Results for “concurrent data structure” — Page 3

DOE OSTI2024

Data-flow parallelism for high-energy and nuclear physics computing frameworks

The processing tasks of a scientific workflow in high-energy and nuclear physics (HENP) can typically be represented as a directed acyclic graph formed according to the data flow—i.e. the data dependencies among algorithms executed as part of the workflow. With this representation, an HENP computing framework can optimally execute a workflow, exploiting the parallelism inherent among independent tasks. Despite such a natural description of a workflow, most HENP frameworks do not make use of technologies that provide concurrent execution of graph-based tasking structures. In this session, we describe Fermilab efforts to adopt a graph-based technology (specifically Intel’s oneTBB flow graph) for meeting the framework needs of its experiments, notably DUNE. After introducing the physics DUNE intends to explore, we will show that all common processing idioms supported by current HENP frameworks can naturally be supported by oneTBB’s data-flow technology, optimally leveraging the concurrent capabilities of the machine. In addition, we discuss collaborative efforts between Fermilab and the Intel oneTBB development team, who is considering improvements to the flow-graph technology to better support HENP use cases.

43 PARTICLE ACCELERATORS↗

DOE OSTI2025

Three-dimensional lattice modulations in the charge density wave system Lu 2 Ir 3 Si 5

Using total and resonant x-ray scattering coupled to large-scale computer modeling, we study the lattice modulations in the complex charge density wave (CDW) material Lu 2 ⁢Ir 3 ⁢Si 5 . Here, we find that it is a unique quantum system where periodic lattice modulations related to emergent CDW order occur in three orthogonal atomic planes of the crystal lattice, leading to the emergence of an unusual three-dimensional (3D) pattern of short and long Ir-Ir and Lu-Lu bonds. The 3D character of observed lattice modulations explains the largely isotropic character of the changes in the electronic properties occurring when the CDW order sets in, demonstrating the strong electron-lattice coupling in Lu 2 ⁢Ir 3 ⁢Si 5 . The result is supported by DFT calculations based on the experimental structure data. Altogether, our work provides strong evidence for the presence of a relationship between the dimensionality of emergent lattice distortions and that of concurrent changes in the electronic properties of CDW materials. The relationship may need to be accounted for when these materials are explored for practical applications.

36 MATERIALS SCIENCE↗

NASA NTRS1989

FLEXAN (version 2.0) user's guide

The FLEXAN (Flexible Animation) computer program, Version 2.0 is described. FLEXAN animates 3-D wireframe structural dynamics on the Evans and Sutherland PS300 graphics workstation with a VAX/VMS host computer. Animation options include: unconstrained vibrational modes, mode time histories (multiple modes), delta time histories (modal and/or nonmodal deformations), color time histories (elements of the structure change colors through time), and rotational time histories (parts of the structure rotate through time). Concurrent color, mode, delta, and rotation, time history animations are supported. FLEXAN does not model structures or calculate the dynamics of structures; it only animates data from other computer programs. FLEXAN was developed to aid in the study of the structural dynamics of spacecraft.

Stallcup, Scott S.↗

NASA NTRS1992

Evolution of vector magnetic fields and the August 27 1990 X-3 flare

Vector magnetic fields in an active region of the sun are studied by means of continuous observations of magnetic-field evolution emphasizing magnetic shear build-up. The vector magnetograms are shown to measure magnetic fields correctly based on concurrent observations and a comparison of the transverse field with the H alpha fibril structure. The morphology and velocity pattern are examined, and these data and the shear build-up suggest that the active region's two major footprints are separated by a region with flows, new flux emergence, and several neutral lines. The magnetic shear appears to be caused by the collision and shear motion of two poles of opposite polarities. The transverse field is shown to turn from potential to sheared during the process of flux cancellation, and this effect can be incorporated into existing models of magnetic flux cancellation.

Wang, Haimin↗

DOE OSTI2026

Ultrafast x-ray scattering of photodissociation dynamics in 2-iodothiophene

Here, a time-resolved x-ray scattering (TRXS) investigation of the photodissociation dynamics of gas-phase 2-iodothiophene molecules following 252 nm excitation is presented. Structural evolution of the molecule and dynamical information on the resulting photofragments were captured using femtosecond x-ray free-electron laser pulses. Two dissociation pathways were identified, arising via excitation to ππ* and (n/π)σ* states, respectively, yielding distinct interfragment recoil velocities of ∼6.4 Åps −1 and 17.0 Åps −1 . A comparison of asymptotic scattering data with simulated patterns indicates that the thiophene ring remains closed following dissociation at this wavelength. Modeling the experimental data yields a branching ratio of ∼3:1 in favor of the high velocity channel. These findings demonstrate the capability of TRXS to disentangle concurrent ultrafast reaction pathways and provide detailed structural insight into energy redistribution during photoinduced bond fission in complex molecular systems.

