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At least 721 records · Page 40

FORECASTOR – II. Simulating galaxy surveys with the Cosmological Advanced Survey Telescope for Optical and UV Research

The Cosmological Advanced Survey Telescope for Optical and UV Research (CASTOR) is a planned flagship space telescope, covering the blue-optical and UV part of the spectrum. Here, we introduce the CASTOR image simulator, a python GalSim package-based script capable of generating mock CASTOR images from an input catalogue. We generate example images from the CASTOR Wide, Deep, and Ultra-Deep surveys using simulated lightcones from the Santa Cruz semi-analytic model. We make predictions for the performance of these surveys by comparing galaxies that are extracted from each image using Source Extractor to the input catalogue. We find that the Wide, Deep, and Ultra-Deep surveys will be 75 per cent complete for point sources down to $\sim 27$, 29, and 30 mag, respectively, in the UV, u, and g filters, with the UV-split and u-split filters reaching a shallower depth. With a large area of $\sim 2200$ deg$^2$, the Wide survey will detect hundreds of millions of galaxies out to $z\sim 4$, mostly with $M_\ast \gtrsim 10^{9}\,{\rm M}_{\odot }$. The Ultra-Deep survey will probe to $z\sim 5$, detecting galaxies with $M_\ast \gtrsim 10^{7}{\rm M}_{\odot }$. These galaxy samples will enable precision measurements of the distribution of star formation in the cosmic web, connecting the growth of stellar mass to the assembly of dark matter haloes over two thirds of the history of the Universe, and other core goals of CASTOR’s legacy surveys. These image simulations and the tools developed to generate them will be a vital planning tool to estimate CASTOR’s performance and iterate the telescope and survey designs prior to launch.

79 ASTRONOMY AND ASTROPHYSICS↗

The Sloan Digital Sky Survey extended point spread functions

ABSTRACT A robust and extended characterization of the point spread function (PSF) is crucial to extract the photometric information produced by deep imaging surveys. Here, we present the extended PSFs of the Sloan Digital Sky Survey (SDSS), one of the most productive astronomical surveys of all time. By stacking ∼1000 images of individual stars with different brightness, we obtain the bidimensional SDSS PSFs extending over 8 arcmin in radius for all the SDSS filters (u, g, r, i, z). This new characterization of the SDSS PSFs is near a factor of 10 larger in extension than previous PSFs characterizations of the same survey. We found asymmetries in the shape of the PSFs caused by the drift scanning observing mode. The flux of the PSFs is larger along the drift scanning direction. Finally, we illustrate with an example how the PSF models can be used to remove the scattered light field produced by the brightest stars in the central region of the Coma cluster field. This particular example shows the huge importance of PSFs in the study of the low-surface brightness Universe, especially with the upcoming of ultradeep surveys, such as the Large Synoptic Survey Telescope (LSST). Following a reproducible science philosophy, we make all the PSF models and the scripts used to do the analysis of this paper publicly available (snapshot v0.4-0-gd966ad0).

Infante-Sainz, Raúl↗

ProteoSign: an end-user online differential proteomics statistical analysis platform

Profiling of proteome dynamics is crucial for understanding cellular behavior in response to intrinsic and extrinsic stimuli and maintenance of homeostasis. Over the last 20 years, mass spectrometry (MS) has emerged as the most powerful tool for large-scale identification and characterization of proteins. Bottom-up proteomics, the most common MS-based proteomics approach, has always been challenging in terms of data management, processing, analysis and visualization, with modern instruments capable of producing several gigabytes of data out of a single experiment. Here, we present ProteoSign, a freely available web application, dedicated in allowing users to perform proteomics differential expression/abundance analysis in a userfriendly and self-explanatory way. Although several non-commercial standalone tools have been developed for post-quantification statistical analysis of proteomics data, most of them are not end-user appealing as they often require very stringent installation of programming environments, third-party software packages and sometimes further scripting or computer programming. To avoid this bottleneck, we have developed a user-friendly software platform accessible via a web interface in order to enable proteomics laboratories and core facilities to statistically analyse quantitative proteomics data sets in a resource-efficient manner. ProteoSign is available at http://bioinformatics.med.uoc.gr/ProteoSign and the source code at https://github.com/yorgodillo/ ProteoSign.

