Related papers: Oct-tree Method on GPU

Graphics Processing Unit (GPU) computing is becoming an alternate computing platform for numerical simulations. However, it is not clear which numerical scheme will provide the highest computational efficiency for different types of…

We present a GPU solution for exact maximal clique enumeration (MCE) that performs a search tree traversal following the Bron-Kerbosch algorithm. Prior works on parallelizing MCE on GPUs perform a breadth-first traversal of the tree, which…

The ability to timely process significant amounts of continuously updated spatial data is mandatory for an increasing number of applications. In this paper we focus on a specific data-intensive problem concerning the repeated processing of…

We present Particle-Particle-Particle-Mesh (PPPM) and Tree Particle-Mesh (TreePM) implementations on GRAPE-5 and GRAPE-6A systems, special-purpose hardware accelerators for gravitational many-body simulations. In our PPPM and TreePM…

We present a simple $O(n^4)$-time algorithm for computing optimal search trees with two-way comparisons. The only previous solution to this problem, by Anderson et al., has the same running time, but is significantly more complicated and is…

We present a GPU-accelerated version of the real-space SPARC electronic structure code for performing Kohn-Sham density functional theory calculations within the local density and generalized gradient approximations. In particular, we…

We present a MATLAB script which can use GPU acceleration to simulate a trapped ion interacting with a low-density cloud of atoms. This script, called atomiongpu.m, can massively parallelize MD simulations of trajectories of a trapped ion…

Depth first search (DFS) tree is a fundamental data structure for solving various graph problems. The classical DFS algorithm requires $O(m+n)$ time for a graph having $n$ vertices and $m$ edges. In the streaming model, an algorithm is…

An improved implementation of an N-body code for simulating collisionless cosmological dynamics is presented. TPM (Tree-Particle-Mesh) combines the PM method on large scales with a tree code to handle particle-particle interactions at small…

Performance optimization can be a daunting task especially as the hardware architecture becomes more and more complex. This paper takes a kernel from the Materials Science code BerkeleyGW, and demonstrates a few performance analysis and…

Graphics processing units have been extensively used to accelerate classical molecular dynamics simulations. However, there is much less progress on the acceleration of force evaluations for many-body potentials compared to pairwise ones.…

Computing fixed-radius near-neighbor graphs is an important first step for many data analysis algorithms. Near-neighbor graphs connect points that are close under some metric, endowing point clouds with a combinatorial structure. As…

Stencil computation is an important class of scientific applications that can be efficiently executed by graphics processing units (GPUs). Out-of-core approach helps run large scale stencil codes that process data with sizes larger than the…

By a well known result the treewidth of k-outerplanar graphs is at most 3k-1. This paper gives, besides a rigorous proof of this fact, an algorithmic implementation of the proof, i.e. it is shown that, given a k-outerplanar graph G, a tree…

The construction of cut trees (also known as Gomory-Hu trees) for a given graph enables the minimum-cut size of the original graph to be obtained for any pair of vertices. Cut trees are a powerful back-end for graph management and mining,…

We review the recent optimizations of gravitational $N$-body kernels for running them on graphics processing units (GPUs), on single hosts and massive parallel platforms. For each of the two main $N$-body techniques, direct summation and…

Three-dimensional neutron transport calculations using the Method of Characteristics (MOC) are highly regarded for their exceptional computational efficiency, precision, and stability. Nevertheless, when dealing with extensive-scale…

The key challenge in neural architecture search (NAS) is designing how to explore wisely in the huge search space. We propose a new NAS method called TNAS (NAS with trees), which improves search efficiency by exploring only a small number…

We give an algorithm that takes as input an $n$-vertex graph $G$ and an integer $k$, runs in time $2^{O(k^2)} n^{O(1)}$, and outputs a tree decomposition of $G$ of width at most $k$, if such a decomposition exists. This resolves the…

Given a collection of points in R^3, KD-Tree and R-Tree are well-known nearest neighbor search (NNS) algorithms that rely on space partitioning and spatial indexing techniques. However, when the query point is far from the data points or…