Razmus, Weronika O. [Univ. of Southampton (United ↗

DOE OSTI2017

PSelInv—A Distributed Memory Parallel Algorithm for Selected Inversion: The Symmetric Case

We describe an efficient parallel implementation of the selected inversion algorithm for distributed memory computer systems, which we call PSelInv. The PSelInv method computes selected elements of a general sparse matrix Athat can be decomposed as A= LU, where L is lower triangular and U is upper triangular. The implementation described in this article focuses on the case of sparse symmetric matrices. It contains an interface that is compatible with the distributed memory parallel sparse direct factorization SuperLU-DIST. Yet, the underlying data structure and design of PSelInv allows it to be easily combined with other factorization routines, such as PARDISO. We discuss general parallelization strategies such as data and task distribution schemes. Specifically, we describe how to exploit the concurrency exposed by the elimination tree associated with the LU factorization of A. We demonstrate the efficiency and accuracy of PSelInv by presenting several numerical experiments. In particular, we show that PSelInv can run efficiently on more than 4,000 cores for a modestly sized matrix. We also show how PSelInv can be used to accelerate large-scale electronic structure calculations.

97 MATHEMATICS AND COMPUTING↗

NASA NTRS1979

The detection of urban expansion from Landsat imagery

Two methodologies for detecting and mapping land cover changes in and around growing urban regions are being studied at Jet Propulsion Laboratory. Both approaches, primarily based on digital image processing techniques, have been developed to supplement data stored in an Image Based Information System (IBIS). The structure of this information system enables the depiction of land cover changes in image format concurrently with statistical reports in tabular form. To date the expansion of two urban areas, Houston, Texas and Orlando, Florida, has been monitored.

Friedman, S. Z.↗

NASA NTRS1993

Studying Venus using a GIS database

A Geographic Information System (GIS) can significantly enhance geological studies on Venus because it facilitates concurrent analysis of many sources of data, as demonstrated by our work on topographic and deformation characteristics of tesserae. We are creating a database of structures referenced to real-world coordinates to encourage the archival of Venusian studies in digital format and to foster quantitative analysis of many combinations of data. Contributions to this database from all aspects of Venusian science are welcome.

Price, Maribeth↗

DOE OSTI2023

Scalable Incremental Checkpointing using GPU-Accelerated De-Duplication

Writing large amounts of data concurrently to stable storage is a typical I/O pattern of many HPC workflows. This pattern introduces high I/O overheads and results in increased storage space utilization especially for workflows that need to capture the evolution of data structures with high frequency as checkpoints. In this context, many applications, such as graph pattern matching, perform sparse updates to large data structures between checkpoints. For these applications, incremental checkpointing techniques that save only the differences from one checkpoint to another can dramatically reduce the checkpoint sizes, I/O bottlenecks, and storage space utilization. However, such techniques are not without challenges: it is non-trivial to transparently determine what data has changed since a previous checkpoint and assemble the differences in a compact fashion that does not result in excessive metadata. State-of-art data reduction techniques (e.g., compression and de-duplication) have significant limitations when applied to modern HPC applications that leverage GPUs: slow at detecting the differences, generate a large amount of metadata to keep track of the differences, and ignore crucial spatiotemporal checkpoint data redundancy. This paper addresses these challenges by proposing a Merkle tree-based incremental checkpointing method to exploit GPUs' high memory bandwidth and massive parallelism. Experimental results at scale show a significant reduction of the I/O overhead and space utilization of checkpointing compared with state-of-the-art incremental checkpointing and compression techniques.

