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DOE OSTI2023

FrESCO

The National Cancer Institute (NCI) monitors population level cancer trends as part of its Surveillance, Epidemiology, and End Results (SEER) program. This program consists of state or regional level cancer registries which collect, analyze, and annotate cancer pathology reports. From these annotated pathology reports, each individual registry aggregates cancer phenotype information and summary statistics about cancer prevalence to facilitate population level monitoring of cancer incidence. Extracting cancer phenotype from these reports is a labor intensive task, requiring specialized knowledge about the reports and cancer. Automating this information extraction process from cancer pathology reports has the potential to improve not only the quality of the data by extracting information in a consistent manner across registries, but to improve the quality of patient outcomes by reducing the time to assimilate new data and enabling time-sensitive applications such as precision medicine. Here we present FrESCO: Framework for Exploring Scalable Computational Oncology, a modular deep-learning natural language processing (NLP) library for extracting pathology information from clinical text documents.

Spannaus, Adam [Oak Ridge National Lab. (ORNL), Oa↗

DOE OSTI2016

PHYSICS OF ECLIPSING BINARIES. II. TOWARD THE INCREASED MODEL FIDELITY

The precision of photometric and spectroscopic observations has been systematically improved in the last decade, mostly thanks to space-borne photometric missions and ground-based spectrographs dedicated to finding exoplanets. The field of eclipsing binary stars strongly benefited from this development. Eclipsing binaries serve as critical tools for determining fundamental stellar properties (masses, radii, temperatures, and luminosities), yet the models are not capable of reproducing observed data well, either because of the missing physics or because of insufficient precision. This led to a predicament where radiative and dynamical effects, insofar buried in noise, started showing up routinely in the data, but were not accounted for in the models. PHOEBE (PHysics Of Eclipsing BinariEs; http://phoebe-project.org) is an open source modeling code for computing theoretical light and radial velocity curves that addresses both problems by incorporating missing physics and by increasing the computational fidelity. In particular, we discuss triangulation as a superior surface discretization algorithm, meshing of rotating single stars, light travel time effects, advanced phase computation, volume conservation in eccentric orbits, and improved computation of local intensity across the stellar surfaces that includes the photon-weighted mode, the enhanced limb darkening treatment, the better reflection treatment, and Doppler boosting. Here we present the concepts on which PHOEBE is built and proofs of concept that demonstrate the increased model fidelity.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2016

Draco,Version 6.x.x

Draco is an object-oriented component library geared towards numerically intensive, radiation (particle) transport applications built for parallel computing hardware. It consists of semi-independent packages and a robust build system. The packages in Draco provide a set of components that can be used by multiple clients to build transport codes. The build system can also be extracted for use in clients. Software includes smart pointers, Design-by-Contract assertions, unit test framework, wrapped MPI functions, a file parser, unstructured mesh data structures, a random number generator, root finders and an angular quadrature component.

Thompson, Kelly↗

DOE OSTI2012

Effective Software Design and Development for the New Graph Architecture HPC Machines

Software applications need to change and adapt as modern architectures evolve. Nowadays advancement in chip design translates to increased parallelism. Exploiting such parallelism is a major challenge in modern software engineering. Multicore processors are about to introduce a significant change in the way we design and use fundamental data structures. In this work we describe the design and programming principles of a software library of highly concurrent scalable and nonblocking data containers. In this project we have created algorithms and data structures for handling fundamental computations in massively multithreaded contexts, and we have incorporated these into a usable library with familiar look and feel. In this work we demonstrate the first design and implementation of a wait-free hash table. Our multiprocessor data structure design allows a large number of threads to concurrently insert, remove, and retrieve information. Non-blocking designs alleviate the problems traditionally associated with the use of mutual exclusion, such as bottlenecks and thread-safety. Lock-freedom provides the ability to share data without some of the drawbacks associated with locks, however, these designs remain susceptible to starvation. Furthermore, wait-freedom provides all of the benefits of lock-free synchronization with the added assurance that every thread makes progress in a finite number of steps. This implies deadlock-freedom, livelock-freedom, starvation-freedom, freedom from priority inversion, and thread-safety. The challenges of providing the desirable progress and correctness guarantees of wait-free objects makes their design and implementation difficult. There are few wait-free data structures described in the literature. Using only standard atomic operations provided by the hardware, our design is portable; therefore, it is applicable to a variety of data-intensive applications including the domains of embedded systems and supercomputers.Our experimental evaluation shows that our hash table design outperforms the most advanced locking solution, provided by Intel's TBB library, by 22%. When compared to more traditional locking designs we show a performance improvement by a factor of 7.92. When compared to alternative non-blocking designs, our hash table demonstrates solid performance gains in a large majority of cases, typically by a factor of 3.44.

