Irregular Large-Scale Computed Tomography on Multiple Graphics Processors Improves Energy-Efficiency Metrics for Industrial Applications.
Abstract not provided.
Thompson, Kyle Richard↗
SEARCH · Search NASA
Results for “Graphics Processors”
Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.
Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.
Neural Networks and Graph Algorithms with Next-Generation Processors
The use of graphical processors for distributed computation revolutionized the field of high performance scientific computing. As the Moore's Law era of computing draws to a close, the development of non-Von Neumann systems: neuromorphic processing units, and quantum annealers; again are redefining new territory for computational methods. While these technologies are still in their nascent stages, we discuss their potential to advance computing in two domains: machine learning, and solving constraint satisfaction problems. Each of these processors utilize fundamentally different theoretical models of computation. This raises questions about how to best use them in the design and implementation of applications. While many processors are being developed with a specific domain target, the ubiquity of spin-glass models and neural networks provides an avenue for multi-functional applications. This provides hints at the future infrastructure needed to integrate many next-generation processing units into conventional high-performance computing systems.
Hamilton, Kathleen↗
Apparatus and method for implementing power saving techniques when processing floating point values
An apparatus and method are described for reducing power when reading and writing graphics data. For example, one embodiment of an apparatus comprises: a graphics processor unit (GPU) to process graphics data including floating point data; a set of registers, at least one of the registers of the set partitioned to store the floating point data; and encode/decode logic to reduce a number of binary 1 values being read from the at least one register by causing a specified set of bit positions within the floating point data to be read out as 0s rather than 1s.
97 MATHEMATICS AND COMPUTING↗
Unified Memory: GPGPU-Sim/UVM Smart Integration
CPU/GPU heterogeneous compute platforms are an ubiquitous element in computing and a programming model specified for this heterogeneous computing model is important for both performance and programmability. A programming model that exposes the shared, unified, address space between the heterogeneous units is a necessary step in this direction as it removes the burden of explicit data movement from the programmer while maintaining performance. GPU vendors, such as AMD and NVIDIA, have released software-managed runtimes that can provide programmers the illusion of unified CPU and GPU memory by automatically migrating data in and out of the GPU memory. However, this runtime support is not included in GPGPU-Sim, a commonly used framework that models the features of a modern graphics processor that are relevant to non-graphics applications. UVM Smart was developed, which extended GPGPU-Sim 3.x to in- corporate the modeling of on-demand pageing and data migration through the runtime. This report discusses the integration of UVM Smart and GPGPU-Sim 4.0 and the modifications to improve simulation performance and accuracy.
97 MATHEMATICS AND COMPUTING↗
Exploring the interoperability of remote GPGPU virtualization using rCUDA and directive-based programming models
Directive-based programming models, such as OpenMP, OpenACC, and OmpSs, enable users to accelerate applications by using coprocessors with little effort. These devices offer significant computing power, but their use can introduce two problems: an increase in the total cost of ownership and their underutilization because not all codes match their architecture. Remote accelerator virtualization frameworks address those problems. In particular, rCUDA provides transparent access to any graphic processor unit installed in a cluster, reducing the number of accelerators and increasing their utilization ratio. Joining these two technologies, directive-based programming models and rCUDA, is thus highly appealing. In this work, we study the integration of OmpSs and OpenACC with rCUDA, describing and analyzing several applications over three different hardware configurations that include two InfiniBand interconnections and three NVIDIA accelerators. Our evaluation reveals favorable performance results, showing low overhead and similar scaling factors when using remote accelerators instead of local devices.
