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At least 649 records · Page 36

Analysis of metabolomics datasets with high-performance computing and metabolite atlases

Even with the widespread use of liquid chromatography mass spectrometry (LC/MS) based metabolomics, there are still a number of challenges facing this promising technique. Many, diverse experimental workflows exist; yet there is a lack of infrastructure and systems for tracking and sharing of information. Here, we describe the Metabolite Atlas framework and interface that provides highly-efficient, web-based access to raw mass spectrometry data in concert with assertions about chemicals detected to help address some of these challenges. This integration, by design, enables experimentalists to explore their raw data, specify and refine features annotations such that they can be leveraged for future experiments. Fast queries of the data through the web using SciDB, a parallelized database for high performance computing, make this process operate quickly. Furthermore, by using scripting containers, such as IPython or Jupyter, to analyze the data, scientists can utilize a wide variety of freely available graphing, statistics, and information management resources. In addition, the interfaces facilitate integration with systems biology tools to ultimately link metabolomics data with biological models.

59 BASIC BIOLOGICAL SCIENCES↗

The GeantV project: Preparing the future of simulation

Detector simulation is consuming at least half of the HEP computing cycles, and even so, experiments have to take hard decisions on what to simulate, as their needs greatly surpass the availability of computing resources. New experiments still in the design phase such as FCC, CLIC and ILC as well as upgraded versions of the existing LHC detectors will push further the simulation requirements. Since the increase in computing resources is not likely to keep pace with our needs, it is therefore necessary to explore innovative ways of speeding up simulation in order to sustain the progress of High Energy Physics. The GeantV project aims at developing a high performance detector simulation system integrating fast and full simulation that can be ported on different computing architectures, including CPU accelerators. After more than two years of R&D the project has produced a prototype capable of transporting particles in complex geometries exploiting micro-parallelism, SIMD and multithreading. Portability is obtained via C++ template techniques that allow the development of machine- independent computational kernels. Furthermore, a set of tables derived from Geant4 for cross sections and final states provides a realistic shower development and, having been ported into a Geant4 physics list, can be used as a basis for a direct performance comparison.

97 MATHEMATICS AND COMPUTING↗

Quantum Optimal Control Using High Performance Computing

This feasibility study developed numerical methods for the optimal control problem for realizing logical gates in closed quantum systems, where the evolution of the state vector is governed by the time dependent Schrodinger equation. The number of parameters in the control functions is made independent of the number of time steps by expanding them in terms of B-spline basis functions, with and without carrier waves. We use an interior point gradient-based technique from the IPOPT package to minimize the gate infidelity subject to amplitude constraints on the control functions. The symplectic Stromer-Verlet scheme is used to integrate a real-valued formulation of Schrodinger's equation in time and the gradient of the gate infidelity is obtained by solving the corresponding adjoint equation. This allows all components of the gradient to be calculated at the cost of solving three Schrodinger systems, independently of the number of parameters in the control functions. The correctness of the method is verified and applied to Hamiltonians that model the dynamics of coupled super-conducting qubits.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Social energy: mining energy from the society

The inherent nature of energy, i.e., physicality, sociality and informatization, implies the inevitable and intensive interaction between energy systems and social systems. From this perspective, we define 'social energy' as a complex sociotechnical system of energy systems, social systems and the derived artificial virtual systems which characterize the intense intersystem and intra-system interactions. The recent advancement in intelligent technology, including artificial intelligence and machine learning technologies, sensing and communication in Internet of Things technologies, and massive high performance computing and extreme-scale data analytics technologies, enables the possibility of substantial advancement in socio-technical system optimization, scheduling, control and management. In this paper, we provide a discussion on the nature of energy, and then propose the concept and intention of social energy systems for electrical power. A general methodology of establishing and investigating social energy is proposed, which is based on the ACP approach, i.e., 'artificial systems' (A), 'computational experiments' (C) and 'parallel execution' (P), and parallel system methodology. A case study on the University of Denver (DU) campus grid is provided and studied to demonstrate the social energy concept. In the concluding remarks, we discuss the technical pathway, in both social and nature sciences, to social energy, and our vision on its future.

