Kokkos 3: Programming Model Extensions for the Exascale Era
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97 MATHEMATICS AND COMPUTING↗
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Crash–and–dash: a new era in tree genome editing
In less than a decade since the first demonstrations of CRISPR genome editing of agronomic genes in several tree species (Zhou et al., 2015; Jia et al., 2016; Ren et al., 2016), this disruptive technology has been deployed for a growing number of traits in both basic and applied research. The precision and efficiency of CRISPR editing allow for the recovery of null mutants in the first generation (Zhou et al., 2015; Elorriaga et al., 2018; Muhr et al., 2018), which is a significant benefit for perennial trees with long generation times. The stability of editing outcomes over multiple years or clonal propagation cycles (Bewg et al., 2022; Chen et al., 2023; Goralogia et al., 2024) is another key advantage since most woody perennials are vegetatively propagated in commercial operations. However, in many countries, gene-edited trees with stably integrated T-DNA face the same regulatory hurdles as traditional transgenics, slowing field trial characterization and the integration of transgenesis with conventional breeding (Boerjan & Strauss, 2024). In an article recently published in New Phytologist, Hoengenaert et al. (2025; doi: 10.1111/nph.20415) demonstrate transgene-free editing in poplar (Populus tremula × alba) that shows promise for wide adoption. The CRISPR-edited, transgene-free canker-resistant citrus (Citrus sinensis) trees (Su et al., 2023) have recently been approved by USDA-APHIS and are exempt from regulation by the US Environmental Protection Agency (EPA) for commercial production. The work by Hoengenaert et al. (2025) suggests a similar path could be followed for purpose-grown plantations for bioenergy, bioproducts, and biomaterials.
59 BASIC BIOLOGICAL SCIENCES↗
VTK-m: Visualization for the Exascale Era and Beyond
A recent trend in modern high-performance computing is the increasing use of hybrid architectures, where the vast majority of performance comes from accelerators. Modern accelerators are based on Graphics Processing Units (GPU) that contain many low power cores that in their aggregate provides an extremely high computation rate. Current and future CPU processors are requiring more explicit parallelism as each successive version of the hardware packs in more cores, and technologies like hyperthreading and vector operations require even more parallel processing to leverage each core’s full potential. As an example, the Frontier supercomputer installed at Oak Ridge National Laboratories recently hit a record breaking 1.1 exaflops1 on the LINPACK HPC benchmark [Shoemaker 2022]. The system contains 37632 AMD MI250x GPUs which requires more than half a billion threads to keep the system fully utilized [Khizeran 2022].VTK-m is a toolkit of scientific visualization algorithms for these emerging processor architectures. VTK-m supports the fine-grained concurrency for data analysis and visualization algorithms required to drive extreme scale computing by providing abstract models for data and execution that can be applied to a variety of algorithms across many different processor architectures.
Bolstad, Mark↗
The (R)evolution of Scientific Workflows in the Agentic AI Era: Towards Autonomous Science
Modern scientific discovery increasingly requires coordinating distributed facilities and heterogeneous resources, forcing researchers to act as manual workflow coordinators rather than scientists. Advances in AI leading to AI agents show exciting new opportunities that can accelerate scientific discovery by providing intelligence as a component in the ecosystem. However, it is unclear how this new capability would materialize and integrate in the real world. To address this, we propose a conceptual framework where workflows evolve along two dimensions which are intelligence (from static to intelligent) and composition (from single to swarm) to chart an evolutionary path from current workflow management systems to fully autonomous scientific laboratories. With these trajectories in mind, we present an architectural blueprint that can help the community take the next steps towards harnessing the opportunities in autonomous science with the potential for 100x discovery acceleration and transformational scientific workflows.
Shin, Woong [ORNL] (ORCID:0000000172077814)↗
Plant Cell Identity in the Era of Single-Cell Transcriptomics
High-throughput single-cell transcriptomic approaches have revolutionized our view of gene expression at the level of individual cells, providing new insights into their heterogeneity, identities, and functions. Recently, technical challenges to the application of single-cell transcriptomics to plants have been overcome, and many plant organs and tissues have now been subjected to analyses at single-cell resolution. In this review, we describe these studies and their impact on our understanding of the diversity, differentiation, and activities of plant cells. We particularly highlight their impact on plant cell identity, including unprecedented views of cell transitions and definitions of rare and novel cell types. Lastly, we also point out current challenges and future opportunities for the application and analyses of single-cell transcriptomics in plants.