97 MATHEMATICS AND COMPUTING↗
Clinically Applicable Monte Carlo–based Biological Dose Optimization for the Treatment of Head and Neck Cancers With Spot-Scanning Proton Therapy
Purpose: Our aim is to demonstrate the feasibility of fast Monte Carlo (MC)–based inverse biological planning for the treatment of head and neck tumors in spot-scanning proton therapy. Methods and Materials: Recently, a fast and accurate graphics processor unit (GPU)–based MC simulation of proton transport was developed and used as the dose-calculation engine in a GPU-accelerated intensity modulated proton therapy (IMPT) optimizer. Besides dose, the MC can simultaneously score the dose-averaged linear energy transfer (LET{sub d}), which makes biological dose (BD) optimization possible. To convert from LET{sub d} to BD, a simple linear relation was assumed. By use of this novel optimizer, inverse biological planning was applied to 4 patients, including 2 small and 1 large thyroid tumor targets, as well as 1 glioma case. To create these plans, constraints were placed to maintain the physical dose (PD) within 1.25 times the prescription while maximizing target BD. For comparison, conventional intensity modulated radiation therapy (IMRT) and IMPT plans were also created using Eclipse (Varian Medical Systems) in each case. The same critical-structure PD constraints were used for the IMRT, IMPT, and biologically optimized plans. The BD distributions for the IMPT plans were obtained through MC recalculations. Results: Compared with standard IMPT, the biologically optimal plans for patients with small tumor targets displayed a BD escalation that was around twice the PD increase. Dose sparing to critical structures was improved compared with both IMRT and IMPT. No significant BD increase could be achieved for the large thyroid tumor case and when the presence of critical structures mitigated the contribution of additional fields. The calculation of the biologically optimized plans can be completed in a clinically viable time (<30 minutes) on a small 24-GPU system. Conclusions: By exploiting GPU acceleration, MC-based, biologically optimized plans were created for small–tumor target patients. This optimizer will be used in an upcoming feasibility trial on LET{sub d} painting for radioresistant tumors.
62 RADIOLOGY AND NUCLEAR MEDICINE↗
Accelerating solidification process simulation for large-sized system of liquid metal atoms using GPU with CUDA
Molecular dynamics simulation is a powerful tool to simulate and analyze complex physical processes and phenomena at atomic characteristic for predicting the natural time-evolution of a system of atoms. Precise simulation of physical processes has strong requirements both in the simulation size and computing timescale. Therefore, finding available computing resources is crucial to accelerate computation. However, a tremendous computational resource (GPGPU) are recently being utilized for general purpose computing due to its high performance of floating-point arithmetic operation, wide memory bandwidth and enhanced programmability. As for the most time-consuming component in MD simulation calculation during the case of studying liquid metal solidification processes, this paper presents a fine-grained spatial decomposition method to accelerate the computation of update of neighbor lists and interaction force calculation by take advantage of modern graphics processors units (GPU), enlarging the scale of the simulation system to a simulation system involving 10 000 000 atoms. In addition, a number of evaluations and tests, ranging from executions on different precision enabled-CUDA versions, over various types of GPU (NVIDIA 480GTX, 580GTX and M2050) to CPU clusters with different number of CPU cores are discussed. The experimental results demonstrate that GPU-based calculations are typically 9∼11 times faster than the corresponding sequential execution and approximately 1.5∼2 times faster than 16 CPU cores clusters implementations. On the basis of the simulated results, the comparisons between the theoretical results and the experimental ones are executed, and the good agreement between the two and more complete and larger cluster structures in the actual macroscopic materials are observed. Moreover, different nucleation and evolution mechanism of nano-clusters and nano-crystals formed in the processes of metal solidification is observed with large-sized system.
71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
GX: a GPU-native gyrokinetic turbulence code for tokamak and stellarator design
GX is a code designed to solve the nonlinear gyrokinetic system for low-frequency turbulence in magnetized plasmas, particularly tokamaks and stellarators. In GX, our primary motivation and target is a fast gyrokinetic solver that can be used for fusion reactor design and optimization along with wide-ranging physics exploration. Here, this has led to several code and algorithm design decisions, specifically chosen to prioritize time to solution. First, we have used a discretization algorithm that is pseudospectral in the entire phase space, including a Laguerre–Hermite pseudospectral formulation of velocity space, which allows for smooth interpolation between coarse gyrofluid-like resolutions and finer conventional gyrokinetic resolutions and efficient evaluation of a model collision operator. Additionally, we have built GX to natively target graphics processors (GPUs), which are among the fastest computational platforms available today. Finally, we have taken advantage of the reactor-relevant limit of small $\rho _*$ by using the radially local flux-tube approach. In this paper we present details about the gyrokinetic system and the numerical algorithms used in GX to solve the system. We then present several numerical benchmarks against established gyrokinetic codes in both tokamak and stellarator magnetic geometries to verify that GX correctly simulates gyrokinetic turbulence in the small $\rho _*$. Moreover, we show that the convergence properties of the Laguerre–Hermite spectral velocity formulation are quite favourable for nonlinear problems of interest. Coupled with GPU acceleration, which we also investigate with scaling studies, this enables GX to be able to produce useful turbulence simulations in minutes on one (or a few) GPUs and higher fidelity results in a few hours using several GPUs. GX is open-source software that is ready for fusion reactor design studies.
