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All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

New developments including X-ray standing waves in the dynamical Bragg diffraction program of X-ray Server

X-ray Server (https://x-server.gmca.aps.anl.gov) is a collection of programs for online modelling of X-ray diffraction and scattering. Additionally, the dynamical diffraction program is the second most popular Server program, contributing 34% of total Server usage. It models dynamical X-ray diffraction from strained crystals and multilayers for any Bragg-case geometry including grazing incidence and exit. This paper reports on a revision of equations used by the program, which yields ten times faster calculations in most use cases, on implementing calculations of X-ray standing waves and on adding new options for modelling diffraction from monolayers.

36 MATERIALS SCIENCE↗
DOE OSTI2025

DXRD : a user-friendly suite of two- and multiple-beam dynamical X-ray diffraction programs

The DXRD program suite consisting of a series of dynamical theory programs is introduced for computing dynamical X-ray diffraction from single crystals. Its interactive graphical user interfaces (GUIs) allow general users to make complicated calculations with minimal effort. It can calculate plane-wave Darwin curves of single crystals (or multiple crystals) for both the Bragg and Laue cases, including grazing-incidence diffraction and backward diffraction (with Bragg angles approaching 90°). It is also capable of simulating rocking curves for divergent incident X-ray beams with finite bandwidths. A unique feature of DXRD is that it provides a convenient GUI-based multiple-beam diffraction program that can accurately compute arbitrary N-beam diffraction of any geometry using a universal 4N × 4N matrix method. DXRD also provides a mapping program for plotting all the multiple-beam diffraction lines (monochromator glitches) in the azimuth–energy coordinate system. All these functions make DXRD a convenient and powerful software tool for designing crystal-based synchrotron/X-ray optics (monochromators, analyzers, polarizers, phase plates etc.) and for crystal characterization, X-ray spectroscopy and X-ray diffraction teaching.

Bragg reflection↗
DOE OSTI2025

Enabling Scientific Applications with Performance-Portability and High-Productivity for Multi-GPU Programming with JACC.Multi

This work bridges the gap between multi-GPU computing and high-productivity, performance-portable programming solutions. Our goal is to enhance scientific applications with a productive and portable solution—program once, deploy everywhere—for multi-GPU programming with no cost to programmability. To accomplish this, we implemented JACC.Multi, which is part of the Julia for ACCelerators (JACC) performance-portable framework. JACC. Multi is the only high-level, portable metaprogramming solution that targets multi-GPU environments and is integrated in a readily accessible programming language (e.g., Julia language). With transparent GPU-to-GPU communication, JACC. Multi is optimized for scientific application workloads and is portable for NVIDIA and AMD accelerators. For the evaluation, we use two modern multi-GPU systems: Hudson, which features two NVIDIA H100 Hopper GPUs per node, and Frontier, which features four AMD MI250X GPUs per node, each with two Graphics Compute Dies (GCDs) for a total of eight GCDs per node. Additionally, as part of the evaluation, we use JACC (one GPU), MPI+JACC, and JACC. Multi codes that implement well-known and widely used scientific algorithms/kernels such as the conjugate gradient algorithm and an explicit forward Euler solver that requires GPU-to-GPU communication. Overall, JACC. Multi codes achieve better performance than MPI+JACC codes and significant speedups over JACC (one GPU), with up to 1.9× on Hudson and 6× on Frontier.

Valero Lara, Pedro [ORNL] (ORCID:0000000214794310)↗
DOE OSTI2021

IRIS: A Portable Runtime System Exploiting Multiple Heterogeneous Programming Systems

Across embedded, mobile, enterprise, and HPC systems, computer architectures are becoming more heterogeneous and complex. This complexity is causing a crisis in programming systems and performance portability. Several programming systems are working to address these challenges, but the increasing architectural diversity is forcing software stacks and applications to specialize for each architecture. As we show, all of these approaches critically depend on their runtime system for discovery, execution, scheduling, and data orchestration. To address this challenge, we believe that a more agile and proactive runtime system is essential to increase performance portability and improve user productivity. In this regard, we have designed and implemented IRIS: a portable runtime system exploiting multiple heterogeneous programming systems. IRIS can discover available resources, manage multiple diverse programming systems (e.g., CUDA, Hexagon, HIP, Level Zero, OpenCL, OpenMP) simultaneously in the same execution, respect data dependencies, orchestrate data movement proactively, and provide for user-configurable scheduling. Our evaluation on three architectures, ranging from Qualcomm Snapdragon to a Summit supercomputer node, shows that IRIS improves portability across a wide range of diverse heterogeneous architectures with negligible overhead.

