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At least 343 records · Page 19

OpenMP and MPI implementations of an elasto-viscoplastic fast Fourier transform-based micromechanical solver for fast crystal plasticity modeling

Here, we explore several parallel implementations of an elasto-viscoplastic fast Fourier transform (EVPFFT) model using Message Passing Interface (MPI), OpenMP, and a hybrid of MPI and OpenMP to efficiently predict micromechanical response of polycrystals. Performance studies using EVPFFT are performed based on domain decomposition over voxels of a periodic cell, which is a representative volume element (RVE) of polycrystalline copper. We begin by parallelizing the computationally intensive Newton–Raphson (NR) single crystal solver within EVPFFT. Next, we compare the performance of the serial and parallel FFTW (Fastest Fourier Transform in the West) using OpenMP (OpenMP-FFTW) and MPI (MPI-FFTW) with the original Numerical Recipes-based FOURN routine within EVPFFT. In the parallel environment, we find that the FFT calculations are best performed using the MPI version of FFTW. Finally, the remainder of the code, except read/write subroutines, is parallelized. Significant speedups of the original EVPFFT model are achieved using MPI on shared memory multicore workstations. Furthermore, results achieved on a distributed memory Cray supercomputer show promising strong and weak scalability and in some cases even super scalability for the single crystal NR solver in EVPFFT. MPI-FFTW also scales perfectly for microstructure RVEs larger than 64 3 FFT voxels. For example, the MPI-EVPFFT parallel version of the code accelerates the simulations for approximately two orders of magnitude using 64 cores over the old serial code for an RVE size of 128 3 . Finally, the parallel EVPFFT code developed in this work can run massive voxel-based microstructural RVEs taking the advantages of thousands of logical cores provided by more advanced clusters.

42 ENGINEERING↗

Performance modeling of microsecond scale biological molecular dynamics simulations on heterogeneous architectures

Performance improvements in biomolecular simulations based on molecular dynamics (MD) codes are widely desired. Unfortunately, the factors, which allowed past performance improvements, particularly the microprocessor clock frequencies, are no longer increasing. Hence, novel software and hardware solutions are being explored for accelerating performance of widely used MD codes. In this paper, we describe our efforts on porting, optimizing and tuning of Large-scale Atomic/Molecular Massively Parallel Simulator, a popular MD framework, on heterogeneous architectures: multi-core processors with graphical processing unit (GPU) accelerators. Our implementation is based on accelerating the most computationally expensive non-bonded interaction terms on the GPUs and overlapping the computation on the CPU and GPUs. This functionality is built on top of message passing interface that allows multi-level parallelism to be extracted even at the workstation level with the multi-core CPUs and allows extension of the implementation on GPU-enabled clusters. We hypothesize that the optimal benefit of heterogeneous architectures for applications will come by utilizing all possible resources (for example, CPU-cores and GPU devices on GPU-enabled clusters). Benchmarks for a range of biomolecular system sizes are provided, and an analysis is performed on four generations of NVIDIA's GPU devices. On GPU-enabled Linux clusters, by overlapping and pipelining computation and communication, we observe up to 10-folds application acceleration in multi-core and multi-GPU environments illustrating significant performance improvements. Detailed analysis of the implementation is presented that allows identification of bottlenecks in algorithm, indicating that code optimization and improvements on GPUs could allow microsecond scale simulation throughput on workstations and inexpensive GPU clusters, putting widely desired biologically relevant simulation time-scales within reach of a large user community. In order to systematically optimize simulation throughput and to enable performance prediction, we have developed a parameterized performance model that will allow developers and users to explore the performance potential of future heterogeneous systems for biological simulations.

