Related papers: A simple asynchronous replica-exchange implementat…
Asynchronous iterations are more and more investigated for both scaling and fault-resilience purpose on high performance computing platforms. While so far, they have been exclusively applied within space domain decomposition frameworks,…
We introduce an algorithm to systematically improve the efficiency of parallel tempering Monte Carlo simulations by optimizing the simulated temperature set. Our approach is closely related to a recently introduced adaptive algorithm that…
We propose a new method for molecular dynamics and Monte Carlo simulations, which is referred to as the replica-permutation method (RPM), to realize more efficient sampling than the replica-exchange method (REM).In RPM not only exchanges…
We present results from our study of the Parallel Tempering algorithm. We examine the swapping acceptance rate of a twin subensemble PT system. We use action matching technology in an attempt to maximise the swap acceptance rate. We model…
We study the 38-atom Lennard-Jones cluster with parallel tempering Monte Carlo methods in the microcanonical and molecular dynamics ensembles. A new Monte Carlo algorithm is presented that samples rigorously the molecular dynamics ensemble…
We present a novel approach to the parallelization of the parabolic fast multipole method for a space-time boundary element method for the heat equation. We exploit the special temporal structure of the involved operators to provide an…
We present a novel implementation of the parallel tempering Monte Carlo method in a multicanonical ensemble. Multicanonical weights are derived by a self-consistent iterative process using a Boltzmann inversion of global energy histograms.…
In finite-size scaling analyses of Monte Carlo simulations of second-order phase transitions one often needs an extended temperature/energy range around the critical point. By combining the replica-exchange algorithm with cluster updates…
Replica Exchange (RE) simulations have emerged as an important algorithmic tool for the molecular sciences. RE simulations involve the concurrent execution of independent simulations which infrequently interact and exchange information. The…
All-atom molecular dynamics (MD) computer simulations are a valuable tool for characterizing the conformational ensembles of intrinsically disordered proteins (IDPs). IDP conformational ensembles are highly heterogeneous and contain…
Markov Chain Monte Carlo methods are algorithms used to sample probability distributions, commonly used to sample the Boltzmann distribution of physical/chemical models (e.g., protein folding, Ising model, etc.). This allows us to study…
In finite-size scaling analyses of Monte Carlo simulations of second-order phase transitions one often needs an extended temperature range around the critical point. By combining the parallel tempering algorithm with cluster updates and an…
In this paper, we address the problem of designing a distributed application meant to run both classical and asynchronous iterations. MPI libraries are very popular and widely used in the scientific community, however asynchronous iterative…
Parallel algorithms designed for simulation and performance evaluation of single-server tandem queueing systems with both infinite and finite buffers are presented. The algorithms exploit a simple computational procedure based on recursive…
Parallel implementations of linear iterative solvers generally alternate between phases of data exchange and phases of local computation. Increasingly large problem sizes on more heterogeneous systems make load balancing and network layout…
We present a new scalable algorithm for short-range molecular dynamics simulations on distributed memory MIMD multicomputer based on a message-passing multi-cell approach. We have implemented the algorithm on the Connection Machine 5 (CM-5)…
State Machine Replication (SMR) is a fundamental approach to designing service with fault tolerance. However, its requirement for the deterministic execution of transactions often results in single-threaded replicas, which cannot fully…
We introduce Lemon, an MPI parallel I/O library that is intended to allow for efficient parallel I/O of both binary and metadata on massively parallel architectures. Motivated by the demands of the Lattice Quantum Chromodynamics community,…
Generation of equilibrium configurations is the major obstacle for numerical investigation of the slow dynamics in supercooled liquid states. The parallel tempering (PT) technique, originally proposed for the numerical equilibration of…
Parallel replica dynamics is a method for accelerating the computation of processes characterized by a sequence of infrequent events. In this work, the processes are governed by the overdamped Langevin equation. Such processes spend much of…