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DOE OSTI2013

KINETIC PLASMA TURBULENCE IN THE FAST SOLAR WIND MEASURED BY CLUSTER

The k-filtering technique and wave polarization analysis are applied to Cluster magnetic field data to study plasma turbulence at the scale of the ion gyroradius in the fast solar wind. Waves are found propagating in directions nearly perpendicular to the background magnetic field at such scales. The frequencies of these waves in the solar wind frame are much smaller than the proton gyrofrequency. After the wavevector k is determined at each spacecraft frequency f{sub sc}, wave polarization property is analyzed in the plane perpendicular to k. Magnetic fluctuations have {delta}B > {delta}B{sub Parallel-To} (here the Parallel-To and refer to the background magnetic field B{sub 0}). The wave magnetic field has right-handed polarization at propagation angles {theta}{sub kB} < 90 Degree-Sign and >90 Degree-Sign . The magnetic field in the plane perpendicular to B{sub 0}, however, has no clear sense of a dominant polarization but local rotations. We discuss the merits and limitations of linear kinetic Alfven waves (KAWs) and coherent Alfven vortices in the interpretation of the data. We suggest that the fast solar wind turbulence may be populated with KAWs, small-scale current sheets, and Alfven vortices at ion kinetic scales.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2018

Unique [Mn 6 Bi 5 ] - Nanowires in KMn 6 Bi 5 : A Quasi-One-Dimensional Antiferromagnetic Metal

In this paper, we report a new quasi-one-dimensional compound KMn 6 Bi 5 composed of parallel nanowires crystallizing in a monoclinic space group C2/m with a = 22.994(2) Å, b = 4.6128(3) Å, c = 13.3830(13) Å and β = 124.578(6)°. The nanowires are infinite [Mn 6 Bi 5 ] - columns each of which is composed of a nanotube of Bi atoms acting as the cladding with a nanorod of Mn atoms located in the central axis of the nanotubes. The nanorods of Mn atoms inside the Bi cladding are stabilized by Mn–Mn bonding and are defined by distorted Mn-centered cluster icosahedra of Mn 13 sharing their vertices along the b axis. The [Mn 6 Bi 5 ] - nanowires are linked with weak internanowire Bi–Bi bonds and charge balanced with K + ions. The [Mn 6 Bi 5 ] - nanowires were directly imaged by high-resolution transmission electron microscopy and scanning transmission electron microscopy. Magnetic susceptibility studies show one-dimensional characteristics with an antiferromagnetic transition at ~75 K and a small average effective magnetic moment (1.56 μ B /Mn for H ∥ b and 1.37 μ B /Mn for H ⊥ b) of Mn from Curie–Weiss fits above 150 K. Specific heat measurements reveal an electronic specific heat coefficient γ of 6.5(2) mJ K –2 (mol-Mn) -1 and a small magnetic entropy change ΔS mag ≈ 1.6 J K –1 (mol-Mn) -1 across the antiferromagnetic transition. Finally, in contrast to a metallic resistivity along the column, the resistivity perpendicular to the column shows a change from a semiconducting behavior at high temperatures to a metallic one at low temperatures, indicating an incoherent-to-coherent crossover of the intercolumn tunneling of electrons.

36 MATERIALS SCIENCE↗

DOE OSTI2018

Electron Distributions in Kinetic Scale Field Line Resonances: A Comparison of Simulations and Observations

Observations in kinetic scale field line resonances, or eigenmodes of the geomagnetic field, reveal highly field-aligned plateaued electron distributions. By combining observations from the Van Allen Probes and Cluster spacecraft with a hybrid kinetic gyrofluid simulation we show how these distributions arise from the nonlocal self-consistent interaction of electrons with the wavefield. This interaction is manifested as electron trapping in the standing wave potential. The process operates along most of the field line and qualitatively accounts for electron observations near the equatorial plane and at higher latitudes. In conjunction with the highly field-aligned plateaus, loss cone features are also evident, which result from the action of the upward-directed wave parallel electric field on the untrapped electron populations.

