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A Cast of Thousands: How the IDEAS Productivity Project Has Advanced Software Productivity and Sustainability
Computational and data-enabled science and engineering are revolutionizing advances throughout science and society, at all scales of computing. For example, teams in the U.S. Department of Energy’s Exascale Computing Project have been tackling new frontiers in modeling, simulation, and analysis by exploiting unprecedented exascale computing capabilities—building an advanced software ecosystem that supports next-generation applications and addresses disruptive changes in computer architectures. However, concerns are growing about the productivity of the developers of scientific software. Members of the Interoperable Design of Extreme-scale Application Software project serve as catalysts to address these challenges through fostering software communities, incubating and curating methodologies and resources, and disseminating knowledge to advance developer productivity and software sustainability. This article discusses how these synergistic activities are advancing scientific discovery—mitigating technical risks by building a firmer foundation for reproducible, sustainable science at all scales of computing, from laptops to clusters to exascale and beyond.
Description of the Three-Dimensional Large-Scale Forcing Data from the 3D Constrained Variational Analysis (VARANAL3D)
This technical report introduces a Three-Dimensional Constrained Variational Analysis (3DCVA) (Tang and Zhang 2015) and its product of three-dimensional large-scale forcing data to drive single-column models (SCM), cloud-resolving models (CRM), and large-eddy simulation (LES) models, and to evaluate model results. The 3DCVA algorithm is an extension of the original 1D constrained variational analysis (1DCVA) (Zhang and Lin 1997, Zhang et al. 2001). The three-dimensional structure of the forcing data allows studies of spatial variation of the large-scale forcing fields and tests of physical parameterizations across scales. In the U.S. Department of Energy Atmospheric Radiation Measurement (ARM) user facility, the 3D forcing data are assigned the datastream name varanal3d. In this technical report, 3DCVA will be used to refer to the algorithm, while VARANAL3D will be used to refer to the data product.
The Role of EGFR in Influenza Pathogenicity: Multiple Network-Based Approaches to Identify a Key Regulator of Non-lethal Infections
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Phase I SBIR Final Scientific/Technical Report: A Climate Impact Assessment Service to Support Urban and Regional Planning
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Modeling and Qualification of a Modified Emission Unit for Radioactive Air Emissions Stack Sampling Compliance
A planned laboratory space and exhaust system modification to the Pacific Northwest National Laboratory Material Science and Technology Building indicated a new evaluation of the mixing at the air sampling system location would be required for compliance to ANSI/HPS N13.1-2011. The modified exhaust system would add a third fan thereby increasing the overall exhaust rate out the stack thus voiding the previous mixing study. Prior to modifying the radioactive air emissions exhaust system, a three-dimensional computational fluid dynamics computer model was used to evaluate the mixing at the sampling system location. Modeling of the new original three-fan system indicated that not all mixing criteria could be met. A second modeling effort was conducted with the addition of an air blender downstream of the confluence of the three fans which then showed satisfactory mixing results. The final installation included an air blender, and the exhaust system underwent full-scale tests to verify velocity, cyclonic flow, gas, and particulate uniformity. The modeling results and those of the full-scale tests show agreement between each of the evaluated criteria. The use of a computational fluid dynamics code was an effective aid in the design process and allowed the sampling system to remain in its original location while still meeting the requirements for sampling at a well-mixed location.
Computational assessment of smooth and rough parameter dependence of statistics in chaotic dynamical systems
An assumption of smooth response to small parameter changes, of statistics or long-time averages of a chaotic system, is generally made in the field of sensitivity analysis, and the parametric derivatives of statistical quantities are critically used in science and engineering. In this paper, we propose a numerical procedure to assess the differentiability of statistics with respect to parameters in chaotic systems. Here, we numerically show that the existence of the derivative depends on the Lebesgue integrability of a certain density gradient function, which we define as the derivative of logarithmic SRB density along the unstable manifold. We develop a recursive formula for the density gradient that can be efficiently computed along trajectories, and demonstrate its use in determining the differentiability of statistics. Our numerical procedure is illustrated on low-dimensional chaotic systems whose statistics exhibit both smooth and rough regions in parameter space.
