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DOE OSTI2024

VerifyIO: Ensuring Correctness of Consistency Semantics in Parallel I/O

Abstract—High-performance computing (HPC) applications generate and consume substantial amounts of data, typically managed by parallel file systems. These applications access file systems either through the POSIX interface or by using highlevel I/O libraries. While the POSIX consistency model remains dominant in HPC, emerging file systems and popular I/O libraries increasingly adopt alternative consistency models that relax semantics in various ways, creating significant challenges for correctness and portability. This paper addresses these challenges by proposing a trace-driven I/O consistency verification workflow, implemented in our open-source tool, VerifyIO, which collects execution traces, detects data conflicts, and verifies proper synchronization against specified consistency models. Our extensive evaluation of 91 test case executions across three widely used I/O libraries with four I/O consistency models reveals critical consistency issues at both application and implementation levels.

Consistency Semantics↗
DOE OSTI2023

2022 American Conference on Neutron Scattering (ACNS 2022)

The 11th American Conference on Neutron Scattering (ACNS 2022) will be held on June 5-9, 2022, in Boulder, CO. The Conference will provide essential information on the breadth and depth of current neutron-related research worldwide. Hosted by the Neutron Scattering Society of America, this year’s Conference will feature a combination of invited and contributed talks, poster sessions, and tutorials. Topics of the conference are: Advances in Neutron Facilities, Instrumentation and Software: Developments in sources, instrumentation, sample environments and control software. Hard Condensed Matter: Magnetism, correlated metals, quantum/topological materials, superconductors, ferroelectrics, multiferroics, glasses, and disorder phenomena. Submissions outlining examples of neutron scattering in industrial and engineering applications involving hard condensed matter systems are also encouraged. Soft Matter: Neutron studies of soft materials and related fields including in situ and in operando studies. Polymers, surfactants, emulsions, gels, nanoparticles, colloidal suspensions and more. Submissions of computational studies or applications of machine learning beneficial to neutron scattering experiments, as well as examples of neutron scattering in industrial and engineering applications are strongly encouraged. Biology, Biophysics and Biotechnology: Neutron studies of biological and biologically relevant systems. Proteins, bio membranes, biological assemblies, natural materials, nucleic acids, drug-delivery platforms and biomedical systems. Submissions of computational studies or applications of machine learning beneficial to biological neutron scattering experiments, as well as examples of neutron scattering in applied research involving biological systems, are strongly encouraged. Materials Chemistry and Energy: Neutron-based studies of functional materials and materials for energy applications. Examples include porous materials such as metal organic frameworks (MOFs), zeolites; phosphors; novel pigments; electrolytes; catalysts; ionic conductors/cathode materials; photovoltaic materials (hybrid perovskites); thermoelectrics; magnetocalorics/electrocalorics. Structural Materials and Engineering: Neutron scattering studies of materials and engineering processes including structural materials, concrete and metals, as well as engineering processes including combustion, corrosion, additive manufacturing, and others. Neutron Physics: Fundamental physical studies of the neutron and related areas. Emerging Applications in Neutron Scattering: Machine Learning and Data Science: Advances in computing power have contributed to rapidly evolving machine learning and data science fields that can be leveraged to the benefit of the neutron scattering community. The purpose of this session is to highlight recent advances in machine learning and data science and to serve as the foundation of a parallel data and computation track highlighting computation advances and applications in neutron scattering throughout the conference.

36 MATERIALS SCIENCE↗
DOE OSTI2015

Enabling Co-Design of Multi-Layer Exascale Storage Architectures

Growing demands for computing power in applications such as energy production, climate analysis, computational chemistry, and bioinformatics have propelled computing systems toward the exascale: systems with 10 18 floating-point operations per second. These systems, to be designed and constructed over the next decade, will create unprecedented challenges in component counts, power consumption, resource limitations, and system complexity. Data storage and access are an increasingly important and complex component in extreme-scale computing systems, and significant design work is needed to develop successful storage hardware and software architectures at exascale. Co-design of these systems will be necessary to find the best possible design points for exascale systems. The goal of this work has been to enable the exploration and co-design of exascale storage systems by providing a detailed, accurate, and highly parallel simulation of exascale storage and the surrounding environment. Specifically, this simulation has (1) portrayed realistic application checkpointing and analysis workloads, (2) captured the complexity, scale, and multilayer nature of exascale storage hardware and software, and (3) executed in a timeframe that enables “what if'” exploration of design concepts. We developed models of the major hardware and software components in an exascale storage system, as well as the application I/O workloads that drive them. We used our simulation system to investigate critical questions in reliability and concurrency at exascale, helping guide the design of future exascale hardware and software architectures. Additionally, we provided this system to interested vendors and researchers so that others can explore the design space. We validated the capabilities of our simulation environment by configuring the simulation to represent the Argonne Leadership Computing Facility Blue Gene/Q system and comparing simulation results for application I/O patterns to the results of executions of these I/O kernels on the actual system.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2017

