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DOE OSTI2021

Unbalanced Parallel I/O: An Often-Neglected Side Effect of Lossy Scientific Data Compression

Lossy compression techniques have demonstrated promising results in significantly reducing the scientific data size while guaranteeing the compression error bounds. However, one important yet often neglected side effect of lossy scientific data compression is its impact on the performance of parallel I/O. Our key observation is that the compressed data size is often highly skewed across processes in lossy scientific compression. To understand this behavior, we conduct extensive experiments where we apply three lossy compressors MGARD, ZFP, and SZ, which are specifically designed and optimized for scientific data, to three real-world scientific applications Gray-Scott simulation, WarpX, and XGC. Our analysis result demonstrates that the size of the compressed data is always skewed even if the original data is evenly decomposed among processes. Such skewness widely exists in different scientific applications using different compressors as long as the information density of the data varies across processes. We then systematically study how this side effect of lossy scientific data compression impacts the performance of parallel I/O. We observe that the skewness in the sizes of the compressed data often leads to I/O imbalance, which can significantly reduce the efficiency of I/O bandwidth utilization if not properly handled. In addition, writing data concurrently to a single shared file through MPI-IO library is more sensitive to the unbalanced I/O loads. Therefore, we believe our research community should pay more attention to the unbalanced parallel I/O caused by lossy scientific data compression.

Wang, Xinying↗

DOE OSTI2021

Resiliency in numerical algorithm design for extreme scale simulations

Here this work is based on the seminar titled ‘Resiliency in Numerical Algorithm Design for Extreme Scale Simulations’ held March 1–6, 2020, at Schloss Dagstuhl, that was attended by all the authors. Advanced supercomputing is characterized by very high computation speeds at the cost of involving an enormous amount of resources and costs. A typical large-scale computation running for 48 h on a system consuming 20 MW, as predicted for exascale systems, would consume a million kWh, corresponding to about 100k Euro in energy cost for executing 10 23 floating-point operations. It is clearly unacceptable to lose the whole computation if any of the several million parallel processes fails during the execution. Moreover, if a single operation suffers from a bit-flip error, should the whole computation be declared invalid? What about the notion of reproducibility itself: should this core paradigm of science be revised and refined for results that are obtained by large-scale simulation? Naive versions of conventional resilience techniques will not scale to the exascale regime: with a main memory footprint of tens of Petabytes, synchronously writing checkpoint data all the way to background storage at frequent intervals will create intolerable overheads in runtime and energy consumption. Forecasts show that the mean time between failures could be lower than the time to recover from such a checkpoint, so that large calculations at scale might not make any progress if robust alternatives are not investigated. More advanced resilience techniques must be devised. The key may lie in exploiting both advanced system features as well as specific application knowledge. Research will face two essential questions: (1) what are the reliability requirements for a particular computation and (2) how do we best design the algorithms and software to meet these requirements? While the analysis of use cases can help understand the particular reliability requirements, the construction of remedies is currently wide open. One avenue would be to refine and improve on system- or application-level checkpointing and rollback strategies in the case an error is detected. Developers might use fault notification interfaces and flexible runtime systems to respond to node failures in an application-dependent fashion. Novel numerical algorithms or more stochastic computational approaches may be required to meet accuracy requirements in the face of undetectable soft errors. These ideas constituted an essential topic of the seminar. The goal of this Dagstuhl Seminar was to bring together a diverse group of scientists with expertise in exascale computing to discuss novel ways to make applications resilient against detected and undetected faults. In particular, participants explored the role that algorithms and applications play in the holistic approach needed to tackle this challenge. This article gathers a broad range of perspectives on the role of algorithms, applications and systems in achieving resilience for extreme scale simulations. The ultimate goal is to spark novel ideas and encourage the development of concrete solutions for achieving such resilience holistically.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2023

Performance Evaluation of Heterogeneous GPU Programming Frameworks for Hemodynamic Simulations

Preparing for the deployment of large scientific and engineering codes on upcoming exascale systems with GPU-dense nodes is made challenging by the unprecedented diversity of device architectures and heterogeneous programming models. In this work, we evaluate the process of porting a massively parallel, fluid dynamics code written in CUDA to SYCL, HIP, and Kokkos with a range of backends, using a combination of automated tools and manual tuning. We use a proxy application along with a custom performance model to inform the results and identify additional optimization strategies. At scale performance of the programming model implementations are evaluated on pre-production GPU node architectures for Frontier and Aurora, as well as on current NVIDIA device-based systems Summit and Polaris. Real-world workloads representing 3D blood flow calculations in complex vasculature are assessed. Our analysis highlights critical trade-offs between code performance, portability, and development time.

