GPU-based Algorithm Research Articles

A GPU Algorithm for Solving the Positions of New Pulsars

Timing newly discovered pulsars requires gradually building up a timing model that connects observations taken days to months apart. This sometimes can be challenging when our initial knowledge of the pulsar’s position is arcminutes off from its true position. Such a position error leads to significant arrival time shifts as a result of the Earth’s orbital motion. Traditional down-hill fitting timing algorithms become ineffective when our model predicts the wrong pulse rotations for our next observation. For some pulsars whose model prediction is not too far off, the correct rotation number could be found by trial-and-error methods. For the remaining challenging pulsars, a more generalized method is called for. This paper proposes a GPU-based algorithm that could exhaustively search a large area of trail positions for probable timing solutions. This could help find phase-connected timing solutions for new pulsars using brute force.

PHUI-GA: GPU-Based Efficiency Evolutionary Algorithm for Mining High Utility Itemsets

PHUI-GA: GPU-Based Efficiency Evolutionary Algorithm for Mining High Utility Itemsets

Graph analysis using a GPU-based parallel algorithm: quantum clustering

Graph analysis using a GPU-based parallel algorithm: quantum clustering

GPU-based parallel programming for FEM analysis in the optimization of steel frames

ABSTRACT Optimization of large-scale frame structures consumes a vast amount of time since the analysis of such complex systems contains several iterative processes. Mitigating computational burden and reducing this time to a reasonable level is possible by running GPU (Graphical Processing Unit) processors, which can be found on standard computers. This study presents an algorithm for the acceleration of size optimization of steel frames by using the BBO (Biogeography-Based Optimization) method that is suitable for GPU architecture. The GPU-based parallel algorithm, designed for FEM (Finite Element Method) analysis, is applied to three hypothetical steel-frame case structures with different numbers of members and nodes; and processed on four different computers which are available on the market. The presented case studies revealed that the proposed solution’s efficiency increases as the number of members increases and confirmed the ability of the acceleration algorithm for optimization of large-scale frame structures and provided time efficiency.

Accelerating Merkle Patricia Trie with GPU

Merkle Patricia Trie (MPT) is a type of trie structure that offers efficient lookup and insert operators for immutable data systems that require multi-version access and tamper-evident controls, such as blockchains and verifiable databases. The performance of these systems is critically dependent on the throughput of the underlying index structure MPT. In this paper, we present a novel approach to accelerate MPT by leveraging the massive parallelism of GPU. However, achieving it is challenging as (i) lock-free data structures are difficult to implement and (ii) traditional fine-grained locking does not scale on GPU. To address them, we first analyze the technical challenges of accelerating MPT via GPU, including node splitting conflicts and hash computing conflicts caused by parallel insert operations. We then propose a lock-free algorithm PhaseNU and a lock-based algorithm LockNU on GPU to resolve the node splitting conflict. We also devise a decision model for users to choose the proper one for different workloads. We next propose a GPU-based hash-compute algorithm PhaseHC to avoid hash computing conflicts. Last, we demonstrate the effectiveness of our proposed techniques by: (i) integrating them into both the real-world blockchain system Geth and verifiable database LedgerDB, and demonstrating its superiority with corresponding workloads; and (ii) conducting extensive experimental studies on two real-world datasets and one synthetic dataset. Our proposed solutions significantly outperform the deployed MPT solution in Geth in all datasets.

Method for GPU-based spectral data cube reconstruction of integral field snapshot imaging spectrometers.

In this paper, the principles of spectral data cube reconstruction based on an integral field snapshot imaging spectrometer and GPU-based acceleration are presented. The primary focus is on improving the reconstruction algorithm using GPU parallel computing technology to enhance the computational efficiency for real-time applications. And the computational tasks of the spectral reconstruction algorithm were transferred to the GPU through program parallelization and memory optimization, resulting in significant performance gains. Experimental results indicate that the average processing time of the GPU-based parallel algorithm is approximately 29.43 ms, showing a substantial acceleration ratio of about 14.27 compared to the traditional CPU serial algorithm with an average processing time of around 420.46 ms. The study aims to refine the GPU parallelization algorithm for continued improvement in computational efficiency and overall performance. The anticipated applications of this research include providing crucial technical support for the perception and monitoring of crop growth traits in agricultural production, contributing to the modernization and advancement of intelligence in the field.

