Related papers: Partitioning 3D space for parallel many-particle s…
Particle-In-Cell (PIC) codes are broadly applied to the kinetic simulation of plasmas, from laser-matter interaction to astrophysics. Their heavy simulation cost can be mitigated by using the Single Instruction Multiple Data (SIMD)…
This article describes a geometric partitioning software that can be used for quick computation of data partitions on many-core HPC machines. It is most suited for dynamic applications with load distributions that vary with time.…
Particle-in-cell (PIC) simulations with Monte-Carlo collisions are used in plasma science to explore a variety of kinetic effects. One major problem is the long run-time of such simulations. Even on modern computer systems, PIC codes take a…
Heterogeneous systems-on-chip (SoCs) are highly favorable computing platforms due to their superior performance and energy efficiency potential compared to homogeneous architectures. They can be further tailored to a specific domain of…
This article describes algorithms for the hybrid parallelization and SIMD vectorization of molecular dynamics simulations with short-range forces. The parallelization method combines domain decomposition with a thread-based parallelization…
The aim of this paper is to develop an approach to visualizations that benefits from distributed computing. Three schemes of process distribution are considered: parallel, pipeline, and expanding pipeline computations. Expanding pipeline…
Cell nuclei segmentation is one of the most important tasks in the analysis of biomedical images. With ever-growing sizes and amounts of three-dimensional images to be processed, there is a need for better and faster segmentation methods.…
Computational chemistry allows researchers to experiment in sillico: by running a computer simulations of a biological or chemical processes of interest. Molecular dynamics with molecular mechanics model of interactions simulates N-body…
In this work I present a technique of construction and fast evaluation of a family of cubic polynomials for analytic smoothing and graphical rendering of particles trajectories for flows in a generic geometry. The principal result of the…
Distributed Computation has been a recent trend in engineering research. Parallel Computation is widely used in different areas of Data Mining, Image Processing, Simulating Models, Aerodynamics and so forth. One of the major usage of…
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…
B-spline based orbital representations are widely used in Quantum Monte Carlo (QMC) simulations of solids, historically taking as much as 50% of the total run time. Random accesses to a large four-dimensional array make it challenging to…
In this paper we describe, implement, and test the performance of distributed memory simulations of quantum circuits on the MSU Laconia Top500 supercomputer. Using OpenMP and MPI hybrid parallelization, we first use a distributed…
Microstructures forming during ternary eutectic directional solidification processes have significant influence on the macroscopic mechanical properties of metal alloys. For a realistic simulation, we use the well established…
In this paper we evaluate the performance of Unified Parallel C (which implements the partitioned global address space programming model) using a numerical method that is widely used in fluid dynamics. In order to evaluate the incremental…
We present a computational algorithm for computing short range forces between particles. The algorithm has two distinguishing features. First, it is optimized for multi-processor computers, and will use as many processors as are available.…
We develop a "semi-parallel" simulation technique suggested by Pretorius and Lehner, in which the simulation spacetime volume is divided into a large number of small 4-volumes which have only initial and final surfaces. Thus there is no…
A highly adaptive load balancing algorithm for parallel simulations using particle methods, such as molecular dynamics and smoothed particle hydrodynamics (SPH), is developed. Our algorithm is based on the dynamic spatial decomposition of…
The Cellular Potts Model (CPM) is a widely used simulation paradigm for systems of interacting cells that has been used to study scenarios ranging from plant development to morphogenesis, tumour growth and cell migration. Despite their wide…
Early but promising results in quantum computing have been enabled by the concurrent development of quantum algorithms, devices, and materials. Classical simulation of quantum programs has enabled the design and analysis of algorithms and…