Martin, Aristotle↗

DOE OSTI2026

Modeling CO 2 flow through faulted/fractured reservoirs using tEDFM in corner-point grids

The interest in underground CO 2 storage has increased significantly over the last decade because of the rising concern about global warming due to the growing levels of greenhouse gases in the atmosphere. Considering that CO 2 accounts for 80% of these greenhouse gases, carbon capture, utilization, and storage (CCUS) is regarded as one of the most direct approaches to achieving the net zero carbon target. Although CO 2 storage in deep saline aquifers and depleted gas reservoirs has been studied extensively, most studies use commercial simulators that model faults/fractures by simply modifying the transmissibility in the direction perpendicular to the fault surfaces. Here, this work shows that this simplistic approach ignores the accelerated flow in the directions parallel to the fault plane, leading to significantly higher leakage along the fault surface. To accurately model the flow of CO 2 in faulted reservoirs, we present the first transient embedded discrete fracture model for corner-point grids (tEDFM-CPG). By comparing the results of the tEDFM-CPG to high-resolution reference solutions, we show that this approach is accurate and efficient at predicting CO 2 flow in faulted/fractured reservoirs. Finally, this work presents the use of mixed reality (MR) to efficiently observe CO 2 gas migration in the interior of these corner-point grid systems.

25 ENERGY STORAGE↗

DOE OSTI2021

Scalable semitransparent prototype organic photovoltaic module with minimal resistance loss

Semi-transparent organic photovoltaic (ST-OPV) cells are regarded as an attractive solution to building-integrated solar energy harvesting. Both the power conversion efficiency (PCE) and average photopic transmission (APT) of ST-OPVs have shown substantial increases in recent years. However, less attention has been paid to the area scaling of ST-OPV cells. In this work, we investigate the scalability of ST-OPV cells from 4 mm 2 to 1 cm 2 , as well as 9 cm 2 active area prototype module. By integrating both top and bottom metal grids onto the transparent electrodes, the series resistance loss of 1 cm 2 ST-OPV cell is significantly reduced, and is comparable to that of the grid-free 4 mm 2 cell. Nine 1 cm 2 cells are then connected in a series-parallel circuit to realize a prototype ST-OPV module. A 100% fabrication yield with only 5% PCE deviation among discrete cells is achieved. The semitransparent module shows PCE = 7.2 ± 0.1% under simulated AM 1.5G illumination at 1 sun intensity, which exhibits no connection resistance loss compared to that of the individual cells. The ST-OPV module exhibits an APT = 38.1 ± 1.1%, which enables a light utilization efficiency, LUE = 2.74 ± 0.09%. Here, the method demonstrates a promising way for ST-OPV modules to scale without compromising performance.

14 SOLAR ENERGY↗

DOE OSTI2021

Modeling of a chain of three plasma accelerator stages with the WarpX electromagnetic PIC code on GPUs

The fully electromagnetic particle-in-cell code WarpX is being developed by a team of the U.S. DOE Exascale Computing Project (with additional non-U.S. collaborators on part of the code) to enable the modeling of chains of tens to hundreds of plasma accelerator stages on exascale supercomputers, for future collider designs. The code is combining the latest algorithmic advances (e.g., Lorentz boosted frame and pseudo-spectral Maxwell solvers) with mesh refinement and runs on the latest computer processing unit and graphical processing unit (GPU) architectures. In this paper, we summarize the strategy that was adopted to port WarpX to GPUs, report on the weak parallel scaling of the pseudo-spectral electromagnetic solver, and then present solutions for decreasing the time spent in data exchanges from guard regions between subdomains. In Sec. IV, we demonstrate the simulations of a chain of three consecutive multi-GeV laser-driven plasma accelerator stages.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2024

Plasma Dynamics and Nonthermal Particle Acceleration in 3D Nonrelativistic Magnetic Reconnection