59 BASIC BIOLOGICAL SCIENCES↗
HDF5 in the exascale era: Delivering efficient and scalable parallel I/O for exascale applications
Accurately modeling real-world systems requires scientific applications at exascale to generate massive amounts of data and manage data storage efficiently. However, parallel input and output (I/O) faces challenges due to new application workflows and the state-of-the-art memory, interconnect, and storage architectures considered in exascale designs. The storage hierarchy has expanded with node-local persistent memory, solid-state storage, and traditional disk and tape-based storage, thus requiring efficiency at each layer and much more efficient data movement among these layers. This paper discusses how the ExaHDF5 project improved the I/O performance and data management for exascale architectures by enhancing HDF5, a widely used parallel I/O library. The team developed an Asynchronous I/O Virtual Object Layer (VOL) connector that allowed overlapping I/O with computation. They also created a Cache VOL to complement asynchronous I/O by incorporating fast storage layers, such as burst buffer and node-local storage, into the parallel I/O workflow through caching and staging data. Additionally, the team enabled data aggregation and I/O at the node level by using a Subfiling Virtual File Driver (VFD). To demonstrate superior I/O performance with HDF5 at exascale, the ExaHDF5 team collaborated with several exascale applications. In this paper, we show I/O performance improvements for three applications: Cabana (a particle-based simulation library), EQSIM (a regional earthquake simulation software), and E3SM (a climate system modeling library).
Asynchronous I/Ol↗
HPC I/O innovations in the exascale era
As high performance computing architecture evolves to deliver ever-increasing performance, the middleware tools also need to adapt in order for applications to better use these higher-performance features. Here, the Adaptable Input Output System (ADIOS), which provides scalable IO performance for exascale HPC applications is one such middleware. During the Exascale Computing Project (ECP), key portions of the ADIOS environment were adapted to respond to ongoing developments in exascale computing and the stresses and opportunities inherent in those changes. This paper examines those changes and where appropriate compares them to pre-exascale implementations.
ADIOS↗
A new era of ferroelectric thin films for nonvolatile memories
Ferroelectric films have potential applications in nonvolatile memory devices. In addition to the well-established perovskite-structure oxide ferroelectrics, hafnia- and wurtzite-based ferroelectrics have recently attracted considerable attention because of the improved scalability of the ferroelectric response (down to nanometer thicknesses), their compatibility with silicon fabrication processes, and the availability of deposition methods that realize three-dimensional structures. Furthermore, due to their high compatibility with silicon processes, these are also expected to be used in emerging energy-efficient applications, such as neuromorphic computing and reservoir computing. In this article, we review the fundamentals of hafnia- and wurtzite-based ferroelectrics and their advantages and issues for developing in nonvolatile memory devices. Then, possible emerging applications are discussed.
36 MATERIALS SCIENCE↗
Directed self-assembly of block copolymers for high-precision patterning in the era of extreme ultraviolet lithography
Extreme ultraviolet (EUV) lithography enables unprecedented resolution in semiconductor patterning but faces critical challenges in developing resist materials that achieve high-precision at economically viable throughput. Directed self-assembly (DSA) of block copolymers (BCPs) offers a promising solution for pattern rectification by leveraging thermodynamically determined domain structures to decouple BCP pattern quality from the imperfect original lithographic pattern. This prospective presents an overview of recent progress on the EUV + DSA strategy, covering advances in BCP material design, processing, metrology, and pattern transfer. We highlight recent advances in high-χ BCPs with perpendicular orientation and domain spacings compatible with EUV dimensions, leveraging A-b-(B-r-C) architectures. We also discuss progress in chemical pre-pattern fabrication using both positive- and negative tone resists, along with processing strategies to minimize defects and roughness based on BCP thermodynamics and assembly kinetics. We further examine metrology platforms for characterizing the thermodynamics of BCP materials and quantifying the size and shape of BCP domains. Lastly, we review pattern transfer strategies for generating functional inorganic masks suitable for semiconductor manufacturing. Together, these advances highlight the potential of DSA to complement EUV lithography, offering a pathway to address critical challenges in achieving high-precision patterning for the semiconductor industry.
Lee, Kyunghyeon [Univ. of Chicago, IL (United Stat↗
Validating Synthetic Galaxy Catalogs for Dark Energy Science in the LSST Era
Large simulation efforts are required to provide synthetic galaxy catalogs for ongoing and upcoming cosmology surveys. These extragalactic catalogs are being used for many diverse purposes covering a wide range of scientific topics. In order to be useful, they must offer realistically complex information about the galaxies they contain. Hence, it is critical to implement a rigorous validation procedure that ensures that the simulated galaxy properties faithfully capture observations and delivers an assessment of the level of realism attained by the catalog. We present here a suite of validation tests that have been developed by the Rubin Observatory Legacy Survey of Space and Time (LSST) Dark Energy Science Collaboration (DESC). We discuss how the inclusion of each test is driven by the scientific targets for static ground-based dark energy science and by the availability of suitable validation data. The validation criteria that are used to assess the performance of a catalog are flexible and depend on the science goals. We illustrate the utility of this suite by showing examples for the validation of cosmoDC2, the extragalactic catalog recently released for the LSST DESC second Data Challenge.
