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At least 1,099 records · Page 61

Portability for GPU-accelerated molecular docking applications for cloud and HPC: can portable compiler directives provide performance across all platforms?

High-throughput structure-based screening of drug-like molecules has become a common tool in biomedical research. Recently, acceleration with graphics processing units (GPUs) has provided a large performance boost for molecular docking programs. Both cloud and high-performance computing (HPC) resources have been used for large screens with molecular docking programs; while NVIDIA GPUs have dominated cloud and HPC resources, new vendors such as AMD and Intel are now entering the field, creating the problem of software portability across different GPUs. Ideally, software productivity could be maximized with portable programming models that are able to maintain high performance across architectures. While in many cases compiler directives have been used as an easy way to offload parallel regions of a CPU-based program to a GPU accelerator, they may also be an attractive programming model for providing portability across different GPU vendors, in which case the porting process may proceed in the reverse direction: from low-level, architecture-specific code to higher-level directive-based abstractions. MiniMDock is a new mini-application (miniapp) designed to capture the essential computational kernels found in molecular docking calculations, such as are used in phar-maceutical drug discovery efforts, in order to test different solutions for porting across GPU architectures. Here we extend MiniMDock to GPU offloading with OpenMP directives, and compare to performance of kernels using CUDA and HIP on NVIDIA and AMD GPUs, respectively, as well as across different compilers, exploring performance bottlenecks. We document this reverse-porting process, from highly optimized device code to a higher-level version using directives, compare code structure, and describe barriers that were overcome in this effort.

Thavappiragasam, Mathialakan↗

Evolution of a minimal parallel programming model

Here, we take a historical approach to our presentation of self-scheduled task parallelism, a programming model with its origins in early irregular and nondeterministic computations encountered in automated theorem proving and logic programming. We show how an extremely simple task model has evolved into a system, asynchronous dynamic load balancing (ADLB), and a scalable implementation capable of supporting sophisticated applications on today’s (and tomorrow’s) largest supercomputers; and we illustrate the use of ADLB with a Green’s function Monte Carlo application, a modern, mature nuclear physics code in production use. Our lesson is that by surrendering a certain amount of generality and thus applicability, a minimal programming model (in terms of its basic concepts and the size of its application programmer interface) can achieve extreme scalability without introducing complexity.

97 MATHEMATICS AND COMPUTING↗

America’s Cutting Edge CNC machining and metrology training

This paper describes the workforce development activities supported by America’s Cutting Edge (ACE), a national initiative for machine tool technology development and advancement. ACE is supported by the Department of Defense Industrial Base Analysis and Sustainment (IBAS) program from the Office of Industrial Policy. Both the online and in-person components of the computer numerically controlled (CNC) machining and metrology training programs are summarized and participation information is provided.

99 GENERAL AND MISCELLANEOUS↗

Using redundant transactions to verify the correctness of program code execution

In the described embodiments, a processor core (e.g., a GPU core) receives a section of program code to be executed in a transaction from another entity in a computing device. The processor core sends the section of program code to one or more compute units in the processor core to be executed in a first transaction and concurrently executed in a second transaction, thereby creating a “redundant transaction pair.” When the first transaction and the second transaction are completed, the processor core compares a read-set of the first transaction to a read-set of the second transaction and compares a write-set of the first transaction to a write-set of the second transaction. When the read-sets and the write-sets match and no transactional error condition has occurred, the processor core allows results from the first transaction to be committed to an architectural state of the computing device.

Gurumurthi, Sudhanva↗

MCNP ® Code Version 6.3.1 Theory & User Manual

This document acts as a repository of knowledge for the Monte Carlo N-Particle (MCNP) transport computer code. It is maintained alongside the source code and attempts to introduce new users and re-familiarize experienced users with the theory and practices of using the MCNP code for the wide range of particle transport analyses that it is appropriate for. The latest version of the MCNP code, version 6.3.1, provides the Monte Carlo particle transport community with the latest feature developments and bug fixes in the MCNP code. The MCNP code version 6.0 and later is also known as the MCNP6 code.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

