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Parallel IO Libraries for Managing HEP Experimental Data

The computing and storage requirements of the energy and intensity frontiers will grow significantly during the Run 4 & 5 and the HL-LHC era. Similarly, in the intensity frontier, with larger trig ger readouts during supernovae explosions, the Deep Underground Neutrino Experiment (DUNE) will have unique computing challenges that could be addressed by the use of parallel and accelerated dataprocessing capabilities. Most of the requirements of the energy and intensity frontier experiments rely on increasing the role of high performance computing (HPC) in the HEP community. In this presentation, we will describe our ongoing efforts that are focused on using HPC resources for the next generation HEP experiments. The HEPCCE (High Energy Physics-Center for Computational Excellence) IOS (Input/Output and Storage) group has been developing approaches to map HEP data to the HDF5 , an IO library optimized for the HPC platforms to store the intermediate HEP data. The complex HEP data products are serialized using ROOT to allow for experiment independent general mapping approaches of the HEP data to the HDF5 format. The mapping approaches can be optimized for high performance parallel IO. Similarly, simpler data can be directly mapped into the HDF5, which can also be suitable for offloading into the GPUs directly. We will present our works on both complex and simple data model models.

Bashyal, Amit↗

Implementation of Parallel Dynamic Simulation on Shared-Memory vs. Distributed-Memory Environments

Power system dynamic simulation computes the system response to a sequence of large disturbance, such as sudden changes in generation or load, or a network short circuit followed by protective branch switching operation. It consists of a large set of differential and algebraic equations, which is computational intensive and challenging to solve using single-processor based dynamic simulation solution. High-performance computing (HPC) based parallel computing is a very promising technology to speed up the computation and facilitate the simulation process. This paper presents two different parallel implementations of power grid dynamic simulation using Open Multi-processing (OpenMP) on shared-memory platform, and Message Passing Interface (MPI) on distributed-memory clusters, respectively. The difference of the parallel simulation algorithms and architectures of the two HPC technologies are illustrated, and their performances for running parallel dynamic simulation are compared and demonstrated.