Science Use Case Design Patterns for Autonomous Experiments
Connecting scientific instruments and robot-controlled laboratories with computing and data resources at the edge, the Cloud or the high-performance computing (HPC) center enables autonomous experiments, self-driving laboratories, smart manufacturing, and artificial intelligence (AI)-driven design, discovery and evaluation. The Self-driven Experiments for Science / Interconnected Science Ecosystem (INTERSECT) Open Architecture enables science breakthroughs using intelligent networked systems, instruments and facilities with a federated hardware/software architecture for the laboratory of the future. It relies on a novel approach, consisting of (1) science use case design patterns, (2) a system of systems architecture, and (3) a microservice architecture. This paper introduces the science use case design patterns of the INTERSECT Architecture. It describes the overall background, the involved terminology and concepts, and the pattern format and classification. It further offers an overview of the 12 defined patterns and 4 examples of patterns of 2 different pattern classes. It also provides insight into building solutions from these patterns. The target audience are computer, computational, instrument and domain science experts working in the field of autonomous experiments.
2016 High Performance Computing Annual Report
Sandia National Laboratories’ California site is celebrating its 60th anniversary (1956 to 2016), and high performance computing has been a key enabler for its scientists and engineers throughout much of its history. Since its founding, Sandia California has helped pioneer the use of HPC platforms including hosting Sandia’s first Cray-1 supercomputer in the 1970s and supporting development of scalable cluster computing platforms to create a new paradigm for cost-effective supercomputing in the 1990s. Recent decades of investment in creation of scalable application frameworks for scientific computing have also enabled new generations of modeling and simulation codes. These resources have facilitated computational analysis of complex phenomena in diverse applications spanning national defense, energy, and homeland security. Today, Sandia California researchers work with partners in academia, industry, and national labs to evolve the state-of-the-art in HPC, modeling, and data analysis (including foundational capabilities for exascale computing platforms) and apply them in transformational ways. Research efforts include mitigating the effects of silent hardware failures that can jeopardize the results of large-scale computations, developing exascale-capable asynchronous task-parallel programming models and runtime systems, formulating new techniques to better explore and analyze extreme-scale data sets, and increasing our understanding of materials and chemical sciences which has applications spanning nuclear weapons stockpile stewardship to more efficient automobile engines. The following section highlights some of these research and applications projects and further illustrates the breadth of our HPC capabilities.
DragonView: Toward Understanding Network Interference in Dragonfly-based Supercomputers
Acquiring and maintaining high performance computing systems represents a substantial, long term investment. Therefore, it is paramount to optimize their utilization in order to maximize the return on investment and the impact on science and engineering. In this context, network congestion and inter-job interference are a major challenge as they can lead to significant systemwide performance degregation. This is especially pertinent in shared interconnects such as the dragonfly network, in which resources are shared by multiple jobs. Since many large-scale applications are communication-bound, a few communication heavy applications can have a large impact on the performance of all jobs and decrease the overall system throughput. In this paper, we describe a web-based visual analytics environment to study congestion and inter-job interference on dragonfly networks. The system enables network architects, system administrators and application developers to explore the potential impact of machine configuration, job placement policies and routing algorithms by visualizing and comparing ensembles of simulated workloads and real world data. We focus on the design of the system and describe the challenges, design decisions and the final implementation. Finally, we present two detailed case studies of prototypical analysis sessions by our stakeholders aimed at exploring the implications of different workloads and machine configurations using ensembles of network simulations.
Chapter 13: Software and Methods for Computational Flux Balance Analysis
As genetic engineering of organisms has grown easier and more precise, computational modeling of metabolic systems has played an increasingly important role in both guiding experimental interventions and in understanding the results of metabolic perturbations.
