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All sourcesNASA NTRSDOE OSTI
DOE OSTI2019

Self-powered Wireless Dual-mode Langasite Sensor for Pressure/Temperature Monitoring of Nuclear Reactors

Safety issues in nuclear power plants are of extreme importance. Numerous sensors are used within nuclear power plants for sensing and monitoring of its critical operation parameters. As currently implemented, during massive losses of power across the plant in accidents, the backup batteries for the monitoring sensors will ultimately be drained and can cease to operate. The overall objective of this NEUP project is to develop a novel self-powered wireless hybrid sensor which can accurately monitor both pressure and temperature using a single device, even in the extreme harsh environments of severe nuclear accidents, without the requirement of external electricity. At Virginia Tech side, a heat pipe assisted thermoelectric generator (TEG) energy harvester and associated power management and data transmission circuits were developed. The energy harvester can produce electrical power continuously, even in loss of plant and external power situations, providing power for important data transmission for accident diagnosis. The self-powered sensing system could be integrated directly onto key nuclear components including pipes, pump housings, heat exchangers, reactor vessels, and shielding structures inside and outside of the reactor core. Two TEG based energy harvesters which can work in relatively low (50-250 ºC) and high temperature ranges (250-350 ºC) were established and tested. In the prototypes, heat pipes were introduced to reduce the heat resistances of the device at the hot and cold ends. The power output of the heat pipe assisted TEG module is 2.22 W, which is 6 times more than one using an aluminum rod. In-lab tests showed that these devices canmeet the requirement to power the sensors and circuit during normal and off-normal conditions.Amodel was then built to analyze the thermal network in the energy harvester, and was used to optimize its performance and reduce its geometry size. The design and testing of the vibrational energy harvester were completed. The harvester, has shown to effectively increase the vibrational potential of the main coolant pump, though it has been shown that thermal energy has a much higher potential for the powering of sensors. In this project, a self-start charger circuit for the energy harvester was designed to regulate and manage the power. An energy storage element was incorporated into the energy harvesting module for sensors and wireless transceivers in an off-normal situation. The signal conditioning and wireless communication electronic circuits were developed and tested in the lab. An important consideration for an energy harvester within a nuclear power plant is the level of radiation it will encounter during operation. The two main sources of radiation in a nuclear power plant are gamma and neutron radiation. Aradiation experiment was conducted in the Westinghouse Electric Company during which the prototypes were placed in a 106 rad radiation environment to test their ability to operate in the extreme environment. The results showed that this level of radiation had little effect on the performance of the TEGmaterial and heat pipe heat exchanging system. Its influence on the circuit was still under research, however the need for more development on radiation hardened electronics is needed. Pressure measurement based on piezoelectric crystal resonators has advantages over the commercially available methods like capacitive, electromagnetic, optical, potentiometric, and piezo resistive strain gauges. Since the output of piezoelectric based sensors are digital in format, it has a very high resolution, high accuracy, and long-term stability. Quartz is one of the commonly used piezoelectric material in digital pressure sensors design. This material is elastic in nature, providing high stability, high repeatability, high elasticity, repeatable mechanical behavior for many cycles of operation, and is free of hysteresis. The quartz resonator has a high Q, which means that very high vibration can be driven with the very low electric power. Langasite (LGS) is a new promising piezoelectric material that combines the advantageous properties of quartz with a better performance at high temperatures. LGS will not undergo any phase transitions up to its melting temperature of 1473 C, and hence, the application of Langasite in measuring pressure at high temperatures is promising. In this project, the design and fabrication of the piezo oscillator crystal for temperature and pressure measurement has been completed. The entire sensor has been fabricated and tested to see its sensitivity to temperature and pressure changes. The design and optimization of the radiation shielding systems that can effective protect the duel-mode Langasite sensor inside reactor core were demonstrated. To maximize the radiation shielding effectiveness, different types of materials are investigated based upon recent developments of radiation shielding systems including aluminum + Boron carbide and bismuth borosilicate glass B2O3 in addition to tungsten/B4C. New materials based upon metatheses is included as potential shielding to mitigate neutron fluencies. The radiation shielding effectiveness of selected composites are evaluated within a broader neutron spectrum from thermal, epithermal, fast (1 MeV) and 15 MeV neutrons. Performance analysis was also conducted to evaluate the effects of selected composite systems.Aconceptual design was also proposed for the packaging and integration of the radiation shielding system with the sensor, and its applicability within the reactor core was discussed. At end of the project, all components necessary for a complete sensing and monitoring system, including a langasite sensor, electrodes, the TEG harvester, an energy storage device, and power management and transmission electronics were integrated to demonstrate feasibility in powering the sensor. Finally, integration of each component into a full package, and a full demonstration were done.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗
DOE OSTI2019