dynamic simulation↗

WE-G-16A-01: Evolution of Radiation Treatment Planning

Welcome and Introduction - Lawrence N. Rothenberg This symposium is one a continuing series of presentations at AAPM Annual Meetings on the historical aspects of medical physics, radiology, and radiation oncology that have been organized by the AAPM History Committee. Information on previous presentations including “Early Developments in Teletherapy” (Indianapolis 2013), “Historical Aspects of Cross-Sectional Imaging” (Charlotte 2012), “Historical Aspects of Brachytherapy” (Vancouver 2011), “50 Years of Women in Medical Physics” (Houston 2008), and “Roentgen's Early Investigations” (Minneapolis 2007) can be found in the Education Section of the AAPM Website. The Austin 2014 History Symposium will be on “Evolution of Radiation Treatment Planning.” Overview - Radhe Mohan Treatment planning is one of the most critical components in the chain of radiation therapy of cancers. Treatment plans of today contain a wide variety of sophisticated information conveying the potential clinical effectiveness of the designed treatment to practitioners. Examples of such information include dose distributions superimposed on three- or even four-dimensional anatomic images; dose volume histograms, dose, dose-volume and dose-response indices for anatomic structures of interest; etc. These data are used for evaluating treatment plans and for making treatment decisions. The current state-of-the-art has evolved from the 1940s era when the dose to the tumor and normal tissues was estimated approximately by manual means. However, the symposium will cover the history of the field from the late-1950's, when computers were first introduced for treatment planning, to the present state involving the use of high performance computing and advanced multi-dimensional anatomic, functional and biological imaging, focusing only on external beam treatment planning. The symposium will start with a general overview of the treatment planning process including imaging, structure delineation, assignment of dose requirements, consideration of uncertainties, selection of beam configurations and shaping of beams, and calculations, optimization and evaluation of dose distributions. This will be followed by three presentations covering the evolution of treatment planning, which parallels the evolution of computers, availability of advanced volumetric imaging and the development of novel technologies such as dynamic multi-leaf collimators and online image guidance. This evolution will be divided over three distinct periods - prior to 1970's, the 2D era; from 1980 to the mid-1990's, the 3D era; and from the mid 1990's to today, the IMRT era. When the World was Flat: The Two-Dimensional Radiation Therapy Era” - Jacob Van Dyk In the 2D era, anatomy was defined with the aid of solder wires, special contouring devices and projection x-rays. Dose distributions were calculated manually from single field, flat surface isodoses on transparencies. Precalculated atlases of generic dose distributions were produced by the International Atomic Energy Agency. Massive time-shared main frames and mini-computers were used to compute doses at individual points or dose distributions in a single plane. Beam shapes were generally rectangular, with wedges, missing tissue compensators and occasional blocks to shield critical structures. Dose calculations were measurement-based or they used primary and scatter calculations based on scatter-air ratio methodologies. Dose distributions were displayed on line printers as alpha-numeric character maps or isodose patterns made with pen plotters. More than Pretty Pictures: 3D Treatment Planning and Conformal Therapy - Benedick A. Fraass The introduction of computed tomography allowed the delineation of anatomy three-dimensionally and, supported partly by contracts from the National Cancer Institute, made possible the introduction and clinical use of 3D treatment planning, leading to development and use of 3D conformal therapy in the 1980's. 3D computer graphics and 3D anatomical structure definitions made possible Beam's Eye View (BEV) displays, making conformal beam shaping and much more sophisticated beam arrangements possible. These conformal plans significantly improved target dose coverage as well as normal tissue sparing. The use of dose volume histograms, gross/clinical/planning target volumes, MRI and PET imaging, multileaf collimators, and computer-controlled treatment delivery made sophisticated planning approaches practical. The significant improvements in dose distributions and analysis achievable with 3D conformal therapy made possible formal dose escalation and normal tissue tolerance clinical studies that set new and improved expectations for improved local control and decreasing complications in many clinical sites. From the Art to the State of the Art: Inverse Planning and IMRT - Thomas R. Bortfeld While the potential of intensity modulation was recognized in the mid- 1980's, intensity-modulated radiotherapy (IMRT) did not become a reality until the mid-1990's. Broad beams of photons could be sub-divided into narrow beamlets whose intensities could be determined using sophisticated optimization algorithms to appropriately balance tumor dose with normal tissue sparing. The development of dynamic multi-leaf collimators (on conventional linear accelerators as well as in helical delivery devices) enabled the efficient delivery of IMRT. The evolution of IMRT planning is continuing in the form of Volumetric Modulated Arc Therapy (VMAT) and through advanced optimization tools, such as multi-criteria optimization, automated IMRT planning, and robust optimization to protect dose distributions against uncertainties. IMRT also facilitates “dose painting” in which different sub-volumes of the target are prescribed different doses. Clearly, these advancements are being made possible by the increasing power and lower cost of computers and developments in other fields such as imaging and operations research. Summary - Radhe Mohan The history does not end here. The advancement of treatment planning is expected to continue, leading to further automation and improvements in conformality and robustness of dose distributions, particularly in the area of particle therapy. Radiobiological modeling will gain emphasis as part of the planning process. Learning Objectives: The scope of changes in technology and the capabilities of radiation treatment planning The impact of these changes in the quality of treatment plans and optimality of dose distributions The impact of development in other fields (imaging, computers, operations research, etc.) on the evolution of radiation treatment planning.

60 APPLIED LIFE SCIENCES↗

HPC-PATTERNS

This repository consists of various code examples demonstrating common patterns used in High-Performance Computing (HPC). Indeed, examples showcasing innovative usage of newly developed capabilities of HPC libraries are highly demanded by the HPC community. This repository's goal is to fulfill those requests.

APPLENCOURT, THOMAS↗

eXascale PRogramming Environment and System Software (XPRESS)

Exascale systems, with a thousand times the compute capacity of today’s leading edge petascale computers, are expected to emerge during the next decade. Their software systems will need to facilitate the exploitation of exceptional amounts of concurrency in applications, and ensure that jobs continue to run despite the occurrence of system failures and other kinds of hard and soft errors. Adapting computations at runtime to cope with changes in the execution environment, as well as to improve power and performance characteristics, is likely to become the norm. As a result, considerable innovation is required to develop system support to meet the needs of future computing platforms. The XPRESS project aims to develop and prototype a revolutionary software system for extreme-­scale computing for both exascale and strong­scaled problems. The XPRESS collaborative research project will advance the state-­of-­the-­art in high performance computing and enable exascale computing for current and future DOE mission-­critical applications and supporting systems. The goals of the XPRESS research project are to: A. enable exascale performance capability for DOE applications, both current and future, B. develop and deliver a practical computing system software X-­stack, OpenX, for future practical DOE exascale computing systems, and C. provide programming methods and environments for effective means of expressing application and system software for portable exascale system execution.

