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DOE OSTI2016

Asynchronous in situ connected-components analysis for complex fluid flows

Fluid flow in porous media is at the heart of problems such as groundwater contamination and carbon sequestration, and presents an important challenge for scientific computing. For this class of problem, large three-dimensional simulations are performed to advance scientific inquiry. On massively parallel computing systems, the volume of data generated by such approaches can become a productivity bottleneck if the raw data generated from the simulation is analyzed in a post-processing step. We present a physics-based framework for in situ data reduction that is theoretically grounded in multiscale averaging theory. We show how task parallelism can be exploited to concurrently perform a variety of analysis tasks with data-dependent costs, including the generation of iso-surfaces, morphological analyses, and connected components analysis. A task management framework is constructed to launch asynchronous analysis threads, manage dependencies between different tasks, promote data locality and hide the impact of data transfers. The framework is applied to analyze GPU-based simulations of two-fluid flow in porous media, generating a set of averaged measures that represents the overall system behavior. We demonstrate how the approach can be applied to perform physically-consistent averaging over fluid subregions using connected components analysis. Simulations performed on Oak Ridge National Lab s Titan supercomputer are profiled to demonstrate the performance of the associated multi-threaded in situ analysis for typical production simulation of two-fluid flow.

Mcclure, James↗

DOE OSTI2016

Asynchronous In Situ Connected-Components Analysis for Complex Fluid flows, In: ISAV '16 Proceedings of the 2nd Workshop on In Situ Infrastructures for Enabling Extreme-scale Analysis and Visualization

The simulation of multiscale physics is an important challenge for scientific computing. For this class of problem, large three-dimensional simulations are performed to advance scientific inquiry. On massively parallel computing systems, the volume of data generated by such approaches can become a productivity bottleneck if the raw data generated from the simulation is analyzed in a post-processing step. To address this, we present a physics-based framework for in situ data reduction that is theoretically grounded in multiscale averaging theory. We show how task parallelism can be exploited to concurrently perform a variety of analysis tasks with data-dependent costs, including the generation of iso-surfaces, morphological analyses, and connected components analysis. All analyses are performed in parallel using distributed memory and use the same domain decomposition as the simulation. A task management framework is constructed to leverage available parallelism within a node for analysis. The capabilities of the framework are to launch asynchronous analysis threads, manage dependencies between different tasks, promote data locality and minimize the impact of data transfers. The framework is applied to analyze GPU-based simulations of two-fluid-phase flow in porous media, generating a set of averaged measures that represents the overall system behavior. We demonstrate how the approach can be applied to perform physically-consistent analysis over fluid sub-regions determined from connected components analysis. Simulations performed on Oak Ridge National Lab's Titan supercomputer are profiled to demonstrate the performance of the associated multi-threaded in situ analysis approach for typical production simulation of two-fluid-phase flow.

Computer Science↗

DOE OSTI2019

PAPI software-defined events for in-depth performance analysis

The methodology and standardization layer provided by the Performance Application Programming Interface (PAPI) has played a vital role in application profiling for almost two decades. It has enabled sophisticated performance analysis tool designers and performance-conscious scientists to gain insights into their applications by simply instrumenting their code using a handful of PAPI functions that “just work” across different hardware components. In the past, PAPI development had focused primarily on hardware-specific performance metrics. However, the rapidly increasing complexity of software infrastructure poses new measurement and analysis challenges for the developers of large-scale applications. In particular, acquiring information regarding the behavior of libraries and runtimes—used by scientific applications—requires low-level binary instrumentation, or APIs specific to each library and runtime. No uniform API for monitoring events that originate from inside the software stack has emerged. In this article, we present our efforts to extend PAPI’s role so that it becomes the de facto standard for exposing performance-critical events, which we refer to as software-defined events (SDEs), from different software layers. Upgrading PAPI with SDEs enables monitoring of both types of performance events—hardware- and software-related events—in a uniform way, through the same consistent PAPI. The goal of this article is threefold. First, we motivate the need for SDEs and describe our design decisions regarding the functionality we offer through PAPI’s new SDE interface. Second, we illustrate how SDEs can be utilized by different software packages, specifically, by showcasing their use in the numerical linear algebra library MAGMA-Sparse, the tensor algebra library TAMM that is part of the NWChem suite, and the compiler-based performance analysis tool Byfl. Third, we provide a performance analysis of the overhead that results from monitoring SDEs and discuss the trade-offs between overhead and functionality.