Agarwal, Pratul K.↗

Parallel multiscale simulations of a brain aneurysm

Cardiovascular pathologies, such as a brain aneurysm, are affected by the global blood circulation as well as by the local microrheology. Hence, developing computational models for such cases requires the coupling of disparate spatial and temporal scales often governed by diverse mathematical descriptions, e.g., by partial differential equations (continuum) and ordinary differential equations for discrete particles (atomistic). However, interfacing atomistic-based with continuum-based domain discretizations is a challenging problem that requires both mathematical and computational advances. We present here a hybrid methodology that enabled us to perform the first multiscale simulations of platelet depositions on the wall of a brain aneurysm. The large scale flow features in the intracranial network are accurately resolved by using the high-order spectral element Navier–Stokes solver NεκTαr. The blood rheology inside the aneurysm is modeled using a coarse-grained stochastic molecular dynamics approach (the dissipative particle dynamics method) implemented in the parallel code LAMMPS. The continuum and atomistic domains overlap with interface conditions provided by effective forces computed adaptively to ensure continuity of states across the interface boundary. A two-way interaction is allowed with the time-evolving boundary of the (deposited) platelet clusters tracked by an immersed boundary method. The corresponding heterogeneous solvers (NεκTαr and LAMMPS) are linked together by a computational multilevel message passing interface that facilitates modularity and high parallel efficiency. Results of multiscale simulations of clot formation inside the aneurysm in a patient-specific arterial tree are presented. We also discuss the computational challenges involved and present scalability results of our coupled solver on up to 300 K computer processors. Validation of such coupled atomistic-continuum models is a main open issue that has to be addressed in future work.

60 APPLIED LIFE SCIENCES↗

Optimized coordinates in vibrational coupled cluster calculations

The use of variationally optimized coordinates, which minimize the vibrational self-consistent field (VSCF) ground state energy with respect to orthogonal transformations of the coordinates, has recently been shown to improve the convergence of vibrational configuration interaction (VCI) towards the exact full VCI [K. Yagi, M. Keçeli, and S. Hirata, J. Chem. Phys. 137, 204118 (2012)]. The present paper proposes an incorporation of optimized coordinates into the vibrational coupled cluster (VCC), which has in the past been shown to outperform VCI in approximate calculations where similar restricted state spaces are employed in VCI and VCC. An embarrassingly parallel algorithm for variational optimization of coordinates for VSCF is implemented and the resulting coordinates and potentials are introduced into a VCC program. The performance of VCC in optimized coordinates (denoted oc-VCC) is examined through pilot applications to water, formaldehyde, and a series of water clusters (dimer, trimer, and hexamer) by comparing the calculated vibrational energy levels with those of the conventional VCC in normal coordinates and VCI in optimized coordinates. For water clusters, in particular, oc-VCC is found to gain orders of magnitude improvement in the accuracy, exemplifying that the combination of optimized coordinates localized to each monomer with the size-extensive VCC wave function provides a supreme description of systems consisting of weakly interacting sub-systems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Solvers for $\mathcal{O} (N)$ Electronic Structure in the Strong Scaling Limit

Here we present a hybrid OpenMP/Charm\tt++ framework for solving the $\mathcal{O} (N)$ self-consistent-field eigenvalue problem with parallelism in the strong scaling regime, $P\gg{N}$, where $P$ is the number of cores, and $N$ is a measure of system size, i.e., the number of matrix rows/columns, basis functions, atoms, molecules, etc. This result is achieved with a nested approach to spectral projection and the sparse approximate matrix multiply [Bock and Challacombe, SIAM J. Sci. Comput., 35 (2013), pp. C72--C98], and involves a recursive, task-parallel algorithm, often employed by generalized $N$-Body solvers, to occlusion and culling of negligible products in the case of matrices with decay. Lastly, employing classic technologies associated with generalized $N$-Body solvers, including overdecomposition, recursive task parallelism, orderings that preserve locality, and persistence-based load balancing, we obtain scaling beyond hundreds of cores per molecule for small water clusters ([H${}_2$O]${}_N$, $N \in \{ 30, 90, 150 \}$, $P/N \approx \{ 819, 273, 164 \}$) and find support for an increasingly strong scalability with increasing system size $N$.

97 MATHEMATICS AND COMPUTING↗

Active Flash: Performance-Energy Tradeoffs for Out-of-Core Processing on Non-Volatile Memory Devices

