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At least 91 records · Page 5

EyeON

EyeON: Eye on Operational technology Software Supply Chain attacks have risen drastically over the past few years, none more well-known and impactful than the SolarWinds compromise. Criminal organizations inserted an attack vector into a specific version of the source code, giving themselves an air of credibility. Once news broke on SolarWinds, identifying compromised sites was very difficult, even knowing the culprit update. Software Bills of Materials (SBOM) have been touted as the solution to reclaiming control of your software supply chain. Deployment of SBOMs has been slow, however, due to conflicting standards, opaque storage requirements, and vendor adoption. Additionally, the path from obtaining an SBOM and securing your supply chain is unclear; how can an SBOM library be leveraged to provide insight to your attack surface? The EyeON tool, sponsored by Department of Energy Cybersecurity, Energy Security, and Emergency Response (DoE CESER), aims to address these gaps by providing an encapsulated solution to tracking which updates have been installed in an enterprise, and alerting system administrators to vulnerabilities as they become known. Similar to a virus scanner, EyeON is a command line tool to parse either a single file, nested directory structure, or filesystem. It collects data such as signature (hashes), version information, VirusTotal tags, compiler, compilation date, and code signing information. Users will anonymously submit scan data periodically to DoE CESER, who will then compile a database of known software products employed by Critical Infrastructure and broadcast alerts based on discovered flaws as they arise.

Tenzing, Wangmo↗

Consist v0.1.0

A Python library for provenance tracking, intelligent caching, and data virtualization in scientific simulation workflows. It automatically records code, configuration, and input data to skip redundant computations and enables querying results across many runs without manual bookkeeping. Designed to support multi-model simulation workflows like the BEAM CORE toolset at LBL, but designed to be extensible to a wide range of research workflows. Combines lineage tracking features as provided by OpenLineage with deterministic hashing like SnakeMake, and adds powerful analysis tools on model outputs.

Needell, Zachary [Lawrence Berkeley National Labor↗

Enhancing reproducibility in scientific computing: Metrics and registry for Singularity containers

Here we present Singularity Hub, a framework to build and deploy Singularity containers for mobility of compute, and the singularity-python software with novel metrics for assessing reproducibility of such containers. Singularity containers make it possible for scientists and developers to package reproducible software, and Singularity Hub adds automation to this workflow by building, capturing metadata for, visualizing, and serving containers programmatically. Our novel metrics, based on custom filters of content hashes of container contents, allow for comparison of an entire container, including operating system, custom software, and metadata. First we will review Singularity Hub’s primary use cases and how the infrastructure has been designed to support modern, common workflows. Next, we conduct three analyses to demonstrate build consistency, reproducibility metric and performance and interpretability, and potential for discovery. This is the first effort to demonstrate a rigorous assessment of measurable similarity between containers and operating systems. We provide these capabilities within Singularity Hub, as well as the source software singularity-python that provides the underlying functionality. Singularity Hub is available at https://singularity-hub.org, and we are excited to provide it as an openly available platform for building, and deploying scientific containers.

97 MATHEMATICS AND COMPUTING↗

SEGUID v2: Extending SEGUID checksums for circular, linear, single- and double-stranded biological sequences