59 BASIC BIOLOGICAL SCIENCES↗

Fringe field maps for symplectic models of general Cartesian dipoles

We present a framework with which to analyze the effects of magnetic fringe fields. The theory defines the fringe field to be the transition between two regions of nearly constant field, and can incorporate constant multipoles in the magnet body. We then analyze Cartesian dipoles and derive symplectic fringe field maps that are applicable to longitudinal and/or transverse gradient dipoles. We verify the fringe maps with tracking, and show how we incorporated the theory into the tracking code ELEGANT. The resulting elements and several supporting scripts are now available for users, and we conclude with several predictions relevant to the APS Upgrade project.

43 PARTICLE ACCELERATORS↗

Nuclear-level effective theory of 𝜇→𝑒 conversion: Formalism and applications

Over the next decade new 𝜇→𝑒 conversion searches at Fermilab (Mu2e) and J-PARC (COMET, DeeMe) are expected to advance limits on charged lepton flavor violation (CLFV) by more than four orders of magnitude. Here, by considering the consequence of 𝑃 and 𝐶⁢𝑃 on elastic 𝜇→𝑒 conversion and the structure of possible charge and current densities, we show that rates are governed by six nuclear responses and a single scale, 𝑞/𝑚 𝑁 , where 𝑞 ≈ 𝑚 𝜇 is the momentum transferred from the leptons to the nucleus. To relate this result to microscopic formulations of CLFV, we construct in nonrelativistic effective theory (NRET) the CLFV nucleon-level interaction, pointing out the relevance of the dimensionless scales 𝑦=($^{𝑞⁢𝑏}_2$) 2 ⁢ > |$\overrightarrow{𝑣}_N$⁢|>|$\overrightarrow{𝑣}_μ$⁢|>|$\overrightarrow{𝑣}_T$| , where 𝑏 is the nuclear size, $\overrightarrow{𝑣}_N$ and $\overrightarrow{𝑣}_μ$ are the nucleon and muon intrinsic velocities, and $\overrightarrow{𝑣}_T$ is the target recoil velocity. We discuss previous work, noting the lack of a systematic treatment of the various small parameters. Because the parameter 𝑦 is not small, a proper calculation of 𝜇→𝑒 conversion requires a full multipole expansion of the nuclear response functions, an apparently daunting task with Coulomb-distorted electron partial waves. We demonstrate that the multipole expansion can be carried out to high precision by introducing a simplifying local momentum 𝑞 eff for the electron. Previous work has been limited to simple charge or spin interactions, thereby treating the nucleus effectively as a point particle. We show that such formulations are not compatible with the general form of the 𝜇→𝑒 conversion rate, failing to generate three of the six allowed nuclear response functions. The inclusion of the nucleon velocity $\overrightarrow{𝑣}_N$ yields an NRET with 16 operators and a rate of the general form. Consequently, in the current discovery era for CLFV, it provides the most sensible starting point for experimental analysis, defining what can and cannot be determined about CLFV from the highly exclusive process of 𝜇→𝑒 conversion. Finally, we expand the NRET operator basis to account for the effects of $\overrightarrow{𝑣}_μ$, associated with the muon's lower component, generating corrections to the CLFV coefficients of the point-nucleus response functions. Using advanced shell-model methods, we compute 𝜇→𝑒 conversion rates for a series of experimental targets, deriving bounds on the coefficients of the CLFV operators. These calculations are the first to include a general basis of CLFV operators, full evaluation of the associated nuclear response functions, and an accurate treatment of electron and muon Coulomb effects. We discuss target selection as an experimental “knob” that can be turned to probe the microscopic origins of CLFV. We describe two types of coherence that enhance certain CLFV operators and selection rules that blind elastic 𝜇→𝑒 conversion to others. We discuss the matching of the NRET onto higher level effective field theories, such as those constructed at the light quark level, noting opportunities to build on existing work in direct detection of dark matter. We discuss the relation of 𝜇→𝑒 conversion to 𝜇→𝑒+𝛾 and 𝜇→3⁢𝑒, showing how MEG II and Mu3e results will complement those of Mu2e and COMET. Finally we describe a accompanying script—in Mathematica and Python versions—that can be used to compute 𝜇→𝑒 conversion rates in various nuclear targets for the full set of NRET operators.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Interactive visualization of multi-data-set Rietveld analyses using Cinema:Debye-Scherrer [nteractive Visualization of Multi-Dataset Rietveld Analyses using Cinema:Debye-Scherrer]