Jagode, Heike↗

DOE OSTI2015

SU-E-T-318: Dosimetric Evaluation of ArcCHECK and 3DVH System Using Customized Polymer Gel Dosimeter

Purpose: ArcCHECK and 3DVH system (Sun Nuclear) can reconstruct the three-dimensional (3D) dose distribution and provide the DVH analysis in a patient. The aim of this study was to evaluate dosimetric accuracy of this system using customized polymer gel dosimeter, and also Gafchromic EBT3 films. Methods: Polyacrylamide-based gel contained magnesium chloride as a sensitizer (iPAGAT) was used in this study. Volumetric-modulated arc therapy (VMAT) plan was performed for the C-shape structure by the Eclipse treatment planning system (Varian) and used to irradiate the ArcCHECK by the Novalis Tx linear accelerator (Varian/BrainLAB). The cubic phantom filled with iPAGAT and EBT3 films placed in three orthogonal planes (axial, sagittal, and coronal) inserted into the I’mRT Phantom (IBA Dosimetry) simulated a patient were irradiated with the same VMAT plan. The measurement-guided 3D dose distribution was reconstructed using 3DVH software from the measured data of the ArcCHECK. The 3D dose distribution in iPAGAT was read out by Signa 1.5 T MRI system (GE), and 2D dose distribution on EBT3 was read out by color scanner (Epson). The comparison of all the dose distributions was performed with dose profiles and gamma index analysis in orthogonal planes using in-house developed software. Results: A good agreement was observed by overlaying the dose profiles of 3DVH, EBT3, and iPAGAT. The mean pass rates by gamma index analysis with 3%/3 mm criteria in orthogonal planes were 94.3% (3DVH vs EBT3), 91.1% (3DVH vs iPAGAT), and 96.4% (iPAGAT vs EBT3), respectively. Conclusion: 3D dose distribution reconstructed by ArcCHECK and 3DVH system was estimated accurately in a patient. However, slightly differences were observed between 3DVH and iPAGAT because of MRI noise, therefore further study is required to improve the accuracy of MRI based polymer gel dosimetry for the DVH analysis.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2021

Performance Analysis of PIConGPU: Particle-in-Cell on GPUs using NVIDIA’s NSight Systems and NSight Compute

PIConGPU, Particle In Cell on GPUs, is an open source simulations framework for plasma and laser-plasma physics used to develop advanced particle accelerators for radiation therapy of cancer, high energy physics and photon science. While PIConGPU has been optimized for at least 5 years to run well on NVIDIA GPU-based clusters, there has been limited exploration by the development team of potential scalability bottlenecks using recently updated and new tools including NVIDIA’s NVProf tool and the brand-new NVIDIA NSight Suite (Systems and Compute) tools. PIConGPU is a highly optimized application that runs production jobs at scale on a system Oak Ridge Leadership Facility’s (OLCF) Summit supercomputer (using the full machine at 4600 nodes; at 98% of GPU utilization on all ~28000 NVIDIA Volta GPUs). PIConGPU has been selected as one of the the eight applications for OLCF’s coveted Center for Accelerated Application Readiness (CAAR) program aimed at the facility’s Frontier supercomputer (OLCF’s first exascale system to launch in 2021), to partner with our vendors (primary vendors: AMD and Cray/HPE) ensuring that Frontier will be able to perform large-scale science when it opens to users in 2022. To this effect, performance engineers on the PIConGPU team wanted to dive deep into the application to understand at the finest granularity, which portions of the code could be further optimized to exploit the hardware on Summit at it’s maximum potential and also to elucidate which key kernels should be tracked and optimized for the CAAR effort to port this code to Frontier. Any bottlenecks that are observed via performance profiling on Summit are likely to also impact scalability on the Frontier-dev system and the Frontier Early Access (EA) system. Additionally, the engineers wanted to take a closer look at the newest NVIDIA profiling tools which allows us to identify the most useful features on these tools and will provide an opportunity to compare it to new AMD and Cray’s performance analysis tool releases and provide feedback to our vendor partners on what features are most important and mission critical for CAAR efforts. The primary goal of this report is to focus on the evaluation of PIConGPU’s most time-intensive kernels using NVProf and NSight Suite. Three kernels, Current Deposition (also known as Compute Current), Particle Push (Move and Mark), and Shift Particles are known to be some of the most time-consuming kernels in PIConGPU. The Current xi Deposition kernel and Particle Push kernel both set up the particle attributes for running any physics simulation with PIConGPU, so it is crucial to improve the performance of these two kernels. In this report, we measure single GPU metrics for the three kernels, offer high level takeaways from the conducted analysis, and compare the profiling data from NSight Compute to that of NVProf. This analysis was performed using a grid size of 240 x 272 x 224, and 10 time steps with the Mid-November Figure of Merit (FOM) run setup. The Traveling Wave Electron Acceleration (TWEAC) science case used in this run is a representative science case for PIConGPU. This execution can also be used for baseline analysis on AMD MI50/ MI60 systems. As of the time of writing, the PIConGPU application has limited use for features of NSight Systems, so this report will mainly focus on insights garnered from NSight Compute. For this analysis, we run the “full” metric set available in NSight Compute version 2020.1.2 and use NSight Systems version 2020.3.1 to generate the application timeline.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2020