Understanding plasma dynamics and nonthermal particle acceleration in 3D magnetic reconnection has been a long-standing challenge. In this paper, we explore these problems by performing large-scale fully kinetic simulations of multi-X-line plasmoid reconnection with various parameters in both the weak- and strong-guide-field regimes. In each regime, we have identified its unique 3D dynamics that lead to field-line chaos and efficient acceleration, and we have achieved nonthermal acceleration of both electrons and protons into power-law spectra. The spectral indices agree well with a simple Fermi acceleration theory that includes guide-field dependence. In the low-guide-field regime, the flux rope kink instability governs the 3D dynamics for efficient acceleration. The weak dependence of the spectra on the ion-to-electron mass ratio and β ($\ll$1) implies that the particles are sufficiently magnetized for Fermi acceleration in our simulations. While both electrons and protons are injected at reconnection exhausts, protons are primarily injected by perpendicular electric fields through Fermi reflections and electrons are injected by a combination of perpendicular and parallel electric fields. The magnetic power spectra agree with in situ magnetotail observations, and the spectral index may reflect a reconnection-driven size distribution of plasmoids instead of the Goldreich–Sridhar vortex cascade. As the guide field becomes stronger, the oblique flux ropes of large sizes capture the main 3D dynamics for efficient acceleration. Intriguingly, the oblique flux ropes can also experience flux rope kink instability, to drive extra 3D dynamics. This work has broad implications for 3D reconnection dynamics and particle acceleration in heliophysics and astrophysics.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2021

Computational design and analysis of modular cells for large libraries of exchangeable product synthesis modules

Microbial metabolism can be harnessed to produce a large library of useful chemicals from renewable resources such as plant biomass. However, it is laborious and expensive to create microbial biocatalysts to produce each new product. To tackle this challenge, we have recently developed modular cell (ModCell) design principles that enable rapid generation of production strains by assembling a modular (chassis) cell with exchangeable production modules to achieve overproduction of target molecules. Previous computational ModCell design methods are limited to analyze small libraries of around 20 products. In this study, we developed a new computational method, named ModCell-HPC, that can design modular cells for large libraries with hundreds of products with a highly-parallel and multi-objective evolutionary algorithm and enable us to elucidate modular design properties. We demonstrated ModCell-HPC to design Escherichia coli modular cells towards a library of 161 endogenous production modules. From these simulations, we identified E. coli modular cells with few genetic manipulations that can produce dozens of molecules in a growth-coupled manner with different types of fermentable sugars. These designs revealed key genetic manipulations at the chassis and module levels to accomplish versatile modular cells, involving not only in the removal of major by-products but also modification of branch points in the central metabolism. We further found that the effect of various sugar degradation on redox metabolism results in lower compatibility between a modular cell and production modules for growth on pentoses than hexoses. To better characterize the degree of compatibility, we developed a method to calculate the minimal set cover, identifying that only three modular cells are all needed to couple with up 85 compatible production modules. By determining the unknown compatibility contribution metric, we further elucidated the design features that allow an existing modular cell to be re-purposed towards production of new molecules. Altogether, ModCell-HPC is a useful tool for understanding modularity of biological systems and guiding more efficient and generalizable design of modular cells that help reduce research and development cost in biocatalysis.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

EUTERPE: A global gyrokinetic code for stellarator geometry

The current state of the EUTERPE code is described with emphasis on the implemented models and their numerical implementation. The code solves the multi-species electromagnetic gyrokinetic equations in the full volume of a three-dimensional domain. Noise reduction of the particle-in-cell method is achieved by using a δf-method and Fourier filters. The field equations are discretized with B-splines and the resulting system of equations is solved iteratively. For linear simulations a phase-factor transformation is applied in order to strongly reduce the necessary grid resolution. Apart from the full gyrokinetic model, other numerically less expensive hybrid models are also implemented. They are mainly tailored for comparison with fluid theory and for studying the interaction of the bulk plasma with fast particles. The code is parallelized for CPUs by particle and domain decomposition. Good scalability up to several thousand nodes is demonstrated.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2021

Tokamak ITG-KBM transition benchmarking with the mixed variables/pullback transformation electromagnetic gyrokinetic scheme