Kim, Jungwon↗
DOE OSTI2017

SharP: Towards Programming Extreme-Scale Systems with Hierarchical Heterogeneous Memory

The pre-exascale systems are expected to have a significant amount of hierarchical and heterogeneous on-node memory, and this trend of system architecture in extreme-scale systems is expected to continue into the exascale era. Along with hierarchical-heterogeneous memory, the system typically has a high-performing network and a compute accelerator. This system architecture is not only effective for running traditional High Performance Computing (HPC) applications (Big-Compute), but also running data-intensive HPC applications and Big-Data applications. As a consequence, there is a growing desire to have a single system serve the needs of both Big-Compute and Big-Data applications. Though the system architecture supports the convergence of the Big-Compute and Big-Data, the programming models have yet to evolve to support either hierarchical-heterogeneous memory systems or the convergence. In this work, we propose and develop the programming abstraction called SHARed data-structure centric Programming abstraction (SharP) to address both of these goals, i.e., provide (1) a simple, usable, and portable abstraction for hierarchical-heterogeneous memory and (2) a unified programming abstraction for Big-Compute and Big-Data applications. To evaluate SharP, we implement a Stencil benchmark using SharP, port QMCPack, a petascale-capable application, and adapt Memcached ecosystem, a popular Big-Data framework, to use SharP, and quantify the performance and productivity advantages. Additionally, we demonstrate the simplicity of using SharP on different memories including DRAM, High-bandwidth Memory (HBM), and non-volatile random access memory (NVRAM).

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2024

Toward Automated Detection of Portability Bugs in Kokkos Parallel Programs

Performance-portable programming frameworks provide abstractions for parallel execution to allow easily porting an application to multiple backend programming models, such as CUDA, HIP, and OpenMP. However, programs may still have portability bugs that manifest only on specific backends. Traditional testing is ineffective in discovering these bugs, as it would require concrete execution on all supported hardware configurations for a potentially infinite set of inputs. To mitigate this issue, we focused on a specific programming framework, Kokkos, and identified several categories of common portability bugs. We then developed Klokkos, a static analysis approach based on symbolic execution that can run on commodity hardware, before execution on supercomputers. As a proof-of-concept, we ran Klokkos on examples encoding the identified bugs. Our results show that Klokkos is effective, efficient, and precise: it detected all the considered bugs, quickly, and without any false positives. Although preliminary, our results motivate further research and development in this direction.

Kale, Vivek↗
DOE OSTI2022

Economic evaluation of the Hepatitis C virus elimination program in the country of Georgia, 2015 to 2017

Abstract Background and Aims In 2015, the country of Georgia launched an elimination program aiming to reduce the prevalence of Hepatitis C virus (HCV) infection by 90% from 5.4% prevalence (~150 000 people). During the first 2.5 years of the program, 770 832 people were screened, 48 575 were diagnosed with active HCV infection, and 41 483 patients were treated with direct‐acting antiviral (DAA)‐based regimens, with a >95% cure rate. Methods We modelled the incremental cost‐effectiveness ratio (ICER) of HCV screening, diagnosis and treatment between April 2015 and November 2017 compared to no treatment, in terms of cost per quality‐adjusted life year (QALY) gained in 2017 US dollars, with a 3% discount rate over 25 years. We compared the ICER to willingness‐to‐pay (WTP) thresholds of US$4357 (GDP) and US$871 (opportunity cost) per QALY gained. Results The average cost of screening, HCV viremia testing, and treatment per patient treated was $386 to the provider, $225 to the patient and $1042 for generic DAAs. At 3% discount, 0.57 QALYs were gained per patient treated. The ICER from the perspective of the provider including generic DAAs was $2285 per QALY gained, which is cost‐effective at the $4357 WTP threshold, while if patient costs are included, it is just above the threshold at $4398/QALY. All other scenarios examined in sensitivity analyses remain cost‐effective except for assuming a shorter time horizon to the end of 2025 or including the list price DAA cost. Reducing or excluding DAA costs reduced the ICER below the opportunity‐cost WTP threshold. Conclusions The Georgian HCV elimination program provides valuable evidence that national programs for scaling up HCV screening and treatment for achieving HCV elimination can be cost‐effective.