In this abstract, we study the performance and energy tradeoffs involved in migrating data analysis into the flash device, a process we refer to as Active Flash. The Active Flash paradigm is similar to 'active disks', which has received considerable attention. Active Flash allows us to move processing closer to data, thereby minimizing data movement costs and reducing power consumption. It enables true out-of-core computation. The conventional definition of out-of-core solvers refers to an approach to process data that is too large to fit in the main memory and, consequently, requires access to disk. However, in Active Flash, processing outside the host CPU literally frees the core and achieves real 'out-of-core' analysis. Moving analysis to data has long been desirable, not just at this level, but at all levels of the system hierarchy. However, this requires a detailed study on the tradeoffs involved in achieving analysis turnaround under an acceptable energy envelope. To this end, we first need to evaluate if there is enough computing power on the flash device to warrant such an exploration. Flash processors require decent computing power to run the internal logic pertaining to the Flash Translation Layer (FTL), which is responsible for operations such as address translation, garbage collection (GC) and wear-leveling. Modern SSDs are composed of multiple packages and several flash chips within a package. The packages are connected using multiple I/O channels to offer high I/O bandwidth. SSD computing power is also expected to be high enough to exploit such inherent internal parallelism within the drive to increase the bandwidth and to handle fast I/O requests. More recently, SSD devices are being equipped with powerful processing units and are even embedded with multicore CPUs (e.g. ARM Cortex-A9 embedded processor is advertised to reach 2GHz frequency and deliver 5000 DMIPS; OCZ RevoDrive X2 SSD has 4 SandForce controllers, each with 780MHz max frequency Tensilica core). Efforts that take advantage of the available computing cycles on the processors on SSDs to run auxiliary tasks other than actual I/O requests are beginning to emerge. Kim et al. investigate database scan operations in the context of processing on the SSDs, and propose dedicated hardware logic to speed up scans. Also, cluster architectures have been explored, which consist of low-power embedded CPUs coupled with small local flash to achieve fast, parallel access to data. Processor utilization on SSD is highly dependent on workloads and, therefore, they can be idle during periods with no I/O accesses. We propose to use the available processing capability on the SSD to run tasks that can be offloaded from the host. This paper makes the following contributions: (1) We have investigated Active Flash and its potential to optimize the total energy cost, including power consumption on the host and the flash device; (2) We have developed analytical models to analyze the performance-energy tradeoffs for Active Flash, by treating the SSD as a blackbox, this is particularly valuable due to the proprietary nature of the SSD internal hardware; and (3) We have enhanced a well-known SSD simulator (from MSR) to implement 'on-the-fly' data compression using Active Flash. Our results provide a window into striking a balance between energy consumption and application performance.

42 ENGINEERING↗

Detecting galaxy–filament alignments in the Sloan Digital Sky Survey III

Abstract Previous studies have shown the filamentary structures in the cosmic web influence the alignments of nearby galaxies. We study this effect in the LOWZ sample of the Sloan Digital Sky Survey using the ‘Cosmic Web Reconstruction' filament catalogue. We find that LOWZ galaxies exhibit a small but statistically significant alignment in the direction parallel to the orientation of nearby filaments. This effect is detectable even in the absence of nearby galaxy clusters, which suggests it is an effect from the matter distribution in the filament. A non-parametric regression model suggests that the alignment effect with filaments extends over separations of 30–40 Mpc. We find that galaxies that are bright and early-forming align more strongly with the directions of nearby filaments than those that are faint and late-forming; however, trends with stellar mass are less statistically significant, within the narrow range of stellar mass of this sample.

Chen, Yen-Chi↗

CSRI Summer Proceedings 2021

The Computer Science Research Institute (CSRI) brings university faculty and students to Sandia National Laboratories for focused collaborative research on Department of Energy (DOE) computer and computational science problems. The institute provides an opportunity for university researches to learn about problems in computer and computational science at DOE laboratories, and help transfer results of their research to programs at the labs. Some specific CSRI research interest areas are: scalable solvers, optimization, algebraic preconditioners, graph-based, discrete, and combinatorial algorithms, uncertainty estimation, validation and verification methods, mesh generation, dynamic load-balancing, virus and other malicious-code defense, visualization, scalable cluster computers, beyond Moore’s Law computing, exascale computing tools and application design, reduced order and multiscale modeling, parallel input/output, and theoretical computer science. The CSRI Summer Program is organized by CSRI and includes a weekly seminar series and the publication of a summer proceedings.

97 MATHEMATICS AND COMPUTING↗

CSRI Summer Proceedings 2021

The Computer Science Research Institute (CSRI) brings university faculty and students to Sandia National Laboratories for focused collaborative research on Department of Energy (DOE) computer and computational science problems. The institute provides an opportunity for university researches to learn about problems in computer and computational science at DOE laboratories, and help transfer results of their research to programs at the labs. Some specific CSRI research interest areas are: scalable solvers, optimization, algebraic preconditioners, graph-based, discrete, and combinatorial algorithms, uncertainty estimation, validation and verification methods, mesh generation, dynamic load-balancing, virus and other malicious-code defense, visualization, scalable cluster computers, beyond Moore’s Law computing, exascale computing tools and application design, reduced order and multiscale modeling, parallel input/output, and theoretical computer science. The CSRI Summer Program is organized by CSRI and includes a weekly seminar series and the publication of a summer proceedings.