97 MATHEMATICS AND COMPUTING↗

Parallel Algorithms for the Exascale Era

New parallel algorithms are needed to reach the Exascale level of parallelism with millions of cores. We look at some of the research developed by students in projects at LANL. The research blends ideas from the early days of computing while weaving in the fresh approach brought by students new to the field of high performance computing. We look at reproducibility of global sums and why it is important to parallel computing. Next we look at how the concept of hashing has led to the development of more scalable algorithms suitable for next-generation parallel computers. Nearly all of this work has been done by undergraduates and published in leading scientific journals.

97 MATHEMATICS AND COMPUTING↗

PETSc Users Manual (Revision 3.15)

This manual describes the use of the Portable, Extensible Toolkit for Scientific Computation (PETSc) for the numerical solution of partial differential equations and related problems on high-performance computers. PETSc is a suite of data structures and routines that provide the building blocks for the implementation of large-scale application codes on parallel (and serial) computers. PETSc uses the MPI standard for all distributed memory communication.

97 MATHEMATICS AND COMPUTING↗

An introduction to developing GitLab/Jacamar runner analyst centric workflows at Sandia

This document provides very basic background information and initial enabling guidance for computational analysts to develop and utilize GitOps practices within the Common Engineering Environment (CEE) and High Performance Computing (HPC) computational environment at Sandia National Laboratories through GitLab/Jacamar runner based workflows.

97 MATHEMATICS AND COMPUTING↗

ECP Software Technology Capability Assessment Report V3.0

The Exascale Computing Project (ECP) Software Technology (ST) focus area is responsible for (1) developing critical software capabilities that will enable the successful execution of ECP applications and (2) providing key components of a productive and sustainable exascale computing ecosystem that will position the US Department of Energy (DOE) and the broader high-performance computing (HPC) community with a firm foundation for future extreme-scale computing capabilities. This ECP ST Capability Assessment Report (CAR) provides an overview and assessment of current ECP ST capabilities and activities, giving stakeholders and the broader HPC community information that can be used to assess ECP ST progress and plan their own efforts accordingly. ECP ST leaders commit to updating this document on regular basis (every 6–12 months). Highlights from this version of the report are presented here. This version of the CAR contains the following updates relative to the previous revision: (1) This report highlights the progress with the Extreme-scale Scientific Software Stack (E4S) efforts. In particular, this report discusses how E4S continues to gain traction as a first-class entity in the HPC ecosystem, enabling new conversations with users, facilities, vendors, other US agencies, and international partners. (2) The several-page summaries of each ECP Level 4 project were updated to reflect recent progress and next steps (Section 4). Of particular note are the experiences of our teams on early-access systems for Frontier. (3) The E4S is described further. E4S is now updated via quarterly releases. E4S is the primary integration and delivery vehicle for ECP ST capabilities (Section 2.1.1). (4) The ECP ST software development kit (SDK) effort further refined its groupings (Section 2.1.2). The ECP ST focus area represents the key bridge between exascale systems and the scientists developing applications that will run on those platforms. ECP ST efforts contribute to approximately 70 software products (Section 2.1.3) in six technical areas (Table 1). Since publishing the previous revision of the CAR, the team has continued to evolve the product dictionary of official product names, which enables more rigorous mapping of ECP ST deliverables to stakeholders (Section 2.1.4).

97 MATHEMATICS AND COMPUTING↗

Computational Requirements in Clean Energy and Manufacturing: Summary report of the virtual workshop held on June 28-29, 2021

On June 28–29, 2021, the US Department of Energy’s (DOE’s) Advanced Scientific Computing Research (ASCR) program in the Office of Science convened a workshop with the Energy Efficiency and Renew able Energy (EERE) program offices to assess the future need for advanced computing resources in the areas of clean energy and advanced manufacturing. In part, this discussion served as an update to earlier workshops and townhalls. ASCR is guided by DOE mission needs as it develops research programs, computers, and networks at the leading edge of technologies. As the exascale computing era dawns, technology changes are creating new opportunities for those who must use high-performance computing (HPC) and data systems effectively. The ASCR computing facilities are augmenting their strategy to adapt to changing science needs and emerging technologies and to leverage the utility of exascale computing across the federal government.

