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At least 91 records · Page 5

GPU-Accelerated Drug Discovery with Docking on the Summit Supercomputer: Porting, Optimization, and Application to COVID-19 Research

Protein-ligand docking is an in silico tool used to screen potential drug compounds for their ability to bind to a given protein receptor within a drug-discovery campaign. Experimental drug screening is expensive and time consuming, and it is desirable to carry out large scale docking calculations in a high-throughput manner to narrow the experimental search space. Few of the existing computational docking tools were designed with high performance computing in mind. Therefore, optimizations to maximize use of high-performance computational resources available at leadership-class computing facilities enables these facilities to be leveraged for drug discovery. Here we present the porting, optimization, and validation of the AutoDock-GPU program for the Summit supercomputer, and its application to initial compound screening efforts to target proteins of the SARS-CoV-2 virus responsible for the current COVID-19 pandemic.

LeGrand, Scott↗

Understanding GPU Memory Corruption at Extreme Scale: The Summit Case Study

GPU memory corruption and in particular double-bit errors (DBEs) remain one of the least understood aspects of HPC system reliability. Albeit rare, their occurrences always lead to job termination and can potentially cost thousands of node-hours, either from wasted computations or as the overhead from regular checkpointing needed to minimize the losses. As supercomputers and their components simultaneously grow in scale, density, failure rates, and environmental footprint, the efficiency of HPC operations becomes both an imperative and a challenge. We examine DBEs using system telemetry data and logs collected from the Summit supercomputer, equipped with 27,648 Tesla V100 GPUs with 2nd-generation high-bandwidth memory (HBM2). Using exploratory data analysis and statistical learning, we extract several insights about memory reliability in such GPUs. We find that GPUs with prior DBE occurrences are prone to experience them again due to otherwise harmless factors, correlate this phenomenon with GPU placement, and suggest manufacturing variability as a factor. On the general population of GPUs, we link DBEs to short- and long-term high power consumption modes while finding no significant correlation with higher temperatures. We also show that the workload type can be a factor in memory’s propensity to corruption.

Oles, Vlad↗

Long Term Per-Component Power and Thermal Measurements of the OLCF Summit System

As we move into the exascale era, the power and energy footprints of high-performance computing (HPC) systems have grown significantly larger. Due to the harsh power and thermal conditions the system, components are exposed to extreme operating conditions. Operation of such modern HPC systems requires deep insights into long term system behavior to maintain its efficiency as well as its longevity. To help the HPC community to gain such insights, we provide a dataset that records the long-term power and thermal behavior of the 200PF pre-exascale supercomputer at the Oak Ridge Leadership Computing Facility (OLCF), Summit. This system is an IBM AC922 based system that has 9,252 IBM Power9 CPUs and 27,756 Nvidia V100 GPUs and can consume up to 13MW power at peak. Heat removal is performed using medium temperature direct liquid cooling and rear-door heat exchanger based secondary cooling loop. Originally extracted from a high-resolution (1Hz) per-component (GPUs, CPUs) measurements from the system, we primarily provide a dataset that has 10-second and 1-minute mean power and thermal measurements selected from five month-long segments over the course of 2020 (January and August), 2021 (February and August), and 2022 (January). For convenience, we also provide various sub datasets randomly sampled from the time and space (hosts) of the cluster. Further details and example code for analysis can be found in the following GitHub repository: https://github.com/at-aaims/summit_power_and_thermal_data

97 MATHEMATICS AND COMPUTING↗

The Suisun Summit 2022: Emerging Themes and Open Questions in qEEG and Neurotherapies

The Suisun Summit 2022 was a gathering of 70 clinicians, educators, and researchers in quantitative electroencephalography and neurofeedback. During this 5-day event, several themes emerged in talks or discussion groups: EEG/qEEG Reading Skills; Medication Effects and Pharmaco-EEG; Technological Advancements; Emerging Concerns; and Growing Community Prestige through Research. Participants were asked to summarize what they believed to be the most important messages from the event to share with colleagues who were not in attendance, resulting in this review. A unifying concept for all the themes was a desire for higher quality, standardized EEG/qEEG education that provides depth as well as breadth. Models of clinical care that encourage open communication with prescribers and functional medicine specialists were strongly emphasized. Abstracts from all presentations are attached in Addendum B.