Electronic excitation spectra of molecular hydrogen in phase I from quantum Monte Carlo and many-body perturbation methods
Here, we study the electronic excitation spectra in solid molecular hydrogen (phase I) at ambient temperature and 5- to 90-GPa pressures using quantum Monte Carlo methods and many-body perturbation theory. In this range, the system changes from a wide-gap molecular insulator to a semiconductor, altering the nature of the excitations from localized to delocalized. Computed gaps and spectra agree with experiments, proving the ability to predict accurately band gaps of many-body systems in the presence of nuclear quantum and thermal effects.
SU-F-T-434: Development of a Fan-Beam Optical Scanner Using CMOS Array for Small Field Dosimetry
Purpose: To design and construct a second generation optical computed tomography (OCT) system using a fan-beam with a CMOS array detector for the 3D dosimetry with polymer gel and radiochromic solid dosimeters. The system was specifically designed for the small field dosimetry. Methods: The optical scanner used a fan-beam laser, which was produced from a collimated red laser beam (λ=620 nm) with a 15-degree laser-line generating lens. The fan-beam was sent through an index-matching bath which holds the sample stage and a sample. The emerging laser light was detected with a 2.54 cm-long CMOS array detector (512 elements). The sample stage rotated through the full 360 degree projection angles at 0.9-degree increments. Each projection was normalized to the unirradiated sample at the projection angle to correct for imperfections in the dosimeter. A larger sample could be scanned by using a motorized mirror and linearly translating the CMOS detector. The height of the sample stage was varied for a full 3D scanning. The image acquisition and motor motion was controlled by a computer. The 3D image reconstruction was accomplished by a fan-beam reconstruction algorithm. All the software was developed inhouse with MATLAB. Results: The scanner was used on both PRESAGE and PAGAT gel dosimeters. Irreconcilable refraction errors were seen with PAGAT because the fan beam laser line refracted away from the detector when the field was highly varying in 3D. With PRESAGE, this type of error was not seen. Conclusion: We could acquire tomographic images of dose distributions by the new OCT system with both polymer gel and radiochromic solid dosimeters. Preliminary results showed that the system was more suited for radiochromic solid dosimeters since the radiochromic dosimeters exhibited minimal refraction and scattering errors. We are currently working on improving the image quality by thorough characterization of the OCT system.
Plasma facing components with capillary porous system and liquid metal coolant flow
Liquid metal can create a renewable protective surface on plasma facing components (PFC), with an additional advantage of deuterium pumping and the prospect of tritium extraction if liquid lithium (LL) is used and maintained below 450 °C, the temperature above which LL vapor pressure begins to contaminate the plasma. LM can also be utilized as an efficient coolant, driven by the Lorentz force created with the help of the magnetic field in fusion devices. Capillary porous systems can serve as a conduit of LM and simultaneously provide stabilization of the LM flow, protecting against spills into the plasma. Recently, a combination of a fast-flowing LM cooling system with a porous plasma facing wall (CPSF) was investigated [A. Khodak and R. Maingi, Nucl. Mater. Energy 26, 100935 (2021)]. The system takes an advantage of a magnetohydrodynamics velocity profile as well as attractive LM properties to promote efficient heat transfer from the plasma to the LL at low pumping energy cost, relative to the incident heat flux on the PFC. In the case of a disruption leading to excessive heat flux from the plasma to the LM PFCs, LL evaporation can stabilize the PFC surface temperature, due to high evaporation heat and apparent vapor shielding. The proposed CPSF was optimized analytically for the conditions of a fusion nuclear science facility [Kessel et al., Fusion Sci. Technol. 75, 886 (2019)]: 10 T toroidal field and 10 MW/m 2 peak incident heat flux. Finally, computational fluid dynamics analysis confirmed that a CPSF system with 2.5 mm square channels can pump enough LL so that no additional coolant is needed.