Tskhomelidze, Irina↗
DOE OSTI2013

Comparative performance of modern digital mammography systems in a large breast screening program

Purpose: To compare physical measures pertaining to image quality among digital mammography systems utilized in a large breast screening program. To examine qualitatively differences in these measures and differences in clinical cancer detection rates between CR and DR among sites within that program. Methods: As part of the routine quality assurance program for screening, field measurements are made of several variables considered to correlate with the diagnostic quality of medical images including: modulation transfer function, noise equivalent quanta, d′ (an index of lesion detectability) and air kerma to allow estimation of mean glandular dose. In addition, images of the mammography accreditation phantom are evaluated. Results: It was found that overall there were marked differences between the performance measures of DR and CR mammography systems. In particular, the modulation transfer functions obtained with the DR systems were found to be higher, even for larger detector element sizes. Similarly, the noise equivalent quanta, d′, and the phantom scores were higher, while the failure rates associated with low signal-to-noise ratio and high dose were lower with DR. These results were consistent with previous findings in the authors’ program that the breast cancer detection rates at sites employing CR technology were, on average, 30.6% lower than those that used DR mammography. Conclusions: While the clinical study was not large enough to allow a statistically powered system-by-system assessment of cancer detection accuracy, the physical measures expressing spatial resolution, and signal-to-noise ratio are consistent with the published finding that sites employing CR systems had lower cancer detection rates than those using DR systems for screening mammography.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2014

TH-C-18A-06: Combined CT Image Quality and Radiation Dose Monitoring Program Based On Patient Data to Assess Consistency of Clinical Imaging Across Scanner Models

Purpose: One of the principal challenges of clinical imaging is to achieve an ideal balance between image quality and radiation dose across multiple CT models. The number of scanners and protocols at large medical centers necessitates an automated quality assurance program to facilitate this objective. Therefore, the goal of this work was to implement an automated CT image quality and radiation dose monitoring program based on actual patient data and to use this program to assess consistency of protocols across CT scanner models. Methods: Patient CT scans are routed to a HIPPA compliant quality assurance server. CTDI, extracted using optical character recognition, and patient size, measured from the localizers, are used to calculate SSDE. A previously validated noise measurement algorithm determines the noise in uniform areas of the image across the scanned anatomy to generate a global noise level (GNL). Using this program, 2358 abdominopelvic scans acquired on three commercial CT scanners were analyzed. Median SSDE and GNL were compared across scanner models and trends in SSDE and GNL with patient size were used to determine the impact of differing automatic exposure control (AEC) algorithms. Results: There was a significant difference in both SSDE and GNL across scanner models (9–33% and 15–35% for SSDE and GNL, respectively). Adjusting all protocols to achieve the same image noise would reduce patient dose by 27–45% depending on scanner model. Additionally, differences in AEC methodologies across vendors resulted in disparate relationships of SSDE and GNL with patient size. Conclusion: The difference in noise across scanner models indicates that protocols are not optimally matched to achieve consistent image quality. Our results indicated substantial possibility for dose reduction while achieving more consistent image appearance. Finally, the difference in AEC methodologies suggests the need for size-specific CT protocols to minimize variability in image quality across CT vendors.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2015

