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All sourcesNASA NTRSDOE OSTI
DOE OSTI2017

It's Indisputable: Five Facts About Planning and Operating Modern Power Systems

An indisputable fact cannot be rebutted. It is supported by theory and experience. Over the past 25 years, wind and solar generation has undergone dramatic growth, resulting in a variety of experiences that model the integration of wind and solar into the planning and operation of modern electric power systems. In this article, we bring together examples from Europe, North America, and Australia to identify five indisputable facts about planning and operating modern power systems. Taken together, we hope these experiences can help build consensus among the engineering and public policy communities about the current state of wind and solar integration and also facilitate conversations about evolving future challenges.

24 POWER TRANSMISSION AND DISTRIBUTION↗
DOE OSTI2020

Evaluating Modern GPU Interconnect: PCIe, NVLink, NV-SLI, NVSwitch and GPUDirect

High performance multi-GPU computing becomes an inevitable trend due to the ever-increasing demand on computation capability in emerging domains such as deep learning, big data and planet-scale simulations. However, the lack of deep understanding on how modern GPUs can be connected and the real impact of state-of-the-art interconnect technology on multi-GPU application performance become a hurdle. In this paper, we fill the gap by conducting a thorough evaluation on five latest types of modern GPU interconnects: PCIe, NVLink-V1, NVLink-V2, NVLink-SLI and NVSwitch, from six high-end servers and HPC platforms: NVIDIA P100-DGX-1, V100-DGX-1, DGX-2, OLCF’s SummitDev and Summit supercomputers, as well as an SLI-linked system with two NVIDIA Turing RTX-2080 GPUs. Based on the empirical evaluation, we have observed four new types of GPU communication network NUMA effects: three are triggered by NVLink’s topology, connectivity and routing, while one is caused by PCIe chipset design issue. These observations indicate that, for a multi-GPU application running in a multi-GPU node, choosing the right GPU combination can impose considerable impact on GPU communication efficiency, as well as an application’s overall performance. Our evaluation can be leveraged in building practical multi-GPU performance models, which are vital for GPU task allocation, scheduling and migration in a shared environment (e.g., AI cloud and HPC centers), as well as communication-oriented performance tuning.

Performance Evaluation, GPU, Interconnect, NUMA, P↗
DOE OSTI2019

Drainage enhances modern soil carbon contribution but reduces old soil carbon contribution to ecosystem respiration in tundra ecosystems

Abstract Warming temperatures are likely to accelerate permafrost thaw in the Arctic, potentially leading to the release of old carbon previously stored in deep frozen soil layers. Deeper thaw depths in combination with geomorphological changes due to the loss of ice structures in permafrost, may modify soil water distribution, creating wetter or drier soil conditions. Previous studies revealed higher ecosystem respiration rates under drier conditions, and this study investigated the cause of the increased ecosystem respiration rates using radiocarbon signatures of respired CO 2 from two drying manipulation experiments: one in moist and the other in wet tundra. We demonstrate that higher contributions of CO 2 from shallow soil layers (0–15 cm; modern soil carbon) drive the increased ecosystem respiration rates, while contributions from deeper soil (below 15 cm from surface and down to the permafrost table; old soil carbon) decreased. These changes can be attributed to more aerobic conditions in shallow soil layers, but also the soil temperature increases in shallow layers but decreases in deep layers, due to the altered thermal properties of organic soils. Decreased abundance of aerenchymatous plant species following drainage in wet tundra reduced old carbon release but increased aboveground plant biomass elevated contributions of autotrophic respiration to ecosystem respiration. The results of this study suggest that drier soils following drainage may accelerate decomposition of modern soil carbon in shallow layers but slow down decomposition of old soil carbon in deep layers, which may offset some of the old soil carbon loss from thawing permafrost.

