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DOE OSTI2014

An MCNP6 Version of the Visual Editor - Paper 2

The Visual Editor is a graphical user interface for working with the MCNP computer code developed at Los Alamos National Laboratory. It consists of a graphical user interface written in C++ that is linked directory to the MCNP Fortran code. Work on the original Visual Editor started in 1992 and was first published in 1993. The original version of the Visual Editor was created on Unix/Linux operating systems and was linked to the MCNP computer code. The Visual Editor was adapted to the Windows operating system in 1999. In 2008 the Visual Editor was adapted to work with the MCNPX computer code. This paper discusses the latest upgrade of the Visual Editor to be compatible with the MCNP6 computer code. Two graphical user interfaces have been created, the Visual MCNP6 Plotter and the Visual MCNP6 Editor. The Visual MCNP6 Plotter includes all of the standard plotting features available in the default MCNP6 plotting package including geometry plotting, tally plotting, cross section plotting, mesh tally plotting and weight window mesh plotting. The Visual MNCP6 Editor has additional capabilities to allow for the creation of MCNP input files with graphical tools. The Visual MCNP6 Editor allows user to create and modify the input file within the Editor. Modifications are not allowed in the Visual MCNP6 Plotter. Both graphical user interfaces allow for advanced plotting features including 3D geometry plots and particle track plotting. Complete details on these tools along with their current status can be found at the Visual Editor website (www.mcnpvised.com). (author)

61 RADIATION PROTECTION AND DOSIMETRY↗
DOE OSTI2014

Towards the clinical implementation of iterative low-dose cone-beam CT reconstruction in image-guided radiation therapy: Cone/ring artifact correction and multiple GPU implementation

Purpose: Compressed sensing (CS)-based iterative reconstruction (IR) techniques are able to reconstruct cone-beam CT (CBCT) images from undersampled noisy data, allowing for imaging dose reduction. However, there are a few practical concerns preventing the clinical implementation of these techniques. On the image quality side, data truncation along the superior–inferior direction under the cone-beam geometry produces severe cone artifacts in the reconstructed images. Ring artifacts are also seen in the half-fan scan mode. On the reconstruction efficiency side, the long computation time hinders clinical use in image-guided radiation therapy (IGRT). Methods: Image quality improvement methods are proposed to mitigate the cone and ring image artifacts in IR. The basic idea is to use weighting factors in the IR data fidelity term to improve projection data consistency with the reconstructed volume. In order to improve the computational efficiency, a multiple graphics processing units (GPUs)-based CS-IR system was developed. The parallelization scheme, detailed analyses of computation time at each step, their relationship with image resolution, and the acceleration factors were studied. The whole system was evaluated in various phantom and patient cases. Results: Ring artifacts can be mitigated by properly designing a weighting factor as a function of the spatial location on the detector. As for the cone artifact, without applying a correction method, it contaminated 13 out of 80 slices in a head-neck case (full-fan). Contamination was even more severe in a pelvis case under half-fan mode, where 36 out of 80 slices were affected, leading to poorer soft tissue delineation and reduced superior–inferior coverage. The proposed method effectively corrects those contaminated slices with mean intensity differences compared to FDK results decreasing from ∼497 and ∼293 HU to ∼39 and ∼27 HU for the full-fan and half-fan cases, respectively. In terms of efficiency boost, an overall 3.1 × speedup factor has been achieved with four GPU cards compared to a single GPU-based reconstruction. The total computation time is ∼30 s for typical clinical cases. Conclusions: The authors have developed a low-dose CBCT IR system for IGRT. By incorporating data consistency-based weighting factors in the IR model, cone/ring artifacts can be mitigated. A boost in computational efficiency is achieved by multi-GPU implementation.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2020

Direct numerical simulations of turbulent reacting flows with shock waves and stiff chemistry using many-core/GPU acceleration

