Student Cluster Competition: A Multi-disciplinary Undergraduate HPC Educational Tool
Abstract Not Provided
Computer Science↗
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High-performance computing leadership to enable advances in artificial intelligence and a thriving compute ecosystem
The past three decades have witnessed the widespread adoption of high-performance computing (HPC) as an essential tool in the advancement of science. From accelerating critical research in the wake of a global pandemic to climate modelling and national security, HPC has become integral to the most cutting-edge scientific research around the world and across application domains. The global competition to debut the next fastest supercomputer keeps pushing the field forward. Meanwhile, increasing capabilities are bringing hallmarks of science fiction, such as artificial intelligence (AI), into daily life. However, the tremendous power of new computing systems comes with an increased concern about equitable access to these resources and their impact on supporting a thriving workforce.
Tourassi, Georgia↗
Model selection and parameter estimation in tumor growth models using approximate Bayesian computation-ABC
Cancer is one of the most fatal diseases in the world. Governments and researchers from various areas have continuously concentrated efforts to better understand the disease and propose diagnostic and treatment techniques. The use of mathematical models of tumor growth is of great importance for the development of such techniques. Due to the variety of models nowadays available in the literature, the problems of model selection and parameter estimation come into picture, aiming at suitably predicting the patient’s status of the disease. As the available data on dependent variables of existing models might not justify the use of common likelihood functions, approximate Bayesian computation (ABC) becomes a very attractive tool for model selection and model calibration (parameter estimation) in tumor growth models. In the present study, a Monte Carlo approximate Bayesian computation (ABC) algorithm is applied to select among competing models of tumor growth, with and without chemotherapy treatment. Simulated measurements are used in this work. The results obtained show that the algorithm correctly selects the model and estimates the parameters used to generate the simulated measurements.
60 APPLIED LIFE SCIENCES↗
Harnessing the Power of Many: Extensible Toolkit for Scalable Ensemble Applications
Many scientific problems require multiple distinct computational tasks to be executed in order to achieve a desired solution. We introduce the Ensemble Toolkit (EnTK) to address the challenges of scale, diversity and reliability they pose. We describe the design and implementation of EnTK, characterize its performance and integrate it with two exemplar use cases: seismic inversion and adaptive analog ensembles. We perform nine experiments, characterizing EnTK overheads, strong and weak scalability, and the performance of the two use case imple-mentations, at scale and on production infrastructures. We show how EnTK meets the following general requirements: (i) imple-menting dedicated abstractions to support the description and execution of ensemble applications; (ii) support for execution on heterogeneous computing infrastructures; (iii) efficient scalability up to O(10 4 ) tasks; and (iv) task-level fault tolerance. We discuss novel computational capabilities that EnTK enables and the scientific advantages arising thereof. We propose EnTK as an important addition to the suite of tools in support of production scientific computing.
Computer Science↗
IMS - MS Data Extractor
An automated drift time extraction and computed associated collision cross section software tool for small molecule analysis with ion mobility spectrometry-mass spectrometry (IMS-MS). The software automatically extracts drift times and computes associated collision cross sections for small molecules analyzed using ion mobility spectrometry-mass spectrometry (IMS-MS) based on a target list of expected ions provided by the user.
Source record↗
IMS - MS Data Extractor
An automated drift time extraction and computed associated collision cross section software tool for small molecule analysis with ion mobility spectrometry-mass spectrometry (IMS-MS). The software automatically extracts drift times and computes associated collision cross sections for small molecules analyzed using ion mobility spectrometry-mass spectrometry (IMS-MS) based on a target list of expected ions provided by the user.
Source record↗
Lightshow: a Python package for generating computational x-ray absorption spectroscopy input files
First-principles computational spectroscopy is a critical tool for interpreting experiment, per- forming structure refinement, and developing new physical understanding. Systematically setting up input files for different simulation codes and a diverse class of materials is a challeng- ing task with a very high barrier-to-entry, given the complexities and nuances of each individual simulation package. This task is non-trivial even for experts in the electronic structure field and nearly formidable for non-expert researchers. Lightshow solves this problem by providing a uniform abstraction for writing computational x-ray spectroscopy input files for multiple popular codes, including FEFF, VASP, OCEAN, exciting and XSpectra. Its extendable framework will also allow the community to easily add new functions and to incorporate new simulation codes.