60 APPLIED LIFE SCIENCES↗

Pacific Northwest Cyber Summit: Summary Report from March 26, 2013 Workshop, Seattle, Washington

On March 26, 2013, the Snohomish County Public Utility District (PUD) and the U.S. Department of Energy’s (DOE’s) Pacific Northwest National Laboratory (PNNL) jointly hosted the Pacific Northwest Cyber Summit with the DOE’s Office of Electricity Delivery and Energy Reliability, the White House, Washington State congressional delegation, Washington State National Guard, and regional energy companies.

24 POWER TRANSMISSION AND DISTRIBUTION↗

DOE Big Idea Summit III: Solving the Information Technology Challenge Beyond Moore's Law: A New Path to Scaling

This report captures the initial conclusions of the DOE seven National Lab team collaborating on the “Solving the Information Technology Energy Challenge Beyond Moore’s Law” initiative from the DOE Big Idea Summit III held in April of 2016. The seven Labs held a workshop in Albuquerque, NM in late July 2016 and gathered 40 researchers into 5 working groups: 4 groups spanning the levels of the co-design framework shown below, and a 5th working group focused on extending and advancing manufacturing approaches and coupling their constraints to all of the framework levels. These working groups have identified unique capabilities within the Labs to support the key challenges of this Beyond Moore’s Law Computing (BMC) vision, as well as example first steps and potential roadmaps for technology development.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

Summit on HPC ML Algorithms and Human Systems Summary

The purpose of this document is to provide an initial overview of (new) information regarding the gaps in DOE's work on High Performance Computing(HPC), Machine Learning and Algorithms (IVILA) and Human Systems(HS) emerging from the Sep. 2018 Summit, and to briefly forecast the attendee community's next steps.

97 MATHEMATICS AND COMPUTING↗

The 2018 U.S. Nuclear Posture Review, NATO's Brussels Summit and Beyond

The NATO allies must react to the nuclear policy and posture choices of the Trump administration. In some respects, there are good reasons why the Alliance should move closer to the Trump Administration. In other cases, Allies should seek agreement on slightly different policies. While it is unrealistic to expect that the NATO allies will be able to resolve all the questions posed by the 2018 Nuclear Posture Review at the Summit in Brussels, there are several things that they should be able to agree upon. This includes more specific language about the Russia nuclear challenges, general recognition of U.S. efforts to bolster NATO nuclear deterrence posture, a clear language on the value of nuclear sharing arrangements, and reaffirmation of some of NATO’s statements on arms control and disarmament. Yet, a signal in Brussels of NATO’s efforts to build a new nuclear consensus would be stronger if heads of state and government initiated a broader process aimed at developing a comprehensive deterrence and defense strategy that would treat nuclear deterrence as an integral part of a multi-domain approach.

98 NUCLEAR DISARMAMENT, SAFEGUARDS, AND PHYSICAL P↗

Evaluation of PETSc on a Heterogeneous Architecture, the OLCF Summit System: Part II - Basic Communication Performance

Nearest-neighbor communication is at the heart of many high-performance parallel computations. We report on the performance of such communication on the Oak Ridge Leadership Computing Facility system Summit in the context of the PETSc communication module. The analysis in this report includes basic Ping-Pong point-to-point communication and regular and irregular nearest-neighbor communication.

97 MATHEMATICS AND COMPUTING↗

Accelerate M-TIP on GPUs and deploy to Summit and NERSC-9 (against simulated data) WBS 2.2.4.05 ExaFEL, Milestone ADSE13-199

We evaluated the orientation matching step in the M-TIP SPI workflow for potential offloading to accelerators. We ported the code to GPUs, benchmarked it, optimized and down-selected the best versions. The accelerated version of the orientation matching code that was developed at LANL (LANL GPU v3) is 34-55X faster than sequential, 2.4-4.9X faster than the fastest OpenMP open source version we found (FAISS OpenMP) and 1.5-4X faster than the fastest GPU open source version we found (FAISS GPU). Summit single-node GPU versions were somewhat faster than Cori GPU. Image size plays a role; mid-range image sizes take more time. The LANL CUDA multi-node, multi-GPU implementation shows mostly linear strong scaling. I/O also plays a large role; splitting data into parts improves read time and burst buffers dramatically improve read times. This work will be integrated into the M-TIP workflow as part of the next milestone ADSE13-193.

