Related papers: Parallel Algorithm for Calculation of the Exact Pa…
The study of approximate matching in the Massively Parallel Computations (MPC) model has recently seen a burst of breakthroughs. Despite this progress, however, we still have a far more limited understanding of maximal matching which is one…
A numerical irreducible decomposition for a polynomial system provides representations for the irreducible factors of all positive dimensional solution sets of the system, separated from its isolated solutions. Homotopy continuation methods…
Lattice models are useful for understanding behaviors of interacting complex many-body systems. The lattice dimer model has been proposed to study the adsorption of diatomic molecules on a substrate. Here we analyze the partition function…
We calculate thermodynamic quantities of HP lattice proteins by means of a multicanonical chain growth algorithm that connects the new variants of the Pruned-Enriched Rosenbluth Method (nPERM) and flat histogram sampling of the entire…
We present a simple and powerful algorithm for parallel black box optimization called Successive Halving and Classification (SHAC). The algorithm operates in $K$ stages of parallel function evaluations and trains a cascade of binary…
Parallel tempering is a meta-algorithm for Markov Chain Monte Carlo that uses multiple chains to sample from tempered versions of the target distribution, enhancing mixing in multi-modal distributions that are challenging for traditional…
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.…
The Cellular Potts Model (CPM) is a lattice based modeling technique which is widely used for simulating cellular patterns such as foams or biological tissues. Despite its realism and generality, the standard Monte Carlo algorithm used in…
We present a new and more efficient implementation of transfer-matrix methods for exact enumerations of lattice objects. The new method is illustrated by an application to the enumeration of self-avoiding polygons on the square lattice. A…
Lattice simulations are an important class of problems in crystalline solids, surface science, alloys, adsorption, absorption, separation, catalysis, to name a few. We describe a fast computational method for performing lattice…
Using (a,b)-trees as an example, we show how to perform a parallel split with logarithmic latency and parallel join, bulk updates, intersection, union (or merge), and (symmetric) set difference with logarithmic latency and with information…
In this work we describe a new technique for numerical exact diagonalization. The method is particularly suitable for cold bosonic atoms in optical lattices, in which multiple atoms can occupy a lattice site. We describe the use of the…
We propose a novel parallel algorithm for decomposing hard CircuitSAT instances. The technique employs specialized constraints to partition an original SAT instance into a family of weakened formulas. Our approach is implemented as a…
We develop the hybrid Monte Carlo method for simulations of single off-lattice polymer chains. We discuss implementation and choice of simulation parameters in some detail. The performance of the algorithm is tested on models for…
We construct a class of lattices in three and higher dimensions for which the number of dimer coverings can be determined exactly using elementary arguments. These lattices are a generalization of the two-dimensional kagome lattice, and the…
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…
A novel approach to parallelize the well-known Hoshen-Kopelman algorithm has been chosen, suitable for simulating huge lattices in high dimensions on massively-parallel computers with distributed memory and message passing. This method…
Specialized function gradient computing hardware could greatly improve the performance of state-of-the-art optimization algorithms, e.g., based on gradient descent or conjugate gradient methods that are at the core of control, machine…
Obtaining reliable estimates of the statistical properties of complex macromolecules by computer simulation is a task that requires high computational effort as well as the development of highly efficient simulation algorithms. We present…
We report the results of intensive numerical calculations for four atomic H2+H2 energy transfer collision. A parallel computing technique based on LAM/MPI functions is used. In this algorithm, the data is distributed to the processors…