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At least 163 records · Page 9

April 2020 Darshan counters from the Summit supercomputer

This dataset is the Darshan counters collected from the Summit supercomputer in a month of April 2020. 1. Description of methods used for collection/generation of data: Job submitted on Summit HPC system when completed successfully and has made I/O calls (captured by Darshan tool) writes a Darshan log file on alpine filesystem. One job can have multiple `jsrun` commands and Darshan will generate separate logs each log corresponding to an `jsrun` command, so a job can have one or more Darshan logs associated with it. 2. Methods for processing the data: To process the data, we first use `darshan-util` tool to parse the Darshan logs. Then we restructure the logs and merge data from multiple Darshan logs if they belong to the same Summit job.

97 MATHEMATICS AND COMPUTING↗

Data Locality Enhancement of Dynamic Simulations for Exascale Computing (Final Report)

The development of modern processors exhibits two trends that complicate the optimizations of modern software. The first is the increasing sensitivity of processors' throughput to irregularities in computation. With more processors produced through a massive integration of simple cores, future systems will increasingly favor regular data-level parallel computations, but deviate from the needs of applications with complex patterns. Some evidences are already shown on Graphic Processing Units (GPU): Irregular data accesses (e.g., indirect references A[D[i]]) and conditional branches are limiting many GPU applications' performance at a level an order of magnitude lower than the peak of GPU. The second hardware trend is the growing gap between memory bandwidth and the aggregate speed—that is, the sum of all cores' computing power—of a Chip Multiprocessor (CMP). Despite the capped growth of the peak CPU speed, the aggregate speed of a CMP keeps increasing as more cores get into a single chip. It is expected that by 2018, node concurrency in an exascale system will increase by hundreds of times, whereas, memory bandwidth will expand by only 10 to 20 times. Consequently, data movement and storage is expected to consume more than 70% of the total system power. Bridging this gap is difficult; the complexities of modern CMP memory hierarchy make it even harder: Data cache becomes shared among computing units, and the sharing is often non-uniform—whether two computing units share a cache depends on their proximity and the level of the cache. On the recent IBM Power7 architecture, for instance, four hardware contexts (or SMT threads) in a core share the entire memory hierarchy, all cores in one chip share an on-chip L3 cache, and cores across chips share L3 and main memory through off-chip connections. These two trends complicate the translation of computing power into performance, especially for a program with either intensive data accesses or complex patterns in data accesses or control flow paths. Unfortunately, both attributes present and will persist in a class of important applications. For instance, many scientific simulations deal with a large volume of data. And meanwhile, as most real-world processes are non-uniform and evolving (e.g., the evolution of a galaxy or the process of a drug injection), both the computations and data accesses of these programs tend to be irregular and dynamically changing. Currently, the lack of support to these applications on modern CMP severely limits their performance. On GPU, as our recent study shows and other studies echo, performance enhancement of a factor of integers is possible when memory accesses or control flows are streamlined for a set of GPU applications. On multicore CPU, our studies show that traditional locality enhancement, for being oblivious to the new features of multicore memory hierarchy, may even cause large slowdown to data-intensive dynamic applications. The severity of the issues is expected to worsen as the two hardware trends continue. Some recent studies try to match software with the trends, but in a limited scope or manner. For irregularities on GPU, most studies focus on irregularities analyzable through static analysis (e.g., data accesses in regular loops). Dynamic irregularities are harder to address because the needed analysis and transformations typically have to happen at run time. Some other research resorts to hardware extensions, an actual adoption of which is unclear for the entailed space cost and complexity. For data locality, recent years have seen some exploitations of the new memory hierarchy on multicore for performance, but most of them are on process or thread scheduling, rather than program transformations. Our recent study reveals that program-level transformations may magnify the scheduling benefits by a factor of seven, concluding that program-level transformation should play a central role for data locality