A tool named Cinema:Debye-Scherrer to visualize the results of a series of Rietveld analyses is presented. The multi-axis visualization of the high-dimensional data sets resulting from powder diffraction analyses allows identification of analysis problems, prediction of suitable starting values, identification of gaps in the experimental parameter space and acceleration of scientific insight from the experimental data. The tool is demonstrated with analysis results from 59 U–Nb alloy samples with different compositions, annealing times and annealing temperatures as well as with a high-temperature study of the crystal structure of CsPbBr 3 . A script to extract parameters from a series of Rietveld analyses employing the widely used GSAS Rietveld software is also described. Finally, both software tools are available for download.

36 MATERIALS SCIENCE↗

Visualization of texture components using MTEX

Knowledge of the appearance of texture components and fibres in pole figures, in inverse pole figures and in Euler space is fundamental for texture analysis. For cubic crystal systems, such as steels, an extensive literature exists and, for example, the book by Matthies, Vinel & Helming [Standard Distributions in Texture Analysis: Maps for the Case of Cubic Orthorhomic Symmetry, (1987), Akademie-Verlag Berlin] provides an atlas to identify texture components. For lower crystal symmetries, however, equivalent comprehensive overviews that can serve as guidance for the interpretation of experimental textures do not exist. Here, this paper closes this gap by providing a set of scripts for the MTEX package [Bachmann, Hielscher & Schaeben (2010). Solid State Phenom.160, 63–68] that allow the texture practitioner to compile such an atlas for a given material system, thus aiding orientation distribution function analysis also for non-cubic systems.

36 MATERIALS SCIENCE↗

General approaches for shear-correcting coordinate transformations in Bragg coherent diffraction imaging. Part II

X-ray Bragg coherent diffraction imaging (BCDI) has been demonstrated as a powerful 3D microscopy approach for the investigation of sub-micrometre-scale crystalline particles. The approach is based on the measurement of a series of coherent Bragg diffraction intensity patterns that are numerically inverted to retrieve an image of the spatial distribution of the relative phase and amplitude of the Bragg structure factor of the diffracting sample. This 3D information, which is collected through an angular rotation of the sample, is necessarily obtained in a non-orthogonal frame in Fourier space that must be eventually reconciled. To deal with this, the approach currently favored by practitioners (detailed in Part I) is to perform the entire inversion in conjugate non-orthogonal real- and Fourier-space frames, and to transform the 3D sample image into an orthogonal frame as a post-processing step for result analysis. In this article, which is a direct follow-up of Part I, two different transformation strategies are demonstrated, which enable the entire inversion procedure of the measured data set to be performed in an orthogonal frame. The new approaches described here build mathematical and numerical frameworks that apply to the cases of evenly and non-evenly sampled data along the direction of sample rotation ( i.e. the rocking curve). The value of these methods is that they rely on the experimental geometry, and they incorporate significantly more information about that geometry into the design of the phase-retrieval Fourier transformation than the strategy presented in Part I. Finally, two important outcomes are (1) that the resulting sample image is correctly interpreted in a shear-free frame and (2) physically realistic constraints of BCDI phase retrieval that are difficult to implement with current methods are easily incorporated. Computing scripts are also given to aid readers in the implementation of the proposed formalisms.