A characterization of workflow management systems for extreme-scale applications

We present that the automation of the execution of computational tasks is at the heart of improving scientific productivity. Over the last years, scientific workflows have been established as an important abstraction that captures data processing and computation of large and complex scientific applications. By allowing scientists to model and express entire data processing steps and their dependencies, workflow management systems relieve scientists from the details of an application and manage its execution on a computational infrastructure. As the resource requirements of today’s computational and data science applications that process vast amounts of data keep increasing, there is a compelling case for a new generation of advances in high-performance computing, commonly termed as extreme-scale computing, which will bring forth multiple challenges for the design of workflow applications and management systems. This paper presents a novel characterization of workflow management systems using features commonly associated with extreme-scale computing applications. We classify 15 popular workflow management systems in terms of workflow execution models, heterogeneous computing environments, and data access methods. Finally, the paper also surveys workflow applications and identifies gaps for future research on the road to extreme-scale workflows and management systems.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

Benchmarking numerical methods for impact and cratering applications

Large scale computational models are important for studying impact cratering events that are prevalent both on Earth and, more broadly, in this solar system. To address these problems, models must reliably account for both large length scales (e.g., kilometers) and relatively long time scales (hundreds of seconds). This work benchmarks two such approaches, a more traditional hydrodynamics approach and a finite-discrete element method (FDEM), for impact cratering applications. Both 2D and 3D results are discussed for two different impact velocities, 5 km/s and 20 km/s, striking normal to the target and, for 3D simulations, 45° from vertical. In addition, comparisons to previously published data are presented. Finally, differences in how these methods model damage are discussed. Ultimately, both approaches show successful modeling of several different impact scenarios.

58 GEOSCIENCES↗
DOE OSTI2024

The ECP SICM project: Managing complex memory hierarchies for exascale applications

The Exascale Computing Project (ECP)’s Simplified Interface to Complex Memories (SICM) effort focuses on developing universal interfaces for discovering, managing, and sharing data across complex memory hierarchies. These facilitate the exploitation of emerging memory technologies and support precise control over their various trade-offs such as high-bandwidth versus low-latency, persistent versus ephemeral, high-capacity versus low-capacity, and near-CPU versus near-GPU. SICM comprises three interrelated components: a low-level interface, a high-level interface, and a persistent-heap interface. The low-level SICM interface is intended for system and run-time developers as well as expert application developers who prefer full control of the memory objects used within their application. The high-level SICM interface builds upon the low-level interface, employing application-level profiling and analysis to optimize data management for complex memory hierarchies. The persistent-heap interface provides applications with a persistent memory allocator that can allocate custom C++ data structures in both block-storage and byte-addressable persistent memories.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2018

Numerical Simulation of Recirculating Flow and Physical Model of Slag–Metal Behavior in an RH Reactor: Application to Desulfurization

Computational fluid dynamics (CFD) techniques and a 1:7.5 physical model of an RH degasser have been used to evaluate the flow of gas and metal inside an RH reactor for vacuum degassing of liquid steel. The effect of gas injection on the gas spatial distribution, steel circulation rate and flow field inside the ladle, snorkels and vacuum chamber have been assessed. N-pentane oil was employed to evaluate the average residence time as well as the slag droplet size distribution. The predicted radial gas distribution and liquid circulation rate have been validated against experimental data from a physical model. The results with incorporation of the virtual mass force coefficient of 0.25 and the turbulence dispersion force showed better predictions of gas distribution in the up-snorkel as well as circulation rate. Full-scale simulations were performed, and the predicted circulation rate was significantly affected by the argon bubble expansion. Data from these simulations were used to analyze the degree of desulfurization performed by the addition of desulfurizing agents inside the vacuum chamber. A model of the kinetics of desulfurization based on the results from the physical model and CFD simulation and on slag dispersion inside liquid steel yields degrees of desulfurization similar to the industrial trials reported in the literature.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Bosonic field digitization for quantum computers