enhancement on modern CMP. But research in this direction has been sparse, and most have focused on data layout or cache performance modeling, rather than program transformations to match with the new memory hierarchy features. Overall, it is still an open question how to bridge the gap between dynamic computations and the two prominent properties of modern processors. The goal of this project is to develop a set of techniques and software tools to enhance the matching between memory accesses in dynamic simulations and the prominent features of modern and future CMP, alleviating the memory performance issues for petascale and exascale computing. This report summarizes the discoveries and products produced throughout this project. It includes free launch, a new software approach to overcoming the shortcomings of both methods; coherence-free multiview, an approach that allows multiple views of a single data object to co-exist on GPU memory during a GPU kernel execution; algorithmic optimizations to data analytics problems, especially those that involve lots of distance calculations. Supporting dynamic parallelism is important for GPU to benefit a broad range of applications. There are currently two fundamental ways for programs to exploit dynamic parallelism on GPU: a software-based approach with software-managed worklists, and a hardware-based approach through dynamic subkernel launches. Neither is satisfactory. The former is complicated to program and is often subject to some load imbalance; the latter suffers large runtime overhead. In this work, we propose free launch, a new software approach to overcoming the shortcomings of both methods. It allows programmers to use subkernel launches to express dynamic parallelism. It employs a novel compiler-based code transformation named subkernel launch removal to replace the subkernel launches with the reuse of parent threads. Coupled with an adaptive task assignment mechanism, the transformation reassigns the tasks in the subkernels to the parent threads with a good load balance. The technique requires no hardware extensions, immediately deployable on existing GPUs. It keeps the programming convenience of the subkernel launch-based approach while avoiding its large runtime overhead. Meanwhile, its superior load balancing makes it outperform manual worklist-based techniques by 3X on average. The work was published at the 48th Annual IEEE/ACM International Symposium on Microarchitecture (Micro'2015). A Graphic Processing Unit (GPU) system is typically equipped with many types of memory (e.g., global, constant, texture, shared, cache). Data placement determines what data are placed on which type of memory, essential for GPU memory performance. Prior optimizations of data placement always require a single view of a data object on memory, which limits the optimization effectiveness. In this work, we propose coherence-free multiview, an approach that allows multiple views of a single data object to co-exist on GPU memory during a GPU kernel execution. We demonstrate that under certain conditions, the multiple views can remain incoherent while facilitating enhanced data placement. We present a theorem and some compiler support to ensure the soundness of the usage of coherence-free multiview. We further develop reference-discerning data placement, a new way to enhance data placements on GPU. It enables more flexible data placements by using coherence-free multiview to leverage the slack in coherence requirement of some GPU programs. Experiments on three types of GPU systems show that, with less than 200KB space cost, the new data placement technique can provide a 1.6X average (up to 4.27X) speedup. In addition, we have examined algorithmic optimizations to data analytics problems, especially those that involve lots of distance calculations. Computing distances among data points is an essential part of many important algorithms in data analytics, graph analysis, and other domains. In each of these domains, developers have spent significant manual effort optimizing algorithms, often through novel applications of the triangle equality, in order to minimize the number of distance computations in the algorithms. In this work, we observe that many algorithms across these domains can be generalized as an instance of a generic distance-related abstraction. Based on this abstraction, we derive seven principles for correctly applying the triangular inequality to optimize distance-related algorithms. Guided by the findings, we develop Triangular OPtimizer (TOP), the first software framework that is able to automatically produce optimized algorithms that either matches or outperforms manually designed algorithms for solving distance-related problems. TOP achieves up to 237x speedups and 2.5X on average. The work has been published at the 32nd International Conference on Machine Learning (ICML'15) and the 41st International Conference on Very Large Data Bases (VLDB'15).