Cataloging the visible universe through Bayesian inference in Julia at petascale

A key task in astronomy is to locate astronomical objects in images and to characterize them according to physical parameters such as brightness, color, and morphology. This task, known as cataloging, is challenging for several reasons: many astronomical objects are much dimmer than the sky background, labeled data is generally unavailable, overlapping astronomical objects must be resolved collectively, and the datasets are enormous – terabytes now, petabytes soon. In this work, we infer an astronomical catalog from 55 TB of imaging data using Celeste, a Bayesian variational inference code written entirely in the high-productivity programming language Julia. Using over 1.3 million threads on 650,000 Intel Xeon Phi cores of the Cori Phase II supercomputer, Celeste achieves a peak rate of 1.54 DP PFLOP/s. Celeste is able to jointly optimize parameters for 188 M stars and galaxies, loading and processing 178 TB across 8192 nodes in 14.6 min. To achieve this, Celeste exploits parallelism at multiple levels (cluster, node, and thread) and accelerates I/O through Cori’s burst buffer. Julia’s native performance enables Celeste to employ high-level constructs without resorting to hand-written or generated low-level code (C/C++/Fortran) while still achieving petascale performance.

Regier, Jeffrey↗
DOE OSTI2022

Optimization Studies for the Long-Baseline Neutrino Facility at Fermilab

The Deep Underground Neutrino Experiment and Long-Baseline Neutrino Facility (DUNE-LBNF) are under development at Fermilab since early 2010s [1]. At present, the work is being performed towards a comprehensive review conducted by US Department of Energy (DOE)-the Critical Decision 2 (CD-2)-that is planned to take place in the middle of 2022. The primary scientific objectives of DUNE are to carry out a comprehensive investigation of neutrino oscillations to test CP violation in the lepton sector, determine the ordering of the neutrino masses, and to test the three-neutrino paradigm (electron, muon and tau neutrino). The LBNF will provide a 120-GeV proton beam on a neutrino production target utilizing a new 800-MeV superconducting Linac which is expected to be completed in 2027 [2]. The neutrino beamline, which utilizes a target and horn systems, decay pipe, hadron absorber and other systems, is a core component of the LBNF. At present-as a result of numerous iterations-there exists an optimized design with a 1.5-m graphite target and focusing system consisting of three horns. Further optimization energy deposition and radiological calculations are performed towards CD-2 and beyond. This paper describes results of the most recent MARS15 [3] optimization studies.

43 PARTICLE ACCELERATORS↗
DOE OSTI2019

Solving a trillion unknowns per second with HPGMG on Sunway TaihuLight

Benchmarks for supercomputers are important tools, not only for evaluating and ranking modern supercomputers, but also for providing hints for future architecture design. As a new benchmark, HPGMG (high performance geometric multigrid) solves a linear equation set with a full geometric multi-grid algorithm. It involves computation on different scales, data movement with various volumes, global communication and neighbor communication with both large and small messages, etc., and is more correlated to real world applications than traditional benchmarks such as LINPACK. Therefore, it is desirable to examine how well HPGMG can perform on leadership supercomputers such as Sunway Taihulight. Sunway Taihulight, the No. 1 supercomputer in the Top 500 list from June 2016 to June 2018, which uses a specially designed many-core architecture SW26010, is of great interest to the community of high performance computing. With careful analysis and code design, we came up with an efficient implementation of HPGMG on SW26010 processors. We not only employed traditional optimization techniques such as 2.5D partitioning, double buffering, and collective data load, but also introduced a micro-benchmark to help with the choice of optimization direction and parameter tuning. Another contribution is that we proposed a new procedure for the major operations, by granulating and reordering the smooth function and the ghost exchange operation, leading to reduced memory copy and accelerated communication process. Our optimized implementation of HPGMG on Sunway TaihuLight achieved a ground-breaking performance of 1.036 × 10 12 Degrees of Freedom per second at the finest level, which is No. 1 on the HPGMG list of Nov 2017.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2016