36 MATERIALS SCIENCE↗
Fast Uncovering of Graph Communities on a Chip: Toward Scalable Community Detection on Multicore and Manycore Platforms
Graph representations are pervasive in scientific and social computing. They serve as vital tools to model the interplay among different interacting entities. In this paper, we visit the problem of community detection, which is one of the most widely used graph operations toward scientific discovery. Community detection refers to the process of identifying tightly-knit subgroups of vertices in a large graph. These sub-groups (or communities) represent vertices that are tied together through common structure or function. Identification of communities could help in understanding the modular organization of complex networks. However, owing to large data sizes and high computational costs, performing community detection at scale has become increasingly challenging. Here, we present a detailed review and analysis of some of the leading computational methods and implementations developed for executing community detection on modern day multicore and manycore architectures. Our goals are to: a) define the problem of community detection and highlight its scientific significance; b) relate to challenges in parallelizing the operation on modern day architectures; c) provide a detailed report and taxonomical classification of the approaches that have been designed for various architectures; and d) finally, provide insights into the strengths and suitability of different architectures for community detection, and a preview into the future trends of the area. It is our hope that this detailed treatment of community detection on parallel architectures can serve as an exemplar study for extending the application of modern day multicore and manycore architectures to other complex graph applications.
community detection, multithreaded platforms↗
Real-Space Quantification of Exciton Localization in Acene Crystals Using Wannier Function Decomposition
Here, we introduce the Wannier function decomposition of excitons (WFDX) method to quantify exciton localization in solids within the ab initio Bethe-Salpeter equation framework. By decomposing each Bloch exciton wave function into products of single-particle electron and hole maximally localized Wannier functions, this real-space approach provides well-defined orbital- and spatial-resolved measures of both Frenkel and charge-transfer excitons at low computational cost. We apply WFDX to excitons in acene crystals, quantifying how the number of rings, the exciton spin state, and the center-of-mass momentum affect spatial localization. Additionally, we show how this real-space representation reflects structural nonsymmorphic symmetries that are hidden in standard reciprocal-space descriptions. We demonstrate how the WFDX framework can be used to efficiently interpolate exciton expansion coefficients in reciprocal-space and outline how it may facilitate evaluation of observables involving position operators, highlighting its potential as a general tool for both analyzing and computing excitonic properties in solids.
Tao, Zui [University of California, Berkeley, CA (↗
Project Description for Student Symposium 2022: Modeling Approach to Critical in the Upcoming CERBERUS Experiment
The Critical Experiment Reflected By copper to BettEr Understand Scattering [CERBERUS] is an integral experiment that will be executed at the end of FY23. The experiment is designed to study the intermediate energy range, in particular elastic and inelastic scattering of neutrons in copper. Approaching criticality safely is of utmost importance, and having a computer mode is a useful tool when determining changes that can safely be made to the experiment. Multiple simulations are needed to analyze the approach to critical, and manually creating MCNP input files is both tedious and error prone. To solve this problem, a python script was created to develop and run these input files.
73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
BARC Element Classifier (barc)
SAND2024-02120O This program enumerates and classifies all possible functional elements in several different categories within the Ballistic Asynchronous Reversible Computing (barc) model of computation. barc software is a research tool that is being used to help document the possible digital behaviors of primitive functional elements in the ABRC a.k.a. BARC model of computation. The method of operation of this software leverages elementary concepts and methods from discrete mathematics: combinatorics (permutations), partitions and equivalence classes, symmetry transformations, and the theory of finite groups. Implementation is in Python programming language. Sandia National Laboratories is a multimission laboratory managed and operated by National Technology & Engineering Solutions of Sandia, LLC, a wholly owned subsidiary of Honeywell International Inc., for the U.S. Department of Energy’s National Nuclear Security Administration under contract DE-NA0003525.