Kwon, Min Jung↗
DOE OSTI2015

WE-G-213-01: Roentgen and the Birth of Modern Medical Physics

Roentgen and the Birth of Modern Medical Physics – Perry Sprawls Wilhelm Roentgen is well known for his discovery of x-radiation. What is less known and appreciated is his intensive research following the discovery to determine the characteristics of the “new kind of radiation” and demonstrate its great value for medical purposes. In this presentation we will imagine ourselves in Roentgen’s mind and follow his thinking, including questions and doubts, as he designs and conducts a series of innovative experiments that provided the foundation for the rapid growth of medical physics. Learning Objectives: Become familiar with the personal characteristics and work of Prof. Roentgen that establishes him as an inspiring model for the medical physics profession. Observe the thought process and experiments that determined and demonstrated the comprehensive characteristics of x-radiation. The AAPM Award Eponyms: William D. Coolidge, Edith H. Quimby, and Marvin M.D. Williams - Who were they and what did they do? – Lawrence N. Rothenberg William David Coolidge (1873–1975) William Coolidge was born in Hudson, NY in 1873. He obtained his BS at the Massacusetts Institute of Technology in 1896. Coolidge then went to the University of Leipzig, Germany for graduate study with physicists Paul Drude and Gustave Wiedemann and received a Ph.D. in 1899. While in Germany he met Wilhelm Roentgen. Coolidge returned to the US to teach at MIT where he was associated with Arthur A. Noyes of the Chemistry Department, working on the electrical conductivity of aqueous solutions. Willis R. Whitney, under whom Coolidge had worked before going to Germany, became head of the newly formed General Electric Research Laboratory and he invited Coolidge to work with him. In 1905, Coolidge joined the staff of the GE laboratory and was associated with it for the remainder of his life. He developed ductile tungsten filaments to replace fragile carbon filaments as the material for electric light bulb filaments. Until that innovation light bulbs had a notoriously short life. He later incorporated the ductile tungsten as a filament material for a hot cathode, fully evacuated x-ray tube, first described in 1912, which allowed higher current and x-ray output, and greater reliability than had previously been possible. These “Coolidge x-ray tubes” were far superior to the cold cathode, partial pressure gas x-ray tubes that had been in use since Roentgen’s discovery of x-rays in 1895. The Coolidge tube with incremental developments is now the key component for x-ray production in all of our modern x-ray imaging devices, such as CT scanners, interventional radiology systems, and mammography units. Coolidge was also involved in the development of sectional x-ray tubes for research and treatment that were initially designed to reach 800 kV. Additional improvements led to 1 MV and 2 MV devices. In 1932 Coolidge became director of the General Electric Research Laboratory, and in 1940, was made Vice-President and Director of Research. In 1945 he retired and was named Director Emeritus of the laboratory. Coolidge held 83 patents and was recognized for these and many other achievements by election to the National Academy of Engineers, a place in the Engineering Hall of Fame and the National Inventor’s Hall of Fame. The AAPM’s highest honor, the Coolidge Award, was named after him. He accepted Honorary Membership in the AAPM and was the first recipient of the AAPM Coolidge Award, which was presented to him in a special ceremony in Schenectady, NY in 1972 when he was 100 years old. Edith Hinckley Quimby (1891–1982) Edith Quimby was born in Rockford, IL in 1891. She graduated from Whitman College in Walla Walla, WA with a B.S. in 1913, and then obtained a masters degree from the University of California at Berkeley. Later in her career, after many significant achievements, Quimby was awarded honorary doctorates by Whitman College and Rutgers University. Edith Quimby was hired by Giacchino Failla as a radiation physicist at Memorial Hospital for Cancer in New York City. Failla had studied with Madame Curie and obtained his doctoral degree in her laboratory. After many groundbreaking medical physics studies from 1919 until 1942, they both moved to Columbia University. Dr. Quimby developed a widely employed dosimetry system for single plane implants with radium and radon seeds, and a dosimetry methodology for internal radionuclides. She was author of more than 75 scientific publications, and of significant textbooks including the first comprehensive physics textbook for radiologists “Physical Foundations of Radiology”, which was co-authored with Otto Glasser, Lauriston Taylor and James Weatherwax in the first edition, with Russell Morgan added for the second edition and Paul Goodwin for the fourth edition. With Sergei Feitelberg, M.D. she published two editions of “Radioactive Isotopes in Medicine and Biology: Basic Physics and Instrumentation”. Quimby became a renowned examiner for the American Board of Radiology when the third ABR examination, given in 1936, added physics. She served as President of the American Radium Society, received the RSNA Gold Medal, and also numerous prestigious awards given to women in science. Edith Quimby was a Charter Member of AAPM. The AAPM Lifetime Achievement Award was renamed the Edith H. Quimby Lifetime Achievement Award in her honor in 2011. Marvin Martin Dixon Williams (1902–1981) Marvin Williams was born in Walla Walla, WA in 1902, and attended the same college as Edith Quimby, graduating from Whitman College in 1926. He was greatly influenced to go into medical physics by her accomplishments. During his early career, Williams worked with James Weatherwax in Philadelphia while he was working toward an M.S. from the University of Pennsylvania. In 1931 Williams was awarded a Ph.D. in Biophysics from the University of Minnesota, with the work actually performed at the Mayo Clinic Graduate School of the University. While completing his Ph.D. studies, Marvin met Dr. Paul Hodges who had returned from the Peiping Union Medical College in Peiping (now Beijing), China. Hodges suggested that a physicist be sent to Peiping to install x-ray therapy equipment and a radon plant. Williams accepted the position and, in 1931, he and his wife Orpha left for China. Before going to China, Williams had spent time with the physics group at Memorial Hospital to learn about the operation of a radon plant. In China, he constructed the radon plant, employing 0.25 g of radium, and also installed the x-ray therapy unit. Williams and his wife returned to the US in 1935, and he accepted a research position at the Mayo Clinic. In 1950, he became Professor of Biophysics at Mayo, where he taught physics and biophysics until his retirement in 1967. Williams was also very active in the American Board of Radiology where, from 1944 through 1977, he examined over 3000 radiologists and 250 physicists. Marvin Williams was a Charter member of AAPM, served as the fourth President of AAPM in 1963, and was the fourth recipient the AAPM Coolidge Award in 1975. The Marvin Williams Award was originally established as the highest award of the American College of Medical Physics. When various functions of the ACMP were absorbed into the AAPM in 2012, the Marvin M D Williams Professional Achievement Award became one of the AAPM’s highest honors. Learning Objectives: Become familiar with the persons in whose honor the three major AAPM Award are named Learn about the achievements and activities which influenced the AAPM to name these awards in their honor.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2016