70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
Modelling excitonic-energy transfer in light-harvesting complexes
The theoretical and experimental study of energy transfer in photosynthesis has revealed an interesting transport regime, which lies at the borderline between classical transport dynamics and quantum-mechanical interference effects. Dissipation is caused by the coupling of electronic degrees of freedom to vibrational modes and leads to a directional energy transfer from the antenna complex to the target reaction-center. The dissipative driving is robust and does not rely on fine-tuning of specific vibrational modes. For the parameter regime encountered in the biological systems new theoretical tools are required to directly compare theoretical results with experimental spectroscopy data. The calculations require to utilize massively parallel graphics processor units (GPUs) for efficient and exact computations.
75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
On implementation of EM-type algorithms in the stochastic models for a matrix computing on GPU
The paper discusses the main ideas of an implementation of EM-type algorithms for computing on the graphics processors and the application for the probabilistic models based on the Cox processes. An example of the GPU’s adapted MATLAB source code for the finite normal mixtures with the expectation-maximization matrix formulas is given. The testing of computational efficiency for GPU vs CPU is illustrated for the different sample sizes.
71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
Alpha particles diffusion due to charge changes
Alpha particles diffusion due to charge changes in a magnetized plasma is studied. Analytical calculations and numerical simulations are employed to show that this process can be very important in the pedestal-edge-SOL regions. This is the first study that presents clear evidence of the importance of atomic processes on the diffusion of alpha particles. A simple 1D model that includes inelastic collisions with plasma species, “cold” neutrals, and partially ionized species was employed. The code, which follows the exact particle orbits and includes the effect of inelastic collisions via a Monte Carlo type random process, runs on a graphic processor unit (GPU). The analytical and numerical results show excellent agreement when a uniform background (plasma and cold species) is assumed. The simulations also show that the gradients in the density of the plasma and cold species, which are large and opposite in the edge region, produce an inward flux of alpha particles. Calculations of the alpha particles flux reaching the walls or divertor plates should include these processes.
70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
HipGISAXS : a high-performance computing code for simulating grazing-incidence X-ray scattering data
This article describes the development of a flexible grazing-incidence small-angle X-ray scattering (GISAXS) simulation code in the framework of the distorted wave Born approximation that effectively utilizes the parallel processing power provided by graphics processors and multicore processors. The code, entitled High-Performance GISAXS , computes the GISAXS image for any given superposition of user-defined custom shapes or morphologies in a material and for various grazing-incidence angles and sample orientations. These capabilities permit treatment of a wide range of possible sample structures, including multilayered polymer films and nanoparticles on top of or embedded in a substrate or polymer film layers. In cases where the material displays regions of significant refractive index contrast, an algorithm has been implemented to perform a slicing of the sample and compute the averaged refractive index profile to be used as the reference geometry of the unperturbed system. A number of case studies are presented, which demonstrate good agreement with the experimental data for a variety of polymer and hybrid polymer/nanoparticle composite materials. The parallelized simulation code is well suited for addressing the analysis efforts required by the increasing amounts of GISAXS data being produced by high-speed detectors and ultrafast light sources.