Tan, Nigel↗

NASA NTRSDate not supplied

Expanding Repository Data Available For Sharing and Knowledge Discovery

Some of the hardest space biology and space health challenges require data-intensive, bioinformatic, meta-analytical, and computer-assisted research approaches. These challenges include examining interdisciplinary space life science research across experiments and across interacting spaceflight hazards (radiation, altered gravity, confinement, hostile-closed environments, distance-duration from Earth). The approaches to confront these challenges involve mining multiple datasets simultaneously from various hierarchical organizations of biological complexity, all while concurrently evaluating how experimental design factors affect endpoints of standard assays. To enable this field, it is essential that principal investigators (PIs) submit data in a structure so it can be maximally re-used. The purpose of the NASA Ames Life Sciences Data Archive (ALSDA) is to collect, curate, and make publicly available all non-human space-relevant biological data. ALSDA must also ensure data are open-access, and maximally findable, accessible, interoperable, and reusable (FAIR). The scope of ALSDA data collected and submitted by PIs include subject and study design metadata, assay metadata parameters, raw and processed assay data, assay imagery/video, and subject-experienced mission data telemetry (radiation, temperature, humidity, acoustics, vibrations, etc.). ALSDA recently integrated into a collaborative group of Open Science projects to facilitate a suite of new tools and workflows that will improve data submission, accessibility, and reusability by implementing digital data submission agreements, and adopting the data management system originally developed by NASA GeneLab. ALSDA intends to bring current biological repository data and all future collected data into this new scientific data reuse reality. This new suite of tools will enable ALSDA to deploy a science curation system using scientific assay configurations for the data submission portal. It will capture essential assay parameters according to established standards in each sub-field within biology. The submission portal expedites data collection by enhancing ease of PI data submission, providing a user interface and specificity for which data is to be submitted. Data submissions can be brought into cutting-edge informatic analysis portals to enable mining of physiological, behavioral, biochemical, and imaging datasets in conjunction with ‘omics-level datasets. As ALSDA datasets are submitted, curated, and published (e.g., micro-computed tomography, histology, pulse oximetry, serum metabolites, magnetic resonance imaging, intraocular pressure, novel object recognition, etc.), the merging together of spaceflight data along this multi-hierarchical complexity of biology will enable informatics and data-intensive approaches resulting in knowledge discoveries across missions, space hazards, and biological disciplines.

Biology↗

NASA NTRSDate not supplied

Expanding Repository Data Available For Sharing And Knowledge Discovery

Some of the hardest space biology and space health challenges require data-intensive, bioinformatic, meta-analytical, and computer-assisted research approaches. These challenges include examining interdisciplinary space life science research across experiments and across interacting spaceflight hazards (radiation, altered gravity, confinement, hostile-closed environments, distance-duration from Earth). The approaches to confront these challenges involve mining multiple datasets simultaneously from various hierarchical organizations of biological complexity, all while concurrently evaluating how experimental design factors affect endpoints of standard assays. To enable this field, it is essential that principal investigators (PIs) submit data in a structure so it can be maximally re-used. The purpose of the NASA Ames Life Sciences Data Archive (ALSDA) is to collect, curate, and make publicly available all non-human space-relevant biological data. ALSDA must also ensure data are open-access, and maximally findable, accessible, interoperable, and reusable (FAIR). The scope of ALSDA data collected and submitted by PIs include subject and study design metadata, assay metadata parameters, raw and processed assay data, assay imagery/video, and subject-experienced mission data telemetry (radiation, temperature, humidity, acoustics, vibrations, etc.). ALSDA recently integrated into a collaborative group of Open Science projects to facilitate a suite of new tools and workflows that will improve data submission, accessibility, and reusability by implementing digital data submission agreements, and adopting the data management system originally developed by NASA GeneLab. ALSDA intends to bring current biological repository data and all future collected data into this new scientific data reuse reality. This new suite of tools will enable ALSDA to deploy a science curation system using scientific assay configurations for the data submission portal. It will capture essential assay parameters according to established standards in each sub-field within biology. The submission portal expedites data collection by enhancing ease of PI data submission, providing a user interface and specificity for which data is to be submitted. Data submissions can be brought into cutting-edge informatic analysis portals to enable mining of physiological, behavioral, biochemical, and imaging datasets in conjunction with ‘omics-level datasets. As ALSDA datasets are submitted, curated, and published (e.g., micro-computed tomography, histology, pulse oximetry, serum metabolites, magnetic resonance imaging, intraocular pressure, novel object recognition, etc.), the merging together of spaceflight data along this multi-hierarchical complexity of biology will enable informatics and data-intensive approaches resulting in knowledge discoveries across missions, space hazards, and biological disciplines.

life science↗

DOE OSTI2018

Accelerating nuclear configuration interaction calculations through a preconditioned block iterative eigensolver