On hybrid scenarios in KSTAR

We report the status of hybrid scenario experiments in Korea Superconducting Tokamak Advanced Research (KSTAR). The hybrid scenario is defined as stationary discharges with ${\beta _{\rm{N}}}$ $ \geqslant $ 2.4 and ${H_{89}}$ $ \geqslant $ 2.0 at ${q_{95}}$ < 6.5 without or with very mild sawtooth activities in KSTAR. It is being developed towards reactor-relevant conditions. High performance of ${\beta _{\rm{N}}} \lesssim 3.0$, ${H_{89}} \lesssim 2.4$ and G-factor ($ \equiv {\beta _{\rm{N}}}{H_{89}}/q_{95}^2$) $ \lesssim 0.4$6 has been achieved and sustained for $ \gtrsim 40{{\tau }_{\text{E}}}$ at ne/nGW ~ 0.7 with heating power of $ \lesssim $5 MW. Some KSTAR hybrid discharges exhibit a unique feature of a slow transition from conventional H-mode to hybrid mode after the third neutral beam injection. The reason for the confinement enhancement is extensively studied in this transition period of a representative discharge exhibiting a common feature of KSTAR hybrid scenarios. 0D performance analysis with magnetohydrodynamic activities, 1D kinetic profile dynamics, power balance analysis, linear gyro-kinetic analysis and edge pedestal stability analysis were conducted. The enhancement is thought to be from both the core and the pedestal. The improvement in the core region of the ion energy channel is observed from the linear gyro-kinetic analysis considering the electromagnetic, the fast ion, the Shafranov shift, ${\it{\omega }_{E \times B}}$, and the magnetic shear effect. The electromagnetic finite $\beta $ stabilisation plays a role in the inner core region at ${\rho _{\rm{tor}}}\sim0.35$ together with the fast ion effect. The alpha stabilisation effect is also found at ${\rho _{\rm{tor}}}\sim0.5$. ${\omega _{E \times B}}$, which could reduce the linear growth of the ion temperature gradient mode in the outer core region at ${\rho _{\rm{tor}}}\sim0.5 - 0.7$ with the highest contribution from the toroidal rotation. Furthermore, regarding the improvement in the pedestal, Shafranov shift broadens the stability boundary of the pedestal in support of the diamagnetic effect. The pedestal height and width could be reproduced by the EPED model, while a realistic current profile is used to calculate the internal inductance for Shafranov shift. Based on these findings, a comprehensive confinement enhancement mechanism has been proposed by considering the core-edge interplay.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2018

Phase and Relaxation Transitions in Poly(tetrafluoroetylene)

Comparative analysis of phase and relaxation transitions in poly(tetrafluoroethylene) by differential scanning calorimetry and dynamic mechanical analysis has been carried out. Elimination of procedural errors in the first case has allowed us to obtain true values of thermodynamic parameters for phase transitions and reveal their nature. Quantitative analysis of heat capacity peak profile was performed on the basis of smeared first-order phase transition theory and relaxation glass transition has been characterized.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2022

Correlations between Texture Profile Analysis and Sensory Evaluation of Cured Largemouth Bass Meat (Micropterus salmoides)