Compressible reacting flows may display sharp spatial variation related to shocks, contact discontinuities or reactive zones embedded within relatively smooth regions. The presence of such phenomena emphasizes the relevance of shock-capturing schemes such as the weighted essentially non-oscillatory (WENO) scheme as an essential ingredient of the numerical solver. However, these schemes are complex and have more computational cost than the simple high-order compact or non-compact schemes. In this paper, we present the implementation of a seventh-order, minimally-dissipative mapped WENO (WENO7M) scheme in a newly developed direct numerical simulation (DNS) code called KAUST Adaptive Reactive Flows Solver (KARFS). In order to make efficient use of the computer resources and reduce the solution time, without compromising the resolution requirement, the WENO routines are accelerated via graphics processing unit (GPU) computation. The performance characteristics and scalability of the code are studied using different grid sizes and block decomposition. Furthermore, the performance portability of KARFS is demonstrated on a variety of architectures including NVIDIA Tesla P100 GPUs and NVIDIA Kepler K20X GPUs. In addition, the capability and potential of the newly implemented WENO7M scheme in KARFS to perform DNS of compressible flows is also demonstrated with model problems involving shocks, isotropic turbulence, detonations and flame propagation into a stratified mixture with complex chemical kinetics.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2015

Accelerating population balance-Monte Carlo simulation for coagulation dynamics from the Markov jump model, stochastic algorithm and GPU parallel computing

This paper proposes a comprehensive framework for accelerating population balance-Monte Carlo (PBMC) simulation of particle coagulation dynamics. By combining Markov jump model, weighted majorant kernel and GPU (graphics processing unit) parallel computing, a significant gain in computational efficiency is achieved. The Markov jump model constructs a coagulation-rule matrix of differentially-weighted simulation particles, so as to capture the time evolution of particle size distribution with low statistical noise over the full size range and as far as possible to reduce the number of time loopings. Here three coagulation rules are highlighted and it is found that constructing appropriate coagulation rule provides a route to attain the compromise between accuracy and cost of PBMC methods. Further, in order to avoid double looping over all simulation particles when considering the two-particle events (typically, particle coagulation), the weighted majorant kernel is introduced to estimate the maximum coagulation rates being used for acceptance–rejection processes by single-looping over all particles, and meanwhile the mean time-step of coagulation event is estimated by summing the coagulation kernels of rejected and accepted particle pairs. The computational load of these fast differentially-weighted PBMC simulations (based on the Markov jump model) is reduced greatly to be proportional to the number of simulation particles in a zero-dimensional system (single cell). Finally, for a spatially inhomogeneous multi-dimensional (multi-cell) simulation, the proposed fast PBMC is performed in each cell, and multiple cells are parallel processed by multi-cores on a GPU that can implement the massively threaded data-parallel tasks to obtain remarkable speedup ratio (comparing with CPU computation, the speedup ratio of GPU parallel computing is as high as 200 in a case of 100 cells with 10 000 simulation particles per cell). These accelerating approaches of PBMC are demonstrated in a physically realistic Brownian coagulation case. The computational accuracy is validated with benchmark solution of discrete-sectional method. The simulation results show that the comprehensive approach can attain very favorable improvement in cost without sacrificing computational accuracy.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2016

Large Eddy Simulation of a Supercritical Fuel Jet in Cross Flow using GPU-Acceleration

Fuel is routinely injected into combustion chambers at elevated pressures resulting in formation of supercritical fluid flow. The dispersion of fuel and the combustion processes are significantly different in high pressure conditions as the raditional liquid atomization and evaporation are replaced by diffusion-dominated mixing. Modeling supercritical flow is challenging due to the complex thermodynamics and transport properties of the fluids and in most cases high fidelity numerical simulations are prohibitively expensive. However, numerical investigations must incorporate the flow properties appropriate for the regime for accurate description of the physical processes involved. In this paper, we consider real-fluid properties and simulate the turbulent mixing of fuel jet in cross flow at high ambient pressure. In order to make efficient use of the computer resources and reduce the time to solution, without compromising the resolution requirements, the real-fluid property routines are accelerated via Graphics Processing Unit (GPU) computation. The numerical simulations performed at different resolutions suggest that the high fidelity computations with refined mesh are essential to capture the non-linear dynamics of vortex evolution downstream of the fuel jet and signifies the necessity for an accelerated code. The code is accelerated using the Kokkos C++ library and is demonstrated to be about 2 times faster than the non-accelerated version. Considerable computational cost associated with the thermodynamics routines is reduced in the accelerated version. The results also suggest the resource requirements to compute turbulent closures and the need for acceleration of the routines associated with the sub-grid scale closures.

