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All sources NASA NTRS DOE OSTI

DOE OSTI2021

A Survey: Handling Irregularities in Neural Network Acceleration with FPGAs

In the last decade, Artificial Intelligence (AI) through Deep Neural Networks (DNNs) has penetrated virtually every aspect of science, technology, and business. Many types of DNNs have been and continue to be developed, including Convolutional Neural Networks (CNNs), Recurrent Neural Net- works (RNNs), and Graph Neural Networks (GNNs). The overall problem for all of these Neural Networks (NNs) is that their target applications generally pose stringent constraints on latency and throughput, while also having strict accuracy requirements. There have been many previous efforts in creating hardware to accelerate NNs. The problem designers face is that optimal NN models typically have significant irregularities, making them hardware-unfriendly. In this paper, we first define the problems in NN acceleration by characterizing common irregularities in NN processing into 4 types; then we summarize the existing works that handle the four types of irregularities efficiently using hardware, especially FPGAs; finally, we provide a new vision of next-generation FPGA-based NN acceleration: that the emerging heterogeneity in the next-generation FPGAs is the key to achieving higher performance.

Geng, Tong↗

DOE OSTI2018

Random Walk on a Perturbation of the Infinitely-Fast Mixing Interchange Process

We consider a random walk in dimension d≥1 in a dynamic random environment evolving as an interchange process with rate γ>0. We prove that, if we choose γ large enough, almost surely the empirical velocity of the walker X{sub t}/t eventually lies in an arbitrary small ball around the annealed drift. This statement is thus a perturbation of the case γ=+∞ where the environment is refreshed between each step of the walker. We extend three-way part of the results of Huveneers and Simenhaus (Electron J Probab 20(105):42, 2015), where the environment was given by the 1-dimensional exclusion process: (i) We deal with any dimension d≥1; (ii) We treat the much more general interchange process, where each particle carries a transition vector chosen according to an arbitrary law μ; (iii) We show that X{sub t}/t is not only in the same direction of the annealed drift, but that it is also close to it.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2023

Effects of Dead‐End Fractures on Non‐Fickian Transport in Three‐Dimensional Discrete Fracture Networks

Abstract Understanding mechanistic causes of non‐Fickian transport in fractured media is important for many hydrogeologic processes and subsurface applications. This study elucidates the effects of dead‐end fractures on non‐Fickian transport in three‐dimensional (3D) fracture networks. Although dead‐end fractures have been identified as low‐velocity regions that could delay solute transport, the direct relation between dead‐end fractures and non‐Fickian transport has been elusive. We systematically generate a large number of 3D discrete fracture networks with different fracture length distributions and fracture densities. We then identify dead‐end fractures using a novel graph‐based method. The effect of dead‐end fractures on solute residence time maximizes at the critical fracture density of the percolation threshold, leading to strong late‐time tailing. As fracture density increases beyond the percolation threshold, the network connectivity increases, and dead‐end fractures diminish. Consequently, the increase in network connectivity leads to a reduction in the degree of late‐time tailing. We also show that dead‐end fractures can inform about main transport paths, such as the mean tortuosity of particle trajectories. This study advances our mechanistic understanding of solute transport in 3D fracture networks.

58 GEOSCIENCES↗

DOE OSTI2019

STEMDL

The code "STEMDL" provides highly-optimized multi-gpu implementations of DL models of applicability in electron microscopy via the use of mixed-precision arithmetic, native graph construction and evaluation in Tensorflow, and adaptive scaling of learning parameters to avoid numerical instabilities due to reduced precision. STEMDL also uses low-level methods from the Horovod library for gradient communication and reduction and adds an additional optimization by allowing the user to scheduling the gradient reduction operations based on their position within the layers of a neural net. STEMDL provides optimized I/O routines for data staging and data reading/writing in both Tensorflow and Pytorch using multi-processing and asynchronous transfer between host and device. .