SU-F-P-09: A Global Medical Physics Collaboration for Implementation of Modern Radiotherapy in Botswana

Purpose: The global burden of cancer is considerable, particularly in low and middle-income countries. Massachusetts General Hospital (MGH) and Botswana-Harvard AIDS Institute have partnered with the oncology community and government of Botswana to form BOTSOGO (BOTSwana Oncology Global Outreach) to address the rising burden of cancer in Botswana. Currently, radiation therapy (RT) is only available at a single linear accelerator (LINAC) in Gaborone Private Hospital (GPH). BOTSOGO worked to limit the absence of RT during a LINAC upgrade and ensure a safe transition to modern radiotherapy techniques. Methods: The existing Elekta Precise LINAC was decommissioned in November 2015 and replaced with a new Elekta VERSA-HD with IMRT/VMAT/CBCT capability. Upgraded treatment planning and record-and-verify systems were also installed. Physicists from GPH and MGH collaborated during an intensive on-site visit in Botswana during the commissioning process. Measurements were performed using newly purchased Sun Nuclear equipment. Photon beams were matched with an existing model to minimize the time needed for beam modeling and machine down time. Additional remote peer review was also employed. Independent dosimetry was performed by irradiating OSLDs, which were subsequently analyzed at MGH. Results: Photon beam quality agreed with reference data within 0.2%. Electron beam data agreed with example clinical data within 3%. Absolute dose calibration was performed using both IAEA and AAPM protocols. Absolute dose measurements with OSLDs agreed within 5%. Quentry cloud-based software was installed to facilitate remote review of treatment plans. Patient treatments resumed in February 2016. The time without RT was reduced, therefore likely resulting in reduced patient morbidity/mortality. Conclusion: A global physics collaboration was utilized to commission a modern LINAC in a resource-constrained setting. This can be a useful model in other areas with limited resources. Further use of technology and on-site exchanges will facilitate the introduction of more advanced techniques in Botswana. We acknowledge funding support from the AAPM International Educational Activities Committee and the NCI Federal Share Proton Beam Program Income Grant.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2016

SU-F-P-19: Fetal Dose Estimate for a High-Dose Fluoroscopy Guided Intervention Using Modern Data Tools

Purpose: An accurate dose estimate is necessary for effective patient management after a fetal exposure. In the case of a high-dose exposure, it is critical to use all resources available in order to make the most accurate assessment of the fetal dose. This work will demonstrate a methodology for accurate fetal dose estimation using tools that have recently become available in many clinics, and show examples of best practices for collecting data and performing the fetal dose calculation. Methods: A fetal dose estimate calculation was performed using modern data collection tools to determine parameters for the calculation. The reference point air kerma as displayed by the fluoroscopic system was checked for accuracy. A cumulative dose incidence map and DICOM header mining were used to determine the displayed reference point air kerma. Corrections for attenuation caused by the patient table and pad were measured and applied in order to determine the peak skin dose. The position and depth of the fetus was determined by ultrasound imaging and consultation with a radiologist. The data collected was used to determine a normalized uterus dose from Monte Carlo simulation data. Fetal dose values from this process were compared to other accepted calculation methods. Results: An accurate high-dose fetal dose estimate was made. Comparison to accepted legacy methods were were within 35% of estimated values. Conclusion: Modern data collection and reporting methods ease the process for estimation of fetal dose from interventional fluoroscopy exposures. Many aspects of the calculation can now be quantified rather than estimated, which should allow for a more accurate estimation of fetal dose.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2016

