Related papers: Cornerstone: Octree Construction Algorithms for Sc…
Gravitational $N$-body simulations calculate numerous interactions between particles. The tree algorithm reduces these calculations by constructing a hierarchical oct-tree structure and approximating gravitational forces on particles. Over…
Computer simulation with Monte Carlo is an important tool to investigate the function and equilibrium properties of many systems with biological and soft matter materials solvable in solvents. The appropriate treatment of long-range…
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…
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 have newly developed a Parallelized Particle-Particle Particle-tree code for Planet formation, PENTACLE, which is a parallelized hybrid $N$-body integrator executed on a CPU-based (super)computer. PENTACLE uses a 4th-order Hermite…
We present an MPI-parallel algorithm for the in-situ visualization of computational data that is built around a distributed linear forest-of-octrees data structure. Such octrees are frequently used in element-based numerical simulations;…
We propose a hybrid tree algorithm for reducing calculation and communication cost of collision-less N-body simulations. The concept of our algorithm is that we split interaction force into two parts: hard-force from neighbor particles and…
We describe the implementation and performance of the ${\rm P^3T}$ (Particle-Particle Particle-Tree) scheme for simulating dense stellar systems. In ${\rm P^3T}$, the force experienced by a particle is split into short-range and long-range…
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…
One of the key problems in tensor network based quantum circuit simulation is the construction of a contraction tree which minimizes the cost of the simulation, where the cost can be expressed in the number of operations as a proxy for the…
Most of the existing clustering methods are based on a single granularity of information, such as the distance and density of each data. This most fine-grained based approach is usually inefficient and susceptible to noise. Therefore, we…
This paper presents \pandora, a novel parallel algorithm for efficiently constructing dendrograms for single-linkage hierarchical clustering, including \hdbscan. Traditional dendrogram construction methods from a minimum spanning tree…
I describe here the performances of a parallel treecode with individual particle timesteps. The code is based on the Barnes-Hut algorithm and runs cosmological N-body simulations on parallel machines with a distributed memory architecture…
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…
In this paper, we present a novel massively parallel algorithm for accelerating the decision tree building procedure on GPUs (Graphics Processing Units), which is a crucial step in Gradient Boosted Decision Tree (GBDT) and random forests…
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.…
This Article presents two optimized multi-GPU algorithms for Fock matrix construction, building on the work of Ufimtsev et al. and Barca et al. The novel algorithms, opt-UM and opt-Brc, introduce significant enhancements, including improved…
The forest-of-octrees approach to parallel adaptive mesh refinement and coarsening (AMR) has recently been demonstrated in the context of a number of large-scale PDE-based applications. Although linear octrees, which store only leaf…
Scalable and efficient numerical simulations continue to gain importance, as computation is firmly established as the third pillar of discovery, alongside theory and experiment. Meanwhile, the performance of computing hardware grows through…
We present an MPI + OpenACC implementation of the kernel-independent barycentric Lagrange treecode (BLTC) for fast summation of particle interactions on GPUs. The distributed memory parallelization uses recursive coordinate bisection for…