WE-A-BRE-01: Debate: To Measure or Not to Measure

Recent studies have highlighted some of the limitations of patient-specific pre-treatment IMRT QA measurements with respect to assessing plan deliverability. Pre-treatment QA measurements are frequently performed with detectors in phantoms that do not involve any patient heterogeneities or with an EPID without a phantom. Other techniques have been developed where measurement results are used to recalculate the patient-specific dose volume histograms. Measurements continue to play a fundamental role in understanding the initial and continued performance of treatment planning and delivery systems. Less attention has been focused on the role of computational techniques in a QA program such as calculation with independent dose calculation algorithms or recalculation of the delivery with machine log files or EPID measurements. This session will explore the role of pre-treatment measurements compared to other methods such as computational and transit dosimetry techniques. Efficiency and practicality of the two approaches will also be presented and debated. The speakers will present a history of IMRT quality assurance and debate each other regarding which types of techniques are needed today and for future quality assurance. Examples will be shared of situations where overall quality needed to be assessed with calculation techniques in addition to measurements. Elements where measurements continue to be crucial such as for a thorough end-to-end test involving measurement will be discussed. Operational details that can reduce the gamma tool effectiveness and accuracy for patient-specific pre-treatment IMRT/VMAT QA will be described. Finally, a vision for the future of IMRT and VMAT plan QA will be discussed from a safety perspective. Learning Objectives: Understand the advantages and limitations of measurement and calculation approaches for pre-treatment measurements for IMRT and VMAT planning Learn about the elements of a balanced quality assurance program involving modulated techniques Learn how to use tools and techniques such as an end-to-end test to enhance your IMRT and VMAT QA program.

60 APPLIED LIFE SCIENCES↗

Reducing the small-heart effect in pediatric gated myocardial perfusion single-photon emission computed tomography

Background: We compared two reconstruction algorisms and two cardiac functional evaluation software programs in terms of their accuracy for estimating ejection fraction (EF) of small hearts (SH). Methods: The study group consisted of 66 pediatric patients. Data were reconstructed using a filtered back projection (FBP) method without the resolution correction (RC) and an iterative method based on an ordered subset expectation maximization (OSEM) algorithm with the RC. EF was evaluated using two software programs of quantitative gated single-photon emission computed tomography (SPECT) (QGS) and cardioREPO. We compared the EF of gated myocardial perfusion SPECT to echocardiographic measurement (Echo). Results: Forty-eight of 66 patients had an end-systolic volume < 20 mL which was used as the criterion for being included in the SH group, and the SH effect led to an overestimation of EF. While significant differences were observed between Echo (66.9 ± 5.0%) and QGS-FBP without RC (76.9 ± 8.4%, P < .0001), QGS-OSEM with RC (76.6 ± 8.6%, P < .0001), and cardioREPO-FBP without RC (72.1 ± 10.0%, P = .0011), no significant difference was observed between Echo and cardioREPO-OSEM with RC (67.4 ± 6.1%) in SH group. Conclusions: In pediatric gated myocardial perfusion SPECT, the SH effect can be significantly reduced when an OSEM algorithm is used with RC in combination with the specific cardioREPO algorithm.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

Design, Control and Application of Next Generation Qubits

Design, Control and Application of Next Generation Qubits Arun Bansil, Northeastern University (Principal Investigator) Claudio Chamon, Boston University (Co-Investigator) Adrian Feiguin, Northeastern University (Co-Investigator) Liang Fu, MIT (Co-Investigator) Eduardo Mucciolo, Univ. of Central Florida (Co-Investigator) Qimin Yan, Temple University (Co-Investigator) The quest for developing technologies for manipulating and storing information quantum mechanically is currently led by approaches that include Josephson-junctions, ion-traps, and qubits generated by defect spins in solids. Topological qubits, however, are inherently more robust to decoherence by environmental effects, and should be able to sprint ahead once practical barriers have been overcome. At the present stage of the development of the field, it is important to explore a variety of architectures and materials beyond the conventional paradigms in order to seed breakthroughs toward building a scalable quantum computer. Our comprehensive theoretical research program involved four interconnected thrusts as follows. • A materials discovery effort in two-dimensional compounds in search of materials to support Majorana zero modes and defect structures suitable as qubits. • Exploration of architectures for topological quantum computation by investigating both superconducting Majorana qubits, and robust platforms for braiding with new “meta-materials” built of arrays of Majorana qubits. • Investigation of properties of hybrid metal-organic qubits based on transition-metal centers in graphene, and molecular crystals of polyaromatic complexes with embedded transition-metal atoms. • Development of tensor-network and semiclassical approaches to study decoherence in the presence of random and dispersive spin baths, and NV centers in diamond. The full spectrum of theoretical and numerical approaches was used to address the goals of this project including first-principles, density-matrix-renormalization group, tensor networks, and data-driven high-throughput approaches using materials database and machine-learning.