WE-A-201-00: Anne and Donald Herbert Distinguished Lectureship On Modern Statistical Modeling

Chris Marshall: Memorial Introduction Donald Edmonds Herbert Jr., or Don to his colleagues and friends, exemplified the “big tent” vision of medical physics, specializing in Applied Statistics and Dynamical Systems theory. He saw, more clearly than most, that “Making models is the difference between doing science and just fooling around [ref Woodworth, 2004]”. Don developed an interest in chemistry at school by “reading a book” - a recurring theme in his story. He was awarded a Westinghouse Science scholarship and attended the Carnegie Institute of Technology (later Carnegie Mellon University) where his interest turned to physics and led to a BS in Physics after transfer to Northwestern University. After (voluntary) service in the Navy he earned his MS in Physics from the University of Oklahoma, which led him to Johns Hopkins University in Baltimore to pursue a PhD. The early death of his wife led him to take a salaried position in the Physics Department of Colorado College in Colorado Springs so as to better care for their young daughter. There, a chance invitation from Dr. Juan del Regato to teach physics to residents at the Penrose Cancer Hospital introduced him to Medical Physics, and he decided to enter the field. He received his PhD from the University of London (UK) under Prof. Joseph Rotblat, where I first met him, and where he taught himself statistics. He returned to Penrose as a clinical medical physicist, also largely self-taught. In 1975 he formalized an evolving interest in statistical analysis as Professor of Radiology and Head of the Division of Physics and Statistics at the College of Medicine of the University of South Alabama in Mobile, AL where he remained for the rest of his career. He also served as the first Director of their Bio-Statistics and Epidemiology Core Unit working in part on a sickle-cell disease. After retirement he remained active as Professor Emeritus. Don served for several years as a consultant to the Nuclear Regulatory Commission and may be remembered for his critique of the National Academy of Sciences BEIR III report (stating that their methodology “imposes a Delphic quality to the .. risk estimates”.) This led to his appointment as a member of the BEIR V committee. Don presented refresher courses at the AAPM, ASTRO and RSNA meetings and was active in the AAPM as a member or chair of several committees. He was the principal author of AAPM Report 43, which is essentially a critique of established clinical studies prior to 1992. He was co-editor of the Proceedings of many symposia on Time, Dose and Fractionation held in Madison, Wisconsin. He received the AAPM lifetime Achievement award in 2004. Don’s second wife of 46 years, Ann, predeceased him and he is survived by daughters Hillary and Emily, son John and two grandsons. Don was a true gentleman with a unique and erudite writing style illuminated by pithy quotations. If he had a fault it was, perhaps, that he did not realize how much smarter he was than the rest of us. This presentation draws heavily on a biography and video interview in the History and Heritage section of the AAPM website. The quote is his own. Andrzej Niemierko: Statistical modeling plays an essential role in modern medicine for quantitative evaluation of the effect of treatment. This session will feature an overview of statistical modeling techniques used for analyzing the many types of research data and an exploration of recent advances in new statistical modeling methodologies. Learning Objectives: To learn basics of statistical modeling methodology. To discuss statistical models that are frequently used in radiation oncology To discuss advanced modern statistical modeling methods and applications.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2016