99 GENERAL AND MISCELLANEOUS↗

DOE OSTI2025

Flexible and Effective Object Tiering for Heterogeneous Memory Systems

Computing platforms that package multiple types of memory, each with their own performance characteristics, are quickly becoming mainstream. To operate efficiently, heterogeneous memory architectures require new data management solutions that are able to match the needs of each application with an appropriate type of memory. As the primary generators of memory usage, applications create a great deal of information that can be useful for guiding memory management, but the community still lacks tools to collect, organize, and leverage this information effectively. To address this gap, this work introduces a novel software framework that collects and analyzes object-level information to guide memory tiering. The framework includes tools to monitor the capacity and usage of individual data objects, routines that aggregate and convert this information into tier recommendations for the host platform, and mechanisms to enforce these recommendations according to user-selected policies. Moreover, the developed tools and techniques are fully automatic, work on standard Linux systems, and do not require modification or recompilation of existing software. Using this framework, this study evaluates and compares the impact of a variety of design choices for memory tiering, including different policies for prioritizing objects for the fast memory tier as well as the frequency and timing of migration events. In conclusion, the results, collected on a modern Intel platform with conventional DDR4 SDRAM as well as Intel Optane NVRAM, show that guiding data tiering with object-level information can enable significant performance and efficiency benefits compared with standard hardware- and software-directed data-tiering strategies for a diverse set of memory-intensive workloads.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2011

Position Verification for the Prostate: Effect on Rectal Wall Dose

Purpose: To evaluate the effect of gold marker (GM)-based position correction on the cumulative dose in the anorectal wall compared with traditional bony anatomy (BA)-based correction, taking into account changes in anorectal shape and position. Methods and Materials: A total of 20 consecutive prostate cancer patients, treated with curative external beam radiotherapy, were included. Four fiducial GMs were implanted in the prostate. Positioning was verified according to the shift in BA and GMs on daily electronic portal images. Position corrections were determined using on- and off-line position verification protocols according to the position of the GMs (GM-on and GM-off) and BA (BA-off). For all patients, intensity-modulated radiotherapy plans were made for the GM (8-mm planning target volume margin) and BA (10-mm planning target volume margin) protocols. The dose distribution was recomputed on 11 repeat computed tomography scans to estimate the accumulated dose to the prostate and anorectal wall while considering internal organ motion. Results: The dose that is at least received by 99% of the prostate was, on average, acceptable for all protocols. The individual patient data showed the best coverage for both GM protocols, with >95% of the prescribed dose for all patients. The anorectal wall dose was significantly lower for the GM protocols. The dose that is at least received by 30% of the rectal wall was, on average, 54.6 Gy for GM-on, 54.1 Gy for GM-off, and 58.9 Gy for BA-off (p <.001). Conclusion: Position verification with GM and reduced planning target volume margins yielded adequate treatment of the prostate and a lower rectal wall dose, even when accounting for independent movement of the prostate and anorectal wall.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

DOE OSTI2015

A new development on measurement and control software of SANS BATAN spectrometer (SMARTer) in Serpong, Indonesia

