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At least 109 records · Page 6

Scalable and accurate multi-GPU-based image reconstruction of large-scale ptychography data

Abstract While the advances in synchrotron light sources, together with the development of focusing optics and detectors, allow nanoscale ptychographic imaging of materials and biological specimens, the corresponding experiments can yield terabyte-scale volumes of data that can impose a heavy burden on the computing platform. Although graphics processing units (GPUs) provide high performance for such large-scale ptychography datasets, a single GPU is typically insufficient for analysis and reconstruction. Several works have considered leveraging multiple GPUs to accelerate the ptychographic reconstruction. However, most of these works utilize only the Message Passing Interface to handle the communications between GPUs. This approach poses inefficiency for a hardware configuration that has multiple GPUs in a single node, especially while reconstructing a single large projection, since it provides no optimizations to handle the heterogeneous GPU interconnections containing both low-speed (e.g., PCIe) and high-speed links (e.g., NVLink). In this paper, we provide an optimized intranode multi-GPU implementation that can efficiently solve large-scale ptychographic reconstruction problems. We focus on the maximum likelihood reconstruction problem using a conjugate gradient (CG) method for the solution and propose a novel hybrid parallelization model to address the performance bottlenecks in the CG solver. Accordingly, we have developed a tool, called PtyGer ( Pty chographic G PU(multipl e )-based r econstruction), implementing our hybrid parallelization model design. A comprehensive evaluation verifies that PtyGer can fully preserve the original algorithm’s accuracy while achieving outstanding intranode GPU scalability.

97 MATHEMATICS AND COMPUTING↗

Iraq/Afghanistan war lung injury reflects burn pits exposure

This descriptive case series retrospectively reviewed medical records from thirty-one previously healthy, war-fighting veterans who self-reported exposure to airborne hazards while serving in Iraq and Afghanistan between 2003 and the present. They all noted new-onset dyspnea, which began during deployment or as a military contractor. Twenty-one subjects underwent non-invasive pulmonary diagnostic testing, including maximum expiratory pressure (MEP) and impulse oscillometry (IOS). In addition, five soldiers received a lung biopsy; tissue results were compared to a previously published sample from a soldier in our Iraq Afghanistan War Lung Injury database and others in our database with similar exposures, including burn pits. We also reviewed civilian control samples (5) from the Stony Brook University database. Military personnel were referred to our International Center of Excellence in Deployment Health and Medical Geosciences, Donald and Barbara Zucker School of Medicine at Hofstra/Northwell under the auspices of Northwell IRB: 17-0140-FIMR Feinstein Institution for Medical Research “Clinicopathologic characteristics of Iraq Afghanistan War Lung Injury.” We retrospectively examined medical records, including exposure data, radiologic imaging, and non-invasive pulmonary function testing (MGC Diagnostic Platinum Elite Plethysmograph) using the American Thoracic Society (ATS) standard interpretation based on Morgan et al., and for a limited cohort, biopsy data. Lung tissue, when available, was examined for carbonaceous particles, polycyclic aromatic hydrocarbons (Raman spectroscopy), metals, titanium connected to iron (Brookhaven National Laboratory, National Synchrotron Light Source II, Beamline 5-ID), oxidized metals, combustion temperature, inflammatory cell accumulation and fibrosis, neutrophil extracellular traps, Sirius red, Prussian Blue, as well as polarizable crystals/particulate matter/dust. Among twenty-one previously healthy, deployable soldiers with non-invasive pulmonary diagnostic tests, post-deployment, all had severely decreased MEP values, averaging 42% predicted. These same patients concurrently demonstrated abnormal airways reactance (X5Hz) and peripheral/distal airways resistance (D5–D20%) via IOS, averaging – 1369% and 23% predicted, respectively. These tests support the concept of airways hyperresponsiveness and distal airways narrowing, respectively. Among the five soldiers biopsied, all had constrictive bronchiolitis. We detected the presence of polycyclic aromatic hydrocarbons (PAH)—which are products of incomplete combustion—in the lung tissue of all five warfighters. All also had detectable titanium and iron in the lungs. Metals were all oxidized, supporting the concept of inhaling burned metals. Combustion temperature was consistent with that of burned petrol rather than higher temperatures noted with cigarettes. All were nonsmokers. Neutrophil extracellular traps were reported in two biopsies. Compared to our prior biopsies in our Middle East deployment database, these histopathologic results are similar, since all database biopsies have constrictive bronchiolitis, one has lung fibrosis with titanium bound to iron in fixed mathematical ratios of 1:7 and demonstrated polarizable crystals. These results, particularly constrictive bronchiolitis and polarizable crystals, support the prior data of King et al. (N. Engl. J. Med. 365:222–230, 2011) Soldiers in this cohort deployed to Iraq and Afghanistan since 2003, with exposure to airborne hazards, including sandstorms, burn pits, and improvised explosive devices, are at high risk for developing chronic clinical respiratory problems, including: (1) reduction in respiratory muscle strength; (2) airways hyperresponsiveness; and (3) distal airway narrowing, which may be associated with histopathologic evidence of lung damage, reflecting inhalation of burned particles from burn pits along with particulate matter/dust. Non-invasive pulmonary diagnostic tests are a predictor of burn pit-induced lung injury