Advantages gained by Optimized ZIRLO and AXIOM PWR cladding materials

In support of industry's demands for higher performance cladding alloy materials, the Optimized ZIRLO alloy was developed as an evolutionary improvement of the ZIRLO alloy to obtain a significant improvement in corrosion performance and hydrogen pickup while maintaining the overall robust performance of ZIRLO alloy. Currently with operating experience in over 40 plants and burnup reaching over 70 GWd/MTU, a majority of the Westinghouse-fueled US PWR fleet, covering almost all Westinghouse fuel designs, has adopted full regions of Optimized ZIRLO cladding. Across all of these applications, Optimized ZIRLO cladding has demonstrated greatly improved corrosion performance and structural stability. These demonstrated improvements offer increased operational margin and flexibility, in support of industry trends toward increased core operating fuel duties and evolving regulatory requirements such as accident scenarios. Underpinning these benefits are the extensive post irradiation exam (PIE) data obtained from both pool-side and hot-cell exams for Optimized ZIRLO cladding. Building on the successes of Optimized ZIRLO cladding, and in recognition of increasingly challenging fuel management practices, and revised LOCA regulatory rules restricting cladding hydrogen content, AXIOM cladding is being rolled out for full lead test assembly irradiation. The AXIOM alloy, Westinghouse's next generation robust alloy targeting very high fuel duties, is designed to provide improved corrosion resistance, lower hydrogen pick-up, and lower creep and growth compared to current Westinghouse products. AXIOM cladding has been irradiated in a variety of reactors worldwide, including both commercial and test reactors. Extensive PIE data is available for various burnup levels, with leading rods approaching 75 GWd/MTU. The AXIOM composition was selected to ensure enhanced operating performance on multiple fronts, including the optimum combination of corrosion resistance and wear resistance, reduced hydrogen pick-up, improved dimensional stability, and robustness in aggressive coolant chemistry conditions. The present paper provides high burnup performance data, capturing the advantages gained by introducing Optimized ZIRLO and AXIOM alloy as PWR cladding materials. (authors)

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2018

On Data Transfers Over Wide-Area Dedicated Connections

Dedicated wide-area network connections are employed in big data and high-performance computing scenarios, since the absence of cross-traffic promises to make it easier to analyze and optimize data transfers over them. However, nonlinear transport dynamics and end-system complexity due to multi-core hosts and distributed file systems make these tasks surprisingly challenging. We present an overview of methods to analyze memory and disk file transfers using extensive measurements over 10 Gbps physical and emulated connections with 0–366 ms round trip times (RTTs). For memory transfers, we derive performance profiles of TCP and UDT throughput as a function of RTT, which show concave regions in contrast to entirely convex regions predicted by previous models. These highly desirable concave regions can be expanded by utilizing large buffers and more parallel flows. We also present Poincar´e maps and Lyapunov exponents of TCP and UDT throughputtraces that indicate complex throughput dynamics. For disk file transfers, we show that throughput can be optimized using a combination of parallel I/O and network threads under direct I/O mode. Our initial throughput measurements of Lustre filesystems mounted over long-haul connections using LNet routers show convex profiles indicative of I/O limits.

Rao, Nageswara S.↗
DOE OSTI2015

DOE site remedial management optimization utilizing on the cloud computing systems - 15676