Parallel optimization approaches for scattering source term and angle merging in MOC high-order anisotropic computation on GPUs

The introduction of high-order anisotropic scattering and thousand-group calculations significantly increases the computational workload of the MOC method, posing difficulties for practical parallel computation on GPUs. In this paper, a GPU-based MOC algorithm is optimized, focusing on the performance optimization of the kernel function that merges high-order anisotropic angular flux density into scalar flux density moments, as well as the optimization of the scattering source term calculation method in thousand-group calculations. Two parallel algorithms based on azimuthal and polar angles are proposed for high-order anisotropic scattering. For the thousand-group calculation, a data structure is designed according to the physical characteristics of the anisotropic scattering matrix, and then two optimization algorithms are proposed from the perspectives of memory access and parallelism. Based on the KAIST-3A reference problem, the parallel expansion of the polar angle in the merging calculation is more advantageous. Based on the KAIST-3A reference problem, the parallel expansion of the polar angle in the merging calculation is found to be more advantageous. Based on a self-designed fast reactor fuel lattice, it is concluded that the parallelism-oriented calculation method for the thousand-group anisotropic scattering source term is more efficient. Finally, the Roofline model is used to analyze the advantages of the algorithm.

SeedHit: A GPU Friendly Pre-Align Filtering Algorithm.

The amount of genetic data generated by Next Generation Sequencing (NGS) technologies grows faster than Moore's law. This necessitates the development of efficient NGS data processing and analysis algorithms. A filter before the computationally-costly analysis step can significantly reduce the run time of the NGS data analysis. As GPUs are orders of magnitude more powerful than CPUs, this paper proposes a GPU-friendly pre-align filtering algorithm named SeedHit for the fast processing of NGS data. Inspired by BLAST, SeedHit counts seed hits between two sequences to determine their similarity. In SeedHit, a nucleic acid in a gene sequence is presented in binary format. By packaging data and generating a lookup table that fits into the L1 cache, SeedHit is GPU-friendly and high- throughput. Using three 16s rRNA datasets from Greengenes as input SeedHit can reject 84%-89% dissimilar sequence pairs on average when the similarity is 0.9-0.99. The throughput of SeedHit achieved 1T/s (Tera base per second) on 3080 Ti. Compared with the other two GPU-based filtering algorithms, GateKeeper and SneakySnake, SeedHit has the highest rejection rate and throughput. By incorporating SeedHit into our in-house clustering algorithm nGIA, the modified nGIA achieved a 1.6-2.1 times speedup compared to the original version.

Run-3 Commissioning of CMS Online HLT reconstruction using GPUs

The software-based High-Level Trigger (HLT) of CMS reduces the data readout rate from 100 kHz (obtained from Level 1 trigger) to around 5 kHz. It makes use of all detector subsystems and runs a streamlined version of CMS reconstruction. Run-2 of the LHC saw the reconstruction algorithms run on a CPU farm. However, the need to have increased computational power as we approach the high luminosity phase of LHC demands the use of Graphical Processing Units (GPUs) to reign in the cost, size and power consumption of the HLT farm. Parallelization of the reconstruction algorithms, on top of the multi-threading functionality introduced in Run-2, allowed parts of the Hadronic Calorimeter (HCAL), Electromagnetic Calorimeter (ECAL) and Pixel Tracker reconstruction to be offloaded to NVIDIA GPUs. In order to ensure the reproducibility of physics results on any machine, the HLT configuration was designed to run seamlessly with and without GPUs, that is, the algorithms were automatically offloaded to a GPU when one was available and otherwise fell back to running on the CPU. This contribution will describe the development of GPU-based algorithms for the HLT and the challenges they presented, along with the comprehensive validation and commissioning activity undertaken by CMS to ensure the successful operations of the new HLT farm.