Texture is an important factor in evaluating the quality of aquatic products. To evaluate the texture properties of cured large mouth bass, edible sodium chloride (0, 1.0, 2.0, and 3.0%) was smeared to the bass meat. Texture profile analysis (TPA) and sensory evaluation were performed to evaluate the quality of the cured samples, and the correlations of the indexes in the two methods were analyzed. Two principal components were obtained from the TPA indexes and sensory evaluation indexes, and the cumulative variance contribution rates were 73.87% and 72.99%, respectively. Results from the principal component analysis showed that the main indicators that affected the TPA were gumminess and springiness, while those that affected sensory evaluation were chewiness and adhesiveness. The TPA index and sensory evaluation could be effectively improved when the sodium chloride added to the bass meat was 1%. In the correlation analysis, sensory springiness was negatively correlated with TPA hardness ( P < 0.05 , r = −0.553) but positively correlated with TPA chewiness ( P < 0.05 , r = 0.596). After stepwise regression analysis, the prediction equation between the sensory springiness and TPA hardness was obtained as SSp=5.770−0.002Ha. These results provide a basis for predicting the quality of large mouth bass cured products.

Li, Meijin↗

DOE OSTI2022

Astronauts Plasma-Derived Exosomes Induced Aberrant EZH2-Mediated H3K27me3 Epigenetic Regulation of the Vitamin D Receptor

There are unique stressors in the spaceflight environment. Exposure to such stressors may be associated with adverse effects on astronauts' health, including increased cancer and cardiovascular disease risks. Small extracellular vesicles (sEVs, i.e., exosomes) play a vital role in intercellular communication and regulate various biological processes contributing to their role in disease pathogenesis. To assess whether spaceflight alters sEVs transcriptome profile, sEVs were isolated from the blood plasma of 3 astronauts at two different time points: 10 days before launch (L-10) and 3 days after return (R+3) from the Shuttle mission. AC16 cells (human cardiomyocyte cell line) were treated with L-10 and R+3 astronauts-derived exosomes for 24 h. Total RNA was isolated and analyzed for gene expression profiling using Affymetrix microarrays. Enrichment analysis was performed using Enrichr. Furthermore, transcription factor (TF) enrichment analysis using the ENCODE/ChEA Consensus TF database identified gene sets related to the polycomb repressive complex 2 (PRC2) and Vitamin D receptor (VDR) in AC16 cells treated with R+3 compared to cells treated with L-10 astronauts-derived exosomes. Further analysis of the histone modifications using datasets from the Roadmap Epigenomics Project confirmed enrichment in gene sets related to the H3K27me3 repressive mark. Interestingly, analysis of previously published H3K27me3–chromatin immunoprecipitation sequencing (ChIP-Seq) ENCODE datasets showed enrichment of H3K27me3 in the VDR promoter. Collectively, our results suggest that astronaut-derived sEVs may epigenetically repress the expression of the VDR in human adult cardiomyocytes by promoting the activation of the PRC2 complex and H3K27me3 levels.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2015

MO-D-213-08: Remote Dosimetric Credentialing for Clinical Trials with the Virtual EPID Standard Phantom Audit (VESPA)

Purpose: Report on implementation of a Virtual EPID Standard Phantom Audit (VESPA) for IMRT to support credentialing of facilities for clinical trials. Data is acquired by local facility staff and transferred electronically. Analysis is performed centrally. Methods: VESPA is based on published methods and a clinically established IMRT QA procedure, here extended to multi-vendor equipment. Facilities, provided with web-based comprehensive instructions and CT datasets, create IMRT treatment plans. They deliver the treatments directly to their EPID without phantom or couch in the beam. They also deliver a set of simple calibration fields. Collected EPID images are uploaded electronically. In the analysis, the dose is projected back into a virtual phantom and 3D gamma analysis is performed. 2D dose planes and linear dose profiles can be analysed when needed for clarification. Results: Pilot facilities covering a range of planning and delivery systems have performed data acquisition and upload successfully. Analysis showed agreement comparable to local experience with the method. Advantages of VESPA are (1) fast turnaround mainly driven by the facility’s capability to provide the requested EPID images, (2) the possibility for facilities performing the audit in parallel, as there is no need to wait for a phantom, (3) simple and efficient credentialing for international facilities, (4) a large set of data points, and (5) a reduced impact on resources and environment as there is no need to transport heavy phantoms or audit staff. Limitations of the current implementation of VESPA for trials credentialing are that it does not provide absolute dosimetry, therefore a Level 1 audit still required, and that it relies on correctly delivered open calibration fields, which are used for system calibration. Conclusion: The implemented EPID based IMRT audit system promises to dramatically improve credentialing efficiency for clinical trials and wider applications. VESPA for VMAT will follow soon.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2016