Electromagnetic gyrokinetic simulation of high temperature plasma is required to predict confinement in magnetic fusion devices and has posed challenges for existing codes. In this paper, we demonstrate successful global gyrokinetic simulation of the ion temperature gradient-driven mode-kinetic ballooning mode transition in a toroidal fusion plasma test case using the mixed variables/pullback transformation (MV/PT) scheme with the particle-in-cell codes XGC and ORB5, and compare to results from a conventional continuum code from the literature. Furthermore, the MV/PT scheme combines explicit time integration with mitigation of the well-known electromagnetic gyrokinetic “cancelation problem.” We calculate eigenmodes in the electrostatic and parallel vector potentials, and find good agreement in growth rate, real frequency, and the normalized plasma pressure of mode transition.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2020

An active learning high-throughput microstructure calibration framework for solving inverse structure–process problems in materials informatics

Determining a process–structure–property relationship is the holy grail of materials science, where both computational prediction in the forward direction and materials design in the inverse direction are essential. Problems in materials design are often considered in the context of process–property linkage by bypassing the materials structure, or in the context of structure–property linkage as in microstructure-sensitive design problems. However, there is a lack of research effort in studying materials design problems in the context of process–structure linkage, which has a great implication in reverse engineering. In this paper, given a target microstructure, we propose an active learning high-throughput microstructure calibration framework to derive a set of processing parameters, which can produce an optimal microstructure that is statistically equivalent to the target microstructure. The proposed framework is formulated as a noisy multi-objective optimization problem, where each objective function measures a deterministic or statistical difference of the same microstructure descriptor between a candidate microstructure and a target microstructure. Furthermore, to significantly reduce the physical waiting wall-time, we enable the high-throughput feature of the microstructure calibration framework by adopting an asynchronously parallel Bayesian optimization to exploit high-performance computing resources. Case studies in additive manufacturing and grain growth are used to demonstrate the applicability of the proposed framework, where kinetic Monte Carlo (kMC) simulation is used as a forward predictive model, such that for a given target microstructure, the target processing parameters that produced this microstructure are successfully recovered.

36 MATERIALS SCIENCE↗

DOE OSTI2026

Ion Cyclotron Heating in a Levitated Dipole Fusion Reactor

OpenStar Technologies is pursuing the levitated dipole (LD) as a highly modular, loosely-coupled system that leverages their expertise in high temperature superconductor (HTS) technology. The next generation experiment at OpenStar, Tahi (Ma¯ori for “first”), will demonstrate the generation and confinement of fast ions in a levitated dipole for the first time. Ion cyclotron range of frequency (ICRF) heating is a leading candidate for energetic ion formation in Tahi. A frequency in the 10 MHz range will be used for H minority heating or D majority heating with waves launched from an antenna located above the floating coil. Unlike a tokamak, where the targeted cyclotron resonance is typically a vertical path through the center of the plasma, in a dipole the resonance location follows a C-shaped path from the separatrix to the center of the plasma. The value of B also varies significantly within the confined plasma resulting in a large number of cyclotron harmonics present in the low field region. Furthermore, levitated dipoles contain a “first closed flux surface” surrounding the floating coil, in addition to the traditional separatrix /last closed flux surface. Simulation e ff orts using full-wave ICRF codes show that ICRF heating of a levitated dipole reactor is feasible using a pair of toroidal current straps phased to launch the appropriate parallel ( i.e. poloidal) refractive index.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2024

Overview of physics results from MAST upgrade towards core-pedestal-exhaust integration

Recent results from MAST Upgrade are presented, emphasising understanding the capabilities of this new device and deepening understanding of key physics issues for the operation of ITER and the design of future fusion power plants. The impact of MHD instabilities on fast ion confinement have been studied, including the first observation of fast ion losses correlated with Compressional and Global Alfvén Eigenmodes. High-performance plasma scenarios have been developed by tailoring the early plasma current ramp phase to avoid internal reconnection events, resulting in a more monotonic q profile with low central shear. The impact of m/n = 3/2, 2/1 and 1/1 modes on thermal plasma confinement and rotation profiles has been quantified, and scenarios optimised to avoid them have transiently reached values of normalised beta approaching 4.2. In pedestal and ELM physics, a maximum pedestal top temperature of ~350 eV has been achieved, exceeding the value achieved on MAST at similar heating power. Mitigation of type-I ELMs with n = 1 RMPs has been observed. Studies of plasma exhaust have concentrated on comparing conventional and Super-X divertor configurations, while X-point target, X-divertor and snowflake configurations have been developed and studied in parallel. In L-mode discharges, the separatrix density required to detach the outer divertors is approximately a factor 2 lower in the Super-X than the conventional configuration, in agreement with simulations. Detailed analysis of spectroscopy data from studies of the Super-X configuration reveal the importance of including plasma-molecule interactions and D 2 Fulcher band emission to properly quantify the rates of ionisation, plasma-molecule interactions and volumetric recombination processes governing divertor detachment. In H-mode with conventional and Super-X configurations, the outer divertors are attached in the former and detached in the latter with no impact on core or pedestal confinement.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2024