Autonomous GPU-based UAS for inspection of confined spaces: Application to marine vessel classification

Inspection of confined spaces poses a series of health risks to human surveyors, and therefore a need for robotic solutions arises. In this paper, we design and demonstrate a real-time system for collecting 3D structural and visual data from a series of inspection points within a prior map of a confined space. The system consists of a GPU accelerated 3D point cloud registration and a visual inertial odometry estimate fused in an Unscented Kalman Filter. Using the state-of-the-art deep learning-based feature descriptors, FCGF –and the robust Teaser++ 3D registration algorithm– point clouds from a narrow field of view, time-of-flight, camera can be registered to a prior map of the environment, to provide accurate cm-level absolute pose estimates. The uncertainty of the system is furthermore estimated on the basis of the novel GPU-based Stein ICP algorithm. Visual defects, represented by augmented reality fiducial markers, are automatically detected during inspection, and their positions are estimated in the map frame of the confined space. The performance of the system has been evaluated in realtime onboard a small UAV, within a mock-up model of a water ballast tank from a marine vessel, where the UAV was able to navigate and inspect the ambiguous and featureless environment. All defects were estimated within ＋/−10 cm of their actual position.

Soft- and Hard-Kill Hybrid GPU-based Bi-Directional Evolutionary Structural Optimization

Abstract Bi-directional evolutionary structural optimization (BESO) is a well-recognized method for generating optimal topologies of structures. Its soft-kill variant has a high computational cost, especially for large-scale structures, whereas the hard-kill variant often faces convergence issues. Addressing these issues, this paper proposes a hybrid BESO model tailored for graphics processing units (GPUs) by combining the soft-kill and hard-kill approaches for large-scale structures. A GPU-based algorithm is presented for dynamically isolating the solid/hard elements from the void/soft elements in the finite element analysis (FEA) stage. The hard-kill approach is used in the FEA stage with an assembly-free solver to facilitate the use of high-resolution meshes without exceeding the GPU memory limits, whereas for the rest of the optimization procedure, the soft-kill approach with a material interpolation scheme is implemented. Furthermore, the entire BESO method pipeline is accelerated for both the proposed hybrid and the standard soft-kill BESO. The comparison of the hybrid BESO with the GPU-accelerated soft-kill BESO using four benchmark problems with more than two million degrees of freedom reveals three key benefits of the proposed hybrid model: reduced execution time, decreased memory consumption, and improved FEA convergence, all of which mitigate the major computational issues associated with BESO.

GPU-acceleration of the distributed-memory database peptide search of mass spectrometry data

Database peptide search is the primary computational technique for identifying peptides from the mass spectrometry (MS) data. Graphical Processing Units (GPU) computing is now ubiquitous in the current-generation of high-performance computing (HPC) systems, yet its application in the database peptide search domain remains limited. Part of the reason is the use of sub-optimal algorithms in the existing GPU-accelerated methods resulting in significantly inefficient hardware utilization. In this paper, we design and implement a new-age CPU-GPU HPC framework, called GiCOPS, for efficient and complete GPU-acceleration of the modern database peptide search algorithms on supercomputers. Our experimentation shows that the GiCOPS exhibits between 1.2 to 5times speed improvement over its CPU-only predecessor, HiCOPS, and over 10times improvement over several existing GPU-based database search algorithms for sufficiently large experiment sizes. We further assess and optimize the performance of our framework using the Roofline Model and report near-optimal results for several metrics including computations per second, occupancy rate, memory workload, branch efficiency and shared memory performance. Finally, the CPU-GPU methods and optimizations proposed in our work for complex integer- and memory-bounded algorithmic pipelines can also be extended to accelerate the existing and future peptide identification algorithms. GiCOPS is now integrated with our umbrella HPC framework HiCOPS and is available at: https://github.com/pcdslab/gicops.

Rapid 3D lidar change detection for geohazard identification using GPU-based alignment and M3C2 algorithms

Topographic change detection is increasingly being used to identify and monitor landslides and other geohazards in support of risk-informed decision-making. Expanding change detection from site specific to regional scales enables increasingly proactive asset management and contributes to improving the resilience of infrastructure to extreme events. It is widely known that change detection precision can be improved by applying three-dimensional algorithms, such as iterative closest point (ICP) and M3C2, directly to raw point clouds. However, this also increases the computational requirements compared to alternatives such as digital elevation model differencing. This study presents a novel graphics processing unit (GPU)-based implementation of the ICP-M3C2 workflow to address this limitation. In the proposed algorithm, point cloud data segments are automatically queued and served to the working GPU, which efficiently performs point cloud processing operations, while the central processing unit (CPU) performs data management operations in parallel. The developed method is estimated to be up to 54 times faster than CPU-based versions of the same algorithm. In this study, we present how the workflow has been applied to six regional-scale landslide identification and monitoring case studies in which landslides are causing the disruption of pipelines, highways, and rail corridors. Overall, in 2021 and 2022, over 17 500 linear km of change detection were processed using the demonstrated method.