97 MATHEMATICS AND COMPUTING↗

Hybridization Assessment of Trybrid Pumped Storage Hydropower System—Part 1: A Case Study of Corral Summit

This report is a part of the deliverables for technical assistance provided to Cat Creek Energy for the Coral Summit Trybrid (Triple Hybrid-Pumped Storage Hydropower, Battery Energy Storage System, and photovoltaic solar energy) energy project. This report explores the operational benefits and challenges of hybridizing an open loop PSH (200MW) located at Mackay, Custer County, Idaho with solar PV (Ground mount 300MW and floating 40MW) and battery (720MWhr). This document reports two activities performed as a part of the hybridization assessment task 1) optimal resource allocation and energy management strategy, and 2) power quality and reliability assessment. From optimal resource allocation and energy management strategy (activity 1), the following key findings can be observed: • Conventional PSH (CPSH) with two reversible pump turbines and separate penstocks can provide required flexibility equivalent to that from two ternary PSH with separate penstock. With single unit CPSH, upper reservoir head cannot be maintained accurately, the variation of water level is rapid and pump mode flexibility is not available. These disadvantages can be overcome by single unit TPSH. However, using two CPSH units with separate penstocks also overcome these disadvantages with the formation of the hydraulic short circuit between two conventional units. • Flooding of the lower reservoir is a severe concern when considering continuous operation for black start. This limits the duration of continuous operation from PSH alone to around 50 hours. Due to the complementary PV and battery action, the duration of continuous operation and smooth power output can be extended. • An optimization problem is framed that maximizes the power output on an hourly basis while minimizing constraint violations and respecting seasonal variations of solar PV and load profiles . Two value streams, arbitrage and baseload generation are served by this profile. It was uncovered that for smooth power output during regular operation, PV curtailment will be required, or the battery capacity needs to be increased above 90MW to accommodate additional PV. From power quality and reliability assessment (activity 2) the following takeaway points can be observed: • The Trybrid, when integrated at the Lost River bus, and limited to 250MW in generation mode and -150MW in the pump mode, causes no violation of voltage or flow.

13 - HYDRO ENERGY↗

Mineralogy of three slightly palagonitized basaltic tephra samples from the summit of Mauna Kea, Hawaii

The paper characterizes the mineralogy and spectral properties of three slightly palagonitized basaltic tephra samples collected near the summit of Mauna Kea in order to contribute to the basis for inferring mineralogy and processes for Martian surface materials. The mineralogy of size fractions of these samples is examined by diffuse reflectance and FIR spectroscopy, optical microscopy, X-ray diffraction, Moessbauer spectroscopy, magnetic analysis, EMPA, TEM, and SEM. For the 20-1000 micron size fraction, sample HWMK11 (red) is essentially completely oxidized and has a hematite (Ti-hematite) pigment dispersed throughout the silicate matrix. Sample HWMK12 (black) has the lowest proportion of ferric-bearing phases and is thus least weathered. For HWMK11, the amount of hematite is essentially constant, and mica is present only in the coarse clay-sized fraction; smectites are low in structural Fe.