Laanait, Nouamane↗

DOE OSTI2016

Quantum Graph Analysis

In recent years, advanced network analytics have become increasingly important to na- tional security with applications ranging from cyber security to detection and disruption of ter- rorist networks. While classical computing solutions have received considerable investment, the development of quantum algorithms to address problems, such as data mining of attributed relational graphs, is a largely unexplored space. Recent theoretical work has shown that quan- tum algorithms for graph analysis can be more efficient than their classical counterparts. Here, we have implemented a trapped-ion-based two-qubit quantum information proces- sor to address these goals. Building on Sandia's microfabricated silicon surface ion traps, we have designed, realized and characterized a quantum information processor using the hyperfine qubits encoded in two 171 Yb + ions. We have implemented single qubit gates using resonant microwave radiation and have employed Gate set tomography (GST) to characterize the quan- tum process. For the first time, we were able to prove that the quantum process surpasses the fault tolerance thresholds of some quantum codes by demonstrating a diamond norm distance of less than 1 . 9 x 10 [?] 4 . We used Raman transitions in order to manipulate the trapped ions' motion and realize two-qubit gates. We characterized the implemented motion sensitive and insensitive single qubit processes and achieved a maximal process infidelity of 6 . 5 x 10 [?] 5 . We implemented the two-qubit gate proposed by Molmer and Sorensen and achieved a fidelity of more than 97 . 7%.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2019

An Agile Design-to-Simulation Workflow Using a New Conforming Moving Least Squares Method

This report summarizes the accomplishments and challenges of a two year LDRD effort focused on improving design-to-simulation agility. The central bottleneck in most solid mechanics simulations is the process of taking CAD geometry and creating a discretization of suitable quality, i.e., the "meshing" effort. This report revisits meshfree methods and documents some key advancements that allow their use on problems with complex geometries, low quality meshes, nearly incompressible materials or that involve fracture. The resulting capability was demonstrated to be an effective part of an agile simulation process by enabling rapid discretization techniques without increasing the time to obtain a solution of a given accuracy. The first enhancement addressed boundary-related challenges associated with meshfree methods. When using point clouds and Euclidean metrics to construct approximation spaces, the boundary information is lost, which results in low accuracy solutions for non-convex geometries and mate rial interfaces. This also complicates the application of essential boundary conditions. The solution involved the development of conforming window functions which use graph and boundary information to directly incorporate boundaries into the approximation space.

42 ENGINEERING↗

DOE OSTI2020

Evaluation of Methods for Causal Discovery in Hydrometeorological Systems

Understanding causal relations is of utmost importance in hydrology and climate research for systems identification, prediction, and understanding systems behavior in a changing climate. Traditionally, researchers in hydrometeorology attempted to study causal questions by conducting controlled experiments using numerical models. This approach, however, in most cases of interest provides uncertain results because the models are approximate representation of the natural system. An alternative approach that has recently drawn significant attention in several fields is to infer causal relations from purely observational data. It possesses several traits to its utility particularly in hydrometeorology due to the rapid accumulation of in situ and remotely sensed data records. The first objective of this study is to present a brief description of four causal discovery methods (Granger causality, Transfer Entropy, graph-based algorithms, and Convergent Cross Mapping) with special emphasis on the assumptions on which they are built. Second, using synthetic data generated from a hydrological model, we assess their performance in retrieving causal information taking into account sensitivity to sample size and presence of noise. Last, we use causal analysis to examine and formulate hypotheses on causal drivers of evapotranspiration in a shrubland region during summer and winter seasons. An interpretation of the hypotheses based on canopy seasonal dynamics and evapotranspiration processes is presented. It is hoped that the results presented here can be useful in guiding researchers studying hydrometeorological systems as to which causal method is most appropriate to the characteristics of the system under study.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2022

MOFSimplify, machine learning models with extracted stability data of three thousand metal–organic frameworks