Quantum simulation of quantum field theory is a flagship application of quantum computers that promises to deliver capabilities beyond classical computing. The realization of quantum advantage will require methods that can accurately predict error scaling as a function of the resolution and parameters of the model and that can be implemented efficiently on quantum hardware. In this paper, we address the representation of lattice bosonic fields in a discretized field amplitude basis, develop methods to predict error scaling, and present efficient qubit implementation strategies. A low-energy subspace of the bosonic Hilbert space, defined by a boson occupation number cutoff, can be represented with exponentially good accuracy by a low-energy subspace of a finite-size Hilbert space. The finite representation construction and the associated errors are directly related to the accuracy of the Nyquist-Shannon sampling and the finite Fourier transforms of the boson number states in the field and the conjugate-field bases. We analyze the relation between the boson mass, the discretization parameters used for wave function sampling, and the finite representation size. Numerical simulations of small size Φ 4 problems demonstrate that the boson mass optimizing the sampling of the ground state wave function is a good approximation to the optimal boson mass yielding the minimum low-energy subspace size. However, we find that accurate sampling of general wave functions does not necessarily result in accurate representation. Finally, we develop methods for validating and adjusting the discretization parameters to achieve more accurate simulations.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2024

Q4Q: Quantum Computation for Quantum Prediction of Materials and Molecular Properties

We aim at exploring the potential of quantum computation to solve practical problems that are currently targeted by “traditional” high performance computing (HPC). Along the way, we will develop theoretical frameworks and algorithmic strategies. We propose computational research activities that will advance the application of quantum computers to selected materials/molecular properties: (1) Band structure of solids; (2) Molecular electronic/vibronic properties; (3) Free energies and phase transitions.

36 MATERIALS SCIENCE↗
DOE OSTI2016

Design, Creep Performance and Deformation Behavior of an Eta-Phase Strengthened Nickel-Base Alloy for A-USC Power Plant Applications

By utilizing computational thermodynamics in a Design of Experiments approach, it was possible to design and manufacture nickel-base superalloys that are strengthened by the eta phase (Ni3Ti), and that contain no gamma prime (Ni3Al,Ti). The compositions are similar to Nimonic 263, and should be cost-effective, and have more stable microstructures. By varying the aging temperature, the precipitates took on either cellular or Widmanstätten morphologies. The Widmanstätten-based microstructure is thermally stable at high temperatures, and was found to have superior ductility, so development efforts were focused on that microstructure. High temperature tensile test and creep test results indicated that the performance of the new alloys was competitive with Nimonic 263. SEM and TEM microscopy were utilized to determine the deformation mechanisms during creep.

36 MATERIALS SCIENCE↗
DOE OSTI2016

Final Technical Report: Sparse Grid Scenario Generation and Interior Algorithms for Stochastic Optimization in a Parallel Computing Environment

The support from this grant resulted in seven published papers and a technical report. Two papers are published in SIAM J. on Optimization [87, 88]; two papers are published in IEEE Transactions on Power Systems [77, 78]; one paper is published in Smart Grid [79]; one paper is published in Computational Optimization and Applications [44] and one in INFORMS J. on Computing [67]). The works in [44, 67, 87, 88] were funded primarily by this DOE grant. The applied papers in [77, 78, 79] were also supported through a subcontract from the Argonne National Lab. We start by presenting our main research results on the scenario generation problem in Sections 1–2. We present our algorithmic results on interior point methods for convex optimization problems in Section 3. We describe a new ‘central’ cutting surface algorithm developed for solving large scale convex programming problems (as is the case with our proposed research) with semi-infinite number of constraints in Section 4. In Sections 5–6 we present our work on two application problems of interest to DOE.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

DenKv: Addressing Design Trade-offs of Key-value Stores for Scientific Applications

