7 Search Results

Journal article detailing how AI/ML and data science tools can be deployed for understanding multiple systems in offshore geologic carbon storage.

The Exascale Computing Project (ECP) Software Technology and Co-Design teams addressed the growing complexities in high-performance computing (HPC) by developing scalable software libraries and tools that leverage exascale system capabilities. As we enter the exascale era, the need for reusable, optimized software solutions that can handle the unique challenges posed by these systems becomes increasingly important. The primary challenges the ECP teams faced were to create software libraries and tools that are performant on exascale architectures and portable and usable across diverse hardware platforms. Efforts addressed issues related to concurrent execution, memory management, and the integration of heterogeneous computing resources,more » such as GPUs from multiple vendors. The ECP’s strategy involved a structured development process encompassing the creation, optimization, and deployment of software in collaboration with industry, academia, and national laboratories. The project was organized into several technical areas: co-design of domain-specific suites with target applications, programming models and runtimes, development tools, mathematical libraries, data and visualization tools, and software ecosystem and delivery mechanisms. ECP has successfully developed a large portfolio of software libraries and tools that demonstrate significant improvements in performance and scalability on exascale systems. These products have been integrated into the Department of Energy’s computing facilities, supporting various scientific applications and ensuring robust performance across different hardware setups. ECP advancements in software development for exascale computing highlight the importance of a collaborative and adaptive approach to handling next-generation HPC systems complexities. The lessons learned emphasize the need for continuous engagement with end-users and vendors, and the importance of maintaining a balance between innovation and practical implementation. Future efforts will focus on ensuring scalability, keeping pace with rapid hardware advancements, and further enhancing the interoperability and usability of the software ecosystem. In conclusion, subsequent articles in this special issue provide in-depth discussions and case studies into specific library and tool efforts.« less

WormBase (www.wormbase.org) is the central repository for the genetics and genomics of the nematode Caenorhabditis elegans. We provide the research community with data and tools to facilitate the use of C. elegans and related nematodes as model organisms for studying human health, development, and many aspects of fundamental biology. Throughout our 22-year history, we have continued to evolve to reflect progress and innovation in the science and technologies involved in the study of C. elegans. We strive to incorporate new data types and richer data sets, and to provide integrated displays and services that avail the knowledge generated by themore » published nematode genetics literature. Here, we provide a broad overview of the current state of WormBase in terms of data type, curation workflows, analysis, and tools, including exciting new advances for analysis of single-cell data, text mining and visualization, and the new community collaboration forum. Concurrently, we continue the integration and harmonization of infrastructure, processes, and tools with the Alliance of Genome Resources, of which WormBase is a founding member.« less

Calling context trees (CCTs) couple performance metrics with call paths, helping understand the execution and performance of parallel programs. To identify performance bottlenecks, programmers and performance analysts visually explore CCTs to form and validate hypotheses regarding degraded performance. However, due to the complexity of parallel programs, existing visual representations do not scale to applications running on a large number of processors. In this work, we present CallFlow, an interactive visual analysis tool that provides a high-level overview of CCTs together with semantic refinement operations to progressively explore CCTs. Using a flow-based metaphor, we visualize a CCT by treating execution timemore » as a resource spent during the call chain, and demonstrate the effectiveness of our design with case studies on large-scale, production simulation codes.« less

In this study, a method is described for deriving two levels of action—an investigation level (IL) and an immediate action level (IAL)—for different forms and mixtures of the natural uranium (U) isotopes ²³⁴U, ²³⁵U, and ²³⁸U in air in the workplace. An IL indicates the need to confirm the validity of moderately elevated measurements of airborne U and adequacy of confinement controls and determine whether work limitations are appropriate. An IAL indicates that safeguards should be put into place immediately, including removal of workers from further exposure until conditions are acceptable. Derivations of ILs and IALs are based on latestmore » radiation protection guidance, information on chemical toxicity of U, and biokinetic models for U. An action level (IL or IAL) is the more restrictive of two derived values, the action level based on U as a chemical hazard and the action level based on U as a radiation hazard.« less

We explored microbial contributions to decomposition using a sophisticated approach to DNA Stable Isotope Probing (SIP). Our experiment evaluated the dynamics and ecological characteristics of functionally defined microbial groups that metabolize labile and structural C in soils. We added to soil a complex amendment representing plant derived organic matter substituted with either ¹³C-xylose or ¹³C-cellulose to represent labile and structural C pools derived from abundant components of plant biomass. We found evidence for ¹³C-incorporation into DNA from ¹³C-xylose and ¹³C-cellulose in 49 and 63 operational taxonomic units (OTUs), respectively. The types of microorganisms that assimilated ¹³C in the ¹³C-xylose treatmentmore » changed over time being predominantly Firrnicutes at day 1 followed by Bacteroidetes at day 3 and then Actinobacteria at day 7. These ¹³C-labeling dynamics suggest labile C traveled through different trophic levels. In contrast, microorganisms generally metabolized cellulose-C after 14 days and did not change to the same extent in phylogenetic composition over time. Furthermore, microorganisms that metabolized cellulose-C belonged to poorly characterized but cosmopolitan soil lineages including Verrucomicrobia, Chlorotlexi, and Planctomycetes.« less