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DOE OSTI2024

Performance Results on CPU/GPU Exascale Architectures for OMEGA: The Ocean Model for E3SM Global Applications

The US Department of Energy (DOE) conducts climate simulations on some of the world’s largest supercomputers. These exascale machines use heterogeneous architectures with both CPUs and GPUs, and scientific codes must adapt to make full use of this computing power. Los Alamos National Lab is developing Omega: The Ocean Model for E3SM Global Applications, which is specifically designed for modern exascale computers. It uses external libraries that have been optimized for a variety of architectures to run on different supercomputers. Omega is an unstructured-mesh ocean model based on TRiSK numerical methods. It will be the new ocean component of the DOE’s Energy Exascale Earth System Model (E3SM). The algorithms in Omega follow those of the current ocean component, MPAS-Ocean, but it will be written in C++ rather than Fortran to take advantage of the Kokkos performance portability library. Omega spatial operators are written as Kokkos kernels to run efficiently on both CPUs and GPUs. Work on Omega began in 2023 with a new C++ framework for unstructured mesh partitioning, halo exchanges, parallel IO, and Kokkos interfaces. The current version, Omega-0, is being developed to solve the shallow water equations and at present includes all of the tendency terms but not time stepping. Here we share the results of Omega-0 verification and performance testing. Verification includes unit tests implemented with CTest as well as convergence tests in Polaris, an in-house python package with a large suite of test problems. Performance tests compare simulations conducted on CPUs versus GPUs and across different architectures: tests are run on Frontier, which has AMD “Optimized 3rd Gen EPYC” CPUs and AMD MI250X GPUs, as well as Perlmutter, which is composed of AMD EPYC 7763 CPUs and NVIDIA A100 GPUs.

58 GEOSCIENCES↗

DOE OSTI2024

Entanglement Renormalization for Quantum Field Theories with Discrete Wavelet Transforms

We propose an adaptation of Entanglement Renormalization for quantum field theories that, through the use of discrete wavelet transforms, strongly parallels the tensor network architecture of the Multiscale Entanglement Renormalization Ansatz (a.k.a. MERA). Our approach, called wMERA, has several advantages of over previous attempts to adapt MERA to continuum systems. In particular, (i) wMERA is formulated directly in position space, hence preserving the quasi-locality and sparsity of entanglers; and (ii) it enables a built-in RG flow in the implementation of real-time evolution and in computations of correlation functions, which is key for efficient numerical implementations. As examples, we describe in detail two concrete implementations of our wMERA algorithm for free scalar and fermionic theories in (1+1) spacetime dimensions. Possible avenues for constructing wMERAs for interacting field theories are also discussed.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2022

PythonFOAM: In-situ data analyses with OpenFOAM and Python

Here, we outline the development of a general-purpose Python-based data analysis tool for OpenFOAM. Our implementation relies on the construction of OpenFOAM applications that have bindings to data analysis libraries in Python. Double precision data in OpenFOAM is cast to a NumPy array using the NumPy C-API and Python modules may then be used for arbitrary data analysis and manipulation on flow-field information. We highlight how the proposed wrapper may be used for an in-situ online singular value decomposition (SVD) implemented in Python and accessed from the OpenFOAM solver PimpleFOAM. Here, 'in-situ' refers to a programming paradigm that allows for a concurrent computation of the data analysis on the same computational resources utilized for the partial differential equation solver. In addition, to demonstrate parallel deployments, we deploy a distributed SVD, which collects snapshot data across the ranks of a distributed simulation to compute the global left singular vectors. Crucially, both OpenFOAM and Python share the same message passing interface (MPI) communicator for this deployment which allows Python objects and functions to exchange NumPy arrays across ranks. Subsequently, we provide scaling assessments of this distributed SVD on multiple nodes of Intel Broadwell and KNL architectures for canonical test cases such as the large eddy simulations of a backward facing step and a channel flow at friction Reynolds number of 395. Finally, we demonstrate the deployment of a deep neural network for compressing the flow-field information using an autoencoder to demonstrate an ability to use state-of-the-art machine learning tools in the Python ecosystem.