97 MATHEMATICS AND COMPUTING↗

Basic Research Needs for Inverse Methods for Complex Systems under Uncertainty [Brochure]

The four priority research directions outlined in this brochure represent a cohesive vision for advancing the science of inverse problems for complex systems under uncertainty. Together, they address the critical challenges of: discovering, exploiting, and preserving physical and problem structure; overcoming model limitations; integrating disparate, multimodal, and/or dynamic data; and tailoring the solution of inverse problems to downstream tasks. While each PRD focuses on a distinct aspect of inverse-problem research, their interconnected nature highlights the importance of a holistic approach that leverages progress across all areas to achieve transformative solutions. This agenda calls for research across mathematics, statistics, and computer science disciplines, which are guided and complemented by rapid advances in artificial intelligence, high-performance computing, and experimental facilities, to unlock new capabilities, maximize scientific impact, and meet the growing demands of inverse problems that arise across applications that are critical to DOE's mission.

97 MATHEMATICS AND COMPUTING↗

Tuning CAS Application using AIMS: An Automated Instrumentation and Monitoring System

To bring together NASA's scientists and engineers and their counterparts in industry, other government agencies, and academia working in the Computational AeroSciences (CAS) field. This workshop is part of the technology transfer plan of the High Performance Computing and Communications Program (HPCCP). Specific objectives of this Workshop are to: (1) communicate the goals and objectives of HPCCP in the area of CAS; (2) promote and disseminate CAS technology within the appropriate technical communities, including NASA, industry, academia, and other government labs; (3) help promote synergy among CAS scientists; and (4) permit feedback from peer researchers in issues pacing the CAS field in general and the HPCCP CAS program in particular.

Mehra, P.↗

Petaflops Computing: The Key Algorithmic Challenges

The prospect of petaflops-class computers brings to the fore some important algorithmic issues that have been considered in the high performance computing community for several years. Key among them are (1) concurrency (whether the fundamental concurrency of an algorithm is sufficient to keep thousands of processors productively busy); (2) data locality; (3) latency tolerance; and (4) memory and operation count scaling. This introductory presentation will give an overview of these issues.

Bailey, David H.↗

Stockpile Stewardship: How We Ensure the Nuclear Deterrent Without Testing

In the 1990s, the U.S. nuclear weapons program shifted emphasis from developing new designs to dismantling thousands of existing weapons and maintaining a much smaller enduring stockpile. The United States ceased underground nuclear testing, and the Department of Energy created the Stockpile Stewardship Program to maintain the safety, security, and reliability of the U.S. nuclear deterrent without full-scale testing. This video gives a behind the scenes look at a set of unique capabilities at Lawrence Livermore that are indispensable to the Stockpile Stewardship Program: high performance computing, the Superblock category II nuclear facility, the JASPER a two stage gas gun, the High Explosive Applications Facility (HEAF), the National Ignition Facility (NIF), and the Site 300 contained firing facility.

98 NUCLEAR DISARMAMENT, SAFEGUARDS, AND PHYSICAL P↗

Efficient Topology Assessment for Integrated Transmission and Distribution Network with 10,000+ Inverter-based Resources

The renewable energy proliferation calls upon the grid operators and planners to systematically evaluate the potential impacts of distributed energy resources (DERs). Considering the significant differences between various inverter-based resources (IBRs), especially the different capabilities between grid-forming inverters and grid-following inverters, it is crucial to develop an efficient and effective assessment procedure besides available co-simulation framework with high computation burdens. This paper presents a streamlined graph-based topology assessment for the integrated power system transmission and distribution networks. Graph analyses were performed based on the integrated graph of modified miniWECC grid model and IEEE 8500-node test feeder model, high performance computing platform with 40 nodes and total 2400 CPUs has been utilized to process this integrated graph, which has 100,000+ nodes and 10,000+ IBRs. The node ranking results not only verified the applicability of the proposed method, but also revealed the potential of distributed grid forming (GFM) and grid following (GFL) inverters interacting with the centralized power plants.