42 ENGINEERING↗

Usage Pattern-Driven Dynamic Data Layout Reorganization

As scientific simulations and experiments move toward extremely large scales and generate massive amounts of data, the data access performance of analytic applications becomes crucial. A mismatch often happens between write and read patterns of data accesses, typically resulting in poor read performance. Data layout reorganization has been used to improve the locality of data accesses. However, current data reorganizations are static and focus on generating a single (or set of) optimized layouts that rely on prior knowledge of exact future access patterns. We propose a framework that dynamically recognizes the data usage patterns, replicates the data of interest in multiple reorganized layouts that would benefit common read patterns, and makes runtime decisions on selecting a favorable layout for a given read pattern. This framework supports reading individual elements and chunks of a multi-dimensional array of variables. Our pattern-driven layout selection strategy achieves multi-fold speedups compared to reading from the original dataset.

97 MATHEMATICS AND COMPUTING↗

Angular Momentum in Rotating Superfluid Droplets

The angular momentum of rotating superfluid droplets originates from quantized vortices and capillary waves, the interplay between which remains to be uncovered. Here, the rotation of isolated submicrometer superfluid 4 He droplets is studied by ultrafast x-ray diffraction using a free electron laser. The diffraction patterns provide simultaneous access to the morphology of the droplets and the vortex arrays they host. In capsule-shaped droplets, vortices form a distorted triangular lattice, whereas they arrange along elliptical contours in ellipsoidal droplets. The combined action of vortices and capillary waves results in droplet shapes close to those of classical droplets rotating with the same angular velocity. The findings are corroborated by density functional theory calculations describing the velocity fields and shape deformations of a rotating superfluid cylinder.

O'Connell, Sean M.O.↗

US NDC Modernization: Service Oriented Architecture Study Status

This report is a progress update on the USNDC Modernization Service Oriented Architecture (SOA) study describing results from Inception Iteration 1, which occurred between October 2012 and March 2013. The goals during this phase are 1) discovering components of the system that have potential service implementations, 2) identifying applicable SOA patterns for data access, service interfaces, and service orchestration/choreography, and 3) understanding performance tradeoffs for various SOA patterns

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗

Spatially Characterizing Effective Timber Supply

The structure of a computer-oriented cartographic model for assessing roundwood supply for generation of base load electricity is discussed. The model provides an analytical procedure for coupling spatial information of harvesting economics and owner willingness to sell stumpages. Supply is characterized in terms of standing timber; of accessibility considering various harvesting and hauling factors; and of availability as affected by ownership and residential patterns. Factors governing accessibility to timber include effective harvesting distance to haulic roads as modified by barriers and slopes. Haul distance is expressed in units that take into account the relative ease of travel along various road types to a central processing facility. Areas of accessible timber are grouped into spatial units, termed 'timbersheds', of common access to particular haul road segments that belong to unique 'transport zones'. Timber availability considerations include size of ownership parcels, housing density and excluded areas. The analysis techniques are demonstrated for a cartographic data base in western Massachusetts.

Berry, J. K.↗

What Use Patterns Were Observed for PEV Drivers at Publicly Accessible AC Level 2 EVSE Sites?

The EV Project deployed over 4,000 ACL2 EVSE for drivers to charge their plug-in electric vehicle (PEV) when away-from-home. The vast majority of these EVSE stations were installed to be available to all PEV drivers at publicly accessible locations. Some were also deployed for use at workplaces and fleets. This paper examines only the use patterns of PEV drivers using the EVSE intended to be publicly accessible.

33 ADVANCED PROPULSION SYSTEMS↗

Geospatial Analysis of Built Infrastructure and Modeled Household Driving Patterns

The level of access to opportunities for a location can be quantified in the amount of time it takes to travel from a departure point to the destinations that somebody would want or need to visit. Isochrone maps are geometric representations of the area accessible from a departure point within a set amount of time. Informed in part by the National Household Travel Survey, this report merges location data for amenities and opportunities across six frequent destination categories – employment, education, health, food, community, and transportation – with isochrone maps generated by the TravelTime API, whose departure points are census tract population-weighted centroids. Using a “Points-In-Polygon” analysis, destinations that fall within a census tract’s isochrone are tallied as accessible from the region within one of three time thresholds: 15-, 30-, and 45-minutes by the walking, cycling, public transit, and driving modes of travel. We find that access to a high number of jobs within a typical commute duration is negatively correlated with annual household vehicle miles traveled (VMT). The spatial distribution of our data suggests that the high household VMT frequently seen surrounding the edges of major cities may be related to worker commutes into the city core, and that the high household VMT frequently seen in rural tracts may be related to the longer travel distances required to access a variety of key opportunities from these areas.

99 GENERAL AND MISCELLANEOUS↗

Solvent Immersion Imprint Lithography

The mechanism of polymer disolution was explored for polymer microsystem prototyping, including microfluidics and optofluidics. Polymer films are immersed in a solvent, imprinted and finally brought into contact with a non-modified surface to permanently bond. The underlying polymer-solvent interactions were experimentally and theoretically investigated, and enabled rapid polymer microsystem prototyping. During imprinting, small molecule integration in the molded surfaces was feasible, a principle applied to oxygen sensing. Polystyrene (PS) was employed for microbiological studies at extreme environmental conditions. The thermophile anaerobe Clostridium Thermocellum was grown in PS pore-scale micromodels, revealing a double mean generation lifetime than under ideal culture conditions. Microsystem prototyping through directed polymer dissolution is simple and accessible, while simultaneous patterning, bonding, and surface/volume functionalization are possible in less than one minute.

