Related papers: On the hierarchical parallelization of ab initio s…
The emergence and understanding of new design paradigms that exploit flow induced mechanical instabilities for propulsion or energy harvesting demands robust and accurate flow structure interaction numerical models. In this context, we…
Pipeline parallelism has been widely explored, but most existing schedules lack a systematic methodology. In this paper, we propose a framework to decompose pipeline schedules as repeating a building block, and show that the lifespan of the…
Unlocking large-scale low-bandwidth decentralized training has the potential to utilize otherwise untapped compute resources. In centralized settings, large-scale multi-node training is primarily enabled by data and pipeline parallelism,…
A new algorithm, "HiER-leap", is derived which improves on the computational properties of the ER-leap algorithm for exact accelerated simulation of stochastic chemical kinetics. Unlike ER-leap, HiER-leap utilizes a hierarchical or…
In many scientific and engineering domains, physical experiments are often costly, non-replicable, or time-consuming. The Kennedy and O'Hagan (KOH) model framework has become a widely used approach for combining simulator runs with limited…
We provided a concise and self-contained introduction to molecular dynamics (MD) simulation, which involves a body of fundamentals needed for all MD users. The associated computer code, simulating a gas of classical particles interacting…
We propose a model to study symmetric binary fluids, based in the mesoscopic molecular simulation technique known as multiparticle collision, where space and state variables are continuous while time is discrete. We include a repulsion rule…
A simple model for simulating flows of active suspensions is investigated. The approach is based on dissipative particle dynamics. While the model is potentially applicable to a wide range of self-propelled particle systems, the specific…
We present an accelerated ``on-the-fly'' coupled-cluster path-integral molecular dynamics (PIMD) method for finite-temperature simulations in which electron correlation and nuclear quantum effects are treated simultaneously. The approach is…
Molecular dynamics (MD) simulation with modified Brenner's reactive empirical bond order (REBO) potential is a powerful tool to investigate plasma wall interaction on divertor plates in a nuclear fusion device. However, MD simulation box's…
Computational intensity and sequential nature of estimation techniques for Bayesian methods in statistics and machine learning, combined with their increasing applications for big data analytics, necessitate both the identification of…
Parallel algorithms for ab initio calculations of vibrations modes of solids are presented and implemented under PVM. Load balancing and communication problems are dealt with in order to increase parallelism efficiency. For accurate time…
Pipeline Parallelism (PP) serves as a crucial technique for training Large Language Models (LLMs), owing to its capability to alleviate memory pressure from model states with relatively low communication overhead. However, in long-context…
In this paper, we design, analyze and implement efficient time parallel method for a class of fourth order time-dependent partial differential equations (PDEs), namely biharmonic heat equation, linearized Cahn-Hilliard (CH) equation and the…
The synchronized molecular dynamics simulation via macroscopic heat and momentum transfer is proposed for the non-isothermal flow behaviors of complex fluids. In this method, the molecular dynamics simulations are assigned to small fluid…
Massively-parallel molecular dynamics simulation is applied to systems containing electrolytes, vapour-liquid interfaces, and biomolecules in contact with water-oil interfaces. Novel molecular models of alkali halide salts are presented and…
This study addresses the challenge of simulating realistic particle systems by proposing a novel particle decomposition scheme that improves the parallel performance of surface resolved particle simulations. Realistic particle systems often…
The persistent homology pipeline includes the reduction of a, so-called, boundary matrix. We extend the work of Bauer et al. (2014) and Chen et al. (2011) where they show how to use dependencies in the boundary matrix to adapt the reduction…
The present paper describes a parallel unstructured-mesh Plasma simulation code based on Finite Volume method. The code dynamically refines and coarses mesh for accurate resolution of the different features regarding the electron density.…
Recent developments in path integral methodology have significantly reduced the computational expense of including quantum mechanical effects in the nuclear motion in ab initio molecular dynamics simulations. However, the implementation of…