36 MATERIALS SCIENCE↗

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↗

Quantum Electromagnetic Transients Program

This work devises a quantum electromagnetic transients program (QEMTP) which is the first attempt to tackle the computational challenges in solving EMTP through quantum computing. The main contributions lie in: (1) A quantum-enabled EMTP formulation with Dommel's model encoded in quantum states; 2) An Harrow-Hassidim-Lloyd (HHL)-based QEMTP to solve the discrete-time nodal equations; 3) An iteration-based HHL revision for mitigating temporal errors to achieve high accuracy of QEMTP with limited quantum resources. Case studies verify the correctness and efficacy of QEMTP in simulating both fast and slow dynamics.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

Noisy-Intermediate-Scale Quantum Electromagnetic Transients Program

Quantum-empowered electromagnetic transients program (QEMTP) is a promising paradigm for tackling EMTP's computational burdens. Nevertheless, no existing studies truly achieve a practical and scalable QEMTP operable on today's noisy-intermediate-scale quantum (NISQ) computers. The strong reliance on noise-free and fault-tolerant quantum devices--which appears to be decades away--hinder practical applications of current QEMTP methods. Here, we devise a NISQ-QEMTP methodology which for the first time transitions the QEMTP operations from ideal, noise-free quantum simulators to real, noisy quantum computers. The main contributions lie in: (1) a shallow-depth QEMTP quantum circuit for mitigating noises on NISQ quantum devices; (2) practical QEMTP linear solvers incorporating executable quantum state preparation and measurements for nodal voltage computations; (3) a noise-resilient QEMTP algorithm leveraging quantum resources logarithmically scaled with power system dimension; (4) a quantum shifted frequency analysis (QSFA) for accelerating QEMTP by exploiting dynamic phasor simulations with larger time steps; (5) a systematical analysis on QEMTPs performance under various noisy quantum environments. Extensive experiments systematically verify the accuracy, efficacy, universality and noise-resilience of QEMTP on both noise-free simulators and IBM real quantum computers.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

High Performance Computing Based Parallel HIearchical Modal Association Clustering (HPAR HMAC)

For many applications, clustering is a crucial step in order to gain insight into the makeup of a dataset. The best approach to a given problem often depends on a variety of factors, such as the size of the dataset, time restrictions, and soft clustering requirements. The HMAC algorithm seeks to combine the strengths of 2 particular clustering approaches: model-based and linkage-based clustering. One particular weakness of HMAC is its computational complexity. HMAC is not practical for mega-scale data clustering. For high-definition imagery, a user would have to wait months or years for a result; for a 16-megapixel image, the estimated runtime skyrockets to over a decade! To improve the execution time of HMAC, it is reasonable to consider an multi-core implementation that utilizes available system resources. An existing imple-mentation (Ray and Cheng 2014) divides the dataset into N partitions - one for each thread prior to executing the HMAC algorithm. This implementation benefits from 2 types of optimization: parallelization and divide-and-conquer. By running each partition in parallel, the program is able to accelerate computation by utilizing more system resources. Although the parallel implementation provides considerable improvement over the serial HMAC, it still suffers from poor computational complexity, O(N2). Once the maximum number of cores on a system is exhausted, the program exhibits slower behavior. We now consider a modification to HMAC that involves a recursive partitioning scheme. Our modification aims to exploit divide-and-conquer benefits seen by the parallel HMAC implementation. At each level in the recursion tree, partitions are divided into 2 sub-partitions until a threshold size is reached. When the partition can no longer be divided without falling below threshold size, the base HMAC algorithm is applied. This results in a significant speedup over the parallel HMAC.