97 MATHEMATICS AND COMPUTING↗

NASA NTRS1990

Supercomputing systems - A projection to 2000

Advances in computer architecture, computer science, computational methods, and constituent technologies are expected to lead to significant advances in the performance of scientific supercomputing system capabilities over the next decade. By the year 2000, single 1-in-sq dies are projected to incorporate four processors, each of which would be operating faster than 750 million instructions per second (MIPS) for a total on-chip processing performance in excess of 2000 MIPS. Scalable parallel processors can be expected to contain thousands of such multiple processor chips. In general, semiconductor performance advances appear to change about one order of magnitude every five years. Rotating magnetic memory and communications technology are not advancing as rapidly, with the result that the allocation of functions within the system configurations fo future supercomputer systems will require important changes. Availability of massively parallel heterogeneous processing capabilities should be a catalyst leading to new approaches for applications.

Lundstrom, S. F.↗

NASA NTRS1994

Very fast motion planning for highly dexterous-articulated robots

Due to the inherent danger of space exploration, the need for greater use of teleoperated and autonomous robotic systems in space-based applications has long been apparent. Autonomous and semi-autonomous robotic devices have been proposed for carrying out routine functions associated with scientific experiments aboard the shuttle and space station. Finally, research into the use of such devices for planetary exploration continues. To accomplish their assigned tasks, all such autonomous and semi-autonomous devices will require the ability to move themselves through space without hitting themselves or the objects which surround them. In space it is important to execute the necessary motions correctly when they are first attempted because repositioning is expensive in terms of both time and resources (e.g., fuel). Finally, such devices will have to function in a variety of different environments. Given these constraints, a means for fast motion planning to insure the correct movement of robotic devices would be ideal. Unfortunately, motion planning algorithms are rarely used in practice because of their computational complexity. Fast methods have been developed for detecting imminent collisions, but the more general problem of motion planning remains computationally intractable. However, in this paper we show how the use of multicomputers and appropriate parallel algorithms can substantially reduce the time required to synthesize paths for dexterous articulated robots with a large number of joints. We have developed a parallel formulation of the Randomized Path Planner proposed by Barraquand and Latombe. We have shown that our parallel formulation is capable of formulating plans in a few seconds or less on various parallel architectures including: the nCUBE2 multicomputer with up to 1024 processors (nCUBE2 is a registered trademark of the nCUBE corporation), and a network of workstations.

Challou, Daniel J.↗

DOE OSTI2025

Bayesian Optimized Deep Ensemble for Uncertainty Quantification of Deep Neural Networks: a System Safety Case Study on Sodium Fast Reactor Thermal Stratification Modeling

Deep neural networks (DNNs) are increasingly important to scientific computing and engineering system simulations. Accurate uncertainty quantification (UQ) for DNNs is critical in safety-sensitive engineering domains. Traditional Deep Ensemble (DE) methods, while easy to implement, frequently suffer from poorly calibrated uncertainty estimates and limited predictive accuracy due to reliance on fixed architectures with varied weight initializations. To address these issues, we introduce a workflow that combines Bayesian Optimization (BO) and DE. The workflow is modular, scalable, and integrates parallel BO initialized with Sobol sequences to individually optimize the hyperparameters of each ensemble member. This method enhances ensemble diversity, improves predictive accuracy, and provides reliable uncertainty estimates. We evaluate the proposed BODE approach in a sodium fast reactor thermal stratification modeling case study, where we used a densely connected convolutional neural network to predict turbulent viscosity during the reactor transient with consideration of data noise. We benchmark its performance against several optimization approaches, including baseline deep ensemble, evolutionary algorithm-optimized ensemble, ensemble formed via random search combined with greedy selection, and a BO ensemble using random initialization. Here, our results demonstrate superior performance of the developed BODE approach. In noise-free scenarios, BODE notably reduces incorrect aleatoric uncertainty and significantly enhances predictive accuracy. Under conditions of 5% and 10% Gaussian noise, BODE adaptively quantifies uncertainty proportional to data noise, achieving up to an 80% reduction in root mean square error compared to baseline methods and producing well-calibrated prediction intervals.