TU-AB-BRD-04: Development of Quality Management Program

Current quality assurance and quality management guidelines provided by various professional organizations are prescriptive in nature, focusing principally on performance characteristics of planning and delivery devices. However, published analyses of events in radiation therapy show that most events are often caused by flaws in clinical processes rather than by device failures. This suggests the need for the development of a quality management program that is based on integrated approaches to process and equipment quality assurance. Industrial engineers have developed various risk assessment tools that are used to identify and eliminate potential failures from a system or a process before a failure impacts a customer. These tools include, but are not limited to, process mapping, failure modes and effects analysis, fault tree analysis. Task Group 100 of the American Association of Physicists in Medicine has developed these tools and used them to formulate an example risk-based quality management program for intensity-modulated radiotherapy. This is a prospective risk assessment approach that analyzes potential error pathways inherent in a clinical process and then ranks them according to relative risk, typically before implementation, followed by the design of a new process or modification of the existing process. Appropriate controls are then put in place to ensure that failures are less likely to occur and, if they do, they will more likely be detected before they propagate through the process, compromising treatment outcome and causing harm to the patient. Such a prospective approach forms the basis of the work of Task Group 100 that has recently been approved by the AAPM. This session will be devoted to a discussion of these tools and practical examples of how these tools can be used in a given radiotherapy clinic to develop a risk based quality management program. Learning Objectives: Learn how to design a process map for a radiotherapy process Learn how to perform failure modes and effects analysis analysis for a given process Learn what fault trees are all about Learn how to design a quality management program based upon the information obtained from process mapping, failure modes and effects analysis and fault tree analysis. Dunscombe: Director, TreatSafely, LLC and Center for the Assessment of Radiological Sciences; Consultant to IAEA and Varian Thomadsen: President, Center for the Assessment of Radiological Sciences Palta: Vice President of the Center for the Assessment of Radiological Sciences.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2016

SU-D-201-07: A Survey of Radiation Oncology Residents’ Training and Preparedness to Lead Patient Safety Programs in Clinics

Purpose: Safety and quality has garnered increased attention in radiation oncology, and physicians and physicists are ideal leaders of clinical patient safety programs. However, it is not clear whether residency programs incorporate formal patient safety training and adequately equip residents to assume this leadership role. A national survey was conducted to evaluate medical and physics residents’ exposure to safety topics and their confidence with the skills required to lead clinical safety programs. Methods: Radiation oncology residents were identified in collaboration with ARRO and AAPM. The survey was released in February 2016 via email using REDCap. This included questions about exposure to safety topics, confidence leading safety programs, and interest in training opportunities (i.e. workshops). Residents rated their exposure, skills, and confidence on 4 or 5-point scales. Medical and physics residents responses were compared using chi-square tests. Results: Responses were collected from 56 of 248 (22%) physics and 139 of 690 (20%) medical residents. More than two thirds of all residents had no or only informal exposure to incident learning systems (ILS), root cause analysis (RCA), failure mode and effects analysis (FMEA), and the concept of human factors engineering (HFE). Likewise, 63% of residents had not heard of RO-ILS. Response distributions were similar, however more physics residents had formal exposure to FMEA (p<0.0001) and felt they were adequately trained to lead FMEAs in clinic (p<0.001) than medical residents. Only 36% of residents felt their patient safety training was adequate, and 58% felt more training would benefit their education. Conclusion: These results demonstrate that, despite increasing desire for patient safety training, medical and physics residents’ exposure to relevant concepts is low. Physics residents had more exposure to FMEA than medical residents, and were more confident in leading FMEA. This suggests that increasing resident exposure to specific topics may increase their confidence.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2016

SU-F-E-12: Elective International Rotations in Medical Physics Residency Programs