97 MATHEMATICS AND COMPUTING↗

The Peculiar Filamentary H i Structure of NGC 6145

In this paper, we report the peculiar H i morphology of the cluster spiral galaxy NGC 6145, which has a 150 kpc H i filament on one side that is nearly parallel to its major axis. This filament is made up of several H i clouds and the diffuse H i gas between them, with no optical counterparts. We compare its H i distribution with other one-sided H i distributions in the literature and find that the overall H i distribution is very different from the typical tidal and ram-pressure stripped H i shape, and that its morphology is inconsistent with that of a pure accretion event. Only ∼30% of the total H i gas is anchored on the stellar disk, while most of the H i gas forms the filament in the west. At a projected distance of 122 kpc, we find a massive elliptical companion (NGC 6146) with extended radio emission whose axis points to an H i gap in NGC 6145. The velocity of the H i filament shows an overall line-of-sight motion of 80–180 km s{sup −1} with respect to NGC 6145. Using the long-slit spectra of NGC 6145 along its major stellar axis, we find that some outer regions show enhanced star formation, while in contrast, almost no star formation activities are found in its center (<2 kpc). Pure accretion, tidal, or ram-pressure stripping are not likely to produce the observed H i filament. An alternative explanation is the jet stripping from NGC 6146, although direct evidence for a jet-cold gas interaction has not been found.

79 ASTRONOMY AND ASTROPHYSICS↗

ARENA: Asynchronous Reconfigurable Accelerator Ring to Enable Data-Centric Parallel Computing

The next generation HPC and data centers are likely to be reconfigurable and data-centric due to the trend of hardware specialization and the emergence of data-driven applications. In this work, we propose ARENA – an asynchronous reconfigurable accelerator ring architecture as a potential scenario on how the future HPC and data centers will be like. Despite using the coarse-grained reconfigurable arrays (CGRAs) as the substrate platform, our key contribution is not only the CGRA-cluster design itself, but also the ensemble of a new architecture and programming model that enables asynchronous tasking across a cluster of reconfigurable nodes, so as to bring specialized computation to the data rather than the reverse. We presume distributed data storage without asserting any prior knowledge on the data distribution. Hardware specialization occurs at runtime when a task finds the majority of data it requires are available at the present node. In other words, we dynamically generate specialized CGRA accelerators where the data reside. The asynchronous tasking for bringing computation to data is achieved by circulating the task token, which describes the dataflow graphs to be executed for a task, among the CGRA cluster connected by a fast ring network. Evaluations on a set of HPC and data-driven applications across different domains show that ARENA can provide better parallel scalability with reduced data movement (53.9 percent). Compared with contemporary compute-centric parallel models, ARENA can bring on average 4.37× speedup. The synthesized CGRAs and their task-dispatchers only occupy 2.93mm 2 chip area under 45nm process technology and can run at 800MHz with on average 759.8mW power consumption. ARENA also supports the concurrent execution of multi-applications, offering ideal architectural support for future high-performance parallel computing and data analytics systems.

97 MATHEMATICS AND COMPUTING↗

PoPLAR: Portal for Petascale Lifescience Applications and Research

Background: We are focusing specifically on fast data analysis and retrieval in bioinformatics that will have a direct impact on the quality of human health and the environment. The exponential growth of data generated in biology research, from small atoms to big ecosystems, necessitates an increasingly large computational component to perform analyses. Novel DNA sequencing technologies and complementary high-throughput approaches–such as proteomics, genomics, metabolomics, and meta-genomics–drive data-intensive bioinformatics. While individual research centers or universities could once provide for these applications, this is no longer the case. Today, only specialized national centers can deliver the level of computing resources required to meet the challenges posed by rapid data growth and the resulting computational demand. Consequently, we are developing massively parallel applications to analyze the growing flood of biological data and contribute to the rapid discovery of novel knowledge. Methods: The efforts of previous National Science Foundation (NSF) projects provided for the generation of parallel modules for widely used bioinformatics applications on the Kraken supercomputer. We have profiled and optimized the code of some of the scientific community’s most widely used desktop and small-cluster-based applications, including BLAST from the National Center for Biotechnology Information (NCBI), HMMER, and MUSCLE; scaled them to tens of thousands of cores on high-performance computing (HPC) architectures; made them robust and portable to next-generation architectures; and incorporated these parallel applications in science gateways with a web-based portal. Results: This paper will discuss the various developmental stages, challenges, and solutions involved in taking bioinformatics applications from the desktop to petascale with a front-end portal for very-large-scale data analysis in the life sciences. Conclusions: This research will help to bridge the gap between the rate of data generation and the speed at which scientists can study this data. The ability to rapidly analyze data at such a large scale is having a significant, direct impact on science achieved by collaborators who are currently using these tools on supercomputers.