Background Synthetic biology involves combining different DNA fragments, each containing functional biological parts, to address specific problems. Fundamental gene-function research often requires cloning and propagating DNA fragments, such as those from the iGEM Parts Registry or Addgene, typically distributed as circular plasmids. Addgene’s repository alone offers around 150,000 plasmids. To ensure data integrity, cryptographic checksums can be calculated for the sequences. Each sequence has a unique checksum, making checksums useful for validation and quick lookups of associated annotations. For example, the SEGUID checksum uniquely identifies protein sequences with a 27-character string. Objectives The original SEGUID, while effective for protein sequences and single-stranded DNA (ssDNA), is not suitable for circular DNA since there is no natural starting position nor for double-stranded DNA (dsDNA) since two separate sequences are present. Challenges include how to uniquely represent linear dsDNA, circular ssDNA, and circular dsDNA. To meet these needs, we propose SEGUID v2, which extends the original SEGUID to handle additional types of sequences. Conclusions SEGUID v2 produces orientation and rotation invariant checksums for single-stranded, double-stranded, possibly staggered, linear, and circular DNA and RNA sequences. Customizable alphabets allow for other types of sequences. In contrast to the original SEGUID, which uses Base64, SEGUID v2 uses Base64url to encode the SHA-1 hash. This ensures SEGUID v2 checksums can be used as-is in filenames, regardless of platform, and in URLs, with minimal friction. Availability SEGUID v2 is readily available for major programming languages, distributed under the MIT license. JavaScript package seguid is available on npm, Python package seguid on PyPi, R package seguid on CRAN, and a Tcl script on GitHub. These tools, along with documentation, examples, and an online SEGUID Calculator , can be found at https://www.seguid.org .

Pereira, Humberto↗

Stacked filters: learning to filter by structure

We present Stacked Filters, a new probabilistic filter which is fast and robust similar to query-agnostic filters (such as Bloom and Cuckoo filters), and at the same time brings low false positive rates and sizes similar to classifier-based filters (such as Learned Filters). The core idea is that Stacked Filters incorporate workload knowledge about frequently queried non-existing values. Instead of learning, they structurally incorporate that knowledge using hashing and several sequenced filter layers, indexing both data and frequent negatives. Stacked Filters can also gather workload knowledge on-the-fly and adaptively build the filter. We show experimentally that for a given memory budget, Stacked Filters achieve end-to-end query throughput up to 130x better than the best alternative for a workload, either query-agnostic or classifier-based filters, and depending on where data is (SSD or HDD).

Computer Science↗

Theoretically and practically efficient parallel nucleus decomposition

This paper studies the nucleus decomposition problem, which has been shown to be useful in finding dense substructures in graphs. We present a novel parallel algorithm that is efficient both in theory and in practice. Our algorithm achieves a work complexity matching the best sequential algorithm while also having low depth (parallel running time), which significantly improves upon the only existing parallel nucleus decomposition algorithm (Sariyüce et al. , PVLDB 2018). The key to the theoretical efficiency of our algorithm is a new lemma that bounds the amount of work done when peeling cliques from the graph, combined with the use of a theoretically-efficient parallel algorithms for clique listing and bucketing. We introduce several new practical optimizations, including a new multi-level hash table structure to store information on cliques space-efficiently and a technique for traversing this structure cache-efficiently. On a 30-core machine with two-way hyper-threading on real-world graphs, we achieve up to a 55x speedup over the state-of-the-art parallel nucleus decomposition algorithm by Sariyüce et al. , and up to a 40x self-relative parallel speedup. We are able to efficiently compute larger nucleus decompositions than prior work on several million-scale graphs for the first time.

Computer Science↗

Microseismic Focal Mechanisms and Implications for Changes in Stress during the 2014 Newberry EGS Stimulation

We adapt the relative polarity method from Shelly et al. (2016) to compute focal mechanisms for microearthquakes associated with the 2014 hydroshearing stimulation at the Newberry volcano geothermal site. We focus the analysis on events relocated by Aguiar and Myers (2018), who report that six event clusters predominantly comprise the 2014 sequence. Data quality allows focal mechanism analysis for four of the six event clusters. We use Hardebeck and Shearer (2002, 2003; hereafter HASH) to compute focal mechanisms based on first–motion polarities and S/P amplitude ratios. We manually determine P– and S–wave polarities for a well–recorded reference event in each cluster, then use waveform cross correlation to determine whether recordings of other events in the cluster are the same or reversed polarity at each network station. Here, most waveform polarities are consistent with the affiliated reference event, indicating similar focal mechanisms within each cluster. The deeper clusters are east–west–striking normal faults, whereas the shallower clusters, close to the top of the open–hole section of the borehole, are strike slip with east–west motion. Regional studies and prestimulation borehole breakouts find the maximum stress direction is vertical and maximum horizontal stress is approximately north–south. Fault geometry and focal mechanisms of microseismicity during the stimulation suggest that increased pressure from fluid injection predominantly caused changes in horizontal stress, consistent with predictions from numerical studies of stress change caused by fluid injection. At shallow depths, where previous studies suggest the difference between vertical and horizontal stress is lowest, injection appears to have rotated the direction of maximum stress from vertical to horizontal, resulting in strike–slip motion. At greater depth, vertical stress continued to be the dominant direction during the stimulation, but fault orientation indicates either reactivation of pre–existing fractures or rotation of the direction of maximum horizontal stress from approximately north–south to east–west.