Golden, D. C.↗

Seasonal and Interannual Variations of Ice Sheet Surface Elevation at the Summit of Greenland: Observed and Modeled

Observed seasonal and interannual variations in the surface elevation over the summit of the Greenland ice sheet are modeled using a new temperature-dependent formulation of firn-densification and observed accumulation variations. The observed elevation variations are derived from ERS (European Remote Sensing)-1 and ERS-2 radar altimeter data for the period between April 1992 and April 1999. A multivariate linear/sine function is fitted to an elevation time series constructed from elevation differences measured by radar altimetry at orbital crossovers. The amplitude of the seasonal elevation cycle is 0.25 m peak-to-peak, with a maximum in winter and a minimum in summer. Inter-annually, the elevation decreases to a minimum in 1995, followed by an increase to 1999, with an overall average increase of 4.2 cm a(exp -1) for 1992 to 1999. Our densification formulation uses an initial field-density profile, the AWS (automatic weather station) surface temperature record, and a temperature-dependent constitutive relation for the densification that is based on laboratory measurements of crystal growth rates. The rate constant and the activation energy commonly used in the Arrhenius-type constitutive relation for firn densification are also temperature dependent, giving a stronger temperature and seasonal amplitudes about 10 times greater than previous densification formulations. Summer temperatures are most important, because of the strong non-linear dependence on temperature. Much of firn densification and consequent surface lowering occurs within about three months of the summer season, followed by a surface build-up from snow accumulation until spring. Modeled interannual changes of the surface elevation, using the AWS measurements of surface temperature and accumulation and results of atmospheric modeling of precipitation variations, are in good agreement with the altimeter observations. In the model, the surface elevation decreases about 20 cm over the seven years due to more compaction driven by increasing summer temperatures. The minimum elevation in 1995 is driven mainly by a temporary accumulation decrease and secondarily by warmer temperatures. However, the overall elevation increase over the seven years is dominated by the accumulation increase in the later years.

Zwally, H. Jay↗

Interannual Variations of Shallow Firn Temperature at Greenland Summit

Firn-temperature profiles are calculated in a thermal model using continuous surface temperatures derived from Automatic Weather Station (AWS) data and passive microwave data in the Greenland Summit region during the period 1987-1999. The results show that significant interannual variations of mean summer (June to August) and annual temperatures occur in the top 15 m, in addition to the normal seasonal cycle of firn temperature. At 5 m depth, the seasonal cycle is damped to 13% of the surface seasonal amplitude, but even at 15 m about 1% or 0.6 C of the seasonal cycle persists. Both summer and mean annual temperatures decrease from 1987 to 1992, followed by a general increasing trend. Interannual variability is 5 C at the surface, but only is only dampened to 3.2 C at 10 m depth and 0.7 C at 15 m depth. Dampening of the interannual variability with depth is slower than dampening of the seasonal cycle, because of the longer time constant of the interannual variation. The warmer spring and summer temperatures experienced in the top 5 m, due to both the seasonal cycle and interannual variations, affect the rate of firn densification, which is non-linearly dependent on temperature. During the 12 year period 1987-1999, the mean annual surface temperature is -29.2 C, and the mean annual 15 m temperature is -30. 1 C, which is more than 1 C warmer than a 15-m borehole temperature representing the period of about 1959 and warmer than the best-fit temperature history by Alley and Koci back to 1500 A.D..

Jun, Li↗

Olympus: The Ultimate Summit for Science

High above the world-class observatories that dot Hawaii's dormant Mauna Kea volcano, floating farther yet over the hostile and nearly inaccessible peaks of Mt. Everest, lies a summit waiting to be conquered. Here above the clouds and city lights and over 99.7% of the atmosphere is a platform on the edge of space, home to a broad range of astronomy and physics experiments. Today, balloons are lifting experiments longer, higher and more inexpensively than ever before, and returning them safely to Earth for reuse. Week-long flights at altitudes of approximately 35 kilometers carrying payloads in excess of several tons are the norm. NASA now plans to extend this platform and create a new generation of balloons capable of staying afloat with such cargo for 100 days and ultimately 1,000 days. What do some scientists hope to accomplish with 100 or even 1,000 days at the edge of space? To name but a few proposals on the table: Jupiter-size planet searches, large-aperture solar astronomy, large-aperture infrared astronomy, cosmic-ray investigations, long-duration Earth science missions, and hard x-ray imaging experiments. Olympus defines a new era in scientific ballooning. Advances in material science and trajectory control are enabling revolutionary capabilities. Very large scientific payloads can now be reliably launched and retrieved for reflight at a range of altitudes. Balloon flight still remains a fraction of the cost of a rocket launch. The ultra long duration balloon, with its 100-day maiden flight planned for 2001, provides a long-term facility in a near-space environment for many types of science. This is a stratospheric mountaintop well worth the climb.