Minimizing Grating Slope Errors in the IEX Monochromato at the Advanced Photon Source

The IEX beamline at the APS is currently in the commissioning phase. The energy resolution of the beamline was not meeting original specifications by several orders of magnitude. The monochromator, an in-focus VLS-PGM, is currently configured with a high and a medium-line-density grating. Experimental results indicated that both gratings were contributing to the poor energy resolution and this led to venting the monochromator to investigate. The initial suspicion was that a systematic error had occurred in the ruling process on the VLS gratings, but that proved to not be the case. Instead the problem was isolated to mechanical constraints used to mount the gratings into their respective side-cooled holders. Modifications were made to the holders to eliminate problematic constraints without compromising the rest of the design. Metrology performed on the gratings in the original and modified holders demonstrated a 20-fold improvement in the surface profile error which was consistent with finite element analysis performed in support of the modifications. Two gratings were successfully reinstalled and subsequent measurements with beam show a dramatic improvement in energy resolution.

Fisher, M. V.↗

DOE OSTI2023

EVs@Scale Next-Gen Profiles - EV Profile Capture 2023

As part of the U.S. DOE EVs@Scale consortium Next-Gen Profiles (NGP) project, the profile capture of production electric vehicles undergoing high power charging (HPC) is conducted over a wide range of conditions to explore variance and performance. Charge session parameters are collected from both the electric vehicle (EV) and electric vehicle supply equipment (EVSE) at a rate of 10Hz and entered into a time-series database for analysis. These charge profiles are captured under nominal and off-nominal conditions, exploring the impact of battery state of charge (SOC), battery temperature, vehicle condition, smart charge management (SCM), and EVSE limitations. Nominal conditions are defined to be ideal conditions that should transfer the maximum allowable energy in the minimum possible amount of time. Nominal condition profiles are compared across EVs to characterize state-of-the-art EV charging performance against one another. Off-nominal condition profiles are compared against its nominal condition profile counterpart to highlight the variance across less desirable starting conditions within a single EV. Under nominal conditions, most EVs can achieve the original equipment manufacturer (OEM) rated peak-power and charge times. Peak power across EVs has variance due to the vehicle design, battery topology, charging strategy, etc. These 10-100% nominal preconditioned charge profiles across 13 EVs (11 light-duty (LD), 2 heavy-duty (HD)) were used for analysis in power curve analysis, power distribution, SOC and range comparison, thermal impacts of current draw, battery pack size and energy charged, and ramp rates. Power curve analysis show the uniqueness in power vs time curves across all EVs, breaking down the features of a typical profile and where variation is typically seen. Power distribution results showed that over 50% of charge time is spent below 50kW and only 12.1% is spent above 200kW. SOC and range performance yielded different top performing EVs when exploring goals of performance from SOC and range gained after 10-min (EV2) and 20-min (EV8), and time-to-achieve 80% SOC (EV8) and 200 miles of range (EV1). Current draw from 400-volt EVs had a higher thermal impact to cable/connector temperatures when compared to 800-volt EVs, due to a higher current requirement to achieve similar power levels. There was high variance in C rating, a useful metric when comparing the relationship between peak/average charge session power and relative battery pack size, across EVs under test. Ramp rates during initial power transfer were examined, fastest and slowest speeds ranging from 192.5kW/second to 2.6kW/second respectively. A similar analysis of ramp rates was also conducted for OCPP curtailment testing, where EVs underwent a 2-minute 65A curtailment request before returning to full-power charge. Under off-nominal conditions, most EVs experienced variation from the nominal condition profiles. EVs that underwent the full set of NGP defined testing conditions were compared, analysis of which was categorized by 800-volt and 400-volt EVs. It should be noted that the 800-volt EVs had significantly higher peak power ratings than the 400-volt EVs, and thus were more prone to variance. Initial state of charge, battery temperature, and vehicle condition had a considerable impact on peak power levels and charge time for the 800-volt vehicles under test. EVSE limited tests lowered achievable power down to 200kW, greatly impacted 800-volt charging power, and had little to no effect on 400-volt charging power. Adapter testing was performed on a single 400-volt EV, where power and current limitations were found but overall charge time was not significantly impacted. Adapter and boost converter testing was performed on a single 800-volt EV, where both charge power and charge time were greatly impacted. Charge profiles are unique, and comparing such requires analysis that examines starting conditions, vehicle and battery topologies,