15 GEOTHERMAL ENERGY↗

FleCSPH notes

FleCSI is a compile-time con gurable framework designed to support multi-physics application development. As such, FleCSI provides a very general set of infrastructure design patterns that can be specialized and extended to suit the needs of a broad variety of solver and data requirements. FleCSI currently supports multi-dimensional mesh topology, geometry, and adjacency information, as well as n-dimensional hashed-tree data structures, graph partitioning interfaces, and dependency closures. FleCSI introduces a functional programming model with control, execution, and data abstractions that are consistent both with MPI and with state-of-the-art, task-based runtimes such as Legion and Charm++. The abstraction layer insulates developers from the underlying runtime, while allowing support for multiple runtime systems including conventional models like asynchronous MPI. The intent is to provide developers with a concrete set of user-friendly programming tools that can be used now, while allowing exibility in choosing runtime implementations and optimization that can be applied to future architectures and runtimes. FleCSI's control and execution models provide formal nomenclature for describing poorly understood concepts such as kernels and tasks. FleCSI's data model provides a low-buy-in approach that makes it an attractive option for many application projects, as developers are not locked into particular layouts or data structure representations. FleCSI currently provides a parallel but not distributed implementation of Binary, Quad and Oct-tree topology. This implementation is base on space lling curves domain decomposition, the Morton order. The current FleCSI version requires the implementation of a driver and a specialization driver. The role of the specialization driver is to provide the data distribution. This feature is not complete in FleCSI code and we provide it. The next step will be to incorporate it directly from FleCSPH to FleCSI as we reach a good level of performance. Then the driver represent the general execution of the resolution without worrying of the data locality and communications. As FleCSI is an On-Development code the structure may change in the future and we keep track of these changes in FleCSPH.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

ATDM LANL FleCSI: Topology and Execution Framework

FleCSI is a compile-time configurable C++ framework designed to support multi-physics application development. As such, FleCSI attempts to provide a very general set of infrastructure design patterns that can be specialized and extended to suit the needs of a broad variety of solver and data requirements. This means that FleCSI is potentially useful to many different ECP projects. Current support includes multidimensional mesh topology, mesh geometry, and mesh adjacency information, n-dimensional hashed-tree data structures, graph partitioning interfaces, and dependency closures (to identify data dependencies between distributed-memory address spaces). FleCSI introduces a functional programming model with control, execution, and data abstractions that are consistent with state-of-the-art task-based runtimes such as Legion and Charm++. The model also provides support for fine-grained, data-parallel execution with backend support for runtimes such as OpenMP and C++17. The FleCSI abstraction layer provides the developer with insulation from the underlying runtimes, while allowing support for multiple runtime systems, including conventional models like asynchronous MPI. The intent is to give developers a concrete set of user-friendly programming tools that can be used now, while allowing flexibility in choosing runtime implementations and optimizations that can be applied to architectures and runtimes that arise in the future. This project is essential to the ECP Ristra Next-Generation Code project, part of ASC ATDM, because it provides a hierarchically parallel programming model that is consistent with the design of modern system architectures, but which allows for the straightforward expression of algorithmic parallelism in a portably performant manner.