36 MATERIALS SCIENCE↗

DLSIA: Deep Learning for Scientific Image Analysis

DLSIA (Deep Learning for Scientific Image Analysis) is a Python-based machine learning library that empowers scientists and researchers across diverse scientific domains with a range of customizable convolutional neural network (CNN) architectures for a wide variety of tasks in image analysis to be used in downstream data processing. DLSIA features easy-to-use architectures, such as autoencoders, tunable U-Nets and parameter-lean mixed-scale dense networks (MSDNets). Additionally, this article introduces sparse mixed-scale networks (SMSNets), generated using random graphs, sparse connections and dilated convolutions connecting different length scales. For verification, several DLSIA-instantiated networks and training scripts are employed in multiple applications, including inpainting for X-ray scattering data using U-Nets and MSDNets, segmenting 3D fibers in X-ray tomographic reconstructions of concrete using an ensemble of SMSNets, and leveraging autoencoder latent spaces for data compression and clustering. As experimental data continue to grow in scale and complexity, DLSIA provides accessible CNN construction and abstracts CNN complexities, allowing scientists to tailor their machine learning approaches, accelerate discoveries, foster interdisciplinary collaboration and advance research in scientific image analysis.

97 MATHEMATICS AND COMPUTING↗

Integration of TomoPy and the ASTRA toolbox for advanced processing and reconstruction of tomographic synchrotron data

The processing of tomographic synchrotron data requires advanced and efficient software to be able to produce accurate results in reasonable time. In this paper, the integration of two software toolboxes, TomoPy and the ASTRA toolbox, which, together, provide a powerful framework for processing tomographic data, is presented. The integration combines the advantages of both toolboxes, such as the user-friendliness and CPU-efficient methods of TomoPy and the flexibility and optimized GPU-based reconstruction methods of the ASTRA toolbox. It is shown that both toolboxes can be easily installed and used together, requiring only minor changes to existing TomoPy scripts. Furthermore, it is shown that the efficient GPU-based reconstruction methods of the ASTRA toolbox can significantly decrease the time needed to reconstruct large datasets, and that advanced reconstruction methods can improve reconstruction quality compared with TomoPy's standard reconstruction method.

Pelt, Daniël M.↗

Robust framework and software implementation for fast speciation mapping

One of the greatest benefits of synchrotron radiation is the ability to perform chemical speciation analysis through X-ray absorption spectroscopies (XAS). XAS imaging of large sample areas can be performed with either full-field or raster-scanning modalities. A common practice to reduce acquisition time while decreasing dose and/or increasing spatial resolution is to compare X-ray fluorescence images collected at a few diagnostic energies. In this work, several authors have used different multivariate data processing strategies to establish speciation maps. Furthermore, the theoretical aspects and assumptions that are often made in the analysis of these datasets are focused on. A robust framework is developed to perform speciation mapping in large bulk samples at high spatial resolution by comparison with known references. Two fully operational software implementations are provided: a user-friendly implementation within the MicroAnalysis Toolkit software, and a dedicated script developed under the R environment. The procedure is exemplified through the study of a cross section of a typical fossil specimen. Additionally, the algorithm provides accurate speciation and concentration mapping while decreasing the data collection time by typically two or three orders of magnitude compared with the collection of whole spectra at each pixel. Whereas acquisition of spectral datacubes on large areas leads to very high irradiation times and doses, which can considerably lengthen experiments and generate significant alteration of radiation-sensitive materials, this sparse excitation energy procedure brings the total irradiation dose greatly below radiation damage thresholds identified in previous studies. This approach is particularly adapted to the chemical study of heterogeneous radiation-sensitive samples encountered in environmental, material, and life sciences.