High-performance computing (HPC) facilities have employed flash-based storage tier near to compute nodes to absorb high I/O demand by HPC applications during periodic system-level checkpoints. To accelerate these checkpoints, proxy-based distributed key-value stores (PD-KVS) gained particular attention for their flexibility to support multiple backends and different network configurations. PD-KVS rely internally on monolithic KVS, such as LevelDB or RocksDB, to exploit the KV interface and query support. However, PD-KVS are unaware of the high redundancy factor in checkpoint data, which can be up to GBs to TBs, and therefore, tend to generate high write and space amplification on these storage layers. In this paper, we propose DenKv which is deduplication-extended node-local LSM-tree-based KVS. DenKv employs asynchronous partially inline dedup (APID) and aims to maintain the performance characteristics of LSM-tree-based KVS while reducing the write and space amplification problems. We implemented DenKv atop BlobDB and showed that our proposed solution maintains performance while reducing write amplification up to 2× and space amplification by 4× on average.

Khan, Awais↗
DOE OSTI2022

Code Verification and Solution Verification framework in pin-resolved neutron transport code MPACT

Program verification in scientific computing encompasses the application of formal and mathematical techniques to a scientific computing code for its credibility, accuracy, and validity. Code Verification identifies bugs and performance issues in the software development stage. Solution Verification assesses the applicability of the code and the accuracy of the solution to problems of interest. Both activities utilize application cases and quantify the error against prescribed acceptance criteria. However, simply executing more application cases does not guarantee stronger or more comprehensive credibility. Here, we establish a verification framework that involves Code Verification and Solution Verification, both of which work together such that the overarching goal of “converge to the correct answer for the intended application” can be reasonably inferred. The application of such a verification framework is demonstrated using the pin-resolved neutron transport code MPACT, where standard unit tests and regression tests are covered, and where the Method of Exact Solutions and the Method of Manufactured Solutions are successfully used. Additionally, the applicability of Method of Manufactured Solutions is extended to the OECD/NEA C5G7 benchmark problems of practical material and geometric configurations. Solution Verification activities are demonstrated on a practical hierarchy of application models of increasing complexity ranging from 2D pin cell problems to 3D assembly problems. The convergence behavior and rate of convergence with respect to each individual variable are studied and provided. This framework can be adapted broadly to other fields involving scientific computing codes.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

Proton Tunable Analog Transistor for Low Power Computing

This project was broadly motivated by the need for new hardware that can process information such as images and sounds right at the point of where the information is sensed (e.g. edge computing). The project was further motivated by recent discoveries by group demonstrating that while certain organic polymer blends can be used to fabricate elements of such hardware, the need to mix ionic and electronic conducting phases imposed limits on performance, dimensional scalability and the degree of fundamental understanding of how such devices operated. As an alternative to blended polymers containing distinct ionic and electronic conducting phases, in this LDRD project we have discovered that a family of mixed valence coordination compounds called Prussian blue analogue (PBAs), with an open framework structure and ability to conduct both ionic and electronic charge, can be used for inkjet-printed flexible artificial synapses that reversibly switch conductance by more than four orders of magnitude based on electrochemically tunable oxidation state. Retention of programmed states is improved by nearly two orders of magnitude compared to the extensively studied organic polymers, thus enabling in-memory compute and avoiding energy costly off-chip access during training. We demonstrate dopamine detection using PBA synapses and biocompatibility with living neurons, evoking prospective application for brain - computer interfacing. By application of electron transfer theory to in-situ spectroscopic probing of intervalence charge transfer, we elucidate a switching mechanism whereby the degree of mixed valency between N-coordinated Ru sites controls the carrier concentration and mobility, as supported by density functional theory (DFT) .

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

HIBP Applications to Advance Understanding of Plasma Transport Physics (2011-2017) (and subsequently titled) Development of Beam Measurements to Advance Understanding of Transients and Improve Validation (2017-2020) (Final Technical Report)