Charging↗

DOE OSTI2011

Report on INL Activities for Uncertainty Reduction Analysis of FY11

This report presents the status of activities performed at INL under the ARC Work Package on "Uncertainty Reduction Analyses" that has a main goal the reduction of uncertainties associated with nuclear data on neutronic integral parameters of interest for the design of advanced fast reactors under consideration by the ARC program. First, an analysis of experiments was carried out. For both JOYO (the first Japanese fast reactor) and ZPPR-9 (a large size zero power plutonium fueled experiment performed at ANL-W in Idaho) the performance of ENDF/B-VII.0 is quite satisfying except for the sodium void configurations of ZPPR-9, but for which one has to take into account the approximation of the modeling. In fact, when one uses a more detailed model (calculations performed at ANL in a companion WP) more reasonable results are obtained. A large effort was devoted to the analysis of the irradiation experiments, PROFIL-1 and -2 and TRAPU, performed at the French fast reactor PHENIX. For these experiments a pre-release of the ENDF/B-VII.1 cross section files was also used, in order to provide validation feedback to the CSWEG nuclear data evaluation community. In the PROFIL experiments improvements can be observed for the ENDF/B-VII.1 capture data in 238 Pu, 241 Am, 244 Cm, 97 Mo, 151 Sm, 153 Eu, and for 240 Pu(n,2n). On the other hand, 240,242 Pu, 95 Mo, 133 Cs and 145 Nd capture C/E results are worse. For the major actinides 235 U and especially 239 Pu capture C/E's are underestimated. For fission products, 105,106 Pd, 143,144 Nd and 147,149 Sm are significantly underestimated, while 101 Ru and 151 Sm are overestimated. Other C/E deviations from unity are within the combined experimental and calculated statistical uncertainty. From the TRAPU analysis, the major improvement is in the predicted 243 Cm build-up, presumably due to an improved 242 Cm capture evaluation. The COSMO experiment was also analyzed in order to provide useful feedback on fission cross sections. It was found out that ENDF/B-VII.1 238,240 Pu fission cross sections have improved with respect to VII.0 files while 242 Pu's fission cross section has not.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

DOE OSTI2015

Self-assembled Ag nanoparticle network passivated by a nano-sized ZnO layer for transparent and flexible film heaters

We investigated a self-assembled Ag nanoparticle network electrode passivated by a nano-sized ZnO layer for use in high-performance transparent and flexible film heaters (TFFHs). The low temperature atomic layer deposition of a nano-sized ZnO layer effectively filled the uncovered area of Ag network and improved the current spreading in the self-assembled Ag network without a change in the sheet resistance and optical transmittance as well as mechanical flexibility. The time-temperature profiles and heat distribution analysis demonstrate that the performance of the TFTH with the ZnO/Ag network is superior to that of a TFFH with Ag nanowire electrodes. In addition, the TFTHs with ZnO/Ag network exhibited better stability than the TFFH with a bare Ag network due to the effective current spreading through the nano-sized ZnO layer.

36 MATERIALS SCIENCE↗

DOE OSTI2022

Approach to using 3D laser-induced breakdown spectroscopy (LIBS) data to explore the interaction of FLiNaK and FLiBe molten salts with nuclear-grade graphite

Nuclear graphite has historically been a key component of many nuclear reactor designs and has emerged as key to numerous advanced nuclear reactor design concepts. Molten salt reactors (MSRs) are one broad group of advanced reactor designs currently being pursued by industry for commercialization. Several MSR designs under consideration use graphitic materials that directly interface with a molten salt, whether it is a fuel salt, coolant salt, or both. Therefore, the interaction of graphite materials with molten salts must be understood. To gain this required understanding, a range of data is needed including porosity, strength, and composition as a function of different salt exposure parameters. In this study, a laser-induced breakdown spectroscopy (LIBS) measurement and data analysis methodology was developed to obtain spatially resolved elemental composition information for graphite samples exposed to a molten fluoride salt. Traditional univariate emission line analysis of atomic, ionic, and molecular optical emission signals was coupled via correlation analysis with spectral decomposition of the data using principal component analysis. Elemental depth profiling and elemental mapping were also performed to visualize salt–graphite interactions. LIBS was demonstrated to be useful for measuring key analytes such as fluorine and hydrogen, which are troublesome for other analysis techniques. Evidence for complex behavior was found, thereby demonstrating the usefulness of the developed approach for future systematic studies.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

