Related papers: Partitioning 3D space for parallel many-particle s…
Several methods for density matrix propagation in distributed computing environments, such as clusters and graphics processing units, are proposed and evaluated. It is demonstrated that the large communication overhead associated with each…
Partitioning graphs into blocks of roughly equal size such that few edges run between blocks is a frequently needed operation in processing graphs. Recently, size, variety, and structural complexity of these networks has grown dramatically.…
Rigorous computer simulations of propagating electromagnetic fields have become an important tool for optical metrology and design of nanostructured optical components. A vectorial finite element method (FEM) is a good choice for an…
Partitioned Global Address Space (PGAS) integrates the concepts of shared memory programming and the control of data distribution and locality provided by message passing into a single parallel programming model. The purpose of allying…
We demonstrate that general-purpose memory allocation involving many threads on many cores can be done with high performance, multicore scalability, and low memory consumption. For this purpose, we have designed and implemented scalloc, a…
We present and compare distributed parallelization strategies for the particle-in-Fourier (PIF) schemes used in kinetic plasma simulations. The different strategies are i) domain decomposition, where both the particles and Fourier modes are…
Simulation of a multicomponent lipid bilayer having a fixed percentage of cholesterol is done to study phase transition leading to domain formation. The concept of random lattice has been used in simulation to account for the coupling…
Multiscale and inhomogeneous molecular systems are challenging topics in the field of molecular simulation. In particular, modeling biological systems in the context of multiscale simulations and exploring material properties are driving a…
A fully parallel version of the contact dynamics (CD) method is presented in this paper. For large enough systems, 100% efficiency has been demonstrated for up to 256 processors using a hierarchical domain decomposition with dynamic load…
This article presents new algorithms for massively parallel granular dynamics simulations on distributed memory architectures using a domain partitioning approach. Collisions are modelled with hard contacts in order to hide their…
In this tutorial paper, we will firstly review some basic simulation concepts and then introduce the parallel and distributed simulation techniques in view of some new challenges of today and tomorrow. More in particular, in the last years…
Medical images such as 3D computerized tomography (CT) scans and pathology images, have hundreds of millions or billions of voxels/pixels. It is infeasible to train CNN models directly on such high resolution images, because neural…
We study the opportunities for parallelism for the simulation of surface reactions. We introduce the concept of a partition and we give new simulation methods based on Cellular Automaton using partitions. We elaborate on the advantages and…
The aim of the paper is to introduce general techniques in order to optimize the parallel execution time of sorting on a distributed architectures with processors of various speeds. Such an application requires a partitioning step. For…
Optical networks with parallel processing capabilities are significant in advancing high-speed data computing and large-scale data processing by providing ultra-width computational bandwidth. In this paper, we present a photonic integrated…
The cell membrane is inherently asymmetric and heterogeneous in its composition, a feature that is crucial for its function. Using atomistic molecular dynamics simulations, the physical properties of a 3-component asymmetric mixed lipid…
The size distributions of 2D and 3D Voronoi cells and of cells of $V_p(2,3)$,--2D cut of 3D Voronoi diagram--are explored, with the single-parameter (re-scaled) gamma distribution playing a central role in the analytical fitting.…
Parallel programming is emerging fast and intensive applications need more resources, so there is a huge demand for on-chip multiprocessors. Accessing L1 caches beside the cores are the fastest after registers but the size of private caches…
The need for computational resources grows as computational algorithms gain popularity in different sectors of the scientific community. This search has stimulated the development of several cloud platforms that abstract the complexity of…
This paper presents our work on developing parallel computational methods for two-phase flow on modern parallel computers, where techniques for linear solvers and nonlinear methods are studied and the standard and inexact Newton methods are…