97 MATHEMATICS AND COMPUTING↗

Side Channel Considerations for SHA-512

We consider a theoretical side-channel attack on SHA-512; the attack should easily generalize to other algorithms in the SHA-2 family. Rather than looking at a side-channel attack on an HMAC, which has been done in various papers, we assume that the targeted device is applying the hash function as a pseudo-random function (prf) in order to generate a secret key from a secret seed, as recommended by NIST. The analyst uses side-channel information to try to recover the secret seed. We use entropy/information theory to show how one might judge whether or not a side-channel attack might be possible and/or feasible, and we show how the design of the implementation can affect the feasibility of an attack.

97 MATHEMATICS AND COMPUTING↗

Development of High-efficiency and Cost-effective Forged Ingot Niobium Technology for Science Frontiers and Accelerator Applications

Development of Forged Ingot Niobium Technology: Worlds science frontier programs and SRF accelerator applications demand high performance and cost-effective SRF accelerator technology [1-8]. Fine-grain (FG) and Large-grain (LG) ingot niobium technologies have been very well developed and implemented in all the present-day accelerator projects. However, forged ingot niobium technology which is the focus of this development proposal will be much more cost-effective and expected to have several technical advantages. FG niobium sheet production is very complex involving more than ten processing steps making them prone to contamination. As a result, they are very expensive to produce and require stringent QA procedure to be ready for SRF cavity production. The accelerating cavity process steps are also numerous and require strict procedures in order to achieve high accelerating gradients and quality factors needed for science frontier programs. LG niobium disc production, directly sliced from the ingot, is relatively simple and straight forward to keep surface cleanness. The disc production cost is significantly low compared to FG niobium sheet production. However, there are (some) draw backs due to non-homogeneity of the grain boundary distribution, resulting in non-uniform mechanical properties and complex cavity fabrication, although the LG cavities achieve the expected high-gradient performance goals with lower cost. Medium-grain (MG) niobium disk production may be realized with a new approach/process, the disc directly sliced from the forged ingot, involves a simpler process steps contributing major production cost reduction [9]. These discs are expected to be superior as they tend to be homogenous with uniform sub millimeter grains and mechanical properties. We are eagerly looking forward to developing the forged ingot niobium SRF accelerator technology for the benefit of the world-wide science frontier programs, green energy subcritical nuclear energy systems and a wide variety of industrial applications including the production of radio isotopes and nuclear transmutation applications. Measurement of thermal characteristics of the forged ingot niobium: Measurement of the thermal diffusivity, D, of superconducting MG niobium is important to be understood in comparison with FG sheet and LG disc, as well as that of advanced composite material of Nb3Sn film sputtered on forged ingot Nb, which will be determined using transient pump-probe thermo-modulation [10,11]. Transient thermo-modulation is based on using an ultrafast laser pulse to heat the superconducting materials by a few K, then a synchronized laser pulse probes the reflectance of the heated material. For thin films on a substrate (e.g, 100-nm Nb3Sn on Nb), it takes <100 ps for the heat to reach the substrate by diffusion. Therefore, an ultrafast method is needed to probe D of the studied material. D will be measured from room temperature to liquid helium temperatures. Fundamental Research: The increase of rf loss in SRF cavities is related to trapping of residual magnetic field during the cavity cool-down. The study suggested that the micro structure plays the role in flux trapping sensitivity. The research includes the flux trapping and expulsion study as forged ingot niobium goes through several mechanical deformations, crystallization leading to the optimal SRF cavity performance. Furthermore, the cavity made from FG, MG, and LG sheet/disc will be compared to understand the optimal re-crystallization temperature that cavity needed to be heat treated which minimize the flux trapping and increase SRF cavity performance. References: 1. S. Belomestnykh, Overview of recent SRF developments for ERLs, presented at the SRF 2015, Whistler, BC, Canada (2015). 2. A. Yamamoto, M. Yamanaka and G. Myneni, Ingot Nb based SRF Technology for the International Linear Collider, in Science and Technology of Ingot Niobium for Superconducting Radio Frequency Applications, AIP Conf. Proc. 1687, 030005-1 ? 03005-6, 2015 3. Report of the Workshop on Energy and Environmental Applications of Accelerators, DOE Workshop Report. https://science.osti.gov/-/media/hep/pdf/Reports/2020/CASM_WorkshopReport.pdf? la=en&hash=AEB0B318ED0436B1C5FF4EE0FDD6DEB84C2F15B2 4. G. Ciovati, et al., Design of a cw, low-energy, high-power superconducting linac for environmental applications, Phys. Rev. Accel. Beams 21, 091601 (2018). 5. P. Dhakal, et al., Effect of high temperature heat treatments on the quality factor of a large-grain superconducting radio-frequency niobium cavity, Phys. Rev. ST Accel. Beams 16, 042001 (2013). 6. P. Kneisel et al., Review of ingot niobium as a material for superconducting radio frequency accelerating cavities, Nuclear Instruments and Methods in Physics Research A 774, 133 (2015). 7. G. Ciovati, P. Dhakal, and G. R, Myneni, Superconducting radio-frequency cavities made from medium and low-purity niobium ingots, Supercond. Sci. Technol. 29, 064002 (2016). 8. M. Drury et al., commissioning of the prototype C75 cavities in a CEBAF cryomodule, in Proc. of IPAC 2018, Vancouver, BC, Canada (2018) 9. Feasibility of forged-ingot niobium disc and SRF cavity fabrication technology recently demonstrated in cooperation of ATI, BSCE, and KEK (2020). 10. Hani E. Elsayed-Ali, ?Measurements of heat transport in thin films by ultrafast laser-based techniques,? 3rd International Conference on Thermal Issues in Emerging Technologies Theory and Applications, Cairo, Egypt, pp. 347 ? 350 (2010). DOI: 10.1109/ThETA17616.2010 11. W. M. G. Ibrahim, H. E. Elsayed-Ali, M. Schinn, and C. A. Bonner, Jr., ?Ultrafast investigation of electron dynamics in multilayer metals,? Int. J. Heat and Mass Transfer, 47(10?11), 2261?2268 (2004).