Neutrons in Structural Biology: Challenges and Opportunities (Workshop Report)
Gaining a thorough understanding of biological systems requires building our knowledge about biological processes from the level of atoms and electrons, and up to whole organisms. Such comprehensive knowledge will allow for a predictive understanding of complex biological systems behavior. It will guide us in the design and development of novel therapeutics and vaccines to tackle existing health threats and to prepare for future pandemics, and it will provide information necessary to create new biomaterials and bio-inspired technologies through manipulation of biological macromolecules, their assemblies, single cells and even microorganisms. Reaching these goals will require a synergistic combination of multiple experimental techniques with molecular calculations and predictive simulations, and the design and development of new techniques and capabilities that bridge current knowledge and technology gaps. Neutron scattering provides unique information about the biomacromolecular structure and function and can play a major role in achieving these goals. A workshop was held to engage the scientific community in identifying pressing challenges in biochemistry, structural biology, enzymology and structure-guided drug design not solved with the current neutron scattering technologies or utilizing other structural biology techniques such as X-ray crystallography, NMR, and cryo-EM. The workshop brought together structural biology, biochemistry and computational experts, as well as early career researchers and students, creating a forum for discussing scientific advancement and collaboration. The workshop included a one-day satellite training workshop where graduate students and postdoctoral researchers were educated in the application of neutron crystallography and small-angle scattering in structural biology. Furthermore, the Instrument Scientific Advisory Board (ISAB) for the development of a macromolecular neutron diffractometer at ORNL’s Second Target Station was introduced at the workshop. The major outcome was that neutrons can provide atomic-level understanding of biomacromolecular structure, function and dynamics which is of paramount importance for addressing the identified challenges. Neutron crystallography, in particular, can resolve long-standing biochemical issues regarding enzyme function by delineating the underlying chemistry and can have a major impact on the design of small-molecule therapeutics, especially in combination with molecular computation (quantum chemistry and molecular dynamics simulations) and the emerging artificial intelligence (AI)-assisted drug design technologies. The unique properties of neutrons, including their high sensitivity to hydrogen and their non-destructive nature, make them ideal probes of biological matter. There is a palpable need in the scientific community to expand and enhance the impact of neutron sciences on biology. Neutron crystallography is the only structural biology method capable of determining positions of all hydrogen atoms in proteins, nucleic acids and their complexes at near-physiological temperatures and of unstable species at cryogenic temperatures. Moreover, neutron analysis is non-ionizing, non-destructive and does not perturb the structure or redox chemistry of active site metal centers and clusters in proteins, which can be invaluable for studying radiation-sensitive metalloprotein complexes. Further, neutron energies used in scattering applications are similar to atomic motions, permitting neutron spectroscopies to characterize the dynamics of biomacromolecules on the picosecond to microsecond timescales. The different sensitivities of neutrons to protium (H) and deuterium (D) isotopes of hydrogen allow enhanced visibility of specific parts of biological complexes through isotopic labeling. The impact of neutrons will be most powerful when neutron scattering is combined with complementary experimental techniques that use photons and electrons, and with high-performance computing. The interconnection and mutuality of the experimental and theoretical capabilities will drive discoveries in biological and health sciences to generate more complete picture of complex biological systems. The major limitation in the field of biological neutron crystallography has been signal-to-noise, demanding large samples that are difficult to produce for the majority of biomacromolecules and limiting the applicability of this technique in biological sciences. A neutron crystallography instrument at the Second Target Station will revolutionize biological science with neutrons by engaging a large scientific community of structural biologists, enabling successful neutron diffraction experiments from radically smaller biomacromolecular crystals, resolving unanswered biochemical questions, and meaningfully contributing to rational drug design. The meeting highlighted 10 grand challenges that will be addressed with this advanced capability over the next decade and beyond, and the recommendations required to help address them are given below.