Abstract We report a workflow and the output of a natural language processing (NLP)-based procedure to mine the extant metal–organic framework (MOF) literature describing structurally characterized MOFs and their solvent removal and thermal stabilities. We obtain over 2,000 solvent removal stability measures from text mining and 3,000 thermal decomposition temperatures from thermogravimetric analysis data. We assess the validity of our NLP methods and the accuracy of our extracted data by comparing to a hand-labeled subset. Machine learning (ML, i.e. artificial neural network) models trained on this data using graph- and pore-geometry-based representations enable prediction of stability on new MOFs with quantified uncertainty. Our web interface, MOFSimplify, provides users access to our curated data and enables them to harness that data for predictions on new MOFs. MOFSimplify also encourages community feedback on existing data and on ML model predictions for community-based active learning for improved MOF stability models.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2018

High performance Data Driven Agent-based Modeling Framework for Simulation of Commute Mode Choices in Metropolitan Area

Active transportation, human-powered transportation modes such as walking and bicycling, not only reduces the carbon footprint from the transportation sector but also promotes healthy living by offering opportunities for people to build physical activity into their daily routine. To encourage active transportation through urban planning and public campaigns, it is of significant importance to infer factors that substantially influence commuters in their transportation mode choice process. This necessitates a flexible and repeatable tool that can evaluate how a policy is perceived by individual commuters and convert their decisions into macro level understanding. This paper introduces one such effort that is specifically designed for studies of transportation mode choices in metropolitan areas. It provides results from a high-resolution data driven simulation based on high performance computing implementation of the agent-based model framework for home-to-work commute trips. The framework uses a graph-partition based technique that can leverage the interaction structure of agents within a geographic proximity and can boost the simulation execution time. Further, based on a flexible design, it can run ABM with different levels of computing resources-from multi core workstations to an HPC grid. The framework has been tested on the Titan Cray XK7 supercomputer of the Oak Ridge Leadership Computing Facility.

Park, Byung↗

DOE OSTI2019

Parsl: Pervasive Parallel Programming in Python

High-level programming languages such as Python are increasingly used to provide intuitive interfaces to libraries written in lower-level languages and for assembling applications from various components. This migration towards orchestration rather than implementation, coupled with the growing need for parallel computing (e.g., due to big data and the end of Moore's law), necessitates rethinking how parallelism is expressed in programs. Here, we present Parsl, a parallel scripting library that augments Python with simple, scalable, and flexible constructs for encoding parallelism. These constructs allow Parsl to construct a dynamic dependency graph of components that it can then execute efficiently on one or many processors. Parsl is designed for scalability, with an extensible set of executors tailored to different use cases, such as low-latency, high-throughput, or extreme-scale execution. We show, via experiments on the Blue Waters supercomputer, that Parsl executors can allow Python scripts to execute components with as little as 5 ms of overhead, scale to more than 250000 workers across more than 8000 nodes, and process upward of 1200 tasks per second. Other Parsl features simplify the construction and execution of composite programs by supporting elastic provisioning and scaling of infrastructure, fault-tolerant execution, and integrated wide-area data management. We show that these capabilities satisfy the needs of many-task, interactive, online, and machine learning applications in fields such as biology, cosmology, and materials science.

parallel programming↗

DOE OSTI2021

A Systems Approach to Estimating the Uncertainty Limits of X-Ray Radiographic Metrology