24 POWER TRANSMISSION AND DISTRIBUTION↗

Understanding Soot Development and Thermal Stratification in Combustion Engines through Hyperspectral Non-linear Optical Diagnostics Development

Progress towards next-generation internal combustion engine technologies is dramatically hindered by the complexity of both simulating and measuring key processes, such as thermal stratification and soot formation, in an operating prototype. In general, spectroscopic methods for in-operando probing become limitingly complex at the high pressures and temperature encountered in such systems, and numerical methods for simulating device performance become computationally expensive due to the turbulent flow field, detailed chemistry, and range of important length-scales involved. This report presents parallel experimental and theoretical advances to conquer these limitations. We report the development of high pressure and high temperature ultrafast coherent anti-Stokes Raman spectroscopy measurements, up to a pressure and temperature regime relevant to engine conditions. This report also presents theoretical results using a stochastic one-dimensional turbulence (ODT) model providing insight into the local thermochemical state and its consequences by resolving the full range of reaction-diffusion scales in a stochastic model.

36 MATERIALS SCIENCE↗

Integrated Direct Air Capture and H₂-Free CO₂ Valorization

This project advances fundamental understanding of a novel integrated direct air capture (DAC) and CO₂ conversion process that valorizes atmospheric CO₂ without external H₂. The research encompasses four critical components: (1) design of task-specific ionic liquids for efficient CO₂ capture under ambient conditions, (2) development of H₂-free tandem catalytic systems using ethane as a reductant, (3) advanced operando characterization to elucidate capture and conversion mechanisms, and (4) data science-driven predictive computation to accelerate material discovery. Over the project period, we developed five high-performance DAC sorbent systems—including CaO/superbase ionic liquid composites, Ni-MOF/Ionic Liquid (IL) hybrids, fluorinated covalent organic frameworks with ion-pair functional groups, defect-engineered UiO-66, and a validated kinetic model for humid-condition operation, achieving CO₂ capacities up to 1.86 mmol/g at 400 ppm with excellent cycling stability. For H₂-free conversion, we constructed atomically synergistic Zn–O–Cr binuclear catalytic sites that achieve 100% ethylene selectivity, ~9.6% ethane conversion, and 99% CO₂ utilization in equimolar co-conversion of ethane and CO₂. We further demonstrated downstream valorization pathways converting CO and C₂H₄ into polyketones and C₃ chemicals. These advances strengthen the scientific foundation for producing value-added materials from ambient CO₂.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

The Kokkos Ecosystem [Brief]

In 2016/2017, the field of High-Performance Computing (HPC) entered a new era driven by fundamental physics challenges to produce ever more energy and cost-efficient processors. Since the convergence on the Message-Passing Interface (MPI) standard in the mid-1990s, application developers enjoyed a seemingly static view of the underlying machine — that of a distributed collection of homogeneous nodes executing in collaboration. However, after almost two decades of dominance, the sole use of MPI to derive parallelism acted as a limiter to improved future performance. While MPI is widely expected to continue to function as the basic mechanism for communication between compute nodes for the immediate future, additional parallelism is required on the computing node itself if high performance and efficiency goals are to be realized. When reviewing the architectures of the top HPC systems today, the change in paradigm is clear: the compute nodes of the leading machines in the world are either powered by many-core chips with a few dozen cores each, or use heterogeneous designs, where traditional CPUs marshal work to massively parallel compute accelerators which has as many as 200,000 processing threads in flight simultaneously. Complicating matters further for application developers, each processor vendor has its own preferred way of writing code for their architecture.The Kokkos EcoSystem was released by Sandia in 2017 to address this new era in HPC system design by providing a vendor independent performance portable programming system for scientific, engineering, and mathematical software applications written in the C++ programming language. Using Kokkos, application developers can be more productive because they will not have to create and maintain separate versions of their software for each architecture, nor will they have to be experts in each architecture's peculiar requirements. Instead, they will have a single method of programming for the diverse set of modern HPC architectures. While Kokkos started in 2011 as a programming model only, it soon became clear that complex applications needed more. It is also critical to have a portable mathematical functions and developers need tools to debug their applications, gain insight into the performance characteristics of their codes and tune algorithm performance parameters through automated processes. The Kokkos EcoSystem addresses those needs through its three main components: the Kokkos Core programming model, the Kokkos Kernels math library, and the Kokkos Tools project.

