Related papers: A fast recursive coordinate bisection tree for nei…
We describe a parallel, cosmological N-body code based on a hybrid scheme using the particle-mesh (PM) and Barnes-Hut (BH) oct-tree algorithm. We call the algorithm GOTPM for Grid-of-Oct-Trees-Particle-Mesh. The code is parallelized using…
We suggest a new non-recursive algorithm for constructing a binary search tree given an array of numbers. The algorithm has $O(N)$ time and $O(1)$ memory complexity if the given array of $N$ numbers is sorted. The resulting tree is of…
A combined N--body/SPH code is presented which benefits from the high speed of the special purpose hardware GRAPE (GRAvity PipE). Besides gravitational forces, GRAPE also returns the list of neighbours and can, therefore, be used to speed…
We present tests of comparison between our versions of the Fast Multipole Algorithm (FMA) and ``classic'' tree-code to evaluate gravitational forces in particle systems. We have optimized the Greengard's original version of FMA allowing for…
We describe a new method to accelerate neighbor searches on GRAPE, i.e. a special purpose hardware that efficiently calculates gravitational forces and potentials in $N$-body simulations. In addition to the gravitational calculations, GRAPE…
We continue our presentation of VINE. We begin with a description of relevant architectural properties of the serial and shared memory parallel computers on which VINE is intended to run, and describe their influences on the design of the…
We present a Fortran 95 code for simulating the evolution of astrophysical systems using particles to represent the underlying fluid flow. The code is designed to be versatile, flexible and extensible, with modular options that can be…
The Stokeslet and stresslet kernels are commonly used in boundary element simulations and singularity methods for slow viscous flow. Evaluating the velocity induced by a collection of Stokeslets and stresslets by direct summation requires…
We describe the TreePM method for carrying out large N-Body simulations to study formation and evolution of the large scale structure in the Universe. This method is a combination of Barnes and Hut tree code and Particle-Mesh code. It…
Many data-based statistical algorithms require that one find \textit{near or nearest neighbors} to a given vector among a set of points in that vector space, usually with Euclidean topology. The k-d data structure and search algorithms are…
We describe a new implementation of a parallel Tree-SPH code with the aim to simulate Galaxy Formation and Evolution. The code has been parallelized using SHMEM, a Cray proprietary library to handle communications between the 256 processors…
N-body codes to perform simulations of the origin and evolution of the Large Scale Structure of the Universe have improved significantly over the past decade both in terms of the resolution achieved and of reduction of the CPU time.…
Retrosynthesis, the process of deconstructing a target molecule into simpler precursors, is crucial for computer-aided synthesis planning (CASP). Widely adopted tree-search methods often suffer from exponential computational complexity. In…
The kd-tree is a fundamental tool in computer science. Among others, an application of the kd-tree search (oct-tree method) to fast evaluation of particle interactions and neighbor search is highly important since computational complexity…
Avraham et al. [AFK+15] presented an alternative approach to parametric search, called \emph{bifurcation}, that performs faster under certain circumstances. Intuitively, when the underlying decider execution can be rolled back cheaply and…
We describe a kernel of size 9k-8 for the NP-hard problem of computing the Tree Bisection and Reconnect (TBR) distance k between two unrooted binary phylogenetic trees. We achieve this by extending the existing portfolio of reduction rules…
We describe a new implementation of a parallel Tree-SPH code with the aim to simulate Galaxy Formation and Evolution. The code has been parallelized using SHMEM, a Cray proprietary library to handle communications between the 256 processors…
We present approximation algorithms for the following NP-hard optimization problems related to bottleneck spanning trees in metric spaces. 1. The disjoint bottleneck spanning tree problem: Given $n$ pairs of points in a metric space, find…
We present parallel algorithms for constructing and traversing sparse octrees on graphics processing units (GPUs). The algorithms are based on parallel-scan and sort methods. To test the performance and feasibility, we implemented them in…
We introduce a new code for cosmological simulations, PHoToNs, which has features on performing massive cosmological simulations on heterogeneous high performance Computer (HPC) and threads oriented programming. PHoToNs adopts a hybrid…