Environmental Molecular Sciences Laboratory↗

Modeling Distributed Computing Infrastructures for HEP Applications

Predicting the performance of various infrastructure design options in complex federated infrastructures with computing sites distributed over a wide area network that support a plethora of users and workflows, such as the Worldwide LHC Computing Grid (WLCG), is not trivial. Due to the complexity and size of these infrastructures, it is not feasible to deploy experimental test-beds at large scales merely for the purpose of comparing and evaluating alternate designs. An alternative is to study the behaviours of these systems using simulation. This approach has been used successfully in the past to identify efficient and practical infrastructure designs for High Energy Physics (HEP). A prominent example is the Monarc simulation framework, which was used to study the initial structure of the WLCG. New simulation capabilities are needed to simulate large-scale heterogeneous computing systems with complex networks, data access and caching patterns. A modern tool to simulate HEP workloads that execute on distributed computing infrastructures based on the SimGrid and WRENCH simulation frameworks is outlined. Studies of its accuracy and scalability are presented using HEP as a case-study. Hypothetical adjustments to prevailing computing architectures in HEP are studied providing insights into the dynamics of a part of the WLCG and candidates for improvements.

Horzela, Maximilian↗

US NDC Modernization: Service Oriented Architecture Proof of Concept

This report is a progress update on the US NDC Modernization Service Oriented Architecture (SOA) study describing results from a proof of concept project completed from May through September 2013. Goals for this proof of concept are 1) gain experience configuring, using, and running an Enterprise Service Bus (ESB), 2) understand the implications of wrapping existing software in standardized interfaces for use as web services, and 3) gather performance metrics for a notional seismic event monitoring pipeline implemented using services with various data access and communication patterns. The proof of concept is a follow on to a previous SOA performance study. Work was performed by four undergraduate summer student interns under the guidance of Sandia staff.

97 MATHEMATICS AND COMPUTING↗

Satellite Data Applications for Sustainable Energy Transitions

Transitioning to a sustainable energy system poses a massive challenge to communities, nations, and the global economy in the next decade and beyond. A growing portfolio of satellite data products is available to support this transition. Satellite data complement other information sources to provide a more complete picture of the global energy system, often with continuous spatial coverage over targeted areas or even the entire Earth. We find that satellite data are already being applied to a wide range of energy issues with varying information needs, from planning and operation of renewable energy projects, to tracking changing patterns in energy access and use, to monitoring environmental impacts and verifying the effectiveness of emissions reduction efforts. While satellite data could play a larger role throughout the policy and planning lifecycle, there are technical, social, and structural barriers to their increased use. We conclude with a discussion of opportunities for satellite data applications to energy and recommendations for research to maximize the value of satellite data for sustainable energy transitions.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

Performance of the Galley Parallel File System

As the input/output (I/O) needs of parallel scientific applications increase, file systems for multiprocessors are being designed to provide applications with parallel access to multiple disks. Many parallel file systems present applications with a conventional Unix-like interface that allows the application to access multiple disks transparently. This interface conceals the parallism within the file system, which increases the ease of programmability, but makes it difficult or impossible for sophisticated programmers and libraries to use knowledge about their I/O needs to exploit that parallelism. Furthermore, most current parallel file systems are optimized for a different workload than they are being asked to support. We introduce Galley, a new parallel file system that is intended to efficiently support realistic parallel workloads. Initial experiments, reported in this paper, indicate that Galley is capable of providing high-performance 1/O to applications the applications that rely on them. In Section 3 we describe that access data in patterns that have been observed to be common.