Environmental cleanups at complex sites necessarily address many competing demands and answer questions such as: 'What is the best way and in a sustainable manner to minimize risk to human health and the environment during active restoration efforts and/or long term legacy management, while incorporating parameter uncertainty, management considerations, and stakeholder concerns into the process?' Physics Based Management Optimization (PBMO{sup TM}) provides a means to answer such questions. 'Physics Based' indicates incorporation of numerically computed groundwater flow and transport processes into the analysis. This enables optimal remedy design based on comprehensive mass removal/destruction metrics and optimal monitoring strategies. 'Management Optimization' indicates the ability to incorporate objective functions (e.g., management constraints, sustainability considerations) into the evaluation. PBMO{sup TM} components have been successfully implemented for optimal plume delineation (points of compliance) and monitoring, for optimal system design and to optimize existing active treatment systems in the US at multiple DOE, DOD and industrial sites since the mid 1990's. PBMO{sup TM} has been recently extended and implemented on multi-core, multi-CPU grid computing systems including computational clusters, local area networks and the Cloud. This extension allows for increased flexibility and adaptation of computational resources which can now support optimal remedy design and long term management strategies for complex soil and groundwater sites. In the PBMO{sup TM} -Grid case study, we evaluate flow and transport for a typical optimization search for a realistic project against sequential optimization. PBMO{sup TM}-Grid reduces the CPU time required to solve the optimization problem by more than a factor of 14 X compared to sequential optimization. PBMO{sup TM}-Grid can be deployed for deterministic or stochastic optimization and formally computes design risk and predicted degree of remedial action success. The numerical models used can consist of a single 'mega' model (aka a monolith), or a mixture of models and other calculations or expert systems. PBMO{sup T}M-Grid integrates the computational models in a seamless manner, and models run on the Cloud can be implemented in Windows or Linux platforms. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2017

Exploring performance and energy tradeoffs for irregular applications: A case study on the Tilera many-core architecture

High performance, parallel applications with irregular data accesses are becoming a critical workload class for modern systems. In particular, the execution of such workloads on emerging many-core systems is expected to be a significant component of applications in data mining, machine learning, scientific computing and graph analytics. However, power and energy constraints limit the capabilities of individual cores, memory hierarchy and on-chip interconnect of such systems, thus leading to architectural and software trade-os that must be understood in the context of the intended application’s behavior. Irregular applications are notoriously hard to optimize given their data-dependent access patterns, lack of structured locality and complex data structures and code patterns. We have ported two irregular applications, graph community detection using the Louvain method (Grappolo) and high-performance conjugate gradient (HPCCG), to the Tilera many-core system and have conducted a detailed study of platform-independent and platform-specific optimizations that improve their performance as well as reduce their overall energy consumption. To conduct this study, we employ an auto-tuning based approach that explores the optimization design space along three dimensions - memory layout schemes, GCC compiler flag choices and OpenMP loop scheduling options. We leverage MIT’s OpenTuner auto-tuning framework to explore and recommend energy optimal choices for different combinations of parameters. We then conduct an in-depth architectural characterization to understand the memory behavior of the selected workloads. Finally, we perform a correlation study to demonstrate the interplay between the hardware behavior and application characteristics. Using auto-tuning, we demonstrate whole-node energy savings and performance improvements of up to 49:6% and 60% relative to a baseline instantiation, and up to 31% and 45:4% relative to manually optimized variants.

auto tuning↗
DOE OSTI2018

Metal Amorphous Nanocomposite (MANC) Alloy Cores with Spatially Tuned Permeability for Advanced Power Magnetics Applications

Metal amorphous nanocomposite (MANC) alloys are an emerging class of soft magnetic materials showing promise for a range of inductive components targeted for higher power density and higher efficiency power conversion applications including inductors, transformers, and rotating electrical machinery. Magnetization reversal mechanisms within these alloys are typically determined by composition optimization as well as controlled annealing treatments to generate a nanocomposite structure composed of nanocrystals embedded in an amorphous precursor. Here in this paper we demonstrate the concept of spatially varying the permeability within a given component for optimization of performance by using the strain annealing process. The concept is realized experimentally through the smoothing of the flux profile from the inner to outer core radius achieved by a monotonic variation in tension during the strain annealing process. Great potential exists for an extension of this concept to a wide range of other power magnetic components and more complex spatially varying permeability profiles through advances in strain annealing techniques and controls.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Implications of parasitic absorption of electron cyclotron waves on ITER operation around half-field

The ITER Research Plan envision operation around half of the nominal magnetic field (i.e. around B = 2.65 T) as a path to baseline operation. This work discusses constraints on the optimal range of magnetic field, which is bounded in the lower limit by the presence of the third-harmonic electron cyclotron resonance at half field, and on the upper limit by the loss of core heating and current drive. Additionally, it will be shown that increasing the magnetic field by only 3%, i.e. to 2.75 T, eliminates the third harmonic parasitic absorption without compromising demonstration of access to H-mode, while operating at a magnetic field of 3.0 T—previously proposed for optimal use of the ion cyclotron system—would impair the use of the electron cyclotron system for core-heating and current drive. Operation at 2.65 T would still be possible if the polarization of the equatorial launcher is changed from X-mode to O-mode in the current flattop phase.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2024