Kelly, Darrell↗

A WOUND CARE AND INTRAVENOUS ACCESS SUMMIT FOR ON-ORBIT CARE

Wound care issues and the ability to establish intravenous (IV) access among injured or ill crew members are a source of concern for NASA flight surgeons. Indeed, the microgravity environment and the remote nature of the International Space Station (ISS) pose unique challenges in diagnosing and treating an injured astronaut. Therefore, it is necessary to identify and adapt the best evidence based terrestrial practices regarding wound care, hemostasis, and IV access for use on the ISS. Methods: A panel of consultants was convened to evaluate the adequacy of the current ISS in-flight medical system for diagnosis and treatment of wounds and establishing IV access by a nonclinician crew medical officer. Participants were acknowledged experts in terrestrial wound care and/or operational medicine. Prior to the meeting, each panelist was encouraged to participate in a pre-summit online forum. Results: Eight external experts participated in a face-to-face meeting held at NASA-Johnson Space Center. Recommendations were made to augment the space station pharmacopoeia, as well as current wound care diagnostic, therapeutic, and deorbit criteria protocols. Additionally, suggestions were offered regarding IV access techniques and devices for use in the microgravity environment. Discussion: The results of the expert panel provide an evidence-based approach to the diagnosis and care of wounds in an injured astronaut on aboard the ISS. The results of the panel underscored the need for further research in wound therapy and IV access devices.

Scheuring, R.↗

Comparison of Satellite, Thermochron and Air Temperatures at Summit, Greenland, During the Winter of 2008/09

Current trends show rise in Arctic surface and air temperatures, including over the Greenland ice sheet where rising temperatures will contribute to increased sea-level rise through increased melt. We aim to establish the uncertainties in using satellite-derived surface temperature for measuring Arctic surface temperature, as satellite data are increasingly being used to assess temperature trends. To accomplish this, satellite-derived surface temperature, or land-surface temperature (LST), must be validated and limitations of the satellite data must he assessed quantitatively. During the 2008/09 boreal winter at Summit, Greenland, we employed data from standard US National Oceanic and Atmospheric Administration (NOAA) air-temperature instruments, button-sized temperature sensors called thermochrons and the Moderate Resolution Imaging Spectroradiometer (MODIS) satellite instrument to (1) assess the accuracy and utility of thermochrons in an ice-sheet environment and (2) compare MODIS-derived LSTs with thermochron-derived surface and air temperatures. The thermochron-derived air temperatures were very accurate, within 0.1+/-0.3 C of the NOAA-derived air temperature, but thermochron-derived surface temperatures were approx. 3 C higher than MODIS-derived LSTs. Though the surface temperature is largely determined by air temperature, these variables can differ significantly. Furthermore, we show that the winter-time mean air temperature, adjusted to surface temperature was approx. 11 C higher than the winter-time mean MODIS-derived LST. This marked difference occurs largely because of satellite-derived LSTs cannot be measured through cloud cover, so caution must be exercised in using time series of satellite LST data to study seasonal temperature trends.

Koenig, Lora S.↗

Comparison of Near-Surface Air Temperatures and MODIS Ice-Surface Temperatures at Summit, Greenland (2008-2013)

We have investigated the stability of the MODerate resolution Imaging Spectroradiometer (MODIS) infrared-derived ice surface temperature (IST) data from Terra for use as a climate quality data record. The availability of climate quality air temperature data (TA) from a NOAA Global Monitoring Division observatory at Greenlands Summit station has enabled this high temporal resolution study of MODIS ISTs. During a 5 year period (July 2008 to August 2013), more than 2500 IST values were compared with 3-minute average TA values derived from the 1-minute data from NOAAs primary 2 m air temperature sensor. These data enabled an expected small offset between air and surface temperatures at this the ice sheet location to be investigated over multiple annual cycles.

Greenland↗