Gottiparthi, Kalyana C.↗
DOE OSTI2016

A Study of Complex Deep Learning Networks on High Performance, Neuromorphic, and Quantum Computers

Current Deep Learning models use highly optimized convolutional neural networks (CNN) trained on large graphical processing units (GPU)-based computers with a fairly simple layered network topology, i.e., highly connected layers, without intra-layer connections. Complex topologies have been proposed, but are intractable to train on current systems. Building the topologies of the deep learning network requires hand tuning, and implementing the network in hardware is expensive in both cost and power.In this paper, we evaluate deep learning models using three different computing architectures to address these problems: quantum computing to train complex topologies, high performance computing (HPC) to automatically determine network topology, and neuromorphic computing for a low-power hardware implementation. Due to input size limitations of current quantum computers we use the MNIST dataset for our evaluation.The results show the possibility of using the three architectures in tandem to explore complex deep learning networks that are untrainable using a von Neumann architecture. We show that a quantum computer can find high quality values of intra-layer connections and weights, while yielding a tractable time result as the complexity of the network increases; a high performance computer can find optimal layer-based topologies; and a neuromorphic computer can represent the complex topology and weights derived from the other architectures in low power memristive hardware.This represents a new capability that is not feasible with current von Neumann architecture. It potentially enables the ability to solve very complicated problems unsolvable with current computing technologies.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2016

A Study of Complex Deep Learning Networks on High Performance, Neuromorphic, and Quantum Computers

Current Deep Learning models use highly optimized convolutional neural networks (CNN) trained on large graphical processing units (GPU)-based computers with a fairly simple layered network topology, i.e., highly connected layers, without intra-layer connections. Complex topologies have been proposed, but are intractable to train on current systems. Building the topologies of the deep learning network requires hand tuning, and implementing the network in hardware is expensive in both cost and power. In this paper, we evaluate deep learning models using three different computing architectures to address these problems: quantum computing to train complex topologies, high performance computing (HPC) to automatically determine network topology, and neuromorphic computing for a low-power hardware implementation. Due to input size limitations of current quantum computers we use the MNIST dataset for our evaluation. The results show the possibility of using the three architectures in tandem to explore complex deep learning networks that are untrainable using a von Neumann architecture. We show that a quantum computer can find high quality values of intra-layer connections and weights, while yielding a tractable time result as the complexity of the network increases; a high performance computer can find optimal layer-based topologies; and a neuromorphic computer can represent the complex topology and weights derived from the other architectures in low power memristive hardware. This represents a new capability that is not feasible with current von Neumann architecture. It potentially enables the ability to solve very complicated problems unsolvable with current computing technologies.

Potok, Thomas E↗
DOE OSTI2021

Mesoscopic Modeling and Rapid Simulation of Incremental Changes in Epidemic Scenarios on GPUs

In simulation-based studies and analyses of epidemics, a major challenge lies in resolving the conflict between fidelity of models and the speed of their simulation. Another related challenge arises in dealing with the large number of what–if scenarios that need to be explored. Here, we describe new computational methods that together provide an approach to dealing with both challenges. A mesoscopic modeling approach is described that strikes a middle ground between macroscopic models based on coupled differential equations and microscopic models built on fine-grained behaviors at the individual entity level. The mesoscopic approach offers the ability to incorporate complex compositions of multiple layers of dynamics even while retaining the potential for aggregate behaviors at varying levels. It also is an excellent match to the accelerator-based architectures of modern computing platforms in which graphical processing units (GPUs) can be exploited for fast simulation via the parallel execution mode of single instruction multiple thread (SIMT). The challenge of simulating a large number of scenarios is addressed via a method of sharing model state and computation across a tree of what–if scenarios that are localized, incremental changes to a large base simulation. A combination of the mesoscopic modeling approach and the incremental what–if scenario tree evaluation has been implemented in the software on modern GPUs. Synthetic simulation scenarios are presented to demonstrate the computational characteristics of our approach. Results from the experiments with large population data, including USA, UK, and India, illustrate the modeling methodology and computational performance on thousands of synthetically generated what–if scenarios. Execution of our implementation scaled to 8192 GPUs of supercomputing platforms demonstrates the ability to rapidly evaluate what–if scenarios several orders of magnitude faster than the conventional methods.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2015

GPU-based simulation of the two-dimensional unstable structure of gaseous oblique detonations