In 2005, the main computer for data acquisition and control system of Small-angle Neutron Scattering (SANS) BATAN Spectrometer (SMARTer) was replaced since it halted to operate the spectrometer. According to this replacement, the new software for data acquisition and control system has been developed in-house. Visual Basic programming language is used in developing the software. In the last two years, many developments have been made both in the hardware and also the software to conduct the experiment is more effective and efficient. Lately, the previous motor controller card (ISA Card) was replaced with the programmable motor controller card (PCI Card) for driving one motor of position sensitive detector (PSD), eight motors of four collimators, and six motors of six pinhole discs. This new control system software makes all motors can be moved simultaneously, then it reduces significantly the consuming time of setting up the instrument before running the experiment. Along with that development, the new data acquisition software under MS Windows operating system is also developed to drive a beam stopper in X-Y directions as well as to read the equipment status such as position of the collimators and PSD, to acquire neutron counts on monitor and PSD detectors, and also to manage 12 samples position automatically. A timer object which is set in one second to read the equipment status via serial port of the computer (RS232C), and general purpose interface board (GPIB) for reading the total counts of each pixel of the PSD from histogram memory was used in this new software. The experiment result displayed in real time on the main window, and the data is saved in the special format for further data reduction and analysis. The new software has been implemented and performed for experiment using a preset count or preset time mode for absolute scattering intensity method.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2017

Final Report: Quantification of Uncertainty in Extreme Scale Computations (QUEST)

QUEST (\url{www.quest-scidac.org}) is a SciDAC Institute that is focused on uncertainty quantification (UQ) in large-scale scientific computations. Our goals are to (1) advance the state of the art in UQ mathematics, algorithms, and software; and (2) provide modeling, algorithmic, and general UQ expertise, together with software tools, to other SciDAC projects, thereby enabling and guiding a broad range of UQ activities in their respective contexts. QUEST is a collaboration among six institutions (Sandia National Laboratories, Los Alamos National Laboratory, the University of Southern California, Massachusetts Institute of Technology, the University of Texas at Austin, and Duke University) with a history of joint UQ research. Our vision encompasses all aspects of UQ in leadership-class computing. This includes the well-founded setup of UQ problems; characterization of the input space given available data/information; local and global sensitivity analysis; adaptive dimensionality and order reduction; forward and inverse propagation of uncertainty; handling of application code failures, missing data, and hardware/software fault tolerance; and model inadequacy, comparison, validation, selection, and averaging. The nature of the UQ problem requires the seamless combination of data, models, and information across this landscape in a manner that provides a self-consistent quantification of requisite uncertainties in predictions from computational models. Accordingly, our UQ methods and tools span an interdisciplinary space across applied math, information theory, and statistics. The MIT QUEST effort centers on statistical inference and methods for surrogate or reduced-order modeling. MIT personnel have been responsible for the development of adaptive sampling methods, methods for approximating computationally intensive models, and software for both forward uncertainty propagation and statistical inverse problems. A key software product of the MIT QUEST effort is the MIT Uncertainty Quantification library, called MUQ (\url{muq.mit.edu}).

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2011

U.S. Department of Energy Best Practices Workshop onFile Systems & Archives San Francisco, CA September 26-27, 2011 Position Paper

This position paper discusses issues of usability of the large parallel file systems in the Livermore Computing Center. The primary uses of these file systems are for storage and access of data that is created during the course of a simulation running on an LC system. The Livermore Computing Center has multiple, globally mounted parallel file systems in each of its computing environments. The single biggest issue of file system usability that we have encountered through the years is to maintain continuous file system responsiveness. Given the back end storage hardware that our file systems are provisioned with, it is easily possible for a particularly I/O intensive application or one with particularly inefficiently coded I/O operations to bring the file system to an apparent halt. The practice that we will be addressing is one of having an ability to indentify, diagnose, analyze and optimize the I/O quickly and effectively.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2021