59 BASIC BIOLOGICAL SCIENCES↗

Reducing Communication in Graph Neural Network Training

Graph Neural Networks (GNNs) are powerful and flexible neural networks that use the naturally sparse connectivity information of the data. GNNs represent this connectivity as sparse matrices, which have lower arithmetic intensity and thus higher communication costs compared to dense matrices, making GNNs harder to scale to high concurrencies than convolutional or fully-connected neural networks. Here, we introduce a family of parallel algorithms for training GNNs and show that they can asymptotically reduce communication compared to previous parallel GNN training methods. We implement these algorithms, which are based on 1D, 1. 5D, 2D, and 3D sparse-dense matrix multiplication, using torch.distributed on GPU-equipped clusters. Our algorithms optimize communication across the full GNN training pipeline. We train GNNs on over a hundred GPUs on multiple datasets, including a protein network with over a billion edges.

97 MATHEMATICS AND COMPUTING↗

Cluster analysis of accelerated molecular dynamics simulations: A case study of the decahedron to icosahedron transition in Pt nanoparticles

Modern molecular-dynamics-based techniques are extremely powerful to investigate the dynamical evolution of materials. With the increase in sophistication of the simulation techniques and the ubiquity of massively parallel computing platforms, atomistic simulations now generate very large amounts of data, which has to be carefully analyzed in order to reveal key features of the underlying trajectories, including the nature and characteristics of the relevant reaction pathways. We show that clustering algorithms, such as the Perron Cluster Cluster Analysis, can provide reduced representations that greatly facilitate the interpretation of complex trajectories. To illustrate this point, clustering tools are used to identify the key kinetic steps in complex Accelerated Molecular Dynamics trajectories exhibiting shape uctuations in Pt nanoclusters. This analysis provides an easily-interpretable coarse representation of the reaction pathways in terms of a handful of clusters, in contrast to the raw trajectory that contains thousands of unique states and tens of thousands of transitions.

74 ATOMIC AND MOLECULAR PHYSICS↗

Computational Particle Dynamic Simulations on Multicore Processors (CPDMu) Final Report Phase I

Statement of Problem - Department of Energy has many legacy codes for simulation of computational particle dynamics and computational fluid dynamics applications that are designed to run on sequential processors and are not easily parallelized. Emerging high-performance computing architectures employ massively parallel multicore architectures (e.g., graphics processing units) to increase throughput. Parallelization of legacy simulation codes is a high priority, to achieve compatibility, efficiency, accuracy, and extensibility. General Statement of Solution - A legacy simulation application designed for implementation on mainly-sequential processors has been represented as a graph G. Mathematical transformations, applied to G, produce a graph representation {und G} for a high-performance architecture. Key computational and data movement kernels of the application were analyzed/optimized for parallel execution using the mapping G {yields} {und G}, which can be performed semi-automatically. This approach is widely applicable to many types of high-performance computing systems, such as graphics processing units or clusters comprised of nodes that contain one or more such units. Phase I Accomplishments - Phase I research decomposed/profiled computational particle dynamics simulation code for rocket fuel combustion into low and high computational cost regions (respectively, mainly sequential and mainly parallel kernels), with analysis of space and time complexity. Using the research team's expertise in algorithm-to-architecture mappings, the high-cost kernels were transformed, parallelized, and implemented on Nvidia Fermi GPUs. Measured speedups (GPU with respect to single-core CPU) were approximately 20-32X for realistic model parameters, without final optimization. Error analysis showed no loss of computational accuracy. Commercial Applications and Other Benefits - The proposed research will constitute a breakthrough in solution of problems related to efficient parallel computation of particle and fluid dynamics simulations. These problems occur throughout DOE, military and commercial sectors: the potential payoff is high. We plan to license or sell the solution to contractors for military and domestic applications such as disaster simulation (aerodynamic and hydrodynamic), Government agencies (hydrological and environmental simulations), and medical applications (e.g., in tomographic image reconstruction). Keywords - High-performance Computing, Graphic Processing Unit, Fluid/Particle Simulation. Summary for Members of Congress - Department of Energy has many simulation codes that must compute faster, to be effective. The Phase I research parallelized particle/fluid simulations for rocket combustion, for high-performance computing systems.