Frank, Michael↗
QUIC-fire: A fast-running simulation tool for prescribed fire planning
Coupled fire-atmospheric modeling tools are increasingly used to understand the complex and dynamic behavior of wildland fires. Multiple research tools linking combustion to fluid flow use Navier-Stokes numerical solutions coupled to a thermodynamic model to understand fire-atmospheric feedbacks, but these computational fluid dynamics approaches require high-performance computing resources. We present a new simulation tool called QUIC-Fire to rapidly solve these feedbacks by coupling the mature 3-D rapid wind solver QUIC-URB to a physics-based cellular automata fire spread model Fire-CA. QUIC-Fire uses 3-D fuels inputs similar to the CFD model FIRETEC, allowing this tool to simulate effects of fuel structure on local winds and fire behavior. Results comparing fire behavior metrics to the computational fluid dynamic model FIRETEC show strong agreement. As a result, QUIC-Fire is the first tool intended to provide an opportunity for prescribed fire planners to compare, evaluate and design burn plans, including complex ignition patterns and coupled fire atmospheric feedbacks.
54 ENVIRONMENTAL SCIENCES↗
Materials Challenges and Opportunities for Energy Generation, Conversion, Delivery, and Storage (Applied Energy Tri-Laboratory Consortium Workshop Report)
This report documents the outcomes of the Tri-Laboratory Materials Workshop that was held July 31 and August 1, 2019 to begin addressing the needs, opportunities, and challenges associated with the development, fabrication, and testing of the needed materials and components for integrated hybrid energy systems (i.e., incorporating nuclear, fossil, and renewables for electric and thermal applications). This was accomplished by assembling the research program leads and principal investigators at Idaho National Laboratory (INL), National Energy Technology Laboratory (NETL), and National Renewable Energy Laboratory (NREL), who support the research and development of new technology and system integration. The team then identified and prioritized key materials development needs. This effort was intended to enhance communications and synergy among the Tri-Lab partners. Advanced functional and structural materials are central to transformative energy technologies for energy generation, conversion, delivery, and storage. With that in mind, the workshop focused on identifying and assessing the foundational materials research needs at both the basic and applied levels. Materials challenges include the ability to withstand harsh environments, such as high temperatures and pressures, corrosion, oxidation, or irradiation while maintaining flexible mission profiles and long service lifespans. Advanced energy system material challenges and needs range from materials for the capture, upgrading/concentration, storage, and delivery of low-grade heat to materials for high temperature environments that involve liquid metals, molten salt, and very high temperature gas heat delivery and storage systems. Material improvements are needed for hybrid energy systems due to accelerated corrosion and stress-fatigue failure of materials and equipment, which results from increased frequency and amplitude of thermal, mechanical, and electrical cycling of systems components. Multifunctional materials are needed for high temperature solid-oxide fuel cells, advanced electrochemical reactors, and in-process separation. Relative to materials manufacturing, application of advanced additive and subtractive methods need to be understood to develop both thin-layer homogenous materials and materials of graded composition. Materials modeling and machine learning will be critical to accelerate the design and production of power electronics, and nuclear reactor materials and fuel, as well as to gain an understanding of beneficial materials phenomena or deleterious microstructure evolution. There is also a need for standardized models, computational structures, data reporting protocols and modeling tools across the three laboratories. This would allow consistent results, analysis, and data sharing. Combining computational capabilities between the three laboratories (e.g., hardware, software) would greatly increase computational capabilities and throughput. The workshop identified the need for laboratories to anticipate and address problems that will occur during scale-up. Laboratory work must connect with industry to ensure that research focuses on processes that are scalable and marketable. Industry input and perspective are essential to guide laboratory research to meet these requirements and deploy new technology in industrial demonstrations. Another aspect of scale-up is the integration of multiple systems since new challenges often arise at the subsystem interfaces. Establishing a scale-up manufacturing demonstration/pilot plant, potentially as an industrial user facility, would be beneficial to the laboratories and industry. That modular scale-up manufacturing demonstration/pilot plant would allow researchers to find and resolve interface problems that cannot be identified by focusing only on individual parts. Communication exchanges among the organizers, attendees, and workshop survey responses indicate that the workshop was successful in achieving its goal to identify key technology gaps and research needs. Strong positive feedback was received on the sharing of ideas, capabilities, talent, and passion to move forward on the materials-related action items.
36 MATERIALS SCIENCE↗
Temperature dependent structural behavior of Mg{sub 70}Zn{sub 30}: A molecular dynamics study
Mg{sub 70}Zn{sub 30} is simplest of metallic glasses having good mechanical properties, biocompatibility with human body and is biodegradable, so it is widely studied material in its class. We present in this paper first principle calculations showing the change in the structure of the system with temperature. The computations are performed using PWSCF tool of Quantum ESPRESSO package, which uses density functional theory for calculations of electronic ground state properties and dynamical structures. With increasing temperature the number of peaks in RDFs reduce in number leaving only a single peak,the system thus makes a transition from non-crystalline solid to liquid state within the range of 300–1000K. First coordination number was found to decrease with rising temperature.