97 MATHEMATICS AND COMPUTING↗

A Typology of Quantum-Classical Faults

This paper introduces an extended taxonomy of faults specific to hybrid quantum-classical systems, addressing the unique challenges that arise from integrating quantum accelerators into high-performance computing (HPC) infrastructures. Building on the foundational fault classification by Avizienis et al., we incorporate fault types unique to quantum computing-such as qubit decoherence, spontaneous gate errors, and photon loss-alongside traditional and human-induced faults including development errors, operational mistakes, and malicious attacks. Our taxonomy classifies faults by their origin (natural vs. human-made), intent (accidental, deliberate non-malicious, or malicious), system boundaries (internal vs. external), and persistence (transient to permanent). We also explore how different architectural integration patterns-ranging from tight coupling to loose on-premise and cloud-based configurations-shape the manifestation and propagation of faults. These scenarios are analyzed in terms of timing mismatches, interface inconsistencies, and security threats such as data tampering and denial-of-service attacks. Through this fault-centric lens, we aim to support the co-design of dependable quantum-classical systems and highlight the critical role that integration strategies play in ensuring reproducibility, resilience, and security across hybrid computing platforms.

Giusto, Edorado [University of Naples Federico II,↗

Residential Natural Gas Demand Response Potential during Extreme Cold Events in Electricity-Gas Coupled Energy Systems

In regions where natural gas is used for both power generation and heating buildings, extreme cold weather events can place the electrical system under enormous stress and challenge the ability to meet residential heating and electric demands. Residential demand response has long been used in the power sector to curtail summer electric load, but these types of programs in general have not seen adoption in the natural gas sector during winter months. Natural gas demand response (NG-DR) has garnered interest given recent extreme cold weather events in the United States; however, the magnitude of savings and potential impacts—to occupants and energy markets—are not well understood. We present a case-study analysis of the technical potential for residential natural gas demand response in the northeast United States that utilizes diverse whole-building energy simulations and high-performance computing. Our results show that NG-DR applied to residential heating systems during extreme cold-weather conditions could reduce natural gas demand by 1–29% based on conservative and aggressive strategies, respectively. This indicates a potential to improve the resilience of gas and electric systems during stressful events, which we examine by estimating the impact on energy costs and electricity generation from natural gas. We also explore relationships between hourly indoor temperatures, demand response, and building envelope efficiency.

03 NATURAL GAS↗

Sensitivity Analysis of an Electrospray Dehumidification System

Electrically enhanced condensation achieved by an electrospray system can enhance dehumidification in HVAC applications if successfully scaled up. The first step towards scale-up is identifying critical design and operating parameters that significantly impact dehumidification for the electrospray system. Sensitivity analysis is one approach for identifying critical parameters. This paper presents a methodology that can efficiently perform quantitative sensitivity analysis on a computationally expensive high fidelity simulation model, which is a computational fluid dynamics (CFD) model of the electrospray system. The methodology employs surrogate modeling and Sobol sensitivity analysis. We estimate the main and total effect Sobol sensitivity indices of four operating parameters of the electrospray system. The results reveal that the most important parameter is the size of the sprayed droplets, followed by the volumetric flow rate of the bulk air and injected water in the system. The water injection velocity of the spray was found to have little to no impact on dehumidification.