JSPEC – An Open Source Program for IBS and Electron Cooling Simulation

The intrabeam scattering can affect the accumulation, the lifetime, and the property of a high-intensity beam. Electron cooling is a method to mitigate the intrabeam scattering effect. JSPEC (JLab Simulation Package on Electron Cooling) is an open-source program developed at Jefferson Lab, which includes various numerical models and friction force formulas for intrabeam scattering and electron cooling simulations. JSPEC has been benchmarked with BETACOOL and experimental data. In this report, we will introduce what features JSPEC provides to the users and how it carries out the computations. Numerical examples are presented to demonstrate the performance and the validity of JSPEC.

Zhang, He↗

DOE OSTI2024

Real World Use Case Evaluation of Radar Retro-reflectors for Autonomous Vehicle Lane Detection Applications

Lane detection plays a critical role in autonomous vehicles for safe and reliable navigation. Lane detection is traditionally accomplished using a camera sensor and computer vision processing. The downside of this traditional technique is that it can be computationally intensive when high quality images at a fast frame rate are used and has reliability issues from occlusion such as, glare, shadows, active road construction, and more. This study addresses these issues by exploring alternative methods for lane detection in specific scenarios caused from road construction-induced lane shift and sun glare. Specifically, a U-Net, a convolutional network used for image segmentation, camera-based lane detection method is compared with a radar-based approach using a new type of sensor previously unused in the autonomous vehicle space: radar retro-reflectors. This evaluation is performed using ground truth data, obtained by measuring the lane positions and transforming them into pixel coordinates. The performance of each method is assessed using the statistical R2 score, indicating the correlation between the detected lane lines and the ground truth. The results show that the U-Net camera-based method exhibits limitations in accurately detecting and aligning the lane lines, particularly in challenging scenarios. However, the radar-based lane detection method demonstrates a strong correlation with the ground truth which implies that the use of this sensor may improve current reliability issues from conventional camera lane detection approach. Furthermore, the study highlights the limitations of the U-Net model for camera lane detection, especially in scenarios with sun glare. This study shows that infrastructure-based radar retro-reflectors can improve autonomous vehicle lane detection reliability. The integration of different sensor modalities and the development of advanced computer vision algorithms are crucial for improving the accuracy, reliability, and energy efficiency of lane detection systems. Addressing these challenges contributes to the advancement of autonomous vehicles and the realization of safer and more efficient transportation systems.

Brown, Nicolas E.↗

DOE OSTI2012

Cyber security best practices for the nuclear industry

When deploying software based systems, such as, digital instrumentation and controls for the nuclear industry, it is vital to include cyber security assessment as part of architecture and development process. When integrating and delivering software-intensive systems for the nuclear industry, engineering teams should make use of a secure, requirements driven, software development life cycle, ensuring security compliance and optimum return on investment. Reliability protections, data loss prevention, and privacy enforcement provide a strong case for installing strict cyber security policies. (authors)

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

DOE OSTI2013

On Eliminating Synchronous Communication in Molecular Simulations to Improve Scalability

Molecular dynamics simulation, as a complementary tool to experimentation, has become an important methodology for the understanding and design of molecular systems as it provides access to properties that are difficult, impossible or prohibitively expensive to obtain experimentally. Many of the available software packages have been parallelized to take advantage of modern massively concurrent processing resources. The challenge in achieving parallel efficiency is commonly attributed to the fact that molecular dynamics algorithms are communication intensive. This paper illustrates how an appropriately chosen data distribution and asynchronous one-sided communication approach can be used to effectively deal with the data movement within the Global Arrays/ARMCI programming model framework. A new put_notify capability is presented here, allowing the implementation of the molecular dynamics algorithm without any explicit global or local synchronization or global data reduction operations. In addition, this push-data model is shown to very effectively allow hiding data communication behind computation. Rather than data movement or explicit global reductions, the implicit synchronization of the algorithm becomes the primary challenge for scalability. Without any explicit synchronous operations, the scalability of molecular simulations is shown to depend only on the ability to evenly balance computational load.