42 ENGINEERING↗

DOE OSTI2014

OpenSHMEM over MPI-3

OpenSHMEM is a community effort to unifyt and standardize the SHMEM programming model. MPI (Message Passing Interface) is a well-known community standard for parallel programming using distributed memory. The most recen t release of MPI, version 3.0, was designed in part to support programming models like SHMEM.OSHMPI is an implementation of the OpenSHMEM standard using MPI-3 for the Linux operating system. It is the first implementation of SHMEM over MPI one-sided communication and has the potential to be widely adopted due to the portability and widely availability of Linux and MPI-3. OSHMPI has been tested on a variety of systems and implementations of MPI-3, includingInfiniBand clusters using MVAPICH2 and SGI shared-memory supercomputers using MPICH. Current support is limited to Linux but may be extended to Apple OSX if there is sufficient interest. The code is opensource via https://github.com/jeffhammond/oshmpi

Sayan Ghosh, JeffHammond↗

DOE OSTI2014

OpenSHMEM over MPI-3

Sayan Ghosh, Jeff Hammond↗

NASA NTRS2003

Cluster electric current density measurements within a magnetic flux rope in the plasma sheet

On August 22, 2001 all 4 Cluster spacecraft nearly simultaneously penetrated a magnetic flux rope in the tail. The flux rope encounter took place in the central plasma sheet, Beta(sub i) approx. 1-2, near the leading edge of a bursty bulk flow. The "time-of-flight" of the flux rope across the 4 spacecraft yielded V(sub x) approx. 700 km/s and a diameter of approx.1 R(sub e). The speed at which the flux rope moved over the spacecraft is in close agreement with the Cluster plasma measurements. The magnetic field profiles measured at each spacecraft were first modeled separately using the Lepping-Burlaga force-free flux rope model. The results indicated that the center of the flux rope passed northward (above) s/c 3, but southward (below) of s/c 1, 2 and 4. The peak electric currents along the central axis of the flux rope predicted by these single-s/c models were approx.15-19 nA/sq m. The 4-spacecraft Cluster magnetic field measurements provide a second means to determine the electric current density without any assumption regarding flux rope structure. The current profile determined using the curlometer technique was qualitatively similar to those determined by modeling the individual spacecraft magnetic field observations and yielded a peak current density of 17 nA/m2 near the central axis of the rope. However, the curlometer results also showed that the flux rope was not force-free with the component of the current density perpendicular to the magnetic field exceeding the parallel component over the forward half of the rope, perhaps due to the pressure gradients generated by the collision of the BBF with the inner magnetosphere. Hence, while the single-spacecraft models are very successful in fitting flux rope magnetic field and current variations, they do not provide a stringent test of the force-free condition.

Slavin, J. A.↗

DOE OSTI2023

Distributed out-of-memory NMF on CPU/GPU architectures

We propose an efficient distributed out-of-memory implementation of the non-negative matrix factorization (NMF) algorithm for heterogeneous high-performance-computing systems. The proposed implementation is based on prior work on NMFk, which can perform automatic model selection and extract latent variables and patterns from data. In this work, we extend NMFk by adding support for dense and sparse matrix operation on multi-node, multi-GPU systems. The resulting algorithm is optimized for out-of-memory problems where the memory required to factorize a given matrix is greater than the available GPU memory. Memory complexity is reduced by batching/tiling strategies, and sparse and dense matrix operations are significantly accelerated with GPU cores (or tensor cores when available). Input/output latency associated with batch copies between host and device is hidden using CUDA streams to overlap data transfers and compute asynchronously, and latency associated with collective communications (both intra-node and inter-node) is reduced using optimized NVIDIA Collective Communication Library (NCCL) based communicators. Benchmark results show significant improvement, from 32X to 76x speedup, with the new implementation using GPUs over the CPU-based NMFk. Good weak scaling was demonstrated on up to 4096 multi-GPU cluster nodes with approximately 25,000 GPUs when decomposing a dense 340 Terabyte-size matrix and an 11 Exabyte-size sparse matrix of density 10 -6 .

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2016

Closeout Report ARRA supplement to DE-FG02-08ER41546, 03/15/2010 to 03/14/2011 - Advanced Transfer Map Methods for the Description of Particle Beam Dynamics

The ARRA funds were utilized to acquire a cluster of high performance computers, consisting of one Altus 2804 Server based on a Quad AMD Opteron 6174 12C with 4 2.2 GHz nodes of 12 cores each, resulting in 48 directly usable cores; as well as a Relion 1751 Server using an Intel Xeon X5677 consisting of 4 3.46 GHz cores supporting 8 threads. Both systems run the Unix flavor CentOS, which is designed for use without need of updates, which greatly enhances their reliability. The systems are used to operate our COSY INFINITY environment which supports MPI parallelization. The units arrived at MSU in September 2010, and were taken into operation shortly thereafter.

43 PARTICLE ACCELERATORS↗

DOE OSTI2025

Multi-GPU porting of a phase-change cascaded lattice Boltzmann method for three-dimensional pool boiling simulations

The Lattice Boltzmann method (LBM) has proven effective in simulating phase-change phenomena, such as melting, solidification, evaporation, and boiling. In this work, we develop a highly parallelized multi-GPU implementation of LBM for three-dimensional pool boiling simulations. The code is based on the OpenACC programming model, which enables the code to be deployed efficiently on multi-core CPUs, GPUs, and potentially other accelerators, without the need for architecture-specific rewrites. To support large-scale simulations, the domain is decomposed and distributed across multiple compute nodes using MPI. We demonstrate that the code exhibits excellent scaling properties, with ideal strong-scaling running with up to 256 GPUs on the MareNostrum5 cluster.