Micro- and nanomanufacturing capabilities have rapidly expanded over the past decade to include complex three-dimensional (3D) structure fabrication; however, the metrology required to accurately assess these processes via part inspection and characterization has struggled to keep pace. X-ray computed tomography (CT) is considered an ideal candidate for providing the critically needed metrology on the smallest scales, especially internal features, or inaccessible regions. X-ray CT supporting micro- and nanomanufacturing often push against the poorly understood resolution and variation limits inherent to the machines, which can distort or hide fine structures. In this study, we have developed and experimentally verify a comprehensive analytical uncertainty propagation signal variation flow graph (SVFG) model for X-ray radiography in this work to better understand resolution and image variability limits on the small scale. The SVFG approach captures, quantifies, and predicts variations occurring in the system that limit metrology capabilities, particularly in the micro/nanodomain. This work is the first step to achieving full uncertainty modeling of CT reconstructions and provides insight into improving X-ray attenuation imaging systems. The SVFG methodology framework is applied to generate a complete basis set of functions describing the major sources of variation in radiographs. Five models are identified, covering variation in energy, intensity, length, blur, and position. Radiographic system experiments are defined to measure the parameters required by the SVFGs. Best practices are identified for these measurements. The SVFG models are confirmed via direct measurement of variation to predict variation within 30% on average.

47 OTHER INSTRUMENTATION↗

DOE OSTI2018

A multiscale multi-permeability poroplasticity model linked by recursive homogenizations and deep learning

Many geological materials, such as shale, mudstone, carbonate rock, limestone and rock salt are multi-porosity porous media in which pores of different scales may co-exist in the host matrix. When fractures propagate in these multi-porosity materials, these pores may enlarge and coalesce and therefore change the magnitude and the principal directions of the effective permeability tensors. The pore-fluid inside the cracks and the pores of host matrix may interact and exchange fluid mass, but the difference in hydraulic properties of these pores often means that a single homogenized effective permeability tensor field is insufficient to characterize the evolving hydraulic properties of these materials at smaller time scale. Furthermore, the complexity of the hydro-mechanical coupling process and the induced mechanical and hydraulic anisotropy originated from the micro-fracture and plasticity at grain scale also makes it difficult to propose, implement and validate separated macroscopic constitutive laws for numerical simulations. Here this article presents a hybrid data-driven method designed to capture the multiscale hydro-mechanical coupling effect of porous media with pores of various different sizes. At each scale, data-driven models generated from supervised machine learning are hybridized with classical constitutive laws in a directed graph that represents the numerical models. By using sub-scale simulations to generate database to train material models, an offline homogenization procedure is used to replace the up-scaling procedure to generate cohesive laws for localized physical discontinuities at both grain and specimen scales. Through a proper homogenization procedure that preserves spatial length scales, the proposed method enables field-scale simulations to gather insights from meso-scale and grain-scale micro-structural attributes. This method is proven to be much more computationally efficient than the classical DEM–FEM or FEM2 approach while at the same time more robust and flexible than the classical surrogate modeling approach. Due to the usage of bridging-scale technique, the proposed model may provide multiple opportunities to incorporate different types of simulations and experimental data across different length scales for machine learning. Numerical issues will also be discussed.

42 ENGINEERING↗

DOE OSTI2013

Toward a Data Scalable Solution for Facilitating Discovery of Scientific Data Resources

Science is increasingly motivated by the need to process larger quantities of data. It is facing severe challenges in data collection, management, and processing, so much so that the computational demands of "data scaling" are competing with, and in many fields surpassing, the traditional objective of decreasing processing time. Example domains with large datasets include astronomy, biology, genomic, climate and weather, and material sciences. This paper presents a real-world use case in which we wish to answer queries provided by domain scientists in order to facilitate discovery of relevant science resources. The problem is that the metadata for these science resources is very large and is growing quickly, rapidly increasing the need for a data scaling solution. We propose the use of our SGEM stack -- a system designed for answering graph-based queries over large datasets on cluster architectures -- for answering complex queries over the metadata, and we report early results for our current capability.