We describe a number of recently developed techniques for improving the performance of large-scalenuclear configuration interaction calculations on high performance parallel computers. We show thebenefit of using a preconditioned block iterative method to replace the Lanczos algorithm that hastraditionally been used to perform this type of computation. The rapid convergence of the block iterativemethod is achieved by a proper choice of starting guesses of the eigenvectors and the construction of aneffective preconditioner. These acceleration techniques take advantage of special structure of the nuclearconfiguration interaction problem which we discuss in detail. The use of a block method also allows usto improve the concurrency of the computation, and take advantage of the memory hierarchy of modernmicroprocessors to increase the arithmetic intensity of the computation relative to data movement. Wealso discuss the implementation details that are critical to achieving high performance on massivelyparallel multi-core supercomputers, and demonstrate that the new block iterative solver is two to threetimes faster than the Lanczos based algorithm for problems of moderate sizes on a Cray XC30 system.

Shao, Meiyue↗

NASA NTRS1991

Microphysical and radiative characteristics of convective clouds during COHMEX

This paper has two purposes: first, to document the structure and evolution of two strong thunderstorms in Alabama using radar multiparameter data; and second, to relate the inferred microphysics to the resulting upwelling microwave radiance observed concurrently by high altitude aircraft. These measurements were collected during the COHMEX field program in the summer of 1986. The radar analysis includes a description of the parameters reflectivity Z, differential reflectivity Z(DR), linear depolarization ratio LDR, and hail signal HS for two thunderstorm cases on July 11, 1986. The simultaneous aircraft data include passive microwave brightness temperature, T(B), measurements at four frequencies ranging from 18 to 183 GHz, as well as visible and infrared data. The remote radar observations reveal the existence of large ice particles within the storms, which is likely to have caused the observed low microwave brightness temperatures. By relating the evolution of the radar measureables to the microwave T(B)s it has been found that knowledge of the storm microphysics and its evolution is important to adequately understand the microwave T(B)s.

Fulton, Richard↗

DOE OSTI2021

Combining the Best of Two Chelating Titans: A Hydroxypyridinone-Decorated Macrocyclic Ligand for Efficient and Concomitant Complexation and Sensitized Luminescence of f-Elements

An ideal chelator for f-elements features rapid kinetics of complexation, high thermodynamic stability, and slow kinetics of dissociation. Here we present the facile synthesis of a macrocyclic ligand bearing four 1-hydroxy-2-pyridinone units linked to a cyclen scaffold that rapidly forms thermodynamically stable complexes with lanthanides (Sm 3+ , Eu 3+ , Tb 3+ , Dy 3+ ) and a representative late actinide (Cm 3+ ) in aqueous media and concurrently sensitizes them. Extended X-ray absorption fine structure (EXAFS) spectroscopy revealed an increase in the Ln/An-O bond lengths following the trend Cm>Eu>Tb and EXAFS data were compatible with time-resolved luminescence studies, which indicated one to two water molecules in the inner metal coordination sphere of Eu(III) and two water molecules for the Cm(III) complex. Spectrofluorimetric ligand competition titrations against DTPA confirmed the high thermodynamic stability of DOTHOPO complexes, with pM values between 19.9(1) and 21.9(2).

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2024

In Situ Insights into Cathode Calcination for Predictive Synthesis: Kinetic Crystallization of LiNiO 2 from Hydroxides

Abstract Calcination is a solid‐state synthesis process widely deployed in battery cathode manufacturing. However, its inherent complexity associated with elusive intermediates hinders the predictive synthesis of high‐performance cathode materials. Here, correlative in situ X‐ray absorption/scattering spectroscopy is used to investigate the calcination of nickel‐based cathodes, focusing specifically on the archetypal LiNiO 2 from Ni(OH) 2 . Combining in situ observation with data‐driven analysis reveals concurrent lithiation and dehydration of Ni(OH) 2 and consequently, the low‐temperature crystallization of layered LiNiO 2 alongside lithiated rocksalts. Following early nucleation, LiNiO 2 undergoes sluggish crystallization and structural ordering while depleting rocksalts; ultimately, it turns into a structurally‐ordered layered phase upon full lithiation but remains small in size. Subsequent high‐temperature sintering induces rapid crystal growth, accompanied by undesired delithiation and structural degradation. These observations are further corroborated by mesoscale modeling, emphasizing that, even though calcination is thermally driven and favors transformation towards thermodynamically equilibrium phases, the actual phase propagation and crystallization can be kinetically tuned via lithiation, providing freedom for structural and morphological control during cathode calcination.

