupled…

Hardware Architecture · Computer Science 2025-07-28 Minnan Pei , Gang Li , Junwen Si , Zeyu Zhu , Zitao Mo , Peisong Wang , Zhuoran Song , Xiaoyao Liang , Jian Cheng

Improving time-to-solution in molecular dynamics simulations often requires strong scaling due to fixed-sized problems. GROMACS is highly latency-sensitive, with peak iteration rates in the sub-millisecond, making scalability on…

Distributed, Parallel, and Cluster Computing · Computer Science 2025-09-29 Mahesh Doijade , Andrey Alekseenko , Ania Brown , Alan Gray , Szilárd Páll

We present Version 3.0 of the GLoBES (``General Long Baseline Experiment Simulator'') software, which is a simulation tool for short- and long-baseline neutrino oscillation experiments. As a new feature, GLoBES 3.0 allows for user-defined…

High Energy Physics - Phenomenology · Physics 2008-11-26 Patrick Huber , Joachim Kopp , Manfred Lindner , Mark Rolinec , Walter Winter

We present the public data release of the AbacusSummit cosmological $N$-body simulation suite, produced with the $\texttt{Abacus}$ $N$-body code on the Summit supercomputer of the Oak Ridge Leadership Computing Facility. $\texttt{Abacus}$…

Cosmology and Nongalactic Astrophysics · Physics 2021-10-25 Nina A. Maksimova , Lehman H. Garrison , Daniel J. Eisenstein , Boryana Hadzhiyska , Sownak Bose , Thomas P. Satterthwaite

We introduce CRK-HACC, an extension of the Hardware/Hybrid Accelerated Cosmology Code (HACC), to resolve gas hydrodynamics in large-scale structure formation simulations of the universe. The new framework couples the HACC gravitational…

Cosmology and Nongalactic Astrophysics · Physics 2023-02-01 Nicholas Frontiere , J. D. Emberson , Michael Buehlmann , Joseph Adamo , Salman Habib , Katrin Heitmann , Claude-André Faucher-Giguère

Upcoming Large Scale Structure surveys aim to achieve an unprecedented level of precision in measuring galaxy clustering. However, accurately modeling these statistics may require theoretical templates that go beyond second-order…

Cosmology and Nongalactic Astrophysics · Physics 2023-11-21 M. Icaza-Lizaola , Yong-Seon Song , Minji Oh , Yi Zheng

We describe a parallel version of our tree-code for the simulation of self-gravitating systems in Astrophysics. It is based on a dynamic and adaptive method for the domain decomposition, which exploits the hierarchical data arrangement used…

Astrophysics · Physics 2007-05-23 P. Miocchi , R. Capuzzo-Dolcetta

This work is devoted to the thermodynamics of gravitational clustering, a collective phenomenon with a great relevance in the $N$-body cosmological problem. We study a classical self-gravitating gas of identical non-relativistic particles…

Statistical Mechanics · Physics 2016-11-03 F. Tello-Ortiz , L. Velazquez

We describe source code level parallelization for the {\tt kira} direct gravitational $N$-body integrator, the workhorse of the {\tt starlab} production environment for simulating dense stellar systems. The parallelization strategy, called…

As an entry for the 2012 Gordon-Bell performance prize, we report performance results of astrophysical N-body simulations of one trillion particles performed on the full system of K computer. This is the first gravitational trillion-body…

Cosmology and Nongalactic Astrophysics · Physics 2015-04-14 Tomoaki Ishiyama , Keigo Nitadori , Junichiro Makino

Numerical simulations of self-gravitating systems are generally based on N-body codes, which solve the equations of motion of a large number of interacting particles. This approach suffers from poor statistical sampling in regions of low…

Cosmology and Nongalactic Astrophysics · Physics 2016-04-27 Giovanni Manfredi , Jean-Louis Rouet , Bruce Miller , Yui Shiozawa

The increasing complexity and scale of cosmological N-body simulations, driven by astronomical surveys like Euclid, call for a paradigm shift towards more sustainable and energy-efficient high-performance computing (HPC). The rising energy…

We introduce the Generalised Lensing and Shear Spectra GLaSS code which is available for download from https://github.com/astro-informatics/GLaSS It is a fast and flexible public code, written in Python, that computes generalized spherical…

Cosmology and Nongalactic Astrophysics · Physics 2018-07-31 Peter L. Taylor , Thomas D. Kitching , Jason D. McEwen , Thomas Tram

LLMs excel in localized code completion but struggle with repository-level tasks due to limited context windows and complex semantic and structural dependencies across codebases. While Retrieval-Augmented Generation (RAG) mitigates context…

Software Engineering · Computer Science 2025-09-09 Xingliang Wang , Baoyi Wang , Chen Zhi , Junxiao Han , Xinkui Zhao , Jianwei Yin , Shuiguang Deng

Modeling of collisionless galactic systems is based on the N-body model, which requires large computational resources due to the long-range nature of gravitational forces. The most common method for calculating gravity is the TreeCode…

Computational Physics · Physics 2024-12-03 Nikolay M. Kuzmin , Danila S. Sirotin , Alexander V. Khoperskov

The performance and accuracy of a GRAPE-3 system for collisionless N-body simulations is discussed. After a description of the hardware configurations available to us at Marseille, and the usefulness of on-line analysis, we concentrate on…

Astrophysics · Physics 2009-10-30 E. Athanassoula , A. Bosma , J. -C. Lambert , J. Makino

Globular cluster stellar streams probe galaxy-formation processes and can potentially reveal the distribution of dark matter in galaxies. In many theoretical studies, streams are modeled with particle-spray or direct N-body codes. But…

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