Straatsma, TP↗

DOE OSTI2013

Independent calculation-based verification of IMRT plans using a 3D dose-calculation engine

Independent monitor unit verification of intensity-modulated radiation therapy (IMRT) plans requires detailed 3-dimensional (3D) dose verification. The aim of this study was to investigate using a 3D dose engine in a second commercial treatment planning system (TPS) for this task, facilitated by in-house software. Our department has XiO and Pinnacle TPSs, both with IMRT planning capability and modeled for an Elekta-Synergy 6 MV photon beam. These systems allow the transfer of computed tomography (CT) data and RT structures between them but do not allow IMRT plans to be transferred. To provide this connectivity, an in-house computer programme was developed to convert radiation therapy prescription (RTP) files as generated by many planning systems into either XiO or Pinnacle IMRT file formats. Utilization of the technique and software was assessed by transferring 14 IMRT plans from XiO and Pinnacle onto the other system and performing 3D dose verification. The accuracy of the conversion process was checked by comparing the 3D dose matrices and dose volume histograms (DVHs) of structures for the recalculated plan on the same system. The developed software successfully transferred IMRT plans generated by 1 planning system into the other. Comparison of planning target volume (TV) DVHs for the original and recalculated plans showed good agreement; a maximum difference of 2% in mean dose, − 2.5% in D95, and 2.9% in V95 was observed. Similarly, a DVH comparison of organs at risk showed a maximum difference of +7.7% between the original and recalculated plans for structures in both high- and medium-dose regions. However, for structures in low-dose regions (less than 15% of prescription dose) a difference in mean dose up to +21.1% was observed between XiO and Pinnacle calculations. A dose matrix comparison of original and recalculated plans in XiO and Pinnacle TPSs was performed using gamma analysis with 3%/3 mm criteria. The mean and standard deviation of pixels passing gamma tolerance for XiO-generated IMRT plans was 96.1 ± 1.3, 96.6 ± 1.2, and 96.0 ± 1.5 in axial, coronal, and sagittal planes respectively. Corresponding results for Pinnacle-generated IMRT plans were 97.1 ± 1.5, 96.4 ± 1.2, and 96.5 ± 1.3 in axial, coronal, and sagittal planes respectively.

61 RADIATION PROTECTION AND DOSIMETRY↗

DOE OSTI2013

Clustering procedures for the optimal selection of data sets from multiple crystals in macromolecular crystallography

A systematic approach to the scaling and merging of data from multiple crystals in macromolecular crystallography is introduced and explained. The availability of intense microbeam macromolecular crystallography beamlines at third-generation synchrotron sources has enabled data collection and structure solution from microcrystals of <10 µm in size. The increased likelihood of severe radiation damage where microcrystals or particularly sensitive crystals are used forces crystallographers to acquire large numbers of data sets from many crystals of the same protein structure. The associated analysis and merging of multi-crystal data is currently a manual and time-consuming step. Here, a computer program, BLEND, that has been written to assist with and automate many of the steps in this process is described. It is demonstrated how BLEND has successfully been used in the solution of a novel membrane protein.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2012

Spherical analyzers and monochromators for resonant inelastic hard X-ray scattering: a compilation of crystals and reflections

Resonant inelastic X-ray scattering (RIXS) experiments require special sets of near-backscattering spherical diced analyzers and high-resolution monochromators for every distinct absorption-edge energy and emission line. For the purpose of aiding the design and planning of efficient RIXS experiments, comprehensive lists of suitable analyzer reflections for silicon, germanium, α-quartz, sapphire and lithium niobate crystals were compiled for a multitude of absorption edges and emission lines. Analyzers made from lithium niobate, sapphire or α-quartz offer many choices of reflections with intrinsic resolutions currently unattainable from silicon or germanium. In some cases these materials offer higher intensities at comparable resolutions. While lithium niobate, sapphire or α-quartz analyzers are still in an early stage of development, the present compilation can serve as a computational basis for assessing expected and actual performance. With regard to high-resolution monochromators, bandpass and throughput calculations for combinations of double-crystal, high-heat-load and near-backscattering high-resolution channel-cuts were assembled. The compilation of these analyzer and monochromator data is publicly available on a website.