Compatibility of divertor detachment and ELM suppression in DIII-D high- β p plasmas with ITER-similar shape

Abstract Integration of transient and steady-state divertor heat fluxes control with a high-performance core is necessary for future fusion reactors. In recent DIII-D high- β p experiments, divertor detachment and simultaneous edge localized mode (ELM) suppression are demonstrated while the plasma confinement quality is maintained high in ITER-similar shape. By optimizing the neon injection in high- β p scenario with ITER-similar shape, deep detachment and ELM suppression are achieved with a high-performance core ( β N ∼ 2.8, β p ∼ 2.3) at q 95 ∼ 7.5. Partial divertor detachment and suppression of large ELMs are achieved at q 95 ∼ 6. The stability analyses suggest that with low neon injection, the density pedestal becomes higher and steeper and the T i profile also increases, therefore the increased edge pressure and higher current density destabilize the Peeling-Ballooning mode (PBM), which would lead to a large ELM collapse. With strong neon gas puffing, the significantly reduced pedestal pressure and current density, due to the degraded T e pedestal, lead to the stabilization of PBM and ELMs are suppressed. For both cases, the coupling between the large radius internal transport barrier (ITB) and edge pedestal is the key reason for maintaining high global performance. The formation of large radius ITB compensates for pedestal degradation. Such results could provide an attractive scenario to well control the transient and steady-state heat flux onto the divertor plates while maintaining good plasma performance, which is an important step toward the steady-state operation of future fusion reactors.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2017

Cryogenic temperature toughening and strengthening due to gradient phase structure

Cold embrittlement is one of the primary concerns challenging the usage of steels in infrastructures like pipelines and ocean platforms. This challenge is also compounded by the limited selection of materials for application in a cold and corrosive environment. Inspired by recent progresses in developing gradient structured materials with extraordinary properties, in this paper we report a class of stainless steels with gradient phase structures achieving a superb combination of strength (1753 MPa) and tensile ductility (>25%) at the cryogenic temperature of 77 K. A set of cylindrical steel samples acquire a graded mixture of hard martensitic and soft austenitic phases through pre-torsion, which results in an optimal stress partition in the material - the hard martensitic structures showing a positive density gradient from core to edge carry higher stress near the edge, while the soft austenitic phase showing a negative density gradient from core to edge serves to retain substantial tensile ductility. Finally, the phase-transformation at low temperature in gradient structures and the resulted work-hardening could be adopted to enhance the ductility and strength of widely used engineering materials for their applications in harsh environment.

36 MATERIALS SCIENCE↗
DOE OSTI2020

The Development of a Generalized Riser Flow Regime Map Based Upon Higher Moment and Chaotic Statistics Using Electrical Capacitance Volume Tomography (ECVT)

Dynamic analyses have been applied to the temporal signals from an Electro Capacitance Volume Tomography instrument located near mid-height on the riser of an industrial-scale cold-flow circulating fluidized bed to characterize gas-solids flow behavior in the riser. Twelve capacitance electrodes surround the cylindrical riser over a height of 1.3 m. The instrument used a neural network deconvolution algorithm to determine the spatially resolved solids fraction recorded at 52 Hz. Experiments were carried out over a range of gas and solids flows in the transport regime using a Geldart Group B bed material, high density polyethylene with mean particle size of 880 μm. The radial solids distribution was found to vary from one-time step to the next between profiles typical of laminar and turbulent flow. The duration of time spent in each of these flow profiles depended upon the operating regime – dilute, core-annular, or fast fluidized bed. The chaotic structure of the temporal data was characterized using the three conventional approaches: the first 4 moments from the distribution of signal in time, system memory parameters from the autocorrelation function and the Hurst exponent, and analysis of the correlationentropy and correlation dimension of the attractor. These signal analysis techniques were used to clearly distinguish differences between different transport operating regimes. Specifically, it was experimentally observed that a riser transitions from core annular flow profile to dilute and dense regimes via increasing the frequency of short term transients to either dilute or dense flow profiles, respectively. A regime map was generated based upon these dynamics using solids flux and gas velocity axes. Fast fluidized, core annular, and dilute each exhibited different degree of dynamic characteristics typical of fluid dominated or particle compromising behavior. It should be noted that the magnitude for the different statistics was in the same range regardless of the regime, it was the radial profile for the statistic that changed and subsequently identified that there was a change in the regime. Finally, a reduced regime map was developed consisting of plotting the gas velocity normalized by the upper transport velocity versus the solids flux normalized by the saturation carrying capacity. The use of this reduced plot allowed the data from widely different conditions to be plotted and compared on the same<p>graph. Note that in many instances, some of the statistics identified the operating point as being in one regime while others indicated that it was in another indicating a transition region between dilute or core annular regimes and between the core annular and fast fluidization regimes. This now provides a tool that can be used to optimize process performance, identify changes in operating states, or replicate process dynamics during process scaling or changing operating parameters. </p>