In this paper, the two-dimensional structure of unstable oblique detonations induced by the wedge from a supersonic combustible gas flow is simulated using the reactive Euler equations with a one-step Arrhenius chemistry model. A wide range of activation energy of the combustible mixture is considered. Computations are performed on the Graphical Processing Unit (GPU) to reduce the simulation runtimes. A large computational domain covered by a uniform mesh with high grid resolution is used to properly capture the development of instabilities and the formation of different transverse wave structures. After the initiation point, where the oblique shock transits into a detonation, an instability begins to manifest and in all cases, the left-running transverse waves first appear, followed by the subsequent emergence of right-running transverse waves forming the dual-head triple point structure. This study shows that for low activation energies, a long computational length must be carefully considered to reveal the unstable surface due to the slow growth rate of the instability. For high activation energies, the flow behind the unstable oblique detonation features the formation of unburnt gas pockets and strong vortex-pressure wave interaction resulting in a chaotic-like vortical structure.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2024

Efficient Parallelization of Irregular Applications on GPU Architectures

With the enlarging computation capacity of general Graphics Processing Units (GPUs), leveraging GPUs to accelerate parallel applications has become a critical topic in academia and industry. However, a wide range of irregular applications with the computation-/memory-intensive nature cannot easily achieve high GPU utilization. The challenges mainly involve the following aspects: first, data dependence leads to coarse-grained kernel and inefficient parallelism; second, heavy GPU memory usage may cause frequent memory evictions and extra overhead of I/O; third, specific computation patterns produce memory redundancies; last, workload balance and data reusability conjunctly benefit the overall performance, but there may exist a dynamic trade-off between them. Targeting these challenges, this dissertation proposes multiple optimizations to accelerate two real-world applications: many-body correlation functions to simulate nuclear physics in a large-scale scientific system; the other is the eALS-based matrix factorization recommendation system. To accelerate the calculations of many-body correlation functions, this dissertation presents three frameworks in GPU memory management and multi-GPU scheduling. Firstly, an optimized systematic GPU memory management framework, MemHC, utilizes a series of new memory reduction designs in GPU memory allocation, CPU/GPU communications, and GPU memory oversubscription. Secondly, an enhanced multi-GPU scheduling framework, MICCO, particularly by taking both data dimension (e.g., data reuse and data eviction) and computation dimension into account. MICCO designs a heuristic scheduling algorithm and a machine learning-based regression model to generate the optimal settings of a proposed new concept to manage the trade-off. Thirdly, a locality-aware multi-GPU scheduling framework. This scheduler leverages pipeline batch generation with a looking-ahead strategy by building local dependency graphs for memory transfer reduction and better data reuse, achieving up to 79.92% memory cost reduction and 1.67x speedup. To parallelize the eALS-based recommendation system, this dissertation proposes an efficient CPU/GPU heterogeneous recommendation system, HEALS. HEALS employs newly designed architecture-adaptive data formats to achieve load balance and good data locality on CPU and GPU. To mitigate the data dependence, HEALS presents a CPU/GPU collaboration model for both task parallelism and data parallelism with multiple kernel computation optimizations. In summary, this dissertation efficiently accelerates two typical irregular applications on GPUs by building four frameworks, including CPU/GPU collaboration, GPU memory management, and multi-GPU scheduling.

Wang, Qihan↗
DOE OSTI2024

GDSA framework, a computational framework for complex modeling problems in radioactive waste management

This paper details a computational framework to produce automated, graphical workflows, and how this framework can be deployed to support complex modeling problems like those in nuclear engineering. Key benefits of the framework include: automating previously manual workflows; intuitive construction and communication of workflows through a graphical interface; and automated file transfer and handling for workflows deployed across heterogeneous computing resources. This paper demonstrates the framework's application to probabilistic post-closure performance assessment of systems for deep geologic disposal of nuclear waste. However, the framework is a general capability that can help users running a variety of computational studies.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2017

Brookhaven Lab Hosts Hackathon Focused on Graphics Processing Units (GPUs)

For five days in June 2017, Brookhaven Lab’s Computational Science Initiative hosted “Brookathon”—a programming workshop where teams of researchers, students, and software developers worked with mentors to accelerate scientific applications on GPUs for high-performance computing.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2020

Collaborative Exploration of Scientific Datasets Using Immersive and Statistical Visualization: Preprint