WE-A-201-02: Modern Statistical Modeling

Chris Marshall: Memorial Introduction Donald Edmonds Herbert Jr., or Don to his colleagues and friends, exemplified the “big tent” vision of medical physics, specializing in Applied Statistics and Dynamical Systems theory. He saw, more clearly than most, that “Making models is the difference between doing science and just fooling around [ref Woodworth, 2004]”. Don developed an interest in chemistry at school by “reading a book” - a recurring theme in his story. He was awarded a Westinghouse Science scholarship and attended the Carnegie Institute of Technology (later Carnegie Mellon University) where his interest turned to physics and led to a BS in Physics after transfer to Northwestern University. After (voluntary) service in the Navy he earned his MS in Physics from the University of Oklahoma, which led him to Johns Hopkins University in Baltimore to pursue a PhD. The early death of his wife led him to take a salaried position in the Physics Department of Colorado College in Colorado Springs so as to better care for their young daughter. There, a chance invitation from Dr. Juan del Regato to teach physics to residents at the Penrose Cancer Hospital introduced him to Medical Physics, and he decided to enter the field. He received his PhD from the University of London (UK) under Prof. Joseph Rotblat, where I first met him, and where he taught himself statistics. He returned to Penrose as a clinical medical physicist, also largely self-taught. In 1975 he formalized an evolving interest in statistical analysis as Professor of Radiology and Head of the Division of Physics and Statistics at the College of Medicine of the University of South Alabama in Mobile, AL where he remained for the rest of his career. He also served as the first Director of their Bio-Statistics and Epidemiology Core Unit working in part on a sickle-cell disease. After retirement he remained active as Professor Emeritus. Don served for several years as a consultant to the Nuclear Regulatory Commission and may be remembered for his critique of the National Academy of Sciences BEIR III report (stating that their methodology “imposes a Delphic quality to the .. risk estimates”.) This led to his appointment as a member of the BEIR V committee. Don presented refresher courses at the AAPM, ASTRO and RSNA meetings and was active in the AAPM as a member or chair of several committees. He was the principal author of AAPM Report 43, which is essentially a critique of established clinical studies prior to 1992. He was co-editor of the Proceedings of many symposia on Time, Dose and Fractionation held in Madison, Wisconsin. He received the AAPM lifetime Achievement award in 2004. Don’s second wife of 46 years, Ann, predeceased him and he is survived by daughters Hillary and Emily, son John and two grandsons. Don was a true gentleman with a unique and erudite writing style illuminated by pithy quotations. If he had a fault it was, perhaps, that he did not realize how much smarter he was than the rest of us. This presentation draws heavily on a biography and video interview in the History and Heritage section of the AAPM website. The quote is his own. Andrzej Niemierko: Statistical modeling plays an essential role in modern medicine for quantitative evaluation of the effect of treatment. This session will feature an overview of statistical modeling techniques used for analyzing the many types of research data and an exploration of recent advances in new statistical modeling methodologies. Learning Objectives: To learn basics of statistical modeling methodology. To discuss statistical models that are frequently used in radiation oncology To discuss advanced modern statistical modeling methods and applications.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2016