47 OTHER INSTRUMENTATION↗

DOE OSTI2019

Provenance–aware workflow for data quality management and improvement for large continuous scientific data streams

Data quality assessment, management and improvement is integral part of any big data intensive scientific research to ensure accurate, reliable and reproducible science discoveries. The task of maintaining the quality of data, however, is non-trivial and pose a challenge for a program like Department of Energy’s Atmospheric Radiation Measurement (ARM) that collects data from hundreds of instruments across the world,and distributes thousands of streaming data products that are continuously growing in near-real-time in an archive 1.7 Petabyte in size and growing. We present a computational data processing workflow to collect the data quality issue via an easy and intuitive web-based portal that allows reporting of any quality issues for any site, facility or instruments at a granularity down to individual variable in the data files. Portal allows instrument specialists and scientists to provide corrective actions in form of symbolic equation. A parallel processing framework applies the data improvement to large volume of data in efficient parallel environment, while optimizing data transfer and file I/O operations. Corrected files are systematically versioned and archived. A provenance tracking module tracks and records any change made to the data during its entire life cycle which are communicated transparently to the scientific users. Developed in Python using open source technologies, software architecture enables efficient and fast management and improvement of data in an operational data center environment.

Kumar, Jitendra↗

DOE OSTI2015

A Hard X-ray Study of a Manganese-Terpyridine Dimer Catalyst in a Chromium-Based Metal Organic Framework

Much of today’s scientific research is geared toward discovering clean energy from renewable sources. A promising approach is to split water into its fundamental elements – hydrogen and oxygen. The hydrogen produced from this process is a source of clean energy. Plants carry out this water splitting routinely as a part of photosynthesis, but we cannot do this readily as the reaction requires a lot of energy, negating the value of cleaner and plentiful energy from hydrogen. Adding a catalyst provides an alternative pathway for the reaction so that it can proceed with lower energy input. Many such catalysts have been developed; the one used in this study is manganese based and is called manganese-terpyridine dimer (MnTD). The problem is that when individual molecules of MnTD interact they destroy each other, which limits practical use of the catalyst. However, by placing the catalyst in a Metal Organic Framework (MOF), the molecules of MnTD can be separated so that, in principle, they do not interact with each other and only interact with water. The MOF is essentially a repetition of boxes, and each box should contain one MnTD molecule. However, preliminary studies showed that a different molecule, not MnTD, may be inside the boxes. My research focused on identifying which molecules are present in the MOF. The primary method of analysis used was x-ray powder diffraction, a technique in which x-rays are scattered by a sample, and the intensity of the scattered radiation is measured as a function of scattering angle. Three samples were analyzed; one contained only the MOF, one contained the MOF and catalyst before catalysis, and one contained the MOF and catalyst during catalysis. The diffraction experiments were carried out at the Stanford Synchrotron Radiation Lightsource (SSRL) at SLAC National Accelerator Laboratory. Initial results revealed that the MOF structure falls apart during catalysis. To further analyze the data, I used several computer programs, including GSAS II, FOX, and VESTA. These programs allowed me to create maps that showed regions of electron density within the MOF and gave me clues as to which molecules were present. I found that MnTD was not the catalytic molecule in the MOF. The preliminary studies showed that manganese oxide is likely present, which is consistent with by data. However, the catalytic rate for this system is much higher than that reported for manganese oxide, and thus future studies are needed to verify the identity of the catalytic molecule and determine the reasons for its unusually high rate of catalysis.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