36 MATERIALS SCIENCE↗

Synchrotron studies of functional interfaces and the state of the art: A perspective

The dramatic improvements in synchrotron light sources across the world imply tremendous opportunities for interface science. In this work, we describe a variety of current scattering and spectroscopic techniques with an eye toward how these will evolve, particularly with the advent of diffraction-limited sources. We also note the importance of in situ and operando methods for both understanding interface creation and interface evolution in different environments. As interfaces are often where critical processes occur, whether in regard to energy/chemical/materials/quantum information science, understanding the utility of these x-ray techniques will be of considerable importance to the cultivation of next-generation scientists.

36 MATERIALS SCIENCE↗

High pressure, high flow rate batch mixing apparatus for high throughput experiments

An automated, high pressure, high flow rate batch mixing apparatus has been designed and constructed for rapid, stable, and repeatable mixing of multiple gases and vapors. The apparatus operates as an intermittent batch mixer with cycles of topping off fresh mixture to maintain pressure in an accumulator tank until consumed in an experimental apparatus. At high duty cycles, the apparatus can also function at steady state. This style of mixing is suitable for experiments such as high repetition rate shock tubes and other devices with intermittent flow demands. It is compact and portable, facilitating use in locations such as synchrotron light sources. The entire apparatus is heated to permit the mixing of vapors from species with low volatilities. The apparatus is fully automated and runs for extended periods with the only intervention being to refresh reagent supplies. Here, the accuracy and repeatability of the apparatus were verified by periodic gas sampling and analysis with gas chromatography. Multi-component mixtures spanning a wide range of complexity, dilution, and volatility of constituents have been prepared. The compositions of the majority of the mixture were found to be stable over several filling cycles, repeatable, and with the proper calibration of set-point conditions, accurate. Challenges were encountered preparing a mixture from multi-component liquids, and potential solutions are discussed.

47 OTHER INSTRUMENTATION↗

Evaluation of crystalline quality of traveling heater method (THM) grown Cd0.9Zn0.1Te0.98Se0.02 crystals

Because of its excellent opto-electronic properties, CdZnTe (CZT) has been the material of choice for x- and gamma-ray detectors operable at room temperature. CZT is the leading commercially available room-temperature radiation detector material today. Although much progress has been made over the past three decades, today's CZT crystals still face certain challenges, especially the presence of the performance-limiting materials defects and the associated relatively high production cost. In this regard, CdxZn1−xTeySe1−y (CZTS) is emerging as a next-generation compound semiconductor, which overcomes some of the limitations of CZT technology for the stated applications. Here, we conducted a study to evaluate the crystalline quality of the traveling heater method grown CZTS with an optimized alloy composition, i.e., Cd0.9Zn0.1Te0.98Se0.02. The as-grown samples were evaluated by low-temperature photoluminescence (PL) spectroscopy and high-resolution x-ray diffraction using the synchrotron light source at Brookhaven National Laboratory. The full width at half maximum of both the PL and x-ray rocking curves was observed to be broadened due to the lattice disorder of the quaternary compound, eventually degrading the crystalline quality. This was consistent with density functional theory calculations.