97 MATHEMATICS AND COMPUTING↗

NASA NTRS2003

Sub-problem Optimization With Regression and Neural Network Approximators

Design optimization of large systems can be attempted through a sub-problem strategy. In this strategy, the original problem is divided into a number of smaller problems that are clustered together to obtain a sequence of sub-problems. Solution to the large problem is attempted iteratively through repeated solutions to the modest sub-problems. This strategy is applicable to structures and to multidisciplinary systems. For structures, clustering the substructures generates the sequence of sub-problems. For a multidisciplinary system, individual disciplines, accounting for coupling, can be considered as sub-problems. A sub-problem, if required, can be further broken down to accommodate sub-disciplines. The sub-problem strategy is being implemented into the NASA design optimization test bed, referred to as "CometBoards." Neural network and regression approximators are employed for reanalysis and sensitivity analysis calculations at the sub-problem level. The strategy has been implemented in sequential as well as parallel computational environments. This strategy, which attempts to alleviate algorithmic and reanalysis deficiencies, has the potential to become a powerful design tool. However, several issues have to be addressed before its full potential can be harnessed. This paper illustrates the strategy and addresses some issues.

Guptill, James D.↗

DOE OSTI2019

Collective nonlinear electric polarization via defect-driven local symmetry breaking

In this work, we report the defect-mediated, abnormal non-linear polarization behavior observed in centrosymmetric rutile TiO 2 where less than 1 at% of sterically mismatched Mg 2+ ions are introduced to create ferroelectric-like polarization hysteresis loops. It is found that the defect cluster produces a dipole moment exceeding 6 Debye, with a rotatable component. Such a polarization is further enhanced by the displacement of neighboring Ti 4+ ions. The coupling between such defect-driven symmetry-breaking regions generates a collective nonlinear electrical polarization state that persists to high temperatures. More importantly, an observation of abnormal bias shift of polarization hysteresis suggests an antiparallel alignment of certain dipoles frozen relative to the external poling electric field, which is associated with oxygen vacancy hopping. This result challenges the long-standing notion of parallel alignment of dipoles with the external electric field in ferroelectrics. Finally, this work also reveals an unexpected new form of non-linear dielectric polarization (non-ferroelectricity) in solid-state materials.

36 MATERIALS SCIENCE↗

DOE OSTI2025

Hubble Space Telescope Observations within the Sphere of Influence of the Powerful Supermassive Black Hole in PKS 0745-191

We present Space Telescope Imaging Spectrograph observations from the Hubble Space Telescope of the supermassive black hole (SMBH) at the center of PKS 0745-191, a brightest cluster galaxy (BCG) undergoing powerful radio-mode active galactic nucleus (AGN) feedback (P cav ~ 5 × 10 45 erg s -1 ). These high-resolution data offer the first spatially resolved map of gas dynamics within an SMBH's sphere of influence under such powerful feedback. Our results reveal the presence of highly chaotic, nondrotational ionized gas flows on subkiloparsec scales, in contrast to the more coherent flows observed on larger scales. While radio-mode feedback effectively thermalizes hot gas in galaxy clusters on kiloparsec scales, within the core, the hot gas flow may decouple, leading to a reduction in angular momentum and supplying ionized gas through cooling, which could enhance accretion onto the SMBH. This process could, in turn, lead to a self-regulating feedback loop. Compared to other BCGs with weaker radio-mode feedback, where rotation is more stable, intense feedback may lead to more chaotic flows, indicating a stronger coupling between jet activity and gas dynamics. Additionally, we observe a sharp increase in velocity dispersion near the nucleus, consistent with a very massive M BH ~ 1.5 × 10 10 M ⊙ SMBH. The density profile of the ionized gas is also notably flat, paralleling the profiles observed in X-ray gas around galaxies where the Bondi radius is resolved. These results provide valuable insights into the complex mechanisms driving galaxy evolution, highlighting the intricate relationship between SMBH fueling and AGN feedback within the host galaxy.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2017

Gene expression differs in codominant prairie grasses under drought

Not provided.