This is the Final Technical Report for the DoE Measurement Innovation (previously Diagnostic Development) grant DE-SC0006077 titled HIBP Applications to Advance Understanding of Plasma Transport Physics (2011-2017), and subsequently titled Development of Beam Measurements to Advance Understanding of Transients and Improve Validation (2017-2020). The grant was funded by the Office of Fusion Energy Sciences (FES) for the period 1 May 2011–17 July 2020. Work performed through the grant has resulted in diagnostic innovations and new measurement capabilities that will improve understanding of transport, magnetic equilibrium, and electric fields in magnetically confined plasmas. We have developed novel hardware and advanced techniques to expand beam-based diagnostic capabilities, and extend measurements to new operating regimes. Some have been realized using a Heavy Ion Beam Probe (HIBP) having traditional features, while other applications have joined our innovations with subsets of advantageous HIBP features. This work has established smaller, more economical detection systems and, in doing so, may enable substantial extension of scenarios in which beam-based diagnostics are deployed. Key Measurement Innovations include: Computer Models and Simulations of HIBP Applications-Computer modeling and simulating of HIBP applications is central to predicting interaction of beam particles with plasmas, designing diagnostic systems, and anticipating measurement characteristics. We have extended the capability and improved measurement fidelity of the HIBP diagnostic on the Madison Symmetric Torus (MST) reversed field pinch (RFP); simulated feasibility of HIBP operation in the Helically Symmetric eXperiment (HSX) optimized stellarator; and investigated the plausibility of HIBP measurements in the ASDEX Upgrade tokamak. We have also developed a new technique that uses ion optics to model a finite phase-space beam. It yields more realistic (than traditional method) estimates of sample volume characteristics, which influence measurement resolution and sensitivity. Extension of Diagnostic Capabilities and Measurements on the MST RFP-Capabilities have been extended using the first and only HIBP installation on an RFP. Challenges associated with operation of the diagnostic on MST include the three-dimensional nature of particle trajectories, temporal topology and amplitude changes in the plasma equilibrium, and strong particle and radiative emission from the plasma. We have addressed these challenges through development of detailed and higher precision diagnostic simulations, calibrated subtraction of noise to resolve secondary ion signals, and implementation of hardware that enables higher fidelity measurement of plasma fluctuations. Development of New Hardware and Measurement Techniques - We have advanced beam-based measurement capabilities via development of new detectors and techniques to determine the poloidal magnetic flux ψ in the plasma, and enable placement of detectors close to the plasma and thus allow a smaller and less expensive diagnostic. We have demonstrated measurement of ψ, an ability that was made possible by development of highly effective noise reduction techniques. We also modeled the effect of non-ideal and instrumentation effects by developing a virtual (simulated) diagnostic. Application of beam-based diagnostics on various devices and multiple magnetic configurations (e.g. stellarator, tokamak, and reversed field pinch) enables investigation of critical physics issues and measurements resulting in the broad parameter space data needed to test and validate theory & modeling.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2016

Cone Beam Computed Tomography: The Challenges and Strategies in Its Application for Dose Accumulation

Online image guidance using cone beam computed tomography (CBCT) has greatly improved the geometric precision of radiotherapy. Changes in anatomy are common during a course of fractionated treatment, resulting in dose deviation from the planned distribution. There is increased interest in performing dose accumulation to compute the actual delivered dose and to adapt the treatment when necessary. This can be achieved by delineating the volume of interest and by generating “dose of the day” through dose computation on the CBCT. However, the image quality and the accuracy of the CT number of CBCT are deemed to be inferior to fan beam CT, which increases the uncertainty associated in this process. A review of literature was conducted to assess the reliability of and to examine strategies for overcoming the challenges in using CBCT for volume delineation and dose computation. The review demonstrates that the uncertainty varies across body sites, and different strategies have been recommended to generate comparable results to images from CT simulators. This facilitates a better understanding of the potential and the limitation of using CBCT for dose accumulation.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2016

Performance analysis and acceleration of explicit integration for large kinetic networks using batched GPU computations

Abstract—We demonstrate the systematic implementation of recently-developed fast explicit kinetic integration algorithms that solve efficiently N coupled ordinary differential equations (subject to initial conditions) on modern GPUs. We take representative test cases (Type Ia supernova explosions) and demonstrate two or more orders of magnitude increase in efficiency for solving such systems (of realistic thermonuclear networks coupled to fluid dynamics). This implies that important coupled, multiphysics problems in various scientific and technical disciplines that were intractable, or could be simulated only with highly schematic kinetic networks, are now computationally feasible. As examples of such applications we present the computational techniques developed for our ongoing deployment of these new methods on modern GPU accelerators. We show that similarly to many other scientific applications, ranging from national security to medical advances, the computation can be split into many independent computational tasks, each of relatively small-size. As the size of each individual task does not provide sufficient parallelism for the underlying hardware, especially for accelerators, these tasks must be computed concurrently as a single routine, that we call batched routine, in order to saturate the hardware with enough work.

Haidar Ahmad, Azzam↗