Visualizing an Exascale Data Center Digital Twin: Considerations, Challenges and Opportunities

Digital twins are an excellent tool to model, visualize, and simulate complex systems, to understand and optimize their operation. In this work, we present the technical challenges of real-time visualization of a digital twin of the Frontier supercomputer.We show the initial prototype and current state of the twin and highlight technical design challenges of visualizing such a large High Performance Computing (HPC) system. The goal is to understand the use of augmented reality as a primary way to extract information and collaborate on digital twins of complex systems. This leverages the spatio-temporal aspect of a 3D representation of a digital twin, with the ability to view historical and real-time telemetry, triggering simulations of a system state and viewing the results, which can be augmented via dashboards for details. Finally, we discuss considerations and opportunities for augmented reality of digital twins of large-scale, parallel computers.

Maiterth, Matthias↗

DOE OSTI2020

CephFS experiments on stria.sandia.gov

This report is an institutional record of experiments conducted to explore performance of a vendor installation of CephFS on the SNL stria cluster. Comparisons between CephFS, the Lustre parallel file system, and NFS were done using the IOR and MDTEST benchmarking tools, a test program which uses the SEACAS/Trilinos IOSS library, and the checkpointing activity performed by the LAMMPS molecular dynamics simulation.

74 ATOMIC AND MOLECULAR PHYSICS↗

DOE OSTI2020

CephFS experiments on stria.sandia.gov

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2024

Airborne LiDAR to Improve Canopy Fuels Mapping for Wildfire Modeling

Increasing conflict between wildfire and the built environment has increased the need for more up-to-date and finer resolution canopy fuels data to improve wildfire modeling and associated risk forecasts. The US Forest Service and US Department of the Interior’s LANDFIRE product, which provides 30-m resolution canopy fuels data for the entire US, is one of the most widely used sources of fuels data. However, the last complete mapping effort for LANDFIRE is based on 2016 conditions, and subsequent updates reflect disturbances 1-2 years behind the release year. Airborne systems equipped with Light Detection and Ranging (LiDAR) sensors can be deployed to actively sense canopy structure and estimate canopy fuels data (cover, height, base height, bulk density) at finer resolutions. Canopy base height (CBH) and canopy bulk density (CBD) are difficult to measure both in the field and in LiDAR point clouds. Still, they are important for accurately modeling crown fires, which are often intense and difficult to contain. Additionally, point cloud datasets are large, and calculations require efficient utilization of computational resources. To address these challenges, we are working on an approach that uses openly available National Ecological Observatory Network (NEON) airborne LiDAR data, with calculations processed in the R programming language and parallelized through the lidR package. CBH and CBD are often derived from tree height, diameter at breast height, and species-specific allometries using the Fire and Fuels Extension of the Forest Vegetation Simulator (FFE-FVS). We aim to test if airborne LiDAR can estimate CBH and CBD without the use of empirical equations. Reliable estimates of canopy fuels data directly from airborne LiDAR could streamline quick, fine-resolution updates for use in wildfire behavior models.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2021

System and method for testing missile components

A testing system for testing a missile component having a sense axis includes a centrifuge, a support arm, an orientation assembly, and a controller. The centrifuge rotates the orientation assembly about a vertical axis in a substantially horizontal plane. The orientation assembly includes a first motor, a first gimbal, and a gimballed support. The first motor has a first rotatable shaft defining a first gimbal axis. The first gimbal is coupled with the first rotatable shaft to rotate about the first gimbal axis while the centrifuge rotates the orientation assembly about the vertical axis such that missile component is simultaneously rotated about both the vertical axis and the first gimbal axis to simulate a missile launch of the missile component. The gimballed support is coupled with the first gimbal for supporting the missile component such that the sense axis of the missile component is not parallel to the substantially horizontal plane. The orientation assembly may also include a second gimbal that is rotated about a second gimbals axis by a second motor.

Prewitt, Steven Forrest↗