The implementation of the three-dimensional unified gas-kinetic wave-particle method on multiple graphics processing units

To further improve the efficiency of the unified gas-kinetic wave-particle (UGKWP) method in hypersonic rarefied non-equilibrium flows, particularly the particle simulation process, we presented the first application of the three-dimensional UGKWP method to multiple graphics processing unit (GPU) devices in this study. The wave and particle evolution components of the method are addressed using cell and particle paralleling strategies, respectively, enabling the primary loop of the GPU-based UPKWP (GPU-UGKWP) to be executed entirely by the compute unified device architecture threads on GPU devices. Concurrently, communication issues between central processing unit (CPU) nodes are resolved by employing the message passing interface model. Additionally, we introduce a tailored memory management scheme for the GPU-UGKWP method, facilitating efficient access to the particle array. Performance comparisons reveal that, relative to a single Intel Xeon Gold 6148 CPU core, the Nvidia Tesla P100 achieves a total speedup of 34 using one GPU device, and 226 with eight GPU devices, and a single Nvidia Titan V GPU device attains a speedup of 62. The speedup outcomes on multiple CPU cores and GPU devices demonstrate that the GPU-based algorithm is better suited for computationally demanding tasks, particularly in particle-dominated simulations. As evidenced by the reduced calculation time for a hypersonic technology vehicle simulation performed on the P100 cluster, GPU devices significantly outperform their CPU counterparts.

A Practical Wave Optics Reflection Model for Hair and Fur

Traditional fiber scattering models, based on ray optics, are missing some important visual aspects of fiber appearance. Previous work [Xia et al. 2020] on wave scattering from ideal extrusions demonstrated that diffraction produces strong forward scattering and colorful effects that are missing from ray-based models. However, that work was unable to include some important surface characteristics such as surface roughness and tilted cuticle scales, which are known to be important for fiber appearance. In this work, we take an important step to study wave effects from rough fibers with arbitrary 3D microgeometry. While the full-wave simulation of realistic 3D fibers remains intractable, we developed a 3D wave optics simulator based on a physical optics approximation, using a GPU-based hierarchical algorithm to greatly accelerate the calculation. It simulates surface reflection and diffractive scattering, which are present in all fibers and typically dominate for darkly pigmented fibers. The simulation provides a detailed picture of first order scattering, but it is not practical to use for production rendering as this would require tabulation per fiber geometry. To practically handle geometry variations in the scene, we propose a model based on wavelet noise, capturing the important statistical features in the simulation results that are relevant for rendering. Both our simulation and practical model show similar granular patterns to those observed in optical measurement. Our compact noise model can be easily combined with existing scattering models to render hair and fur of various colors, introducing visually important colorful glints that were missing from all previous models.

GPU-Based Algorithms for Processing the k Nearest-Neighbor Query on Spatial Data Using Partitioning and Concurrent Kernel Execution

Algorithms for answering the k nearest-neighbor (k-NN) query are widely used for queries in spatial databases and for distance classification of a group of query points against a reference dataset to derive the dominating feature class. GPU devices have significantly more processing cores than CPUs and faster device memory than the main memory accessed by CPUs, thus, providing higher computing power for processing demanding queries like the k-NN. However, since device and/or main memory may not be able to host an entire, rather big, reference and query datasets, storing these datasets in a fast secondary device, like a solid state disk (SSD), and partially retrieve the required, at each stage, partitions is, in many practical cases, a feasible solution. We propose and implement the first GPU-based algorithms for processing the k-NN query for big reference and query spatial data stored on SSDs. Based on 3d synthetic and real big spatial data, we experimentally compare these algorithms and highlight the most efficient algorithmic variation. This variation utilizes a CUDA feature known as Concurrent Kernel Execution, to further improve its performance.

MDSubSampler: a posteriori sampling of important protein conformations from biomolecular simulations.