Purpose: The purpose of this educational program is to motivate talented, intelligent individuals to become stakeholders in the global effort to improve access to radiotherapy. Methods: The need to improve global access to radiotherapy has been clearly established and several organizations are making substantial progress in securing funding and developing plans to achieve this worthwhile goal. The incorporation of elective international rotations in residency programs may provide one possible mechanism to promote and support this future investment. We recently incorporated an elective 1-month international rotation into our CAMPEP accredited Medical Physics residency program, with our first rotation taking place in Vietnam. A unique aspect of this rotation was that it was scheduled collaboratively with our Radiation Oncology residency program such that Radiation Oncology and Medical Physics residents traveled to the same clinic at the same time. Results: We believe the international rotation substantially enhances the educational experience, providing additional benefits to residents by increasing cross-disciplinary learning and offering a shared learning experience. The combined international rotation may also increase benefit to the host institution by modeling positive multidisciplinary working relationships between Radiation Oncologists and Medical Physicists. Our first resident returned with several ideas designed to improve radiotherapy in resource-limited settings – one of which is currently being pursued in collaboration with a vendor. Conclusion: The elective international rotation provides a unique learning experience that has the potential to motivate residents to become stakeholders in the global effort to improve access to radiotherapy. What better way to prepare the next generation of Medical Physicists to meet the challenges of improving global access to radiotherapy than to provide them with training experiences that motivate them to be socially conscious and equip them with the clinical and problem solving skills required to deliver effective treatments in resource limited settings?.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2015

The Clostridium Sporulation Programs: Diversity and Preservation of Endospore Differentiation

Bacillus and Clostridium organisms initiate the sporulation process when unfavorable conditions are detected. The sporulation process is a carefully orchestrated cascade of events at both the transcriptional and posttranslational levels involving a multitude of sigma factors, transcription factors, proteases, and phosphatases. Like Bacillus genomes, sequenced Clostridium genomes contain genes for all major sporulation-specific transcription and sigma factors (spo0A, sigH, sigF, sigE, sigG, and sigK) that orchestrate the sporulation program. However, recent studies have shown that there are substantial differences in the sporulation programs between the two genera as well as among different Clostridium species. First, in the absence of a Bacillus-like phosphorelay system, activation of Spo0A in Clostridium organisms is carried out by a number of orphan histidine kinases. Second, downstream of Spo0A, the transcriptional and posttranslational regulation of the canonical set of four sporulation-specific sigma factors (σF, σE, σG, and σK) display different patterns, not only compared to Bacillus but also among Clostridium organisms. Finally, recent studies demonstrated that σK, the last sigma factor to be activated according to the Bacillus subtilis model, is involved in the very early stages of sporulation in Clostridium acetobutylicum, C. perfringens, and C. botulinum as well as in the very late stages of spore maturation in C. acetobutylicum. Despite profound differences in initiation, propagation, and orchestration of expression of spore morphogenetic components, these findings demonstrate not only the robustness of the endospore sporulation program but also the plasticity of the program to generate different complex phenotypes, some apparently regulated at the epigenetic level.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2016

NVL-C: Static Analysis Techniques for Efficient, Correct Programming of Non-Volatile Main Memory Systems

Computer architecture experts expect that non-volatile memory (NVM) hierarchies will play a more significant role in future systems including mobile, enterprise, and HPC architectures. With this expectation in mind, we present NVL-C: a novel programming system that facilitates the efficient and correct programming of NVM main memory systems. The NVL-C programming abstraction extends C with a small set of intuitive language features that target NVM main memory, and can be combined directly with traditional C memory model features for DRAM. We have designed these new features to enable compiler analyses and run-time checks that can improve performance and guard against a number of subtle programming errors, which, when left uncorrected, can corrupt NVM-stored data. Moreover, to enable recovery of data across application or system failures, these NVL-C features include a flexible directive for specifying NVM transactions. So that our implementation might be extended to other compiler front ends and languages, the majority of our compiler analyses are implemented in an extended version of LLVM's intermediate representation (LLVM IR). We evaluate NVL-C on a number of applications to show its flexibility, performance, and correctness.

