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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.

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At least 19 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Graphics processor unit with opportunistic inter-path reconvergence

A graphics processing unit and methods for comping and executing instructions with opportunistic inter-path reconvergence are provided. A graphics processing unit may access computer executable instructions mapped to code blocks of a control flow for a warp. The code blocks may include an immediate dominator block and an intermediate post dominator block. The graphics processing unit may store a first thread mask associated with the first code block. The first thread mask may include a plurality of bits indicative of the active or non-active status for the threads of the warp, respectively. The graphics processing unit may a second thread mask corresponding to an intermediate code block between the immediate dominator block and intermediate post dominator block. The graphics processing unit may execute, with threads indicated as active by the first thread mask, instructions of the intermediate code block with a first operand or a second operand depending on the second thread mask.

Kulkarni, Milind↗
DOE OSTI2023

Physical vapor deposition simulator by graphical processor unit ray casting

This paper presents fast, accurate software for modeling physical vapor deposition systems over irregular surfaces. The model is implemented using graphics processing unit (GPU) ray casting. Applied models are viewed as a cross section of the area of interest. Given evaporation rate, time, and angular profiles in a vacuum system, an iterative time-step approach for calculating deposition profiles is calculated in the GPU architecture following a ballistic modeling approach. Thin-film technologies for the electronics industry will require evaporations on complex surfaces. Depending on the nature of the surface, a uniform thin film across the topology is wanted for various device parameters. The ray casting method is tested against various profiles. The code is freely distributed on GitHub (see https://github.com/adam-r-thomas/PVDS).

Engineering↗
DOE OSTI2017

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↗
DOE OSTI2016

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↗
DOE OSTI2016

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↗
DOE OSTI2014

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↗
DOE OSTI2014

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↗
DOE OSTI2015

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↗
DOE OSTI2013

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↗
DOE OSTI2016

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↗
DOE OSTI2016

A Deep Generative Deconvolutional Image Model

A deep generative model is developed for representation and analysis of images, based on a hierarchical convolutional dictionary-learning framework. Stochastic unpooling is employed to link consecutive layers in the model, yielding top-down image generation. A Bayesian support vector machine is linked to the top-layer features, yielding max-margin discrimination. Deep deconvolutional inference is employed when testing, to infer the latent features, and the top-layer features are connected with the max-margin classifier for discrimination tasks. The model is efficiently trained using a Monte Carlo expectation-maximization (MCEM) algorithm; the algorithm is implemented on graphical processor units (GPU) to enable large-scale learning, and fast testing. Excellent results are obtained on several benchmark datasets, including ImageNet, demonstrating that the proposed model achieves results that are highly competitive with similarly sized convolutional neural networks.

convolutional neural network↗
DOE OSTI2021

Hardware accelerated dynamic work creation on a graphics processing unit

A processor core is configured to execute a parent task that is described by a data structure stored in a memory. A coprocessor is configured to dispatch a child task to the at least one processor core in response to the coprocessor receiving a request from the parent task concurrently with the parent task executing on the at least one processor core. In some cases, the parent task registers the child task in a task pool and the child task is a future task that is configured to monitor a completion object and enqueue another task associated with the future task in response to detecting the completion object. The future task is configured to self-enqueue by adding a continuation future task to a continuation queue for subsequent execution in response to the future task failing to detect the completion object.

Gutierrez, Anthony↗
DOE OSTI2023

Hardware accelerated dynamic work creation on a graphics processing unit

A processor core is configured to execute a parent task that is described by a data structure stored in a memory. A coprocessor is configured to dispatch a child task to the at least one processor core in response to the coprocessor receiving a request from the parent task concurrently with the parent task executing on the at least one processor core. In some cases, the parent task registers the child task in a task pool and the child task is a future task that is configured to monitor a completion object and enqueue another task associated with the future task in response to detecting the completion object. The future task is configured to self-enqueue by adding a continuation future task to a continuation queue for subsequent execution in response to the future task failing to detect the completion object.