Patlolla, Dilip R↗

Brookhaven Lab Hosts Hackathon Focused on Graphics Processing Units (GPUs)

For five days in June 2017, Brookhaven Lab’s Computational Science Initiative hosted “Brookathon”—a programming workshop where teams of researchers, students, and software developers worked with mentors to accelerate scientific applications on GPUs for high-performance computing.

97 MATHEMATICS AND COMPUTING↗

SRF-Based Quantum Transduction for Quantum Computing and Sensing

The next groundbreaking frontier in Quantum Information Science (QIS) is the development of low-noise interconnections over fiber optics between superconducting radio-frequency (SRF) quantum devices. High-efficiency microwave-optical transduction serves as a pivotal enabler for distributed quantum computing and sensor networks. This presentation will provide a comprehensive overview of quantum transduction achieved by coupling SRF cavities to electro-optic optical resonators, enabling efficient conversion between microwave and optical photons. This research, supported by the DOE Early Career Research Program, advances technologies for quantum computing and sensing, and complements the mission of the Superconducting Quantum Materials and Systems (SQMS) Center at Fermilab.

Zorzetti, Silvia [Fermilab] (ORCID:000000023208338↗

Report on Year-4 of Water NSTF Matrix Testing: Facility Maintenance and Accident Testing

Under support from the Department of Energy (DOE) and the Office of Advanced Reactor Technologies (ART), a large-scale test facility has been constructed at Argonne National Laboratory to generate NQA-1 qualified validation data for passive decay heat removal systems in advanced reactors. The Natural convection Shutdown heat removal Test Facility (NSTF) reflects key features of a ½ scale, water-based, Reactor Cavity Cooling System (RCCS) and is intended to study the behavior, bound performance, and ultimately guide design decisions for passive decay heat removal systems for advanced reactors. In addition to the experimental activities detailed in this report, a supportive computational modeling effort is on-going which has been demonstrated to significantly strengthen the experimental program while also improving accuracy of the computer models. Together these create a mutually beneficial relationship integral to meeting the overall program objective of examining the heat removal performance of the RCCS concept. This report serves as a summary of maintenance and experimental activities during the program’s fourth year of water-based operation. A planned six-month maintenance period began in August 2021, during which major inspections, repairs, cleaning, and installation of new instrumentation and data acquisition hardware were conducted. Most significantly, two heaters that faulted during Year-3 were repaired, allowing the facility to resume use of the full heated section area and full range of available electric power. The remainder of the year consisted of eight months of test operations, during which the facility logged 211 hours of active heating across one bake-out (following the maintenance period) and seven matrix tests; five classifieds as Accepted per NQA-1, one as Trending, and one as Failed. Testing began by performing two repeat cases to confirm expected facility response and behavior during both single- and two-phase flow conditions, ensuring no changes were introduced during the maintenance period that might have altered the thermal-hydraulic characteristics of the facility. In continuation of the power parametric series initiated in previous years, a high-power test case was then performed examining heat removal performance at a decay heat load equivalent to 2.4 MWt, full-scale, a level exceeding maximum design targets. Additional testing then introduced various blockage scenarios along the network piping, examining the effects of partial and complete blockages of the flow paths on the system behavior and heat removal performance. A study of static boiling tests directed at understanding the geysering two-phase instability was also conducted. The loop was filled only to the bottom of the tank outlet, creating an open loop configuration that prevents any natural circulation flow from occurring, and the heaters were powered on until the facility reached saturation conditions. Following, a series of quasi-steady-state conditions were introduced by adjusting the inventory level in the adiabatic chimney piping at decreasingly lower elevations above the heated region. A strong correlation of geysering characteristics and loop level was observed, with flow and temperature excursions decreasing in intensity, but increasing in frequency, as the fill were reduced to lower elevations along the chimney piping. Once the level fell very low in the chimney, at points near the top of the heated section, the system reached a stable state of continuous boiling without any occurrence of geysering eruptions. A final significant testing accomplishment this year was successful completion of an “accident scenario” test, whose operating conditions were based on a prototypic decay heat curve provided by Framatome and scaled for the NSTF. This test began by establishing steady-state, single-phase “normal operation” conditions, before simulating an accident trip where the availability of active cooling systems was lost. Loop temperatures gradually increased until reaching saturation and subsequent two-phase boiling flow. Over the course of an extended operational period along the defined decay heat curve, steam boil-off caused gradual but continued depletion of liquid inventory until reaching a critically low level causing flow stagnation and cessation of natural circulation heat removal. At this point, after nearly 72 hours of continuous operation, a cold refill was performed to replenish the system inventory and allow the facility to re-establish closed loop natural circulation flow and return to a safe operational state.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