We discuss the value of collaborative, immersive visualization for the exploration of scientific datasets and review techniques and tools that have been developed and deployed at the National Renewable Energy Laboratory (NREL). We believe that collaborative visualizations linking statistical interfaces and graphics on laptops and high-performance computing (HPC) with 3D visualizations on immersive displays (head-mounted displays and large-scale immersive environments) enable scientific workflows that further rapid exploration of large, high-dimensional datasets by teams of analysts. We present a framework, PlottyVR, that blends statistical tools, general-purpose programming environments, and simulation with 3D visualizations. To contextualize this framework, we propose a categorization and loose taxonomy of collaborative visualization and analysis techniques. Finally, we describe how scientists and engineers have adopted this framework to investigate large, complex datasets.

collaborative visualization↗
DOE OSTI2021

Collaborative Exploration of Scientific Datasets Using Immersive and Statistical Visualization

We discuss the value of collaborative, immersive visualization for the exploration of scientific datasets and review techniques and tools that have been developed and deployed at the National Renewable Energy Laboratory (NREL). We believe that collaborative visualizations linking statistical interfaces and graphics on laptops and high-performance computing (HPC) with 3D visualizations on immersive displays (head-mounted displays and large-scale immersive environments) enable scientific workflows that further rapid exploration of large, high-dimensional datasets by teams of analysts. We present a framework, PlottyVR, that blends statistical tools, general-purpose programming environments, and simulation with 3D visualizations. To contextualize this framework, we propose a categorization and loose taxonomy of collaborative visualization and analysis techniques. Finally, we describe how scientists and engineers have adopted this framework to investigate large, complex datasets.

collaborative visualization↗
DOE OSTI2022

PeleC: An adaptive mesh refinement solver for compressible reacting flows

Reacting flow simulations for combustion applications require extensive computing capabilities. Leveraging the AMReX library, the Pele suite of combustion simulation tools targets the largest supercomputers available and future exascale machines. We introduce PeleC, the compressible solver in the Pele suite, and detail its capabilities, including complex geometry representation, chemistry integration, and discretization. We present a comparison of development efforts using both OpenACC and AMReX’s C++ performance portability framework for execution on multiple GPU architectures. We discuss relevant details that have allowed PeleC to achieve high performance and scalability. PeleC’s performance characteristics are measured through relevant simulations on multiple supercomputers. The success of PeleC’s design for exascale is exhibited through demonstration of a 160 billion cell simulation and weak scaling onto 100% of Summit, an NVIDIA-based GPU supercomputer at Oak Ridge National Laboratory. Our results provide confidence that PeleC will enable future combustion science simulations with unprecedented fidelity.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2020

Systems and methods for monitoring traffic on industrial control and building automation system networks

Technologies relating to monitoring communications traffic to detect potential attacks on industrial control system networks and building automation system networks are described herein. In an embodiment, a monitoring device receives a plurality of communications from a control network. The monitoring device transmits the communications to a computing device. Based on the communications, the computing device generates a listing of devices that communicated by way of the control network over a period of time, and computes a volume of traffic between each pair of devices in the listing of devices. The computing device then outputs a graphical user interface (GUI) by way of display, the GUI comprising data indicative of the computed volumes of traffic, which may be indicative of a potential attack on the control network.

Jenkins, Chris↗
DOE OSTI2018

Prediction of residual stresses in a multipass pipe weld by a novel 3D finite element approach

Due to enormous computation cost, current residual stress simulation of multipass girth welds are mostly performed using two-dimensional (2D) axisymmetric models. The 2D model can only provide limited estimation on the residual stresses by assuming its axisymmetric distribution. In this study, a highly efficient thermal-mechanical finite element code for three-dimensional (3D) model has been developed based on high performance Graphics Processing Unit (GPU) computers. Our code is further accelerated by considering the unique physics associated with welding processes that are characterized by steep temperature gradient and a moving arc heat source. It is capable of modeling large-scale welding problems that cannot be easily handled by the existing commercial simulation tools. To demonstrate the accuracy and efficiency, our code was compared with a commercial software by simulating a 3D multi-pass girth weld model with over 1 million elements. Our code achieved comparable solution accuracy with respect to the commercial one but with over 100 times saving on computational cost. Moreover, the three-dimensional analysis demonstrated more realistic stress distribution that is not axisymmetric in hoop direction.

Huang, Hui↗