Gutierrez, Anthony T.↗
DOE OSTI2013

Validation of columnar CsI x-ray detector responses obtained with hybridMANTIS, a CPU-GPU Monte Carlo code for coupled x-ray, electron, and optical transport

Purpose: hybridMANTIS is a Monte Carlo package for modeling indirect x-ray imagers using columnar geometry based on a hybrid concept that maximizes the utilization of available CPU and graphics processing unit processors in a workstation. Methods: The authors compare hybridMANTIS x-ray response simulations to previously published MANTIS and experimental data for four cesium iodide scintillator screens. These screens have a variety of reflective and absorptive surfaces with different thicknesses. The authors analyze hybridMANTIS results in terms of modulation transfer function and calculate the root mean square difference and Swank factors from simulated and experimental results. Results: The comparison suggests that hybridMANTIS better matches the experimental data as compared to MANTIS, especially at high spatial frequencies and for the thicker screens. hybridMANTIS simulations are much faster than MANTIS with speed-ups up to 5260. Conclusions: hybridMANTIS is a useful tool for improved description and optimization of image acquisition stages in medical imaging systems and for modeling the forward problem in iterative reconstruction algorithms.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2014

Web-based, GPU-accelerated, Monte Carlo simulation and visualization of indirect radiation imaging detector performance

Purpose: Monte Carlo simulations play a vital role in the understanding of the fundamental limitations, design, and optimization of existing and emerging medical imaging systems. Efforts in this area have resulted in the development of a wide variety of open-source software packages. One such package, hybridMANTIS, uses a novel hybrid concept to model indirect scintillator detectors by balancing the computational load using dual CPU and graphics processing unit (GPU) processors, obtaining computational efficiency with reasonable accuracy. In this work, the authors describe two open-source visualization interfaces, webMANTIS and visualMANTIS to facilitate the setup of computational experiments via hybridMANTIS. Methods: The visualization tools visualMANTIS and webMANTIS enable the user to control simulation properties through a user interface. In the case of webMANTIS, control via a web browser allows access through mobile devices such as smartphones or tablets. webMANTIS acts as a server back-end and communicates with an NVIDIA GPU computing cluster that can support multiuser environments where users can execute different experiments in parallel. Results: The output consists of point response and pulse-height spectrum, and optical transport statistics generated by hybridMANTIS. The users can download the output images and statistics through a zip file for future reference. In addition, webMANTIS provides a visualization window that displays a few selected optical photon path as they get transported through the detector columns and allows the user to trace the history of the optical photons. Conclusions: The visualization tools visualMANTIS and webMANTIS provide features such as on the fly generation of pulse-height spectra and response functions for microcolumnar x-ray imagers while allowing users to save simulation parameters and results from prior experiments. The graphical interfaces simplify the simulation setup and allow the user to go directly from specifying input parameters to receiving visual feedback for the model predictions.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2013

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.↗
DOE OSTI2018

Analyzing the Impact of System Reliability Events on Applications in the Titan Supercomputer

Extreme-scale computing systems employ Reliability, Availability and Serviceability (RAS) mechanisms and infrastructure to log events from multiple system components. In this paper, we analyze RAS logs in conjunction with the application placement and scheduling database, in order to understand the impact of common RAS events on application performance. This study conducted on the records of about 2 million applications executed on Titan supercomputer provides important insights for system users, operators and computer science researchers. Specifically, we investigate the impact of RAS events on application performance and its variability by comparing cases where events are recorded with corresponding cases where no events are recorded. Such a statistical investigation is possible since we observed that system users tend to execute their applications multiple times. Our analysis reveals that most RAS events do impact application performance, although not always. We also find that different system components affect application performance differently. In particular, our investigation includes the following components: parallel file system processor, memory, graphics processing units, system and user software issues. Our work establishes the importance of providing feedback to system users for increasing operational efficiency of extreme-scale systems.

Ashraf, Rizwan↗