47 OTHER INSTRUMENTATION↗

Flexible Data-Aware Scheduling for Workflows over an In-Memory Object Store

This paper explores novel techniques for improving the performance of many-task workflows based on the Swift scripting language. We propose novel programmer options for automated distributed data placement and task scheduling. These options trigger a data placement mechanism used for distributing intermediate workflow data over the servers of Hercules, a distributed key-value store that can be used to cache file system data. We demonstrate that these new mechanisms can significantly improve the aggregated throughput of many-task workflows with up to 86x, reduce the contention on the shared file system, exploit the data locality, and trade off locality and load balance.

Duro, Francisco Rodrigo↗

Running Ensemble Workflows at Extreme Scale: Lessons Learned and Path Forward

The ever-increasing volumes of scientific data combined with sophisticated techniques for extracting information from them have led to the increasing popularity of ensemble workflows which are a collection of runs of individual workflows. A traditional approach followed by scientists to run ensembles is to rely on simple scripts to execute different runs and manage resources. This approach is not scalable and is error-prone, thereby motivating the development of workflow management systems that specialize in executing ensembles on HPC clusters. However, when the size of both the ensemble and the target system reach extreme scales, existing workflow management systems face new challenges that hamper their efficient execution. In this paper, we describe our experience scaling an ensemble workflow from the computational biology domain from the early design stages to the execution at extreme scale on Summit, a leadership class supercomputer at the Oak Ridge National Laboratory. We discuss challenges that arise when scaling ensembles to several million runs on thousands of HPC nodes. We identify challenges with composition of the ensemble itself, its execution at large scale, post-processing of the generated data, and scalability of the file system. Based on the experience acquired, we develop a generic vision of the capabilities and abstractions to add to existing workflow management systems to enable the execution of ensemble workflows at extreme scales. We believe that the understanding of these fundamental challenges will help application teams along with workflow system developers with designing the next generation of infrastructure for composing and executing extreme-scale ensemble workflows.

Mehta, Kshitij↗

Data Jockey: Automatic Data Management for HPC Multi-Tiered Storage Systems

We present the design and implementation of Data Jockey, a data management system for HPC multi-tiered storage systems. As a centralized data management control plane, Data Jockey automates bulk data movement and placement for scientific workflows and integrates into existing HPC storage infrastructures. Data Jockey simplifies data management by eliminating human effort in programming complex data movements, laying datasets across multiple storage tiers when supporting complex workflows, which in turn increases the usability of multitiered storage systems emerging in modern HPC data centers.Specifically, Data Jockey presents a new data management scheme called “goal driven data management” that can automatically infer low-level bulk data movement plans from declarative high-level goal statements that come from the lifetime of iterative runs of scientific workflows. While doing so, Data Jockey aims to minimize data wait times by taking responsibility for datasets that are unused or to be used, and aggressively utilizing the capacity of the upper, higher performant storage tiers.We evaluated a prototype implementation of Data Jockey under a synthetic workload based on a year’s worth of Oak Ridge Leadership Computing Facility’s (OLCF) operational logs. Our evaluations suggest that Data Jockey leads to higher utilization of the upper storage tiers while minimizing the programming effort of data movement compared to human involved, per-domain adhoc data management scripts.

Shin, Woong↗

Distribution Model Creation using Circuit Maps for Applied PV Impact Studies

Photovoltaic (PV) generation is becoming increasingly common on power distribution systems. The output fluctuations of this variable resource necessitate the creation of an accurate model to ensure that any adverse impacts to the distribution system are properly addressed. To reduce model creation time, a method of extracting data from AutoCAD drawings using scripted methods was developed. This paper will present a distribution model creation and validation process, document case studies of evaluating the impact of PV interconnections on utility distribution feeders, and discuss future applications. PV integration was found to be easier on 23 kV circuits compared to 4.16 kV circuits.