Roy, U. N. (ORCID:0000000282089680)↗

Applications of “Synchrotron Radiation Workshop” Code

The “Synchrotron Radiation Workshop” (SRW) computer code was started in the group of Insertion Devices of the European Synchrotron Radiation Facility in 1997. The idea behind it was to combine in one software library electrodynamics methods for calculating electric fields (and derived characteristics) of synchrotron radiation (SR) generated by relativistic electrons moving in magnetic fields of nearly arbitrary configuration with wave-optics methods for simulating propagation of radiation through optical elements of beamlines. Further, the use of this general approach was initially driven by applications in electron beam diagnostics using SR. However, with time it started to be used for more complicated beamlines of synchrotron light sources, and the use of the code for these applications continues to increase, with the new light sources offering brighter and more coherent x ray beams for wide ranges of experiments in different areas of science.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

A compact approach to higher-resolution resonant inelastic x-ray scattering detection using photoelectrons

The detection of inelastically scattered soft x-rays with high energy resolution usually requires large grating spectrometers. Recently, photoelectron spectrometry for analysis of x-rays (PAX) has been rediscovered for modern spectroscopy experiments at synchrotron light sources. By converting scattered photons to electrons and using an electron energy analyser, the energy resolution for resonant inelastic x-ray scattering (RIXS) becomes decoupled from the x-ray spot size and instrument length. In this work, we develop PAX towards high energy resolution using a modern photoemission spectroscopy setup studying Ba 2 Cu 3 O 4 Cl 2 at the Cu L 3 -edge. We measure a momentum transfer range of 24% of the first Brillouin zone simultaneously. Our results hint at the observation of a magnon excitation below 100 meV energy transfer and show intensity variations related to the dispersion of dd-excitations. With dedicated setups, PAX can complement the best and largest RIXS instruments, while at the same time opening new opportunities to acquire RIXS at a range of momentum transfers simultaneously and combine it with angle-resolved photoemission spectroscopy in a single instrument.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Developments in SRW Code and Sirepo Framework Supporting Simulation of Time-Dependent Coherent X-ray Scattering Experiments

Physical optics simulations for beamlines and experiments are essential for the effective use of synchrotron light source facilities such as NSLS-II at BNL. The SRW software package supports such source-to-detector simulations for coherent X-ray scattering and imaging experiments through its Python interface and Sirepo browser-based graphical user interface. This allows one to define custom sample models, assess the feasibility of an experiment, and estimate most appropriate beamline settings before using valuable beamtime. We discuss the recent use of general-purpose GPU resources and coherent mode decomposition algorithms in SRW to accelerate physical optics simulations with partially coherent X-rays. To illustrate these new capabilities, we describe simulations of typical time series of partially coherent scattering images used in X-ray Photon Correlation Spectroscopy (XPCS) experiments; aiming to characterize the nanoscale dynamics of a disordered sample, representing a solution of nanoparticles undergoing Brownian diffusion.

36 MATERIALS SCIENCE↗

Outlook for artificial intelligence and machine learning at the NSLS-II

Abstract We describe the current and future plans for using artificial intelligence and machine learning (AI/ML) methods at the National Synchrotron Light Source II (NSLS-II), a scientific user facility at the Brookhaven National Laboratory. We discuss the opportunity for using the AI/ML tools and techniques developed in the data and computational science areas to greatly improve the scientific output of large scale experimental user facilities. We describe our current and future plans in areas including from detecting and recovering from faults, optimizing the source and instrument configurations, streamlining the pipeline from measurement to insight, through data acquisition, processing, analysis. The overall strategy and direction of the NSLS-II facility in relation to AI/ML is presented.