WE-H-204-01: William D. Coolidge, Inventor of the Modern X-Ray Tube

“William D. Coolidge, Inventor of the Modern X-ray Tube” David J. Allard, M.S., CHP - Director, PA DEP Bureau of Radiation Protection William David Coolidge 1873–1975 was a research scientist and inventor of the modern X-ray tube. Besides Roentgen, with his 1895 discovery and subsequent studies of X-rays, perhaps no other individual contributed more to the advancement of X-ray technology than did Coolidge. He was born in Hudson, MA and received his Bachelor of Science degree from MIT in 1896. That same year he went to Europe to study under renowned physicists of the time. Coolidge received his Ph.D. summa cum laude from the University of Leipzig in 1899 and soon after joined the staff of MIT. While studying at Leipzig, he met Roentgen. In 1905 he was asked to join the newly established General Electric Research Laboratory in Schenectady, NY. He promptly began fundamental work on the production of ductile tungsten filaments as a replacement for fragile carbon filaments used in incandescent light bulbs. This improved light bulb was brought to market by GE in 1911. It was subsequent application of his tungsten work that led Coolidge to his studies in X ray production. Circa 1910, the state-of-the-art X-ray tube was a “gas tube” or “cold cathode” type tube. These crude X-ray tubes relied on residual gas molecules as a source of electrons for bombardment of low to medium atomic number metal targets. In 1912 Coolidge described the use of tungsten as an improved anode target material for X-ray tubes. Shortly after in 1913 he published a paper in Physical Review describing “A Powerful Roentgen Ray Tube With a Pure Electron Discharge.” This tube used a tungsten filament as a thermionic source of electrons under high vacuum to bombard a tungsten anode target. Great improvements in X-ray tube stability, output and performance were obtained with the “hot cathode” or “Coolidge tube.” With some variation in filament and target geometry, this 100 year old invention is the same basic X-ray tube used today in medicine, research and industry. In 1932 Coolidge became Director of the GE Laboratory, then in 1940 Vice-President and Director of Research. In 1941 he was a member of a small committee, appointed by President Franklin D. Roosevelt, to evaluate the military importance of research on uranium. This committee’s report led to the establishment of the Manhattan Engineering District for nuclear weapons development during WWII. Coolidge lived to be over 100 years old, he had 83 patents to his credit, numerous awards and honorary degrees, and in 1975 was elected to the National Inventor’s Hall of Fame. At the time he was the only inventor to receive this honor in his lifetime. Dr. Coolidge was also the first recipient of the AAPM’s highest science award - named in his honor. From notes of a day-long interview with Coolidge’s son Lawrence in the mid-1990s, previous biographies, publications, books, GE literature, historic photographs, e.g., a wonderful 1874 photo stereoview card with 1 year old baby “Willie Coolidge”, and other artifacts in the author’s collection, this presentation will review Dr. Coolidge’s amazing life, work, accomplishments and awards. “History and Archives Resources at AIP for AAPM and its Members” Gregory A. Good, Ph.D. - Director, AIP Center for History of Physics Melanie J. Mueller, MLIS - Acting Director, AIP Niels Bohr Library & Archives The American Institute of Physics established the Center for History of Physics and the Niels Bohr Library & Archives in the 1960s. Our shared mission is: To preserve and make known the history of the physical sciences. This talk will explore the many ways that AIP’s two history programs support the historical and archival activities of AAPM. Topics will include our ongoing oral history program, web outreach through exhibits and teaching guides, and archiving for AAPM and other Member Societies. We will focus in particular on materials in our collections related to the history of medical physics and to the history of AAPM. We will unveil and demonstrate a new “Archives Portal” that we are designing specifically to be useful to AAPM and its members. Learning Objectives: Study the background of the medical physicist - William David Coolidge Examine the time-line for his success Review the publications conceptualizing his works and progressions Realize what he invented Evaluate the importance of the invention Relate the success to national prominence Uncover how he influenced medical physicists today Find out how he was celebrated by the AAPM View the AIP established Center for History of Physics Consider the significant efforts and vision to preserve the history of medical physics Learn about the Niels Bohr Library & Archives Look back in time at medical physics in the 1960s Unveil and demonstrate a new “Archives Portal” that will be useful to AAPM.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2015

Scintillation counters in modern high-energy physics experiments (Review)

Scintillation counters (SCs) based on organic plastic scintillators (OPSs) are widely used in modern high-energy physics (HEP) experiments. A comprehensive review is given to technologies for production of OPS strips and tiles (extrusion, injection molding, etc.), optical and physical characteristics of OPSs, and methods of light collection based on the use of wavelength-shifting (WLS) fibers coupled to multipixel vacuum and silicon PMs. Examples are given of the use of SCs in modern experiments involved in the search for quarks and new particles, including the Higgs boson (D0, CDF, ATLAS, CMS), new states of matter (ALICE), CP violation (LHCb, KLOE), neutrino oscillations (MINOS, OPERA), and cosmic particles in a wide mass and energy interval (AMS-02). Scintillation counters hold great promise for future HEP experiments (at the ILC, NICA, FAIR) due to properties of a high segmentation, WLS fiber light collection, and multipixel silicon PMT readout.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2022

Reproduced Computational Results Report for “Ginkgo: A Modern Linear Operator Algebra Framework for High Performance Computing”

The article titled “Ginkgo: A Modern Linear Operator Algebra Framework for High Performance Computing” by Anzt et al. presents a modern, linear operator centric, C++ library for sparse linear algebra. Experimental results in the article demonstrate that Ginkgo is a flexible and user-friendly framework capable of achieving high-performance on state-of-the-art GPU architectures. In this report, the Ginkgo library is installed and a subset of the experimental results are reproduced. Specifically, the experiment that shows the achieved memory bandwidth of the Ginkgo Krylov linear solvers on NVIDIA A100 and AMD MI100 GPUs is redone and the results are compared to what presented in the published article. Upon completion of the comparison, the published results are deemed reproducible.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2024