Biochemistry & Molecular Biology↗

DOE OSTI2015

TU-CD-BRB-05: Radiation Damage Signature of White Matter Fiber Bundles Using Diffusion Tensor Imaging (DTI)

Purpose: To develop an automated and scalable approach and identify temporal, spatial and dosimetric patterns of radiation damage of white matter (WM) fibers following partial brain irradiation. Methods: An automated and scalable approach was developed to extract DTI features of 22 major WM fibers from 33 patients with low-grade/benign tumors treated by radiation therapy (RT). DTI scans of the patients were performed pre-RT, 3- and 6-week during RT, and 1, 6 and 18 months after RT. The automated tractography analysis was applied to 198 datasets as: (1) intra-subject registration of longitudinal DTI, (2) spatial normalization of individual-patient DTI to the Johns Hopkins WM Atlas, (3) automatic fiber tracking regulated by the WM Atlas, and (4) segmentation of WM into 22 major tract profiles. Longitudinal percentage changes in fractional anisotropy (FA), and mean, axial and radial diffusivity (MD/AD/RD) of each tract from pre-RT were quantified and correlated to 95%, 90% and 80% percentiles of doses and mean doses received by the tract. Heatmaps were used to identify clusters of significant correlation and reveal temporal, spatial and dosimetric signatures of WM damage. A multivariate linear regression was further carried out to determine influence of clinical factors. Results: Of 22 tracts, AD/MD changes in 12 tracts had significant correlation with doses, especially at 6 and 18 months post-RT, indicating progressive radiation damage after RT. Most interestingly, the DTI-index changes in the elongated tracts were associated with received maximum doses, suggesting a serial-structure behavior; while short association fibers were affected by mean doses, indicating a parallel-structure response. Conclusion: Using an automated DTI-tractography analysis of whole brain WM fibers, we reveal complex radiation damage patterns of WM fibers. Damage in WM fibers that play an important role in the neural network could be associated with late neurocognitive function declines after brain irradiation. NIH NS064973.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2023

Parallel measurement of transcriptomes and proteomes from same single cells using nanodroplet splitting

Single-cell multiomics provides comprehensive insights into gene regulatory networks, cellular diversity, and temporal dynamics. While tools for co-profiling single-cell genomes, transcriptomes, and epigenomes are available, accessing proteomes in parallel is more challenging. We developed nanoSPLITS (nanodroplet SPlitting for Linked-multimodal Investigations of Trace Samples), an integrated platform that enables global profiling of the transcriptome and proteome from same single cells using RNA sequencing and mass spectrometry-based proteomics, respectively. nanoSPLITS can precisely quantify over 5000 genes, 2000 proteins, and 140 phosphopeptides per single cell and identify candidate cell markers from these modalities. By exploring Cdk1-mediated cell cycle arrest, we demonstrate how nanoSPLITS single-cell multiomics can provide comprehensive cellular characterization with insights into covarying protein/gene clusters, unique phosphorylation events, and mitotic pathways.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2015

Graph 500 in OpenSHMEM, In: OpenSHMEM 2014: OpenSHMEM and Related Technologies. Experiences, Implementations, and Technologies

This document describes the effort to implement the Graph 500 benchmark using OpenSHMEM based on the MPI-2 one-side version. The Graph 500 benchmark performs a breadth-first search in parallel on a large randomly generated undirected graph and can be implemented using basic MPI-1 and MPI-2 one-sided communication. Graph 500 requires atomic bit-wise operations on unsigned long integers but neither atomic bit-wise operations nor OpenSHMEM for unsigned long are available in OpenSHEM. Such needed bit-wise atomic operations and support for unsigned long are implemented using atomic condition swap (CSWAP) on signed long integers. Preliminary results on comparing the OpenSHMEM and MPI-2 one-sided implementations on a Silicon Graphics Incorporated (SGI) cluster and the Cray XK7 are presented.

Computer Science↗

DOE OSTI2023

$μ^+$ Knight shift in UTe 2 : Evidence for relocalization in a Kondo lattice

The local magnetic susceptibility of the spin-triplet superconductor UTe 2 has been investigated by positive muon (μ + ) Knight shift measurements in the normal state. Three distinct μ + Knight shift components are observed for a magnetic field applied parallel to the c axis. Two of these exhibit a breakdown in the linear relationship with the bulk magnetic susceptibility (χ) below a temperature T*~30K, which points to a gradual emergence of a correlated Kondo liquid. Below T r ~12K linearity is gradually restored, indicating relocalization of the Kondo liquid quasiparticles. The third Knight shift component is two orders of magnitude larger, and despite the c-axis alignment of the external field, scales with the a axis χ above T r ~12K. We conjecture that this component is associated with magnetic clusters and the change in the temperature dependence of all three Knight shift components below T r is associated with a change in magnetic correlations. Finally, our findings indicate that prior to the onset of superconductivity the development of the itinerant heavy-electron fluid is halted by a gradual development of local U 5⁢ƒ-moment fluctuations.

36 MATERIALS SCIENCE↗

DOE OSTI2015

Graph500 in OpenSHMEM

openshmem graph500↗