36 MATERIALS SCIENCE↗

DOE OSTI2020

National Cancer Institute Think-Tank Meeting Report on Proteomic Cartography and Biomarkers at the Single-Cell Level: Interrogation of Premalignant Lesions

A Think-Tank Meeting was convened by the National Cancer Institute (NCI) to solicit experts’ opinion on the development and application of multi-omic single-cell analyses, and especially single-cell proteomics, to improve the development of a new generation of biomarkers for cancer risk, early detection, diagnosis, prognosis as well as to discuss the discovery of new targets for prevention and therapy. It is anticipated that such markers and targets will be based on cellular, subcellular, molecular and functional aberrations within the lesion and within individual cells. Additionally, single-cell proteomic data will be essential for the establishment of new tools that with searchable and scalable features that include spatial and temporal cartographies of premalignant and malignant lesions. Challenges and potential solutions that were discussed included: • The best way/s to analyze single-cells from fresh and preserved tissue • Detection and analysis of secreted molecules and from single cells, especially from a tissue slice • Detection of new, previously undocumented cell type/s in the premalignant and early stage cancer tissue microenvironment • Multi-omic integration of data to support and inform proteomic measurements • Subcellular organelles – identifying abnormal structure, function, distribution and location within individual premalignant and malignant cells • How to improve the dynamic range of single-cell proteomic measurements for discovery of differentially expressed proteins and their post translational modifications (PTM) • The depth of coverage measured concurrently using single-cell techniques • Quantitation - absolute or semiquantitative? • Single methodology or multiplexed combinations? • Application of analytical methods for identification of biologically significant subsets • Data visualization of N-dimensional datasets • How to construct intercellular signaling networks in individual cells within premalignant tumor microenvironments (TME) • Associations between intrinsic cellular processes and extrinsic stimuli • How to predict cellular responses to stress inducing stimuli • Identification of new markers for prediction of progression from precursor, benign and localized lesions to invasive cancer, based on spatial and temporal changes within individual cells • Identification of new targets for immunoprevention or immunotherapy – identification of neoantigens and surfactome of individual cells within a lesion

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS1972

Study on multi-satellite, multi-measurement of the structure of the earth's bow shock

The pulsation model of the earth's bow shock proposed a nonuniform shock having both perpendicular (abrupt, monotonic) and oblique (oscillatory, multigradient) properties simultaneously, depending on local orientation of the shock surface to the interplanetary field B sub sw in parallel planes defined by B sub sw and solar wind velocity. Multiple, concurrent, satellite observations of the shock and solar wind conditions were used. Twenty-six potentially useful intervals of concurrent Explorer 33 and 35 data acquisition were examined, of which six were selected for closer study. In addition, two years of OGO-5 and HEOS 1 magnetometer data were examined for possible conjunctions to these spacecraft having applicable data. One case of clear nonuniformity and several of field-dependent structure were documented. A computational aid, called pulsation index, was developed.

Source record↗

DOE OSTI2015

Glass-forming ability of TeO{sub 2} and temperature induced changes on the structure of the glassy, supercooled, and molten states

Polarized (VV) and depolarized (VH) Raman spectra are obtained for glassy, supercooled, and molten TeO{sub 2} at temperatures up to 1000 K in order to elucidate the temperature evolution of the pertinent structural and vibrational properties. The intrinsic tendency of the system for crystallization is avoided by means of a newly applied protocol, thereby enabling the recording of Raman spectra of pure TeO{sub 2} on going from the molten to the supercooled liquid and to the room temperature glass states. Following an appropriate fitting procedure, the revealed bands are assigned to specific modes of structural polymorphs. A weak polarised band at ∼880 cm{sup −1} is assigned to Te=O terminal stretching in agreement with the literature ab initio molecular orbital calculations. Subtle changes to the relative band intensities within the 550-900 cm{sup −1} stretching region are caused by temperature increase. The network-like structure of the glass/melt is composed by TeO{sub 4} trigonal bipyramid and TeO{sub 3} trigonal pyramid units. With increasing temperature, TeO{sub 4} units convert to TeO{sub 3} units with a concurrent increase in the number of Te=O sites resulting from cleavages within the network structure. The fraction of such terminal oxygen atoms has been directly estimated from the spectroscopic data. The relative populations of the basic building blocks and the average number of O atoms around Te have been estimated for a wide temperature range directly from the Raman spectra, implying a gradual transformation of TeO{sub 4/2} to TeO{sub 2/2}(= O) trigonal pyramid units. The results are discussed in the context of the current phenomenological and theoretical status of the field.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