97 MATHEMATICS AND COMPUTING↗

Gaming the beamlines—employing reinforcement learning to maximize scientific outcomes at large-scale user facilities

Abstract Beamline experiments at central facilities are increasingly demanding of remote, high-throughput, and adaptive operation conditions. To accommodate such needs, new approaches must be developed that enable on-the-fly decision making for data intensive challenges. Reinforcement learning (RL) is a domain of AI that holds the potential to enable autonomous operations in a feedback loop between beamline experiments and trained agents. Here, we outline the advanced data acquisition and control software of the Bluesky suite, and demonstrate its functionality with a canonical RL problem: cartpole. We then extend these methods to efficient use of beamline resources by using RL to develop an optimal measurement strategy for samples with different scattering characteristics. The RL agents converge on the empirically optimal policy when under-constrained with time. When resource limited, the agents outperform a naive or sequential measurement strategy, often by a factor of 100%. We interface these methods directly with the data storage and provenance technologies at the National Synchrotron Light Source II, thus demonstrating the potential for RL to increase the scientific output of beamlines, and layout the framework for how to achieve this impact.

36 MATERIALS SCIENCE↗

Microsecond-latency feedback at a particle accelerator by online reinforcement learning on hardware

The commissioning and operation of future large-scale scientific experiments will challenge current tuning and control methods. Reinforcement learning (RL) algorithms are a promising solution due to their ability to dynamically adapt to changing environments and consider delayed consequences. In many real-world applications, RL policies must produce actions in real time, often within microseconds to milliseconds, imposing significant constraints on system latency and computational overhead that conventional machine learning libraries are not designed to handle. To control phenomena in real time at these timescales, RL needs to be deployed on-the-edge, namely on dedicated hardware located near the system it controls, without relying on a host CPU or cloud-based inference. In this work we present the design and deployment of an experience accumulator system in a particle accelerator. In this system, deep-RL algorithms run using hardware acceleration and act within a few microseconds, enabling the use of RL for control of phenomena like beam instabilities. The training uses the collected data offline to reduce the number of operations carried out on the acceleration hardware. The proposed architecture was tested in real experimental conditions at the Karlsruhe research accelerator, a synchrotron light source, where the system was used to control artificially induced horizontal betatron oscillations in real-time, with a control loop period of just 2.7 μs. The results showed a performance comparable to the commercial feedback system available at the accelerator, demonstrating the viability and potential of this approach. Due to the self-learning and reconfiguration capability of this implementation, a seamless application to other control problems is possible. Applications range from particle accelerators to large-scale research and industrial facilities.

FPGA↗

Approximate entropy analysis for nonlinear beam dynamics

In this paper, we applied an approximate entropy (ApEn) analysis to nonlinear beam dynamics. Due to the presence of strong nonlinear magnets, the degree of chaos in beam motion gradually increases proportionally with its amplitude. Such chaos can be quantitatively characterized with ApEn of beam turn-by-turn readings. ApEn analysis is a technique used to quantify the amount of regularity and the unpredictability of fluctuations with respect to time-series data. The ApEn, when applied as a chaos indicator, can then be used for nonlinear lattice optimization and analysis. The National Synchrotron Light Source II (NSLS-II) electron storage ring lattice was used as an example of a real-world application of our technique. Published by the American Physical Society 2024

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Numerical modeling of a proof-of-principle experiment on optical stochastic cooling at an electron storage ring

Cooling of beams circulating in storage rings is critical for many applications including particle colliders and synchrotron light sources. A method enabling unprecedented beam-cooling rates, optical stochastic cooling (OSC), was recently demonstrated in the Integrable Optics Test Accelerator (IOTA) electron storage ring at Fermilab [J. Jarvis , ]. This paper describes the numerical implementation of the OSC process in the particle-tracking program and discusses the validation of the developed model with available experimental data. The model is also employed to highlight some features associated with different modes of operation of OSC. The developed simulation tool should be valuable in guiding future configurations of optical stochastic cooling and, more broadly, modeling self-field-based beam manipulations. Published by the American Physical Society 2024