Exploring Architectural-Aware Affinity Policies in Modern HPC Runtimes

Modern commodity and High-Performance Computing (HPC) systems are evolving with complex CPU architectures. These architectures now feature higher core and NUMA domain counts and implement features such as hyperthreading. When considering significant differences in hardware configurations, library availability, and hardware-tailored system/software stacks, which could substantially vary from one system to another, performance portability is hard to achieve. Throughout the years, this trend resulted in an increasingly high burden on application developers to fine-tune their workloads for each architecture. This work explores how hardware-dependent aspects such as locality/process/thread affinity affect performance in modern CPU architectures. We focus our study on the Global Memory and Threading (GMT) distributed runtime system as a representative of Partitioned Global Address Space (PGAS) software stacks commonly adopted for productivity. In particular, to appreciate performance implications, we evaluate GMT’s thread affinity policies, and, introduce two new ones which exploit architectural awareness. Finally, we explore alternative NUMA configurations via different process bindings and perform a scalability study on three HPC clusters with varying CPU architectures and NUMA layouts. Our analysis indicates that more complex architectures are more affected by affinity and binding policies and highlights the importance of setting proper runtime configurations to achieve superior performance.

Di Dio Lavore, Ian↗
DOE OSTI2023

Representation of the Convectively Coupled Kelvin Waves in Modern Reanalysis Products

Abstract This study aims to deepen our understanding of the destabilization mechanisms and the mean-state modulation of the convectively coupled Kelvin waves (CCKWs) while testing simple models for CCKWs. We examine CCKW precipitation, vertical structure, and energetics in four modern reanalyses: the fifth version of ECMWF Reanalysis (ERA5), NASA Modern-Era Retrospective Analysis for Research and Applications, version 2 (MERRA-2), the second version of the NCEP Climate Forecast System Reanalysis (CFSR), and the Japanese 55-year Reanalysis (JRA-55). The CCKW precipitation signal strength in the wavenumber–frequency domain and the geographical distribution of CCKW precipitation variability are reasonably represented in all reanalyses, although they commonly underestimate the amplitude of CCKW precipitation. Despite considerable interreanalysis differences in the vertical structure of temperature and diabatic heating anomalies, the eddy available potential energy (EAPE) generation within the CCKWs is found to be associated with the second baroclinic mode whereas the first baroclinic mode damps CCKW EAPE in three out of four reanalyses. Geographically, strong CCKW activity occurs in the areas of high mean-state sea surface temperature (SST), where the second mode EAPE generation is higher, mainly due to a stronger stratiform heating and a tighter wave–convection coupling. Our results are supportive of the simple models for CCKWs in which CCKWs are destabilized within the second baroclinic mode component.

Meteorology & Atmospheric Sciences↗
DOE OSTI2017

Modern gyrokinetic particle-in-cell simulation of fusion plasmas on top supercomputers

The Gyrokinetic Toroidal Code at Princeton (GTC-P) is a highly scalable and portable particle-in-cell (PIC) code. It solves the 5D Vlasov-Poisson equation featuring efficient utilization of modern parallel computer architectures at the petascale and beyond. Motivated by the goal of developing a modern code capable of dealing with the physics challenge of increasing problem size with sufficient resolution, new thread-level optimizations have been introduced as well as a key additional domain decomposition. GTC-P's multiple levels of parallelism, including inter-node 2D domain decomposition and particle decomposition, as well as intra-node shared memory partition and vectorization have enabled pushing the scalability of the PIC method to extreme computational scales. In this paper, we describe the methods developed to build a highly parallelized PIC code across a broad range of supercomputer designs. This particularly includes implementations on heterogeneous systems using NVIDIA GPU accelerators and Intel Xeon Phi (MIC) co-processors and performance comparisons with state-of-the-art homogeneous HPC systems such as Blue Gene/Q. New discovery science capabilities in the magnetic fusion energy application domain are enabled, including investigations of Ion-Temperature-Gradient (ITG) driven turbulence simulations with unprecedented spatial resolution and long temporal duration. Performance studies with realistic fusion experimental parameters are carried out on multiple supercomputing systems spanning a wide range of cache capacities, cache-sharing configurations, memory bandwidth, interconnects and network topologies. Furthermore, these performance comparisons using a realistic discovery-science-capable domain application code provide valuable insights on optimization techniques across one of the broadest sets of current high-end computing platforms worldwide.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2023

An implicit barotropic mode solver for MPAS-ocean using a modern Fortran solver interface