71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
MFANS 2024 - Formally Proving Characteristics of Cyber-Physical Systems
Cyber-physical systems (CPS) are engineered systems that rely on the smooth integration of computational algorithms and physical elements. This integration presents new challenges for verifying that systems will behave as expected. The goal of this presentation is to present current challenges and potential solutions for the formal verification of cyber-physical systems. For cyber systems, formal methods refer to systematically rigorous mathematical techniques employed in the specification, development, analysis, and verification of both software and hardware systems. Recent advancements in computer science have yielded sophisticated tools specifically designed to address challenges associated with formal methods in complex systems. These tools leverage various foundational concepts such as logic, formal languages, program semantics, type systems, type theory, and automata theory. A notable achievement in the application of formal methods is the seL4 microkernel, claimed to be the first general-purpose operating-system kernel to be verified. Its proof implies the absence of bugs and guarantees that the kernel meets specifications. For physical systems, dynamic and control theory has a history of using rigorous analytic techniques to prove functional correctness. Lyapunov, optimal, classical, modern, and robust control theories all provide rigorous mathematical methods both to analyze system performance and to design controller that can be guaranteed to meet certain objectives. Recent computational techniques like level set theory and reachability analysis provide assertions that a system's state will avoid unsafe regions. Even though success has been independently achieved for cyber systems and physical systems, the integration of such systems creates new challenges. In particular, there is an obvious discrepancy between finite-state machines and infinite-state systems, resulting in different approaches for modeling and analyzing these system. While it is possible to simulate hybrid systems, this provides only a demonstration of a performance and not proof. For hybrid systems, current formal methods and system analysis approaches typically require a workarounds to work on hybrid systems like CPS. This paper will outline the state of the art and limits of current practice for formally verifying CPS and will identify possible research directions that require attention.
97 MATHEMATICS AND COMPUTING↗
International Neuroscience Initiatives through the Lens of High-Performance Computing
Neuroscience initiatives aim to develop new technologies and tools to measure and manipulate neuronal circuits. In this paper, to deal with the massive amounts of data generated by these tools, the authors envision the co-location of open data repositories in standardized formats together with high-performance computing hardware utilizing open source optimized analysis codes.
60 APPLIED LIFE SCIENCES↗
Heterogeneous Computing
To leverage the increasing heterogeneity in modern computing resources, Geant4 incorporates advanced software tools and a task-based framework (G4Tasking) that enables efficient parallelism at event, sub-event, and track levels. Ongoing R&D efforts focus on integrating GPUs into high-energy physics (HEP) simulations, including optical photon simulation with Opticks/NVIDIA OptiX, offloading electromagnetic particle transport using G4HepEM/AdePT and Celeritas, and employing advanced surface-based geometry models such as VecGeom2.0 and ORANGE. As Geant4 continues evolving toward high-performance computing (HPC) and heterogeneous architectures, it remains a key tool for large-scale simulations in HEP and beyond.
72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
Automated defect analysis in electron microscopic images
Electron microscopy and defect analysis are a cornerstone of materials science, as they offer detailed insights on the microstructure and performance of a wide range of materials and material systems. Building a robust and flexible platform for automated defect recognition and classification in electron microscopy will result in the completion of analysis orders of magnitude faster after images are recorded, or even online during image acquisition. Automated analysis has the potential to be significantly more efficient, accurate, and repeatable than human analysis, and it can scale with the increasingly important methods of automated data generation. Herein, an automated recognition tool is developed based on a computer vison–based approach; it sequentially applies a cascade object detector, convolutional neural network, and local image analysis methods. We demonstrate that the automated tool performs as well as or better than manual human detection in terms of recall and precision and achieves quantitative image/defect analysis metrics close to the human average. The proposed approach works for images of varying contrast, brightness, and magnification. Furthermore, these promising results suggest that this and similar approaches are worth exploring for detecting multiple defect types and have the potential to locate, classify, and measure quantitative features for a range of defect types, materials, and electron microscopic techniques.
47 OTHER INSTRUMENTATION↗