Breault, Ronald↗
DOE OSTI2024

Stellarators with enhanced tritium confinement and edge radiation control

A stellarator design is described with the purpose of achieving three goals: (1) enhance the confinement time of tritium. (2) Have a sufficient density of high-Z impurities to radiate the thermal power escaping from the core while having an extremely low impurity density in the core. (3) Maintain a large fraction of the plasma in a burning plasma state with an optimal tritium fraction. Some features of this design could be used in tokamaks. Although having three confinement zones is natural for stellarators, it is not for tokamaks.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2024

Compensating slice emittance growth in high brightness photoinjectors using sacrificial charge

Achieving maximum electron beam brightness in photoinjectors requires detailed control of the 3D bunch shape and precise tuning of the beam focusing. Even in state-of-the-art designs, slice emittance growth due to nonlinear space charge forces and partial nonlaminarity often remains non-negligible. In this work, we introduce a new means to linearize the transverse slice phase space: a sacrificial portion of the bunch’s own charge distribution, formed into a wavebroken shock front by highly nonlinear space charge forces within the gun, whose downstream purpose is to dynamically linearize the desired bunch core. We show that linearization of an appropriately prepared bunch can be achieved via strongly nonlaminar focusing of the sacrificial shock front, while the inner core focuses laminarly. This leads to a natural spatial separation of the two distributions: a dense core surrounded by a diffuse halo of sacrificial charge that can be collimated. Multiobjective genetic algorithm optimizations of the ultracompact x-ray free electron laser injector employ this concept, and we interpret it with an analytic model that agrees well with the simulations. In simulation, we demonstrate a final bunch charge of 100 pC, peak current ∼ 30 A, and a sacrificial charge of 150 pC (250 pC total emitted from cathode) with normalized emittance growth of < 20 nm rad due to space charge. This implies a maximum achievable brightness approximately an order of magnitude greater than existing free electron laser injector designs. Published by the American Physical Society 2024

43 PARTICLE ACCELERATORS↗
DOE OSTI2016

TU-AB-BRC-10: Modeling of Radiotherapy Linac Source Terms Using ARCHER Monte Carlo Code: Performance Comparison of GPU and MIC Computing Accelerators

Purpose: (1) To perform phase space (PS) based source modeling for Tomotherapy and Varian TrueBeam 6 MV Linacs, (2) to examine the accuracy and performance of the ARCHER Monte Carlo code on a heterogeneous computing platform with Many Integrated Core coprocessors (MIC, aka Xeon Phi) and GPUs, and (3) to explore the software micro-optimization methods. Methods: The patient-specific source of Tomotherapy and Varian TrueBeam Linacs was modeled using the PS approach. For the helical Tomotherapy case, the PS data were calculated in our previous study (Su et al. 2014 41(7) Medical Physics). For the single-view Varian TrueBeam case, we analytically derived them from the raw patient-independent PS data in IAEA’s database, partial geometry information of the jaw and MLC as well as the fluence map. The phantom was generated from DICOM images. The Monte Carlo simulation was performed by ARCHER-MIC and GPU codes, which were benchmarked against a modified parallel DPM code. Software micro-optimization was systematically conducted, and was focused on SIMD vectorization of tight for-loops and data prefetch, with the ultimate goal of increasing 512-bit register utilization and reducing memory access latency. Results: Dose calculation was performed for two clinical cases, a Tomotherapy-based prostate cancer treatment and a TrueBeam-based left breast treatment. ARCHER was verified against the DPM code. The statistical uncertainty of the dose to the PTV was less than 1%. Using double-precision, the total wall time of the multithreaded CPU code on a X5650 CPU was 339 seconds for the Tomotherapy case and 131 seconds for the TrueBeam, while on 3 5110P MICs it was reduced to 79 and 59 seconds, respectively. The single-precision GPU code on a K40 GPU took 45 seconds for the Tomotherapy dose calculation. Conclusion: We have extended ARCHER, the MIC and GPU-based Monte Carlo dose engine to Tomotherapy and Truebeam dose calculations.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2020