Here, we demonstrate use of a modern Fortran solver interface to manage solver algorithms for an implicit barotropic mode solver in the Model for Predictions Across Scales-Ocean (MPAS-O). ForTrilinos, a Fortran interface to Trilinos that contains a large collection of solver capabilities written in C++, has been implemented in MPAS-O to provide access to a suite of linear solver options. By virtue of the simplified wrapper and interface generator (SWIG) automation tool that generates modern Fortran interfaces to C++ code, we were able to implement the Fortran solver interface in MPAS-O using a familiar Fortran coding style while minimizing performance degradation. The ForTrilinos solver interface is written within MPAS-O’s time stepping modules as a subroutine in conjunction with MPAS-O code. Applied to an idealized ocean and a high-resolution realistic ocean test case, parallel performance of ForTrilinos solvers is examined. It is found that parallel scalability of the ForTrilinos solvers is highly dependent on the number of global synchronization points per solver iteration in each iterative solver algorithm. ForTrilinos solvers perform best compared to the Fortran hand-crafted (FHC) solver when the amount of work per processor is large enough. However, parallel scalability is better with the FHC solver and so when the work per core is modest FHC outperforms ForTrilinos. The intercomparison between the ForTrilinos and FHC solvers reveals that this performance hit in the ForTrilinos solver mostly comes from the global synchronization process, while suggesting that the matrix-vector multiplication process in the FHC solver needs to be optimized for better performance.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2019

Genetics of adaptation in modern chicken

We carried out whole genome resequencing of 127 chicken including red jungle fowl and multiple populations of commercial broilers and layers to perform a systematic screening of adaptive changes in modern chicken ( Gallus gallus domesticus ). We uncovered >21 million high quality SNPs of which 34% are newly detected variants. This panel comprises >115,000 predicted amino-acid altering substitutions as well as 1,100 SNPs predicted to be stop-gain or -loss, several of which reach high frequencies. Signatures of selection were investigated both through analyses of fixation and differentiation to reveal selective sweeps that may have had prominent roles during domestication and breed development. Contrasting wild and domestic chicken we confirmed selection at the BCO2 and TSHR loci and identified 34 putative sweeps co-localized with ALX1 , KITLG , EPGR , IGF1 , DLK1 , JPT2 , CRAMP1 , and GLI3 , among others. Analysis of enrichment between groups of wild vs. commercials and broilers vs. layers revealed a further panel of candidate genes including CORIN , SKIV2L2 implicated in pigmentation and LEPR , MEGF10 and SPEF2 , suggestive of production-oriented selection. SNPs with marked allele frequency differences between wild and domestic chicken showed a highly significant deficiency in the proportion of amino-acid altering mutations (P<2.5×10 -6 ). The results contribute to the understanding of major genetic changes that took place during the evolution of modern chickens and in poultry breeding.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2018

Selection Signatures Underlying Dramatic Male Inflorescence Transformation During Modern Hybrid Maize Breeding

Inflorescence capacity plays a crucial role in reproductive fitness in plants, and in production of hybrid crops. Maize is a monoecious species bearing separate male and female flowers (tassel and ear, respectively). The switch from open-pollinated populations of maize to hybrid-based breeding schemes in the early 20th century was accompanied by a dramatic reduction in tassel size, and the trend has continued with modern breeding over the recent decades. The goal of this study was to identify selection signatures in genes that may underlie this dramatic transformation. Using a population of 942 diverse inbred maize accessions and a nested association mapping population comprising three 200-line biparental populations, we measured 15 tassel morphological characteristics by manual and image-based methods. Genome-wide association studies identified 242 single nucleotide polymorphisms significantly associated with measured traits. We compared 41 unselected lines from the Iowa Stiff Stalk Synthetic (BSSS) population to 21 highly selected lines developed by modern commercial breeding programs, and found that tassel size and weight were reduced significantly. We assayed genetic differences between the two groups using three selection statistics: cross population extended haplotype homozogysity, cross-population composite likelihood ratio, and fixation index. All three statistics show evidence of selection at genomic regions associated with tassel morphology relative to genome-wide null distributions. These results support the tremendous effect, both phenotypic and genotypic, that selection has had on maize male inflorescence morphology.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Modernization Plans for Fermilab’s Accelerator Control System

The control system, ACNET, for Fermilab’s accelerator complex has enabled the lab’s scientific mission for decades. ACNET has evolved over the years to incorporate new technologies. However, as Fermilab prepares to enter a new era with its PIP-II superconducting linear accelerator, ACNET is at a crossroads. There are several components that are either obsolete or outdated, or certainly will be over the long lifetime of PIP-II. We have begun a plan to modernize our accelerator control system. This paper discusses some of the obsolete hardware and software that needs to be replaced, and lays out options and technologies that we might adopt as part of this modernization effort.

43 PARTICLE ACCELERATORS↗