FY23 Report on Water NSTF Testing at Two-Phase Conditions: Off-normal Scenarios

Under support from the Department of Energy (DOE) and the Office of Advanced Reactor Technologies (ART), a large-scale test facility has been constructed at Argonne National Laboratory to generate NQA-1 qualified validation data for passive decay heat removal systems in advanced reactors. The Natural convection Shutdown heat removal Test Facility (NSTF) reflects key features of a ½ scale, water-based, Reactor Cavity Cooling System (RCCS) and is intended to study the behavior, bound performance, and ultimately guide design decisions for passive decay heat removal systems for advanced reactors. In addition to the experimental activities detailed in this report, a supportive computational modeling effort is on-going which has been demonstrated to significantly strengthen the experimental program while also improving accuracy of the computer models. Together these create a mutually beneficial relationship integral to meeting the overall program objective of examining the heat removal performance of the RCCS concept. This report details the experimental activities and upgrades performed during the program’s fifth year of water-based operation. The theme of this year of testing was examining off-normal scenarios. In practice, that meant examining scenarios with blockages or other design basis conditions. From a maintenance and capability standpoint that meant assessing valving options for implementing blockages, assessing drain and refill capabilities, and ensuring in all cases that operators could safely, efficiently, and repeatably bring the facility to an off-normal condition and return it to the normal operating state. In one notable case, no solution existed, nor was a solution commercially available, that met the facility needs for implementing blockages within the two-phase region of the chimney. A valve and feedthrough were custom-designed for NSTF to operate submerged in saturated water while being safely actuated from outside the tank. The fifth year of testing included eight matrix tests consisting of 162 hours of active heating, 9,735 kWh of electrical heating, with seven tests classified as Accepted per NQA-1 and one as Trending. All matrix tests were performed at two-phase flow conditions. The power parametric series from previous years was extended to include another scenario with a decay load equivalent to 1.75 MWt, full scale, further resolving the system flow oscillation response as a function of input power. A depletion test was performed to extend previous work and examine the system’s approach to stagnation and geysering that were not previously observed. This test began at an initial inventory level of 50%, prototypic power of 2.1 MWt, and employed an accelerated drain of 0.75 gpm plus boiloff until stagnation conditions were achieved and multiple geysering events were recorded. Further exploring the geysering phenomenon was a separate effects test examining static boiling in the risers and chimney. This static boiling test was performed at 48 kWe, a higher power than testing in the previous year, and included enhancements to the drain system to remove inventory in a better-controlled and more reliable manner. Two tests were performed, at prototypic conditions of 1.4 MWt and 2.4 MWt, respectively, examining the system response to throttled conditions in the singlephase region of the piping. A ball valve immediately before he riser inlet header was increasingly throttled, progressing the system through a repeatable pattern of two-phase oscillations and stable regimes before ultimately inducing stagnation and geysering. Concluding the year, two tests were performed at baseline conditions of 70% initial inventory level and 2.1 MWt of prototypic decay heat to examine both repeatability and the response to throttling within the two-phase region, at the inventory tank inlet using the custom valve mentioned above. The first such test repeated transient operating conditions and revealed significant sensitivity t

22 GENERAL STUDIES OF NUCLEAR REACTORS↗