DOE OSTI2026

Profile Generation for GPU Targets

GPU accelerators are ubiquitous, but their ecosystem is far less evolved than the host one. Compiler heuristics are often tuned for CPUs and reused for GPU. Similarly, tooling and more evolved optimization techniques are historically not available on GPU targets. In this work, we address one of these shortcomings and enable profile generation and profile-guided optimizations (PGO) for GPU targets. While this is only a single step towards a CPU equivalent ecosystem for offload devices, it shows how old misconceptions on the limitations of GPUs are often not warranted anymore. Through our implementation in LLVM/Offload, we enable device-side PGO for full scientific applications and open up tooling opportunities, including code coverage analysis and compiler-built-in roofline analysis. Our evaluation highlights the performance implications of profile generation, the insights gained from these profiles, and the (missed) opportunities in utilizing the information for GPU compilation.

McDonough, Ethan Luis [Lawrence Livermore National↗

DOE OSTI2018

Biochemical Characterization and Structure-Based Mutational Analysis Provide Insight into the Binding and Mechanism of Action of Novel Aspartate Aminotransferase Inhibitors

Pancreatic cancer cells are characterized by deregulated metabolic programs that facilitate growth and resistance to oxidative stress. Among these programs, pancreatic cancers preferentially utilize a metabolic pathway through the enzyme aspartate aminotransferase 1 [also known as glutamate oxaloacetate transaminase 1 (GOT1)] to support cellular redox homeostasis. As such, small molecule inhibitors that target GOT1 could serve as starting points for the development of new therapies for pancreatic cancer. We ran a high-throughput screen for inhibitors of GOT1 and identified a small molecule, iGOT1-01, with in vitro GOT1 inhibitor activity. Application in pancreatic cancer cells revealed metabolic and growth inhibitory activity reflecting a promiscuous inhibitory profile. We then performed an in silico docking analysis to study inhibitor–GOT1 interactions with iGOT1-01 analogues that possess improved solubility and potency properties. Here, these results suggested that the GOT1 inhibitor competed for binding to the pyridoxal 5-phosphate (PLP) cofactor site of GOT1. To analyze how the GOT1 inhibitor bound to GOT1, a series of GOT1 mutant enzymes that abolished PLP binding were generated. Application of the mutants in X-ray crystallography and thermal shift assays again suggested but were unable to formally conclude that the GOT1 inhibitor bound to the PLP site. Mutational studies revealed the relationship between PLP binding and the thermal stability of GOT1 while highlighting the essential nature of several residues for GOT1 catalytic activity. Insight into the mode of action of GOT1 inhibitors may provide leads to the development of drugs that target redox balance in pancreatic cancer.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2015

Using Coarrays to Parallelize Legacy Fortran Applications: Strategy and Case Study

This paper summarizes a strategy for parallelizing a legacy Fortran 77 program using the object-oriented (OO) and coarray features that entered Fortran in the 2003 and 2008 standards, respectively. OO programming (OOP) facilitates the construction of an extensible suite of model-verification and performance tests that drive the development. Coarray parallel programming facilitates a rapid evolution from a serial application to a parallel application capable of running on multicore processors and many-core accelerators in shared and distributed memory. We delineate 17 code modernization steps used to refactor and parallelize the program and study the resulting performance. Our initial studies were done using the Intel Fortran compiler on a 32-core shared memory server. Scaling behavior was very poor, and profile analysis using TAU showed that the bottleneck in the performance was due to our implementation of a collective, sequential summation procedure. We were able to improve the scalability and achieve nearly linear speedup by replacing the sequential summation with a parallel, binary tree algorithm. We also tested the Cray compiler, which provides its own collective summation procedure. Intel provides no collective reductions. With Cray, the program shows linear speedup even in distributed-memory execution. We anticipate similar results with other compilers once they support the new collective procedures proposed for Fortran 2015.

Radhakrishnan, Hari↗