Graph Analysis, Topology evaluation, Infrastructur↗

EngineSim: Turbojet Engine Simulator Adapted for High School Classroom Use

EngineSim is an interactive educational computer program that allows users to explore the effect of engine operation on total aircraft performance. The software is supported by a basic propulsion web site called the Beginner's Guide to Propulsion, which includes educator-created, web-based activities for the classroom use of EngineSim. In addition, educators can schedule videoconferencing workshops in which EngineSim's creator demonstrates the software and discusses its use in the educational setting. This software is a product of NASA Glenn Research Center's Learning Technologies Project, an educational outreach initiative within the High Performance Computing and Communications Program.

Petersen, Ruth A.↗

Interface tracking simulations of bubbly flows in PWR relevant geometries

[en] Highlights: • Simulations were performed for turbulent bubbly flows in PWR subchannel geometry. • Liquid turbulence is fully resolved by direct numerical simulation approach. • Bubble behavior is captured using level-set interface tracking method. • Time-averaged single- and two-phase turbulent flow statistical quantities are obtained. - Abstract: The advances in high performance computing (HPC) have allowed direct numerical simulation (DNS) approach coupled with interface tracking methods (ITM) to perform high fidelity simulations of turbulent bubbly flows in various complex geometries. In this work, we have chosen the geometry of the pressurized water reactor (PWR) core subchannel to perform a set of interface tracking simulations (ITS) with fully resolved liquid turbulence. The presented research utilizes a massively parallel finite-element based code, PHASTA, for the subchannel geometry simulations of bubbly flow turbulence. The main objective for this research is to demonstrate the ITS capabilities in gaining new insight into bubble/turbulence interactions and assisting the development of improved closure laws for multiphase computational fluid dynamics (M-CFD). Both single- and two-phase turbulent flows were studied within a single PWR subchannel. The analysis of numerical results includes the mean gas and liquid velocity profiles, void fraction distribution and turbulent kinetic energy profiles. Two sets of flow rates and bubble sizes were used in the simulations. The chosen flow rates corresponded to the Reynolds numbers of 29,079 and 80,775 based on channel hydraulic diameter (D_h) and mean velocity. The finite element unstructured grids utilized for these simulations include 53.8 million and 1.11 billion elements, respectively. This has allowed to fully resolve all the turbulence scales and the deformable interfaces of individual bubbles. For the two-phase flow simulations, a 1% bubble volume fraction was used which resulted in 17 bubbles in the smaller case and 262 bubbles in the larger case. In the larger simulation case the size of the resolved bubbles is 0.65 mm in diameter, and the bulk mesh cell size is about 30 microns. Those large-scale simulations provide new level of details previously unavailable and were enabled by the excellent scaling performance of our two-phase flow solver and access to the state-of-the-art supercomputing resources. The presented simulations used up to 256 thousand processing threads on the IBM BG/Q supercomputer “Mira” (Argonne National Laboratory).

Nuclear Science & Technology↗

On Concavity and Utilization Analytics of Wide-Area Network Transport Protocols

Wide-area data transfers in high-performance computing infrastructures and big data applications are increasingly carried over dynamically provisioned dedicated network connections, which provide high capacities with no competing traffic. Throughput of TCP and UDT over wide-area connections depends, often in a complex non-linear way, on the congestion control mechanism, buffer sizes, and the number of parallel streams. In addition, our extensive TCP and UDT throughput measurements and time traces over a suite of physical and emulated 10 Gbps connections with 0-366 ms round-trip times (RTTs) show significant statistical and temporal variations. Consequently, parameter selection and optimization for transport methods require data analytics to complement analytical throughput models. We present analytics based on the concavity-convexity of throughput profiles which provide insights into peak throughput and superior/inferior trend compared to linear interpolations based on RTT. In particular, we propose the utilization-concavity coefficient, a scalar metric that incorporates both utilization and concavity profile to characterize the overall performance of a transport protocol. These measurements-based anaytics enable us to select a transport protocol and its parameters for a given host and connection configuration to achieve high throughput with statistical guarantees.

Rao, Nageswara↗