Machine learning in cardiovascular flows modeling: Predicting arterial blood pressure from non-invasive 4D flow MRI data using physics-informed neural networks
Advances in computational science offer a principled pipeline for predictive modeling of cardiovascular flows and aspire to provide a valuable tool for monitoring, diagnostics and surgical planning. Such models can be nowadays deployed on large patient-specific topologies of systemic arterial networks and return detailed predictions on flow patterns, wall shear stresses, and pulse wave propagation. However, their success heavily relies on tedious pre-processing and calibration procedures that typically induce a significant computational cost, thus hampering their clinical applicability. Here, we put forth a machine learning framework that enables the seamless synthesis of non-invasive in-vivo measurement techniques and computational flow dynamics models derived from first physical principles. We illustrate this new paradigm by showing how one-dimensional models of pulsatile flow can be used to constrain the output of deep neural networks such that their predictions satisfy the conservation of mass and momentum principles. Once trained on noisy and scattered clinical data of flow and wall displacement, these networks can return physically consistent predictions for velocity, pressure and wall displacement pulse wave propagation, all without the need to employ conventional simulators. A simple post-processing of these outputs can also provide a relatively cheap and effective way for estimating Windkessel model parameters that are required for the calibration of traditional computational models. Finally, the effectiveness of the proposed techniques is demonstrated through a series of prototype benchmarks, as well as a realistic clinical case involving in-vivo measurements near the aorta/carotid bifurcation of a healthy human subject.
Computationally Guided and Experimentally Validated Design of Custom Chelators for Critical Mineral Recovery
Selective, high throughput separation of target critical metals from complex environments such as fly ash leachates and mining process streams presents a significant challenge for economical production. Custom chelators and sorbents are an attractive technology for selective metal extraction, however it can be difficult to predict their performance, and significant experimental efforts are often required to develop chelating technologies. Here, we present a computational strategy focused on modelling chelator-metal binding interactions and benchmark these results versus experimental data. A computational pipeline combining forcefield, semiempirical, and meta-GGA methods with a thermodynamic framework optimized for error cancellation has been developed to predict binding energies of chelator complexes towards critical mineral recovery applications. This approach, originally validated on [2.2.2] cryptates binding mono- and divalent cations, demonstrated robust predictive capabilities with an R2 of 0.850 against experimental aqueous binding energies. The workflow includes metadynamics for exploring high-dimensional potential energy surfaces and a cluster-continuum model for accurate yet computationally efficient solvation modeling. Error cancellation between solvation energies of free and chelator-coordinated ions enables faster convergence, even with finite cluster sizes. Initial studies on the cryptates revealed consistent metal-ligand coordination patterns, with systematic variations influenced by ion size and charge, highlighting key structural features linked to binding selectivity. Further studies of a proprietary chelator have resulted in identification of previously unreported selectivity towards economically significant metals, which in-house experiments have confirmed, demonstrating the feasibility of this approach. By applying this methodology to new chelators targeting critical minerals such as lithium, cobalt, nickel and other strategic metals, we aim to accelerate the discovery of next-generation chelators for efficient recovery, recycling, and separation processes. This computational framework serves as the backbone of a high-throughput design pipeline tailored for sustainable resource utilization and may be applied to a wide range of systems to meet experimental needs.
INTERSECT Architecture Specification: Use Case Design Patterns (V.0.9)
Connecting scientific instruments and robot-controlled laboratories with computing and data resources at the edge, the Cloud or the high-performance computing (HPC) center enables autonomous experiments, self-driving laboratories, smart manufacturing, and artificial intelligence (AI)-driven design, discovery and evaluation. The Self-driven Experiments for Science / Interconnected Science Ecosystem (INTERSECT) Open Architecture enables science breakthroughs using intelligent networked systems, instruments and facilities with a federated hardware/software architecture for the laboratory of the future. It relies on a novel approach, consisting of (1) science use case design patterns, (2) a system of systems architecture, and (3) a microservice architecture. This document introduces the science use case design patterns of the INTERSECT Architecture. It describes the overall background, the involved terminology and concepts, and the pattern format and classification. It further details the 12 defined patterns and provides insight into building solutions from these patterns. The document also describes the application of these patterns in the context of several INTERSECT autonomous laboratories. The target audience are computer, computational, instrument and domain science experts working in the field of autonomous experiments.