Bayesian optimization↗

NASA NTRS1991

Biological neural networks as model systems for designing future parallel processing computers

One of the more interesting debates of the present day centers on whether human intelligence can be simulated by computer. The author works under the premise that neurons individually are not smart at all. Rather, they are physical units which are impinged upon continuously by other matter that influences the direction of voltage shifts across the units membranes. It is only the action of a great many neurons, billions in the case of the human nervous system, that intelligent behavior emerges. What is required to understand even the simplest neural system is painstaking analysis, bit by bit, of the architecture and the physiological functioning of its various parts. The biological neural network studied, the vestibular utricular and saccular maculas of the inner ear, are among the most simple of the mammalian neural networks to understand and model. While there is still a long way to go to understand even this most simple neural network in sufficient detail for extrapolation to computers and robots, a start was made. Moreover, the insights obtained and the technologies developed help advance the understanding of the more complex neural networks that underlie human intelligence.

Ross, Muriel D.↗

NASA NTRS2010

Reconfigurable Hardware for Compressing Hyperspectral Image Data

High-speed, low-power, reconfigurable electronic hardware has been developed to implement ICER-3D, an algorithm for compressing hyperspectral-image data. The algorithm and parts thereof have been the topics of several NASA Tech Briefs articles, including Context Modeler for Wavelet Compression of Hyperspectral Images (NPO-43239) and ICER-3D Hyperspectral Image Compression Software (NPO-43238), which appear elsewhere in this issue of NASA Tech Briefs. As described in more detail in those articles, the algorithm includes three main subalgorithms: one for computing wavelet transforms, one for context modeling, and one for entropy encoding. For the purpose of designing the hardware, these subalgorithms are treated as modules to be implemented efficiently in field-programmable gate arrays (FPGAs). The design takes advantage of industry- standard, commercially available FPGAs. The implementation targets the Xilinx Virtex II pro architecture, which has embedded PowerPC processor cores with flexible on-chip bus architecture. It incorporates an efficient parallel and pipelined architecture to compress the three-dimensional image data. The design provides for internal buffering to minimize intensive input/output operations while making efficient use of offchip memory. The design is scalable in that the subalgorithms are implemented as independent hardware modules that can be combined in parallel to increase throughput. The on-chip processor manages the overall operation of the compression system, including execution of the top-level control functions as well as scheduling, initiating, and monitoring processes. The design prototype has been demonstrated to be capable of compressing hyperspectral data at a rate of 4.5 megasamples per second at a conservative clock frequency of 50 MHz, with a potential for substantially greater throughput at a higher clock frequency. The power consumption of the prototype is less than 6.5 W. The reconfigurability (by means of reprogramming) of the FPGAs makes it possible to effectively alter the design to some extent to satisfy different requirements without adding hardware. The implementation could be easily propagated to future FPGA generations and/or to custom application-specific integrated circuits.

Aranki, Nazeeh↗

NASA NTRS2015

Biomimetic Fly Eye Sensor for Real-Time Target Tracking

The project objective is to design, build, and demonstrate a biomimetic (inspired by biology) smart sensor based on the common house fly eye for real-time target tracking in three dimensions (3-D). The sensor makes use of revolutionary optical sensor design resulting in significantly improved motion detection capabilities when compared with conventional optical sensors. The design is motivated by the parallel nature of the flys vision system and its demonstrated hyperacuity or precision of visual localization beyond the conventional resolution limit. This means that the sensor is able to accurately detect very fast motion and small changes in motion. The analog architecture of the sensor allows for real-time solution at adjustable bandwidths depending on the application. The low cost, exceptionally lightweight, small form factor, low power requirements, and low computation requirements of the sensor make it ideally suited to many aeronautics applications that have limitations on weight, power, and processing time. The sensor is modular and can be easily adapted in scale and manufactured for a wide variety of sensing applications. Advanced target tracking algorithms will be developed to allow the sensor to track a target in 3-D. These algorithms will be implemented in the smart sensors hardware to enable real-time target tracking.

wing position measurement system↗

NASA NTRS1992

A balanced submatrix merging algorithm for multiprocessor architectures

In this article, a parallel algorithm which applies Givens rotations to selectively annihilate k(k + 1)/2 nonzero elements from two k x n(k not more than n) upper trapezoidal submatrices is described. The new algorithm is suitable for implementation on either a pair of directly connected local-memory processors or two clusters of multiple tightly-coupled processors. Analyses show that in both cases the proposed algorithms achieve optimal speed-up by balancing the work load distribution and masking interprocessor or intercluster communication by computation if k is much small than n. In the context of solving large scale least squares problems, this submatrix merging step is repetitively needed during the entire computation and, furthermore, there are usually many pairs of such submatrices to be merged with each submatrix stored in the memory of a processor or a cluster of processors. The proposed algorithm can be applied to each pair of submatrices concurrently, and thus parallelizes an important step in solving the least squares problems.