Nieuwejaar, Nils↗

Satellite Data Applications for Sustainable Energy Transitions

Transitioning to a sustainable energy system poses a massive challenge to communities, nations, and the global economy in the next decade and beyond. A growing portfolio of satellite data products is available to support this transition. Satellite data complement other information sources to provide a more complete picture of the global energy system, often with continuous spatial coverage over targeted areas or even the entire Earth. We find that satellite data are already being applied to a wide range of energy issues with varying information needs, from planning and operation of renewable energy projects, to tracking changing patterns in energy access and use, to monitoring environmental impacts and verifying the effectiveness of emissions reduction efforts. While satellite data could play a larger role throughout the policy and planning lifecycle, there are technical, social, and structural barriers to their increased use. We conclude with a discussion of opportunities for satellite data applications to energy and recommendations for research to maximize the value of satellite data for sustainable energy transitions.

energy↗

TriC: Distributed-memory Triangle Counting by Exploiting the Graph Structure

Graph analytics has emerged as an important tool in the analysis of large scale data from diverse application domains such as social networks, cyber security and bioinformatics. Counting the number of triangles in a graph is a fundamental kernel with several applications such as detecting the community structure of a graph or in identifying important vertices in a graph. The ubiquity of massive datasets is driving the need to scale graph analytics on parallel systems. However, numerous challenges exist in efficiently parallelizing graph algorithms, especially on distributed-memory systems. Irregular memory accesses and communication patterns, low computation to communication ratios, and the need for frequent synchronization are some of the leading challenges. In this paper, we present TriC, our distributed-memory implementation of triangle counting in graphs using the Message Passing Interface (MPI), as a submission to the 2020 GraphChallenge competition. Using a set of synthetic and real-world inputs from the challenge, we demonstrate a speedup of up to 90x relative to previous work on 32 processor-cores of a NERSC Cori node. We also provide details from distributed runs with up to8192 processes along with strong scaling results. The observations presented in this work provide an understanding of the system-level bottlenecks at scale that specifically impact sparse-irregular workloads and will therefore benefit other efforts to parallelize graph algorithms.

Halappanavar, Mahantesh↗

Global Pattern of Nasopharyngeal Cancer: Correlation of Outcome With Access to Radiation Therapy

Purpose: This study aimed to estimate the treatment outcome of nasopharyngeal cancer (NPC) across the world and its correlation with access to radiation therapy (RT). Methods and Materials: The age-standardized mortality (ASM) and age-standardized incidence (ASI) rates of NPC from GLOBOCAN (2012) were summarized, and [1−(ASM/ASI)] was computed to give the proxy relative survival (RS). Data from the International Atomic Energy Agency (IAEA) and the World Bank were used to assess the availability of RT in surrogate terms: the number of RT equipment units and radiation oncologists per million population. Results: A total of 112 countries with complete valid data were analyzed, and the proxy RS varied widely from 0% to 83% (median, 50%). Countries were categorized into Good, Median, and Poor outcome groups on the basis of their proxy RS (<45%, 45%-55%, and >55%). Eighty percent of new cases occurred in the Poor outcome group. Univariable linear regression showed a significant correlation between outcome and the availability of RT: proxy RS increased at 3.4% (P<.001) and 1.5% (P=.001) per unit increase in RT equipment and oncologist per million population, respectively. The median number of RT equipment units per million population increased significantly from 0.5 in the Poor, to 1.5 in the Median, to 4.6 in the Good outcome groups, and the corresponding number of oncologists increased from 1.1 to 3.3 to 7.1 (P<.001). Conclusions: Nasopharyngeal cancer is a highly treatable disease, but the outcome varies widely across the world. The current study shows a significant correlation between survival and access to RT based on available surrogate indicators. However, the possible reasons for poor outcome are likely to be multifactorial and complex. Concerted international efforts are needed not only to address the fundamental requirement for adequate RT access but also to obtain more comprehensive and accurate data for research to improve cancer outcome.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

Approximating Effect Of Spherical Radiation Pattern

Time-division multiple-access TDMA multichannels radio communication system implements scheme of temporal and spatial multiplexing of signals to approximate effect of spherical antenna radiation pattern. Signal to be transmitted sped up by factor of n and transmitted in n replicas via n antennas. During reception, incoming signal processed by use of maximum-signal-selection or diversity-reception demodulated-signal-combining technique.

Sickles, Louis, II↗

Pattern-aware prefetching using parallel log-structured file system

Techniques are provided for pattern-aware prefetching using a parallel log-structured file system. At least a portion of one or more files is accessed by detecting at least one pattern in a non-sequential access of the one or more files; and obtaining at least a portion of the one or more files based on the detected at least one pattern. The obtaining step comprises, for example, a prefetching or pre-allocation of the at least the portion of the one or more files. A prefetch cache can store the portion of the one or more obtained files. The cached portion of the one or more files can be provided from the prefetch cache to an application requesting the at least a portion of the one or more files.

Bent, John M.↗