43 PARTICLE ACCELERATORS↗

High-Energy Coherent X-Ray Dffraction Microscopy of Polycrystal Grains: First Steps Towards a Multi-Scale Approach

Here, we present proof-of-concept imaging measurements of a polycrystalline material that integrate the elements of conventional high-energy x-ray diffraction microscopy with coherent diffraction-imaging techniques, and that can enable in situ strain-sensitive imaging of lattice structure in ensembles of deeply embedded crystals over five decades of length scale upon full realization. We demonstrate that the combination of these two characterization methods enables a more complete picture of the crystal-lattice strain than either method is capable of providing individually. Such complementary imaging capabilities are critical to addressing questions in a variety of research areas such as materials science and engineering, chemistry, and solid-state physics. Towards this eventual goal, the following key aspects are demonstrated: (1) high-energy Bragg coherent diffraction imaging (HE BCDI) of submicron-scale crystallites at 52 keV at current third-generation synchrotron light sources, (2) HE BCDI performed in conjunction with far-field high-energy diffraction microscopy (FF HEDM) on the grains of a polycrystalline sample in a smoothly integrated manner, and (3) the orientation information of an ensemble of grains obtained via FF HEDM used to perform complementary HE BCDI on multiple Bragg reflections of a single targeted grain. The imaged structures are seen to be 477 ± 50 nm or smaller in size, with an estimated strain resolution of 2.5 x 10 -4 . These steps lay the foundation for integration of HE BCDI, which typically provides a spatial resolution tens of nanometers, into a broad suite of well-established HEDM methods, extending HEDM beyond the few-micrometer resolution bound and into the nanoscale, and positioning the approach to take full advantage of the orders-of-magnitude improvement of x-ray coherence expected at fourth-generation light sources presently being built and commissioned worldwide.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Specimen-displacement correction for powder X-ray diffraction in Debye–Scherrer geometry with a flat area detector

The effect of small changes in the specimen-to-detector distance on the unit-cell parameters is examined for synchrotron powder diffraction in Debye–Scherrer (transmission) geometry with a flat area detector. An analytical correction equation is proposed to fix the shift in 2θ values due to specimen capillary displacement. This equation does not require the use of an internal reference material, is applied during the Rietveld refinement step, and is analogous to the specimen-displacement correction equations for Bragg–Brentano and curved-detector Debye–Scherrer geometry experiments, but has a different functional form. The 2θ correction equation is compared with another specimen-displacement correction based on the use of an internal reference material in which new integration and calibration parameters of area-detector images are determined. Example data sets showing the effect of a 3.3 mm specimen displacement on the unit-cell parameters for 25°C CeO 2 , including both types of displacement correction, are described. These experiments were performed at powder X-ray diffraction beamlines at the National Synchrotron Light Source II at Brookhaven National Laboratory and the Advanced Photon Source at Argonne National Laboratory.

36 MATERIALS SCIENCE↗

Fast digital lossy compression for X-ray ptychographic data

Increases in X-ray brightness from synchrotron light sources lead to a requirement for higher frame rates from hybrid pixel array detectors (HPADs), while also favoring charge integration over photon counting. However, transfer of the full uncompressed data will begin to constrain detector design, as well as limit the achievable continuous frame rate. Here a data compression scheme that is easy to implement in a HPAD's application-specific integrated circuit (ASIC) is described, and how different degrees of compression affect image quality in ptychography, a commonly employed coherent imaging method, is examined. Using adaptive encoding quantization, it is shown in simulations that one can digitize signals up to 16383 photons per pixel (corresponding to 14 bits of information) using only 8 or 9 bits for data transfer, with negligible effect on the reconstructed image.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