Young, David↗

Computational design of high entropy alloy coating for hydrogen turbine applications

This project aims to develop novel high entropy alloy (HEA)-based coatings to protect critical components in hydrogen-fueled turbine power system. The HEA-coatings will demonstrate superior performance in hydrogen combustion environment to commercial NiCoCrAlY coating in current natural gas turbine system. The HEA coating facilitates the formation of a protective scale of alpha-alumina to slow down the inward diffusion of oxidizing species and the outward diffusion of metal elements, and possesses ultrahigh corrosion and spallation resistance to prolong the service lifetime of critical components in hydrogen turbine power system. Aimed to accelerate the discovery of novel HEA coating compositions, high throughput computational modeling including CALPHAD and density functional theory and machine learning are performed to predict phase stability, oxygen permeability, oxidation rate constant, coefficient of thermal expansion, and mechanical properties. Based on the modeling and machine learning prediction, experimental validation is performed. Preliminary results will be presented and approaches to minimize oxidation will be discussed.

alloy design↗

2021 Supercomputer Institute Outbrief [Slides]

An ideal early career candidate for the HPC division is one who has a bachelor’s degree in a related field and experience with concepts of high performance computing. Most programs do not provide a good background on the systems side of HPC in their undergraduate curricula. We are competing for the same candidates that large tech companies are interested in and recruiting into a field that isn’t on the radar of many undergrads.

97 MATHEMATICS AND COMPUTING↗

Can the United States Maintain Its Leadership in High-Performance Computing? - A report from the ASCAC Subcommittee on American Competitiveness and Innovation to the ASCR Office

The United States (U.S.) is no longer the unambiguous leader in the vitally important field of high performance computing (HPC). Japan, the European Union (EU), and China have fielded systems that are on par with our fastest supercomputers. The supply chain for everything from semiconductors to scientific software is globally distributed. Yet our economic future and security depend critically on our ability to innovate faster than our competitors, and the speed of innovation depends increasingly on large-scale computational science and engineering and thus HPC. How should the United States respond to this challenge? This report seeks to initiate a new and potentially transformative national discussion on this vital question. The Department of Energy’s (DOE) Advanced Scientific Computing Research (ASCR) program is well-positioned to make informed, targeted decisions about where the United States should cooperate and where it should compete in the global market for scientific exploration and discovery. By setting its sights on problems critical to our nation and the world, by establishing productive new collaborations, and by making strategic investments, ASCR can restore and maintain U.S. scientific leadership in the critical areas described in this report while strengthening our research infrastructure and training a large, diverse cohort of scientists. In doing so, ASCR and its scientists will pave the way for a secure and prosperous future for America. For more than 30 years, the ASCR program has provided the HPC and networking capabilities and expertise needed to support DOE’s mission to advance the national, economic, and energy security of the United States. The program now faces the challenge of developing and deploying the next generation of HPC systems and technologies, as well as supporting the application of HPC and artificial intelligence (AI) technologies to a wide range of scientific and engineering research problems. Through its research and development efforts, the ASCR program must also advance the state of the art in HPC and accelerate the pace of scientific discovery and technological innovation. Fulfilling this promise will require significantly increased investments, as well as innovative policies and programs. This subcommittee is aware that we are making recommendations and calls for action at a time when federal resources are limited. We understand that a wide range of competing priorities must be balanced by the nation’s leaders and that there is a need to leverage resources in new ways and seek efficiencies in facilities and operations. However, we must not let these realities limit our imagination or silence our advocacy. The ASCR program is a key part of the U.S. research infrastructure and an important component of economic growth and U.S. competitiveness. ASCR has a responsibility to pursue its mission, including advanced scientific computing, applications of AI technologies, and the required advanced research facilities, with determination and enthusiasm. To fulfill the scientific enterprise’s responsibility to the nation, the ASCR program must not only develop and publish a clear vision with an associated list of goals, priorities, and recommendations but also demonstrate scientific leadership by consistently securing long-term funding. This will allow the program to build on its achievements to date, to realize its ambitious vision, and to make lasting contributions to the field.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