72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
Physics motivation and detector upgrades for the new era of the ATLAS experiment
The ATLAS experiment at CERN’s Large Hadron Collider (LHC) will be upgraded in two stages to prepare first for the Run~3 data-taking campaign, during which the integrated luminosity will roughly double, and then for the High-Luminosity LHC program with an ultimate integrated luminosity of up to 4 ab ^{{-1}} − 1 . These upgrades and high-statistics datasets will allow ATLAS to perform searches and precision measurements to constrain the Standard Model in yet-unexplored phase spaces and in the Higgs sector. This contribution summarizes the ATLAS detector upgrades and selected physics prospects for Run~3 and the HL-LHC.
Nielsen, Jason↗
Understanding Structures of Cyber Competition in an Era of Major Power Rivalry
Over the past two decades, the cyber domain has emerged and evolved into a key strategic domain for nations across the globe. Security strategies are espoused by heads of state that focus on how to manage the increasingly enormous, crosscutting impact that the cyber domain has on national security across economic, military, intelligence, intellectual property, and countless other facets. These strategies frequently evolve, and even change entirely, as leaders adapt to new technologies and administrations change. Even if these strategies did not change at all, they would take inordinate amounts of time to effectively implement within the organizational structures of government. The time required to go from setting department and agency-level goals, to the time small teams have well-oiled processes and expertise to accomplish tactical objectives that meet the strategic vision is lengthy. With near certainty, by the time objectives and vision are implemented, the landscape, strategy, or both has changed entirely. While this churn will likely never cease due to the rapidly changing nature of the cyber domain, this problem raises an important question: can governmental structures be organized to rapidly adapt to changing cyber strategies? As offices responsible for particular missions in cyberspace shuffle about within the bureaucracy, are technical capabilities enabled or enhanced? No matter how advanced a particular technical capability is or how adept the staff is at solving problems, they will be ineffective if placed haphazardly within the organization: the right authorities may not exist for their office, the correct lines of interpersonal communication may not be established properly, or insufficient resources have not been allocated to effectively deploy a brilliant technical solution. This concept of organizational agility in the context of national cyber capabilities is important when taking into account the National Defense Strategy’s emphasis on cyber capability and the ability of the United States to compete and rapidly adapt to new challenges posed by rivals. As a nation, we are at a point where technology evolves rapidly enough to warrant thoughtful and nimble changes to the bureaucratic structures that support how cyber operations are carried out. Taking these questions and cross-comparing them to the organizational structures across China, Russia, and the United States provides for an interesting thought experiment. As non-democratic regimes, China and Russia have differing priorities and internal power dynamics than the United States and thus organize their governments differently. By combining known and broadcasted strategies of these nations with the observed technical capabilities demonstrated in the public domain, we can begin to see how organizational structures map to strategic goals and directly enable technical capabilities. Insight can be gained by introducing organizational structures into traditional analysis focusing solely around strategies and capabilities; additionally, otherwise unknown capabilities or intents might be discovered or inferred by analyzing organizational structures alone. Analyzing cyber operations from this oft-overlooked perspective could potentially provide useful insight and more concrete actions that can be undertaken to realize the National Defense Strategy’s goals.
45 MILITARY TECHNOLOGY, WEAPONRY, AND NATIONAL DEF↗
LDRD DR 20200022DR. First year Appraisal: A new era of nuclear physics at the electron-ion collider [PowerPoint]
The first year review of the project is presented, including the following topics: introduction of the EIC; project team and resources; project scope, science and outreach; feasibility review; minimal and stretch goals; organization chart - theory; summary of project deliverables met; detailed account of perturbative QCD accomplishments; and conclusions.
73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
Nuclear Risk Reduction in an Era of Major Power Rivalry: Annotated Bibliography
Abstract not provided.
45 MILITARY TECHNOLOGY, WEAPONRY, AND NATIONAL DEF↗
A new era of observationally-infused E3SM: GANs for unifying imagery archives
This paper presents an idea to develop a “Rosetta Stone” for unifying observations from various satellite or remote sensors into a common format that would vastly advance our ability to exploit existing datasets for improving predictability within Earth System Models (ESMs). While the applications of such a unified archive are broad, we believe it will be a critical step toward ushering in a new generation of ESMs that are richly informed, guided by, and validated by extensive observational data. With the vast quantity of both remotely-sensed and in-situ data streams available and coming online, new approaches are needed that can harmonize and thus fully exploit these expensive datasets. While we present the broader idea, we point to examples of applications that impact the water cycle and its representation in ESMs.
58 GEOSCIENCES↗