Chemistry↗
Fast DRR generation for 2D to 3D registration on GPUs
Purpose: The generation of digitally reconstructed radiographs (DRRs) is the most time consuming step on the CPU in intensity based two-dimensional x-ray to three-dimensional (CT or 3D rotational x-ray) medical image registration, which has application in several image guided interventions. This work presents optimized DRR rendering on graphical processor units (GPUs) and compares performance achievable on four commercially available devices. Methods: A ray-cast based DRR rendering was implemented for a 512 Multiplication-Sign 512 Multiplication-Sign 72 CT volume. The block size parameter was optimized for four different GPUs for a region of interest (ROI) of 400 Multiplication-Sign 225 pixels with different sampling ratios (1.1%-9.1% and 100%). Performance was statistically evaluated and compared for the four GPUs. The method and the block size dependence were validated on the latest GPU for several parameter settings with a public gold standard dataset (512 Multiplication-Sign 512 Multiplication-Sign 825 CT) for registration purposes. Results: Depending on the GPU, the full ROI is rendered in 2.7-5.2 ms. If sampling ratio of 1.1%-9.1% is applied, execution time is in the range of 0.3-7.3 ms. On all GPUs, the mean of the execution time increased linearly with respect to the number of pixels if sampling was used. Conclusions: The presented results outperform other results from the literature. This indicates that automatic 2D to 3D registration, which typically requires a couple of hundred DRR renderings to converge, can be performed quasi on-line, in less than a second or depending on the application and hardware in less than a couple of seconds. Accordingly, a whole new field of applications is opened for image guided interventions, where the registration is continuously performed to match the real-time x-ray.
07 ISOTOPE AND RADIATION SOURCES↗
Combining prior day contours to improve automated prostate segmentation
Purpose: To improve the accuracy of automatically segmented prostate, rectum, and bladder contours required for online adaptive therapy. The contouring accuracy on the current image guidance [image guided radiation therapy (IGRT)] scan is improved by combining contours from earlier IGRT scans via the simultaneous truth and performance level estimation (STAPLE) algorithm. Methods: Six IGRT prostate patients treated with daily kilo-voltage (kV) cone-beam CT (CBCT) had their original plan CT and nine CBCTs contoured by the same physician. Three types of automated contours were produced for analysis. (1) Plan: By deformably registering the plan CT to each CBCT and then using the resulting deformation field to morph the plan contours to match the CBCT anatomy. (2) Previous: The contour set drawn by the physician on the previous day CBCT is similarly deformed to match the current CBCT anatomy. (3) STAPLE: The contours drawn by the physician, on each prior CBCT and the plan CT, are deformed to match the CBCT anatomy to produce multiple contour sets. These sets are combined using the STAPLE algorithm into one optimal set. Results: Compared to plan and previous, STAPLE improved the average Dice's coefficient (DC) with the original physician drawn CBCT contours to a DC as follows: Bladder: 0.81 {+-} 0.13, 0.91 {+-} 0.06, and 0.92 {+-} 0.06; Prostate: 0.75 {+-} 0.08, 0.82 {+-} 0.05, and 0.84 {+-} 0.05; and Rectum: 0.79 {+-} 0.06, 0.81 {+-} 0.06, and 0.85 {+-} 0.04, respectively. The STAPLE results are within intraobserver consistency, determined by the physician blindly recontouring a subset of CBCTs. Comparing plans recalculated using the physician and STAPLE contours showed an average disagreement less than 1% for prostate D98 and mean dose, and 5% and 3% for bladder and rectum mean dose, respectively. One scan takes an average of 19 s to contour. Using five scans plus STAPLE takes less than 110 s on a 288 core graphics processor unit. Conclusions: Combining the plan and all prior days via the STAPLE algorithm to produce treatment day contours is superior to the current standard of deforming only the plan contours to the daily CBCT. STAPLE also improves the precision, with a substantial decrease in standard deviation, a key for adaptive therapy. Geometrically and dosimetrically accurate contours can be automatically generated with STAPLE on prostate region kV CBCT in a time scale suitable for online adaptive therapy.