97 MATHEMATICS AND COMPUTING↗

Modeling a Million-Node Slim Fly Network Using Parallel Discrete-Event Simulation

As supercomputers close in on exascale performance, the increased number of processors and processing power translates to an increased demand on the underlying network interconnect. The Slim Fly network topology, a new lowdiameter and low-latency interconnection network, is gaining interest as one possible solution for next-generation supercomputing interconnect systems. In this paper, we present a high-fidelity Slim Fly it-level model leveraging the Rensselaer Optimistic Simulation System (ROSS) and Co-Design of Exascale Storage (CODES) frameworks. We validate our Slim Fly model with the Kathareios et al. Slim Fly model results provided at moderately sized network scales. We further scale the model size up to n unprecedented 1 million compute nodes; and through visualization of network simulation metrics such as link bandwidth, packet latency, and port occupancy, we get an insight into the network behavior at the million-node scale. We also show linear strong scaling of the Slim Fly model on an Intel cluster achieving a peak event rate of 36 million events per second using 128 MPI tasks to process 7 billion events. Detailed analysis of the underlying discrete-event simulation performance shows that a million-node Slim Fly model simulation can execute in 198 seconds on the Intel cluster.

interconnection networks↗

Modeling optical properties of silicon clusters by first principles: From a few atoms to large nanocrystals

Time dependent density functional tight binding (TDDFTB) method is implemented with sparse matrix techniques and improved parallelization algorithms. The method is employed to calculate the optical properties of various Si nanocrystals (NCs). The calculated light absorption spectra of small Si NCs from TDDFTB were found to be comparable with many body perturbation methods utilizing planewave basis sets. For large Si NCs (more than a thousand atoms) that are beyond the reach of conventional approaches, the TDDFTB method is able to produce reasonable results that are consistent with prior experiments. We also employed the method to study the effects of surface chemistry on the optical properties of large Si NCs. We learned that the optical properties of Si NCs can be manipulated with small molecule passivations such as methyl, hydroxyl, amino, and fluorine. In general, the shifts and profiles in the absorption spectra can be tuned with suitably chosen passivants.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

ArborX 2.0

ArborX library tackles a problem of efficiently finding geometric objects that are close in space. Variations of this problem, such as finding the nearest neighbors of a point, or finding all objects within a certain distance, are inherent components of applications in many fields. The data may be large so that solving the problem efficiently may require significant computational resources, such as multiple processors or accelerators such as general purpose GPUs. ArborX' main advantage in its ability to solve large problems efficiently utilizing a combination of distributed and on-node parallelism. ArborX can be run efficiently on a wide variety of hardware, including GPUs from different vendors, which distinguishes it from other available libraries which typically choose only few of these. The other advantage is that it supports both types of user problems: spatial problems (useful for intersections and finding objects within certain distance), and nearest neighbor problems. ArborX also supports flexible interface in its interaction with a user. Particularly, it allows a user to call user's own function on a positive match, a functionality not rarely available in other libraries. ArborX implements construction and traversal algorithms using efficient tree structures, such as bounding volume hierarchy (BVH). At its core, ArborX uses linear BVH for its low construction cost and sufficient quality. ArborX implements both spatial and nearest-neighbor traversal algorithms. ArborX also provides several clustering algorithms (minimum spanning tree, DBSCAN, HDBSCAN*), interpolation using minimum least squares and ray tracing. ArborX is written using C++, and is parallelized using the message passing interface (MPI) for the distributed communication, and the Kokkos library for on-node parallelism. This approach allows ArborX to be run on a wide variety of hardware, from common laptops and desktops to supercomputers while using the same codebase.

Prokopenko, Andrey [Oak Ridge National Laboratory ↗