integrated circuit modeling↗

Modeling and Automation Framework for High IBR Integration in Large-Scale Power Systems

The increasing prevalence of power electronics- interfaced renewable generation sources is leading to a gradual replacement of traditional thermal generation-based synchronous machines. In this context, the modeling of a large-scale power grid that incorporates a significant number of inverter-based resources is crucial for understanding the dynamics and effects of these resources on the power system. This study investigates the positive sequence model of grid-following and grid-forming inverters. Additionally, this work explores the integration of distributed energy resources using population as an indicator of their relative geographic locations. To address challenge to integrate these inverter based resources into a realistic grid of the US Western interconnection, automation scripts are developed to streamline the process of replacing conventional generators with grid-following and grid-forming inverters, as well as allocating distributed energy resources. Different penetration levels of these inverters are considered, and their frequency regulation support following a disturbance is compared through dynamic simulations.

Lyu, Xue↗

Quantum/AI Topology-Aware Latency-Adaptive HPC Workflow Scheduling Optimization

The growing demand for more powerful high-performance computing (HPC) systems has led to a steady rise in energy consumption by supercomputing worldwide. This study is focused on comparing our Application-Topology Mapper (ATMapper) to the popular Simple Linux Utility for Resource Management (SLURM) for the purpose of exploring methods that can further optimize job-scheduling within HPC systems. ATMapper is an Artificial-Intelligence based approach to job-scheduling that is currently being enhanced with quantum annealing (QA) to generate optimal schedules faster. We are applying QA to speedup our ATMapper process to achieve higher computing efficiency, thereby reducing HPC energy consumption. Here, we examine how four job-scheduling approaches perform in processor node assignment when using an example network architecture of 4 interconnected nodes. Using a specialized script, we are assessing the schedule of a computation flow with 11 interdependent tasks. The data movements among nodes were tracked to count for the number of interactions (network hops) between nodes needed to complete the tasks. The total number of hops and the job completion time were then used to quantify the efficiency of the different mapping approaches. In addition to SLURM, we also compare our ATMapper to the QA-enabled LBNL TIGER and the D-Wave Distributed Computing processor assignment approaches. The preliminary results showed that our topology-aware, latency-adaptive ATMapper is significantly more efficient when compared to the other scheduling approaches due to its load-imbalance network allocation. The scheduler displayed a computing efficiency of 53% by performing significantly fewer network hops than its alternatives. By reducing the number of hops, ATMapper was able to perform all 11 tasks by using only 3 nodes out of given 4. This research indicates the potential to use QA/AI for HPC job-scheduling. Later, we will test a SLURM simulator program to draw further comparisons on the effectiveness of ATMapper's scheduling approach. The results of this comparison will serve as a baseline for later improving SLURM's performance using a QA-enhanced ATMapper approach.

Caraveo, Braulio [University of Huston - Clear Lak↗

STEPS: A Portable Numerical Simulation Toolkit for Electrical Power System Dynamic Studies

Numerical simulation is the key technique for large scale power system analysis. Redistribution of global renewable power via international interconnections requires new simulation tools to study the interconnected systems with different nominal frequencies as a whole. In this paper we introduce an open source simulation toolkit for electrical power systems (STEPS) which is hosted at Github. Its kernel is coded in C++ with major functions of power flow and electro-mechanical dynamic simulation. Flexible options are provided and configurable to improve power flow solution and dynamic simulation. Common devices and models are supported in STEPS for AC/DC hybrid system studies. Studies of interconnected systems with different nominal frequencies is supported in STEPS for research of international interconnection. Application program interfaces are provided and wrapped with Python to enable high-level interfaces for general applications. STEPS is thread safe and parallel computation is supported in both kernel and script levels to accelerate simulation. It is portable and works on Windows and GNU/Linux platforms. Cases from small to large scale systems are thoroughly tested to validate the toolkit with commercial packages as benchmarks.

42 ENGINEERING↗