Related papers: Parallel implementation of three-dimensional molec…
We present a GPU implementation of LAMMPS, a widely-used parallel molecular dynamics (MD) software package, and show 5x to 13x single node speedups versus the CPU-only version of LAMMPS. This new CUDA package for LAMMPS also enables…
Molecular dynamics facilitates the simulation of a complex system to be analyzed at molecular and atomic levels. Simulations can last a long period of time, even months. Due to this cause the graphics processing units (GPUs) and multi-core…
Spatial stochastic molecular simulations in biology are limited by the intense computation required to track molecules in space either in a discrete time or discrete space framework, meaning that the serial limit has already been reached in…
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)…
This paper proposes a general formulation for temporal parallelisation of dynamic programming for optimal control problems. We derive the elements and associative operators to be able to use parallel scans to solve these problems with…
An efficient parallelization approach to simulate optical properties of ensembles of quantum emitters in realistic electromagnetic environments is considered. It relies on balancing computing load of utilized processors and is built into…
Large molecular dynamics simulations (millions of atoms, tens of microseconds, thousands of processors) hit the strong scalability wall: simulation on twice as many processors does not take half the time. Inspired by large N-body space…
Numerical studies of shock waves in large scale systems via kinetic simulations with millions of particles are too computationally demanding to be processed in serial. In this work we focus on optimizing the parallel performance of a…
We discuss the possibility of implementing asynchronous replica-exchange (or parallel tempering) molecular dynamics. In our scheme, the exchange attempts are driven by asynchronous messages sent by one of the computing nodes, so that…
Stochastic, spatial reaction-diffusion simulations have been widely used in systems biology and computational neuroscience. However, the increasing scale and complexity of simulated models and morphologies have exceeded the capacity of any…
In this talk I discuss the general question of the portability of Molecular Dynamics codes for diffusive systems on parallel computers of the APE family. The intrinsic single precision arithmetics of the today available APE platforms does…
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…
Numerical solution of reaction-diffusion equations in three dimensions is one of the most challenging applied mathematical problems. Since these simulations are very time consuming, any ideas and strategies aiming at the reduction of CPU…
In this paper we present results of using parallel supercomputers to simulate beam dynamics in next-generation high intensity ion linacs. Our approach uses a three-dimensional space charge calculation with six types of boundary conditions.…
Micro-macro models provide a powerful tool to study the relationship between microscale mechanisms and emergent macroscopic behavior. However, the detailed microscopic modeling may require tracking and evolving a high-dimensional…
In this work, a new partition-collocation strategy for the parallel execution of CFD--DEM couplings is investigated. Having a good parallel performance is a key issue for an Eulerian-Lagrangian software that aims to be applied to solve…
We present a parallel-scalable method for simulating non-dilute suspensions of deformable particles immersed in Stokesian fluid in three dimensions. A critical component in these simulations is robust and accurate collision handling. This…
Typical biomolecular systems such as cellular membranes, DNA, and protein complexes are highly charged. Thus, efficient and accurate treatment of electrostatic interactions is of great importance in computational modelling of such systems.…
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…
In this paper I describe some results on the use of virtual processors technology for parallelize some SPMD computational programs in a cluster environment. The tested technology is the INTEL Hyper Threading on real processors, and the…