60 APPLIED LIFE SCIENCES↗
SU-G-TeP1-15: Toward a Novel GPU Accelerated Deterministic Solution to the Linear Boltzmann Transport Equation
Purpose: To develop a Graphic Processor Unit (GPU) accelerated deterministic solution to the Linear Boltzmann Transport Equation (LBTE) for accurate dose calculations in radiotherapy (RT). A deterministic solution yields the potential for major speed improvements due to the sparse matrix-vector and vector-vector multiplications and would thus be of benefit to RT. Methods: In order to leverage the massively parallel architecture of GPUs, the first order LBTE was reformulated as a second order self-adjoint equation using the Least Squares Finite Element Method (LSFEM). This produces a symmetric positive-definite matrix which is efficiently solved using a parallelized conjugate gradient (CG) solver. The LSFEM formalism is applied in space, discrete ordinates is applied in angle, and the Multigroup method is applied in energy. The final linear system of equations produced is tightly coupled in space and angle. Our code written in CUDA-C was benchmarked on an Nvidia GeForce TITAN-X GPU against an Intel i7-6700K CPU. A spatial mesh of 30,950 tetrahedral elements was used with an S4 angular approximation. Results: To avoid repeating a full computationally intensive finite element matrix assembly at each Multigroup energy, a novel mapping algorithm was developed which minimized the operations required at each energy. Additionally, a parallelized memory mapping for the kronecker product between the sparse spatial and angular matrices, including Dirichlet boundary conditions, was created. Atomicity is preserved by graph-coloring overlapping nodes into separate kernel launches. The one-time mapping calculations for matrix assembly, kronecker product, and boundary condition application took 452±1ms on GPU. Matrix assembly for 16 energy groups took 556±3s on CPU, and 358±2ms on GPU using the mappings developed. The CG solver took 93±1s on CPU, and 468±2ms on GPU. Conclusion: Three computationally intensive subroutines in deterministically solving the LBTE have been formulated on GPU, resulting in two orders of magnitude speedup. Funding support from Natural Sciences and Engineering Research Council and Alberta Innovates Health Solutions. Dr. Fallone is a co-founder and CEO of MagnetTx Oncology Solutions (under discussions to license Alberta bi-planar linac MR for commercialization).
60 APPLIED LIFE SCIENCES↗
Modern approaches for the theoretical description of multiparticle scattering and nuclear reactions
A review of novel approaches to solution of multiparticle scattering problems in the area above three-body breakup together with the review of new computational technologies which provide very effective and ultrafast realization of the novel approaches with ordinary PC are given. The novel direction presented here is based on two key points: a new formulation of the quantum scattering theory in a discrete Hilbert space of stationary wave packets and the massive-parallel solution of the resulted matrix equations with usage of ultrafast graphic processors (the so called GPU-computations). For the reader's convenience, a short review of the modern GPU calculations for the medicine, physics, military applications etc. is presented.
73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
Model of a Thin Current Sheet in the Earth’s Magnetotail with a Kinetic Description of Magnetized Electrons
Steady-state two-dimensional thin current sheets (TCSs) in collisionless space plasma, similar to the current sheet of the near-Earth magnetotail, are considered. The magnetic field of the sheet is orthogonal to the current and has a nonzero normal component, the electrons are magnetized, and the ions are unmagnetized. To solve the problem of kinetic description of electrons in such current sheets in a general form, they are described by the Vlasov equation in the drift approximation, the general solution to which is found in the form of a function of three independent integrals of the system of drift motion equations. An important case is considered in which the electron guiding centers obey a Maxwell–Boltzmann distribution in a stationary electromagnetic field. The obtained results make it possible to create one- and two-dimensional numerical− analytical models of current sheets in which unmagnetized ions are described by the Vlasov equation, which should be solved numerically, whereas the contribution of magnetized electrons is taken into account analytically. To numerically solve the time-independent Vlasov equation, a new method is proposed that allows one to perform the bulk of computations by using graphic processors. On the basis of the new theory, a one-dimensional numerical−analytical model of a steady-state TCS in the near-Earth magnetotail is presented, TCS configurations are calculated, and the role of electrostatic effects and electron pressure anisotropy is analyzed.
71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
HipGISAXS
Implementation of a flexible Grazing Incidence Small-Angle Scattering (GISAXS). Simulation code based on the Distorted Wave Born Approximation (DWBA) theory that effectively utilizes the parallel processing power provided by graphic processors and multicore processors. This constitutes a handy tool for experimentalists facing a massive flux of data, allowing them to accurately simulate the GISAXS process and analyze the produced data. The software computes the diffraction image for any given super position of custom shapes or morphologies in a user-defined region of the reciprocal space for all possible grazing incidence angles and in-plane sample rotations. This flexibility then allows to easily tackle a wide range of possible sample structures such as nanoparticles o top of or embedded in a substrate or a multilayered structure. In cases where the sample displays regions of significant refractive index contrast, an algorithm has been implemented to perform a slicing of the sample along the vertical direction and compute the averaging refractive index profile to be used as the reference geometry of the unpertubed system. Preliminary tests show good agreement with experimental data for a variety of commonly encountered nanostructures.
Xiaoye, Sherry Li↗