The Radical Atom: Mechanosynthetic 3D Printing of an Atomically Precise SPM Tip

This research effort sought to overcome current limitations in scanning probe-based atomic manipulation to enable atomically precise manufacturing (APM). Previous theoretical and experimental works on atom by atom and molecule by molecule fabrication of precise structures are limited to essentially to two-dimensions. APM will enable a paradigm shift in 21st century manufacturing practices in which every single atom in a electronic chip, device or machine can be placed in an exact and predefined position in three-dimensions. By providing a general method for generating reproducible SPM tip structure, this project will drive forward the entire field of atomically precise scanning probe microscopy, opening the door to positional control of nearly arbitrary covalent chemistry. Such control could, for example, be used in applications such as novel 2.5 or 3D microchip fabrication. The creation of a unique manufacturing method through APM has the potential to impact technologies at the theoretical limits of performance, weight, and utility including: solid-state quantum and spintronic computing systems, high efficiency optical antenna, solar power systems, defect engineered materials and extremely efficient catalysts. Although this experiment focused on pick-and-place non-scalable APM, the better understanding of the chemistry is crucial to the eventual goal of scalable APM. To place individual atoms into a specified location is a seminal aspiration of researchers and engineers in the many fields and may have early premium applications in medical devices and microelectronics.

77 NANOSCIENCE AND NANOTECHNOLOGY↗

Mini-Ckpts: Surviving OS Failures in Persistent Memory

Concern is growing in the high-performance computing (HPC) community on the reliability of future extreme-scale systems. Current efforts have focused on application fault-tolerance rather than the operating system (OS), despite the fact that recent studies have suggested that failures in OS memory are more likely. The OS is critical to a system's correct and efficient operation of the node and processes it governs -- and in HPC also for any other nodes a parallelized application runs on and communicates with: Any single node failure generally forces all processes of this application to terminate due to tight communication in HPC. Therefore, the OS itself must be capable of tolerating failures. In this work, we introduce mini-ckpts, a framework which enables application survival despite the occurrence of a fatal OS failure or crash. Mini-ckpts achieves this tolerance by ensuring that the critical data describing a process is preserved in persistent memory prior to the failure. Following the failure, the OS is rejuvenated via a warm reboot and the application continues execution effectively making the failure and restart transparent. The mini-ckpts rejuvenation and recovery process is measured to take between three to six seconds and has a failure-free overhead of between 3-5% for a number of key HPC workloads. In contrast to current fault-tolerance methods, this work ensures that the operating and runtime system can continue in the presence of faults. This is a much finer-grained and dynamic method of fault-tolerance than the current, coarse-grained, application-centric methods. Handling faults at this level has the potential to greatly reduce overheads and enables mitigation of additional fault scenarios.

Fiala, David↗

Large scale multi-node simulations of $\mathbb{Z}_2$ gauge theory quantum circuits using Google Cloud Platform

Simulating quantum field theories on a quantum computer is one of the most exciting fundamental physics applications of quantum information science. Dynamical time evolution of quantum fields is a challenge that is beyond the capabilities of classical computing, but it can teach us important lessons about the fundamental fabric of space and time. Whether we may answer scientific questions of interest using near-term quantum computing hardware is an open question that requires a detailed simulation study of quantum noise. Here we present a large scale simulation study powered by a multi-node implementation of qsim using the Google Cloud Platform. We additionally employ newly-developed GPU capabilities in qsim and show how Tensor Processing Units -- Application-specific Integrated Circuits (ASICs) specialized for Machine Learning -- may be used to dramatically speed up the simulation of large quantum circuits. We demonstrate the use of high performance cloud computing for simulating $\mathbb{Z}_2$ quantum field theories on system sizes up to 36 qubits. We find this lattice size is not able to simulate our problem and observable combination with sufficient accuracy, implying more challenging observables of interest for this theory are likely beyond the reach of classical computation using exact circuit simulation.

Gustafson, Erik↗