Chappell, Alan R.↗

DOE OSTI2017

Addressing Global Data Dependencies in Heterogeneous Asynchronous Runtime Systems on GPUs

Large-scale parallel applications with complex global data dependencies beyond those of reductions pose significant scalability challenges in an asynchronous runtime system. Internodal challenges include identifying the all-to-all communication of data dependencies among the nodes. Intranodal challenges include gathering together these data dependencies into usable data objects while avoiding data duplication. This paper addresses these challenges within the context of a large-scale, industrial coal boiler simulation using the Uintah asynchronous many-task runtime system on GPU architectures. We show significant reduction in time spent analyzing data dependencies through refinements in our dependency search algorithm. Multiple task graphs are used to eliminate subsequent analysis when task graphs change in predictable and repeatable ways. Using a combined data store and task scheduler redesign reduces data dependency duplication ensuring that problems fit within host and GPU memory. Furthermore, these modifications did not require any changes to application code or sweeping changes to the Uintah runtime system. We report results running on the DOE Titan system on 119K CPU cores and 7.5K GPUs simultaneously. Our solutions can be generalized to other task dependency problems with global dependencies among thousands of nodes which must be processed efficiently at large scale.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2023

Q-BEEP: Quantum Bayesian Error Mitigation Employing Poisson Modeling over the Hamming Spectrum

Quantum computing technology has grown rapidly in recent years, with new technologies being explored, error rates being reduced, and quantum processor’s qubit capacity growing. However, near-term quantum algorithms are still unable to be induced without compounding consequential levels of noise, leading to non-trivial erroneous results. Quantum Error Correction (in-situ error mitigation) and Quantum Error Mitigation (post-induction error mitigation) are promising fields of research within the quantum algorithm scene, aiming to alleviate quantum errors, increasing the overall fidelity and hence the overall quality of circuit induction. Earlier this year, a pioneering work, namely HAMMER, published in ASPLOS-22 demonstrated the existence of a latent structure regarding post-circuit induction errors when mapping to the Hamming spectrum. However, they intuitively assumed that errors occur in local clusters, and that at higher average Hamming distances this structure falls away. In this work, we show that such a correlation structure is not only local but extends certain non-local clustering patterns which can be precisely described by a Poisson distribution model taking the input circuit, the device run time status (i.e., calibration statistics) and qubit topology into consideration. Using this quantum error characterizing model, we developed an iterative algorithm over the generated Bayesian network state-graph for post-induction error mitigation. Thanks to more precise modeling of the error distribution latent structure and the new iterative method, our Q-Beep approach provides state of the art performance and can boost circuit execution fidelity by up to 234.6% on Bernstein-Vazirani circuits and on average 71.0% on QAOA solution quality, using 16 practical IBMQ quantum processors. For other benchmarks such as those in QASMBench, the fidelity improvement is up to 17.8%. Q-Beep is a light-weight post-processing technique that can be performed offline and remotely, making it a useful tool for quantum vendors to integrate and provide more reliable circuit induction results.

Stein, Samuel A.↗

DOE OSTI2014

On the Suitability of MPI as a PGAS Runtime

Partitioned Global Address Space (PGAS) models are emerging as a popular alternative to MPI models for designing scalable applications. At the same time, MPI remains a ubiquitous communication subsystem due to its standardization, high performance, and availability on leading platforms. In this paper, we explore the suitability of using MPI as a scalable PGAS communication subsystem. We focus on the Remote Memory Access (RMA) communication in PGAS models which typically includes {\em get, put,} and {\em atomic memory operations}. We perform an in-depth exploration of design alternatives based on MPI. These alternatives include using a semantically-matching interface such as MPI-RMA, as well as not-so-intuitive interfaces such as MPI two-sided with a combination of multi-threading and dynamic process management. With an in-depth exploration of these alternatives and their shortcomings, we propose a novel design which is facilitated by the data-centric view in PGAS models. This design leverages a combination of highly tuned MPI two-sided semantics and an automatic, user-transparent split of MPI communicators to provide asynchronous progress. We implement the asynchronous progress ranks approach and other approaches within the Communication Runtime for Exascale which is a communication subsystem for Global Arrays. Our performance evaluation spans pure communication benchmarks, graph community detection and sparse matrix-vector multiplication kernels, and a computational chemistry application. The utility of our proposed PR-based approach is demonstrated by a 2.17x speed-up on 1008 processors over the other MPI-based designs.

