Related papers: A simple asynchronous replica-exchange implementat…
The purpose of this article is to lay the mathematical foundations of a well known numerical approach in computational statistical physics and molecular dynamics, namely the parallel replica dynamics introduced by A.F. Voter. The aim of the…
Parallel tempering (PT) methods are a popular class of Markov chain Monte Carlo schemes used to sample complex high-dimensional probability distributions. They rely on a collection of $N$ interacting auxiliary chains targeting tempered…
We have developed molecular dynamics codes for a short-range interaction potential that adopt both the flat-MPI and MPI/OpenMP hybrid parallelizations on the basis of a full domain decomposition strategy. Benchmark simulations involving up…
The parallel linear equations solver capable of effectively using 1000+ processors becomes the bottleneck of large-scale implicit engineering simulations. In this paper, we present a new hierarchical parallel master-slave-structural…
Data structures for efficient sampling from a set of weighted items are an important building block of many applications. However, few parallel solutions are known. We close many of these gaps both for shared-memory and distributed-memory…
Parallel tempering is popular method for allowing MCMC algorithms to properly explore a $d$-dimensional multimodal target density. One problem with traditional power-based parallel tempering for multimodal targets is that the proportion of…
In this paper, we present a communication protocol between a pair of biological nanomachines, transmitter and receiver, built upon molecular communications in an aqueous environment. In our proposal, the receiver, acting as a control node,…
For distributions over discrete product spaces $\prod_{i=1}^n \Omega_i'$, Glauber dynamics is a Markov chain that at each step, resamples a random coordinate conditioned on the other coordinates. We show that $k$-Glauber dynamics, which…
Because of growing interest in temperature-based sampling methods like replica exchange, this note aims to make some observations and raise some potentially important questions which we have not seen addressed sufficiently in the…
Quantum algorithms have the potential to revolutionize our understanding of open quantum systems in chemistry. In this work, we demonstrate that a repeated interaction model, which could serve as the foundation for a digital quantum…
Asynchronous programming models (APM) are gaining more and more traction, allowing applications to expose the available concurrency to a runtime system tasked with coordinating the execution. While MPI has long provided support for…
We present a novel parallel implementation for large-scale three-dimensional electromagnetic inversion based on a Gauss-Newton framework combined with a rational near-best approximation of the matrix exponential for transient simulations.…
Data and pipeline parallelism are key strategies for scaling neural network training across distributed devices, but their high communication cost necessitates co-located computing clusters with fast interconnects, limiting their…
The advent of asynchronous iterative scheme gives high efficiency to numerical computations. However, it is generally difficult to handle the problems of resource management and convergence detection. This paper uses JACK2, an asynchronous…
Processors with large numbers of cores are becoming commonplace. In order to take advantage of the available resources in these systems, the programming paradigm has to move towards increased parallelism. However, increasing the level of…
We investigate the theoretical foundations of the simulated tempering method and use our findings to design efficient algorithms. Employing a large deviation argument first used for replica exchange molecular dynamics [Plattner et al., J.…
A parallel numerical simulation algorithm is presented for fractional-order systems involving Caputo-type derivatives, based on the Adams-Bashforth-Moulton (ABM) predictor-corrector scheme. The parallel algorithm is implemented using…
We present an algorithm for cluster dynamics to efficiently simulate large systems on MIMD parallel computers with large numbers of processors. The method divides physical space into rectangular cells which are assigned to processors and…
Understanding the complex behavior of molecular systems is fundamental to fields such as physics, materials science, and biology. Molecular dynamics (MD) simulations are crucial tools for studying atomic-level dynamics. This work focuses on…
In this paper, we present a parallel algorithm for Monte Carlo simulation of the 2D Ising Model to perform efficiently on a cluster computer using MPI. We use C++ programming language to implement the algorithm. In our algorithm, every…