ADEPT: a domain independent sequence alignment strategy for gpu architectures

Bioinformatic workflows frequently make use of automated genome assembly and protein clustering tools. At the core of most of these tools, a significant portion of execution time is spent in determining optimal local alignment between two sequences. This task is performed with the Smith-Waterman algorithm, which is a dynamic programming based method. With the advent of modern sequencing technologies and increasing size of both genome and protein databases, a need for faster Smith-Waterman implementations has emerged. Multiple SIMD strategies for the Smith-Waterman algorithm are available for CPUs. However, with the move of HPC facilities towards accelerator based architectures, a need for an efficient GPU accelerated strategy has emerged. Existing GPU based strategies have either been optimized for a specific type of characters (Nucleotides or Amino Acids) or for only a handful of application use-cases. In this paper, we present ADEPT, a new sequence alignment strategy for GPU architectures that is domain independent, supporting alignment of sequences from both genomes and proteins. Our proposed strategy uses GPU specific optimizations that do not rely on the nature of sequence. We demonstrate the feasibility of this strategy by implementing the Smith-Waterman algorithm and comparing it to similar CPU strategies as well as the fastest known GPU methods for each domain. ADEPT’s driver enables it to scale across multiple GPUs and allows easy integration into software pipelines which utilize large scale computational systems. We have shown that the ADEPT based Smith-Waterman algorithm demonstrates a peak performance of 360 GCUPS and 497 GCUPs for protein based and DNA based datasets respectively on a single GPU node (8 GPUs) of the Cori Supercomputer. Overall ADEPT shows 10x faster performance in a node-to-node comparison against a corresponding SIMD CPU implementation. ADEPT demonstrates a performance that is either comparable or better than existing GPU strategies. We demonstrated the efficacy of ADEPT in supporting existing bionformatics software pipelines by integrating ADEPT in MetaHipMer a high-performance denovo metagenome assembler and PASTIS a high-performance protein similarity graph construction pipeline. Our results show 10% and 30% boost of performance in MetaHipMer and PASTIS respectively.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2016

Structural Basis for Inhibitor-Induced Aggregation of HIV Integrase

The allosteric inhibitors of integrase (termed ALLINIs) interfere with HIV replication by binding to the viral-encoded integrase (IN) protein. Surprisingly, ALLINIs interfere not with DNA integration but with viral particle assembly late during HIV replication. To investigate the ALLINI inhibitory mechanism, we crystallized full-length HIV-1 IN bound to the ALLINI GSK1264 and determined the structure of the complex at 4.4 Å resolution. The structure shows GSK1264 buried between the IN C-terminal domain (CTD) and the catalytic core domain. In the crystal lattice, the interacting domains are contributed by two different dimers so that IN forms an open polymer mediated by inhibitor-bridged contacts; the N-terminal domains do not participate and are structurally disordered. Engineered amino acid substitutions at the inhibitor interface blocked ALLINI-induced multimerization. HIV escape mutants with reduced sensitivity to ALLINIs commonly altered amino acids at or near the inhibitor-bound interface, and these substitutions also diminished IN multimerization. We propose that ALLINIs inhibit particle assembly by stimulating inappropriate polymerization of IN via interactions between the catalytic core domain and the CTD and that understanding the interface involved offers new routes to inhibitor optimization.

59 BASIC BIOLOGICAL SCIENCES↗