Computational modeling↗

DOE OSTI2025

Optimizing Management of Persistent Data Structures in High-Performance Analytics

Large-scale data analytics workflows ingest massive input data into various data structures, including graphs and key-value datastores. These data structures undergo multiple transformations and computations and are typically reused in incremental and iterative analytics workflows. Persisting in-memory views of these data structures enables reusing them beyond the scope of a single program run while avoiding repetitive raw data ingestion overheads. Memory-mapped I/O enables persisting in-memory data structures without data serialization and deserialization overheads. However, memory-mapped I/O lacks the key feature of persisting consistent snapshots of these data structures for incremental ingestion and processing. The obstacles to efficient virtual memory snapshots using memory-mapped I/O include background writebacks outside the application’s control, and the significantly high storage footprint of such snapshots. To address these limitations, we present Privateer, a memory and storage management tool that enables storage-efficient virtual memory snapshotting while also optimizing snapshot I/O performance. Here, we integrated Privateer into Metall, a state-of-the-art persistent memory allocator for C++, and the Lightning Memory-Mapped Database (LMDB), a widely-used key-value datastore in data analytics and machine learning. Privateer optimized application performance by 1.22× when storing data structure snapshots to node-local storage, and up to 16.7× when storing snapshots to a parallel file system. Privateer also optimizes storage efficiency of incremental data structure snapshots by up to 11× using data deduplication and compression.

Computer science↗

DOE OSTI2021

Nickel(ii) complexes based on dithiolate–polyamine binary ligand systems: crystal structures, hirshfeld surface analysis, theoretical study, and catalytic activity study on photocatalytic hydrogen generation

To ascertain the influence of binary ligand systems [1,1-dicyanoethylene-2,2-dithiolate (i-mnt -2 ) and polyamine {tetraen = tris(2-aminoethyl)amine, tren = diethylene triamine and opda = o-phenylenediamine}] on the coordination modes of the Ni(II) metal center and resulting supramolecular architectures, a series of nickel(II) thiolate complexes [Ni(tetraen)(i-mnt)](DMSO) (1), [Ni 2 (tren) 2 (i-mnt) 2 ] (2), and [Ni 2 (i-mnt) 2 (opda) 2 ] n (3) have been synthesized in high yield in one step in water and structurally characterized by single crystal X-ray crystallography and spectroscopic techniques. X-ray diffraction studies disclose the diverse i-mnt -2 coordination to the Ni +2 center in the presence of active polyamine ligands, forming a slightly distorted octahedral geometry (NiN 4 S 2 ) in 1, square planar (NiS 4 ) and distorted octahedral geometries (NiN 6 ) in the bimetallic co-crystallized aggregate of cationic [Ni(tren) 2 ] +2 and anionic [Ni(i-mnt) 2 ] -2 in 2, and a one dimensional (1D) polymeric chain along the [100] axis in 3, having consecutive square planar (NiS 4 ) and octahedral (NiN 6 ) coordination kernels. The N–H···O, N–H···S, N–H···N, N–H···S, N–H···N, and N–H···O type hydrogen bonds stabilize the supramolecular assemblies in 1, 2, and 3 respectively imparting interesting graph-set-motifs. The molecular Hirshfeld surface analyses (HS) and 2D fingerprint plots were utilized for decoding all types of non-covalent contacts in the crystal networks. Atomic HS analysis of the Ni +2 centers reveals significant Ni–N metal–ligand interactions compared to Ni–S interactions. We have also studied the unorthodox interactions observed in the solid state structures of 1–3 by QTAIM and NBO analyses. Moreover, all the complexes proved to be highly active water reduction co-catalysts (WRC) in a photo-catalytic hydrogen evolution process involving iridium photosensitizers, wherein 2 and 3 having a square planar arrangement around the nickel center(s) – were found to be the most active ones, achieving 1000 and 1119 turnover numbers (TON), respectively.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