Chu, Eleanor↗

NASA NTRS2017

Archive Management of NASA Earth Observation Data to Support Cloud Analysis

NASA collects, processes and distributes petabytes of Earth Observation (EO) data from satellites, aircraft, in situ instruments and model output, with an order of magnitude increase expected by 2024. Cloud-based web object storage (WOS) of these data can simplify the execution of such an increase. More importantly, it can also facilitate user analysis of those volumes by making the data available to the massively parallel computing power in the cloud. However, storing EO data in cloud WOS has a ripple effect throughout the NASA archive system with unexpected challenges and opportunities. One challenge is modifying data servicing software (such as Web Coverage Service servers) to access and subset data that are no longer on a directly accessible file system, but rather in cloud WOS. Opportunities include refactoring of the archive software to a cloud-native architecture; virtualizing data products by computing on demand; and reorganizing data to be more analysis-friendly.

Lynnes, Christopher↗

NASA NTRS2017

Archive Management of NASA Earth Observation Data to Support Cloud Analysis

Lynnes, Christopher↗

NASA NTRS2011

Energy Usage in an Embedded Space Vision Application on a Tiled Architecture

The need for greater autonomy in platforms such as planetary rovers is driving rapidly to codes that far overwhelm the capabilities of conventional space-qualified single core processors to run them in real-time. However, a new generation of potentially space-qualified 2D "tiled" multi-core microprocessor chips is emerging with significant performance potential. Leveraging such inherently parallel hardware for space platforms requires consideration of both time and power limitations - the latter of which is not normally done in conventional parallel computing. This paper takes one such application, Rockster, and analyzes it for energy usage when ported to a multi-core tiled chip such as may come from the Maestro program. The results demonstrate not only the criticality of memory and interconnect in the energy of real-time parallel codes, but also the effects of possible "energy-aware" changes in partitioning and algorithm design.

multi-core processors↗

NASA NTRS1990

Multiprocessor architecture: Synthesis and evaluation

Multiprocessor computed architecture evaluation for structural computations is the focus of the research effort described. Results obtained are expected to lead to more efficient use of existing architectures and to suggest designs for new, application specific, architectures. The brief descriptions given outline a number of related efforts directed toward this purpose. The difficulty is analyzing an existing architecture or in designing a new computer architecture lies in the fact that the performance of a particular architecture, within the context of a given application, is determined by a number of factors. These include, but are not limited to, the efficiency of the computation algorithm, the programming language and support environment, the quality of the program written in the programming language, the multiplicity of the processing elements, the characteristics of the individual processing elements, the interconnection network connecting processors and non-local memories, and the shared memory organization covering the spectrum from no shared memory (all local memory) to one global access memory. These performance determiners may be loosely classified as being software or hardware related. This distinction is not clear or even appropriate in many cases. The effect of the choice of algorithm is ignored by assuming that the algorithm is specified as given. Effort directed toward the removal of the effect of the programming language and program resulted in the design of a high-level parallel programming language. Two characteristics of the fundamental structure of the architecture (memory organization and interconnection network) are examined.

Standley, Hilda M.↗

DOE OSTI2025

Distributed Stochastic Optimization of a Neural Representation Network for Time-Space Tomography Reconstruction