Denny, Joel↗
DOE OSTI2021

Gleipnir: toward practical error analysis for Quantum programs

Practical error analysis is essential for the design, optimization, and evaluation of Noisy Intermediate-Scale Quantum(NISQ) computing. However, bounding errors in quantum programs is a grand challenge, because the effects of quantum errors depend on exponentially large quantum states. In this work, we present Gleipnir, a novel methodology toward practically computing verified error bounds in quantum programs. Gleipnir introduces the (ρ,δ)-diamond norm, an error metric constrained by a quantum predicate consisting of the approximate state ρ and its distance δ to the ideal state ρ. This predicate (ρ,δ) can be computed adaptively using tensor networks based on the Matrix Product States. Gleipnir features a lightweight logic for reasoning about error bounds in noisy quantum programs, based on the (ρ,δ)-diamond norm metric. Furthermore, our experimental results show that Gleipnir is able to efficiently generate tight error bounds for real-world quantum programs with 10 to 100 qubits, and can be used to evaluate the error mitigation performance of quantum compiler transformations.

Tao, Runzhou↗
DOE OSTI2021

Programming Abstractions for Managing Workflows on Tiered Storage Systems

Scientific workflows in High Performance Computing (HPC) environments are processing large amounts of data. The storage hierarchy on HPC systems is getting deeper, driven by new technologies (NVRAMs, SSDs, etc.) There is a need for new programming abstractions that allow users to seamlessly manage data at the workflow level on multi-tiered storage systems, and provide optimal workflow performance and use of storage resources. In previous work, we introduced a software architecture Managing Data on Tiered Storage for Scientific Workflows (MaDaTS) that used a Virtual Data Space (VDS) abstraction to hide the complexities of the underlying storage system while allowing users to control data management strategies. In this article, we detail the data-centric programming abstractions that allow users to manage a workflow around its data on the storage layer. The programming abstractions simplify data management for scientific workflows on multi-tiered storage systems, without affecting workflow performance or storage capacity. We measure the overheads and effectiveness introduced by the programming abstractions of MaDaTS. Our results show that these abstractions can optimally use the storage capacity in lesser capacity storage tiers, and simplify data management without adding any performance overheads.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗
DOE OSTI2023

Evaluation of OpenAI Codex for HPC Parallel Programming Models Kernel Generation

We evaluate AI-assisted generative capabilities on fundamental numerical kernels in high-performance computing (HPC), including AXPY, GEMV, GEMM, SpMV, Jacobi Stencil, and CG. We test the generated kernel codes for a variety of language-supported programming models, including (1) C++ (e.g., OpenMP [including offload], OpenACC, Kokkos, SyCL, CUDA, and HIP), (2) Fortran (e.g., OpenMP [including offload] and OpenACC), (3) Python (e.g., numpy, Numba, cuPy, and pyCUDA), and (4) Julia (e.g., Threads, CUDA.jl, AMDGPU.jl, and KernelAbstractions.jl). We use the GitHub Copilot capabilities powered by the GPT-based OpenAI Codex available in Visual Studio Code as of April 2023 to generate a vast amount of implementations given simple + + prompt variants. To quantify and compare the results, we propose a proficiency metric around the initial 10 suggestions given for each prompt. Results suggest that the OpenAI Codex outputs for C++ correlate with the adoption and maturity of programming models. For example, OpenMP and CUDA score really high, whereas HIP is still lacking. We found that prompts from either a targeted language such as Fortran or the more general purpose Python can benefit from adding code keywords, while Julia prompts perform acceptably well for its mature programming models (e.g., Threads and CUDA.jl). We expect for these benchmarks to provide a point of reference for each programming model's community. Overall, understanding the convergence of large language models, AI, and HPC is crucial due to its rapidly evolving nature and how it is redefining human-computer interactions.

Godoy, William↗
DOE OSTI2017

XACC - eXtreme-scale Accelerator Programming Framework

Hybrid programming models for beyond-CMOS technologies will prove critical for integrating new computing technologies alongside our existing infrastructure. Unfortunately the software infrastructure required to enable this is lacking or not available. XACC is a programming framework for extreme-scale, post-exascale accelerator architectures that integrates alongside existing conventional applications. It is a pluggable framework for programming languages developed for next-gen computing hardware architectures like quantum and neuromorphic computing. It lets computational scientists efficiently off-load classically intractable work to attached accelerators through user-friendly Kernel definitions. XACC makes post-exascale hybrid programming approachable for domain computational scientists.

McCaskey, AlexanderJ.↗