Myneni, G.↗

Data Structure Alchemy

In an increasingly more data-driven world, the project set out to uncover the first principles of data-structure design, chart the immense design space they form, and build automation that can synthesize an optimal structure, or even a whole storage engine, for any given workload, hardware platform, and cost target. Data structures are at the center of every computational system and are directly responsible for its performance. Two core technical thrusts were defined: 1) Mapping design spaces for key data-centric abstractions (filters, hash functions, storage-engine layouts, neural-network topologies, blockchain protocols, image layouts, etc.). 2) Developing search & synthesis algorithms, initially analytical cost models, later neural-guided bi-level optimisers that navigate sextillions of candidate designs in seconds and materialise the best one as ready‐to-run code. This report distills the key insights, accomplishments, and impact.

97 MATHEMATICS AND COMPUTING↗

NEAMS Technical Area Support in MOOSE

The Multiphysics Object-Oriented Simulation Environment (MOOSE) framework is a foundational capability used by the Nuclear Energy Advanced Modeling and Simulation (NEAMS) program to create over 15 different simulation tools for advanced nuclear reactors. Due to this ubiquity, improvements to the framework in support of modeling and simulation goals are critical to the program. These improvements can take many forms, including optimization, improved user experience, streamlined application programming interfaces (APIs), parallelism, and other new capabilities. The work described in this report was conducted in direct support of the simulation tools and has already been deployed. The capabilities outlined in this report include implementing hash table matrix assembly for efficient sparsity pattern construction for contact in BISON, developing re-step testing infrastructure for ensuring the viability of overlapping domain coupling between SAM and Pronghorn, allowing unique preconditioners for single-input multi-system solves, supporting multi-system in MOOSE’s workhorse executioners, and many more smaller feature enhancements and bug fixes.