Molecular dynamics (MD) simulations have become routine tools for the study of protein dynamics and function. Thanks to faster GPU-based algorithms, atomistic and coarse-grained simulations are being used to explore biological functions over the microsecond timescale, yielding terabytes of data spanning multiple trajectories, thereby extracting relevant protein conformations without losing important information is often challenging. We present MDSubSampler, a Python library and toolkit for a posteriori subsampling of data from multiple trajectories. This toolkit provides access to uniform, random, stratified, weighted sampling, and bootstrapping sampling methods. Sampling can be performed under the constraint of preserving the original distribution of relevant geometrical properties. Possible applications include simulations post-processing, noise reduction, and structures selection for ensemble docking. MDSubSampler is freely available at https://github.com/alepandini/MDSubSampler, along with guidance on installation and tutorials on how it can be used.

GPU-based mesh reduction strategy utilizing active nodes for structural topology optimization

This paper presents a novel mesh reduction strategy on graphics processing unit (GPU) that aims to reduce the computational complexity of conventional structural topology optimization. In the proposed strategy, the effective number of design variables is reduced by using the concept of active nodes and active elements in the finite element mesh. A novel mesh numbering scheme is also introduced to facilitate parallel identification of active nodes using a proposed GPU-based algorithm. The preconditioned conjugate gradient (PCG) solver is further developed using the proposed strategy and the numbering scheme. The proposed strategy is tested on three structural topology optimization problems using solid isotropic material with penalization method. Results of the proposed strategy demonstrate up to 8× speedup over the standard GPU implementation considering the entire mesh.

Variable stars in the residual light curves of OGLE-IV eclipsing binaries towards the Galactic Bulge

Context. The Optical Gravitational Lensing Experiment (OGLE) observed around 450 000 eclipsing binaries (EBs) towards the Galactic Bulge. Decade-long photometric observations such as these provide an exceptional opportunity to thoroughly examine the targets. However, observing dense stellar fields such as the Bulge may result in blends and contamination by close objects. Aims. We searched for periodic variations in the residual light curves of EBs in OGLE-IV and created a new catalogue for the EBs that contain ‘background’ signals after the investigation of the source of the signal. Methods. From the about half a million EB systems, we selected those that contain more than 4000 data points. We fitted the EB signal with a simple model and subtracted it. To identify periodical signals in the residuals, we used a GPU-based phase dispersion minimisation python algorithm called cuvarbase and validated the found periods with Lomb-Scargle periodograms. We tested the reliability of our method with artificial light curves. Results. We identified 354 systems where short-period background variation was significant. In these cases, we determined whether it is a new variable or just the result of contamination by an already catalogued nearby one. We classified 292 newly found variables into EB, δ Scuti, or RR Lyrae categories, or their sub-classes, and collected them in a catalogue. We also discovered four new doubly eclipsing systems and one eclipsing multiple system with a δ Scuti variable, and modelled the outer orbits of the components.

Efficient Simulation of Volumetric Deformable Objects in Unity3D: GPU-Accelerated Position-Based Dynamics

This paper proposes an efficient approach for simulating volumetric deformable objects using the Position-Based Dynamics (PBD) method. Volumetric bodies generated by TetGen are used to represent three-dimensional objects, which accurately capture complex shapes and volumes. However, when a large number of constraints are applied to the system to solve using serialized algorithms on central processing units (CPU), the computational cost can become a bottleneck of the simulation. To address this issue, the proposed implementation algorithm takes advantage of graphic processing unit (GPU) acceleration and parallel processing to improve the efficiency of the simulation. We propose two specific contributions: firstly, the use of the PBD method with volume constraint for tetrahedral elements to simulate volumetric deformable objects realistically; secondly, an efficient GPU-accelerated algorithm for implementing the PBD method that significantly improves computational efficiency. We also applied the node-centric and constraint-centric algorithms to solve the stretch constraint in the GPU-based algorithm. The implementation was performed using Unity3D. The compute shader feature of Unity3D was utilized to perform thousands of parallel computations in a single pass, making it possible to simulate large and complex objects in real-time. The performance of the simulation can be accelerated by using GPU-based methods with stretch and bending constraints, which provides significant speedup factors compared to using only the CPU for deformable objects such as Bunny, Armadillo, and Dragon. The constraint-centric and node-centric GPU approaches provide speedup factors of up to 8.9x and 8x, respectively, while the GPU-based methods with all types of constraints exhibit a slight decrease but still operate at real-time speeds. Overall, this approach enables the simulation of complex and irregular shapes with plausible and realistic results, while also achieving speed, robustness, and flexibility. Additionally, the proposed approach can be applied to general simulation and other game engines that support GPU-based acceleration.