4D time-space reconstruction of dynamic events or deforming objects using X-ray computed tomography (CT) is an important inverse problem in non-destructive evaluation. Conventional back-projection based reconstruction methods assume that the object remains static for the duration of several tens or hundreds of X-ray projection measurement images (reconstruction of consecutive limited-angle CT scans). However, this is an unrealistic assumption for many in-situ experiments that causes spurious artifacts and inaccurate morphological reconstructions of the object. To solve this problem, we propose to perform a 4D time-space reconstruction using a distributed implicit neural representation (DINR) network that is trained using a novel distributed stochastic training algorithm. Our DINR network learns to reconstruct the object at its output by iterative optimization of its network parameters such that the measured projection images best match the output of the CT forward measurement model. Here, we use a forward measurement model that is a function of the DINR outputs at a sparsely sampled set of continuous valued 4D object coordinates. Unlike previous neural representation architectures that forward and back propagate through dense voxel grids that sample the object's entire time-space coordinates, we only propagate through the DINR at a small subset of object coordinates in each iteration resulting in an order-of-magnitude reduction in memory and compute for training. DINR leverages distributed computation across several compute nodes and GPUs to produce high-fidelity 4D time-space reconstructions. We use both simulated parallel-beam and experimental cone-beam X-ray CT datasets to demonstrate the superior performance of our approach.

36 MATERIALS SCIENCE↗

NASA NTRS1992

An open, parallel I/O computer as the platform for high-performance, high-capacity mass storage systems

APTEC Computer Systems is a Portland, Oregon based manufacturer of I/O computers. APTEC's work in the context of high density storage media is on programs requiring real-time data capture with low latency processing and storage requirements. An example of APTEC's work in this area is the Loral/Space Telescope-Data Archival and Distribution System. This is an existing Loral AeroSys designed system, which utilizes an APTEC I/O computer. The key attributes of a system architecture that is suitable for this environment are as follows: (1) data acquisition alternatives; (2) a wide range of supported mass storage devices; (3) data processing options; (4) data availability through standard network connections; and (5) an overall system architecture (hardware and software designed for high bandwidth and low latency). APTEC's approach is outlined in this document.

Abineri, Adrian↗

DOE OSTI2020

Evaluation of Graph Analytics Frameworks Using the GAP Benchmark Suite

The analysis of connected data is an increasingly important application in high-performance computing. Such analyses can reveal fraudulent patterns in financial transactions, optimize telecommunications networks, predict information flow in social networks, etc. However, the landscape of graph analytics is highly diverse. Graph algorithms stress processor architectures differently, and no one graph can represent all topologies. Consequently, no single approach or framework is expected to be optimal for all graph analytics problems. To help make sense of this diverse landscape, we evaluated four approaches to graph analytics: GraphBLAS, Galois, BGL17, GraphIt; and compare them against hand-tuned implementations that take advantage of hardware features on our test platform. Graph- BLAS formulates graph analytics as sparse linear algebra. Galois provides syntactic constructs for data parallelism over irregular data structures. BGL17 is a generic C++ template library for implementing graph algorithms. GraphIt provides a domain- specific language to describe and optimize graph algorithms. We use the GAP Benchmark Suite to establish baseline performance and guide the side-by-side evaluation of each framework. GAP consists of 30 tests: six graph analytics algorithms (breadth- first search, single-source shortest path, PageRank, betweenness centrality, connected components, and triangle counting) run on five graphs, each with different topological characteristics (e.g., high diameter, skewed degree distribution, high average degree). High-performance reference implementations are included for each benchmark algorithm. Because a graph can be loaded into memory a number of ways (e.g., flat file on disk, compressed sparse format, data frames, retrieved from SQL or NoSQL databases), our evaluation focused on computational performance rather than I/O. Our results show the relative strengths of each framework.

Graph algorithms, Benchmarking, shared-memory prog↗

DOE OSTI2023

Fast tree-based algorithms for DBSCAN for low-dimensional data on GPUs

DBSCAN is a well-known density-based clustering algorithm to discover arbitrary shape clusters. While conceptually simple in serial, the algorithm is challenging to efficiently parallelize on manycore GPU architectures. Common pitfalls, such as asynchronous range query calls, result in high thread execution divergence in many implementations. In this paper, we propose a new framework for GPU-accelerated DBSCAN, and describe two tree-based algorithms within that framework. Both algorithms fuse the search for neighbors with updating cluster information, but differ in their treatment of dense regions of the data. We show that the time taken to compute clusters is at most twice that of determination of the neighbors. We compare the proposed algorithms with existing CPU and GPU implementations, and demonstrate their competitiveness and performance using a fast traversal structure (bounding volume hierarchy) for low dimensional data. We also show that the memory usage can be reduced by processing object neighbors dynamically without storing them.

Prokopenko, Andrey↗