97 - MATHEMATICS AND COMPUTING↗

The effects of storms and a transient sandy veneer on the interannual planform evolution of a low-relief coastal cliff and shore platform at Sargent Beach, Texas, USA

Coastal cliff erosion is alongshore-variable and episodic, with retreat rates that depend upon sediment as either tools of abrasion or protective cover. However, the feedbacks between coastal cliff planform morphology, retreat rate, and sediment cover are poorly quantified. This study investigates Sargent Beach, Texas, USA, at the annual to interannual scale to explore (1) the relationship between temporal and spatial variability in cliff retreat rate, roughness, and sinuosity and (2) the response of retreat rate and roughness to changes in sand and shell hash cover of the underlying mud substrate as well as the impact of major storms using field measurements of sediment cover, erosion, and aerial images to measure shore platform morphology and retreat. A storm event in 2009 increased the planform roughness and sinuosity of the coastal cliff at Sargent Beach. Following the storm, aerial-image-derived shorelines with annual resolution show a decrease in average alongshore erosion rates from 12 to 4 m yr –1 , coincident with a decrease in shoreline roughness and sinuosity (smoothing). Like the previous storm, a storm event in 2017 increased the planform roughness and sinuosity of the cliff. Over shorter timescales, monthly retreat of the sea cliff occurred only when the platform was sparsely covered with sediment cover on the shore platform, indicating that the tools and cover effects can significantly affect short-term erosion rates. The timescale to return to a smooth shoreline following a storm or roughening event, given a steady-state erosion rate, is approximately 24 years, with the long-term rate suggesting a maximum of ~107 years until Sargent Beach breaches, compromising the Gulf Intracoastal Waterway (GIWW) under current conditions and assuming no future storms or intervention. The observed retreat rate varies, both spatially and temporally, with cliff face morphology, demonstrating the importance of multi-scale measurements and analysis for interpretation of coastal processes and patterns of cliff retreat.

58 GEOSCIENCES↗

Architectural design of an Algol interpreter

The design of a syntax-directed interpreter for a subset of Algol is described. It is a conceptual design with sufficient details and completeness but as much independence of implementation as possible. The design includes a detailed description of a scanner, an analyzer described in the Floyd-Evans productions, a hash-coded symbol table, and an executor. Interpretation of sample programs is also provided to show how the interpreter functions.

Jackson, C. K.↗

Onset phenomena in MPD thrusters

An experimental study has clarified some aspects of MPD thruster onset phenomena. The steep increase in terminal voltage that occurs as the onset current is approached may have different causes, depending on the propellant injection geometry. For propellant injection at the cathode radius, terminal voltage increase corresponds to a growing anode fall voltage; for injection at a larger radius, the increase is related to the back emf in the near-cathode plasma. The formation of the onset current pattern within the arc has been mapped experimentally as the thruster responds to an input current step which rises from below onset to the onset value. The appearance of terminal voltage hash at onset correlates with the extension into the exhaust region of a significant fraction of the arc current.

Barnett, J. W.↗

Segmentation of computer-classified Landsat multispectral scanner data into spatially-connected regions of elk habitat components

Segmentation of computer-classified Landsat multispectral data into spatially-connected regions of ground cover is described. Sorting and hash addressing, techniques commonly used for ordering and searching data records keyed by attributes, are the basis for the region identification and extraction. An example based on the use of spatial regions for evaluating elk habitat components is outlined.

Murray, R.↗

Cross-fertilization between connectionist networks and highly parallel architectures

The theoretical and practical connections between connectionist schemes such as neural-network computers and traditional symbolic processing architectures involving a high degree of parallelism are explored, reviewing the results of recent investigations. Topics addressed include data flow, data structure, and control flow; conventional pointers; associative addressing; hashing and reduced representations; the problem of binding values to variables; and levels of parallelism. It is concluded that connectionism is more closely related to traditional computer science and technology than is generally admitted; more cooperation between followers of the two approaches is recommended.

Barnden, John↗