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At least 163 records · Page 9

Flexible HPC Environments [Poster]

New computational paradigms require new tools and environments. A new class of data-analysis tools are available for scientists. These tools do not integrate well with traditional HPC resource management systems. Differing and often conflicting requirements exist. Some fields require validated environments including high energy physics and cosmology. By adopting cloud technologies in an HPC environment we are merging the compute-intensive and data-intensive worlds in one converged system. HPC Systems will support a Larger Set of Technologies. Scientists will be able to leverage the latest tools on HPC resources at previously unavailable scales. User-defined environments will enable rapid experimentation and adoption of emerging tools. HPC systems will support a consolidated workflow from simulation to analysis and discovery. HPC systems will have increased utility to a broader set of users.

97 MATHEMATICS AND COMPUTING↗

Classification of Cloud Particle Imagery and Thermodynamics (COCPIT): A New Databasing Tool for the Characterization of Cloud Particle Images Captured During DOE Field Campaigns

The Department of Energy for decades has explored the earth system and atmosphere through research and deployment of in-situ and remote sensing platforms during field campaigns. Among these datasets exists a vast supply of cloud particle images that provide visual insight into the complex microphysics in the clouds that span our globe. The millions of images collected over decades of deployments provides a unique opportunity to further our understanding of our atmosphere down to the crystal size. This work over the past 5 years has sought to organize these images into digestible datasets that can then be used by scientists to further our understanding of microphysics. A machine learning model was developed that categorizes over 1.5 million images across 11 weather events with over 90% accuracy according to particle type. The database was then extended to include dimensional characteristics of the particle as well as co-location of environmental properties, such as temperature and water content. Then, to initialize the connection between these data and our understanding of how crystals form and grow, weather research and forecasting simulations were run to generate the growth histories of the classified crystals. This research culminates with 2 databases per event: (1) a database of all classified crystals and their dimensional and environmental properties and (2) simulated growth histories of each crystal. Finally, a user interface was created to allow researchers to explore data statistics.

54 ENVIRONMENTAL SCIENCES↗

SpaRC: scalable sequence clustering using Apache Spark

MOTIVATION: Whole genome shotgun based next-generation transcriptomics and metagenomics studies often generate 100-1000 GB sequence data derived from tens of thousands of different genes or microbial species. Assembly of these data sets requires tradeoffs between scalability and accuracy. Current assembly methods optimized for scalability often sacrifice accuracy and vice versa. An ideal solution would both scale and produce optimal accuracy for individual genes or genomes. RESULTS: In this work we describe an Apache Spark-based scalable sequence clustering application, SparkReadClust (SpaRC), that partitions reads based on their molecule of origin to enable downstream assembly optimization. SpaRC produces high clustering performance on transcriptomes and metagenomes from both short and long read sequencing technologies. It reaches near-linear scalability with input data size and number of compute nodes. SpaRC can run on both cloud computing and HPC environments without modification while delivering similar performance. Our findings demonstrate that SpaRC provides a scalable solution for clustering billions of reads from next-generation sequencing experiments, and Apache Spark represents a cost-effective solution with rapid development/deployment cycles for similar large-scale sequence data analysis problems. AVAILABILITY AND IMPLEMENTATION: https://bitbucket.org/berkeleylab/jgi-sparc.

59 BASIC BIOLOGICAL SCIENCES↗

Cloud-Based Demonstration of the Eastern Interconnection Situational Awareness Monitoring System (ESAMS)

This report describes a cloud-based implementation and field demonstration of the Eastern Interconnection Situational Awareness and Monitoring System (ESAMS). ESAMS was developed to support the detection and source localization of forced oscillations using synchrophasor measurements from tie-lines connecting areas served by different reliability coordinators (RCs), so that RCs could better coordinate their response to wide-area events. A previous effort had identified deployment barriers associated with hosting shared situational awareness tools at a single RC. To address these barriers, ESAMS was migrated to Amazon Web Services and evaluated in a six-month field demonstration. ISO New England (ISO-NE) and PJM streamed data to the platform using AWS Direct Connect and a site-to-site VPN, respectively. The resulting multi-utility measurement footprint enabled regional source localization across major portions of the U.S. Eastern Interconnection and supported routine identification of oscillation events. During the final three months of the trial, 24 events above 2 MW/MVAR were detected. The largest detected oscillation approached a 25 MW peak-to-peak amplitude, and the longest persisted intermittently for more than 11 hours. The demonstration also assessed operational considerations—including data transfer volumes, end-to-end latency, and cloud computing costs—and found that network and compute requirements were modest relative to typical cloud capabilities while providing performance comparable to prior on-premises deployments. Overall, the results indicate that cloud hosting can provide a practical path to shared interconnection-wide oscillation monitoring. The cloud ESAMS demonstration establishes a foundation for broader utility participation and for building future wide-area analytics that leverage measurements across organizational boundaries.

Follum, James D.↗

Improving Cyber Situational Understanding

Effective cybersecurity operations require the ability to analyze large amounts of information to assess security risks and formulate defensive strategies against adversaries. This has become more complex in recent years as the sprawl and interconnectivity of devices grows through implementation of virtualization, cloud computing, and Internet of Things (IoT). The amount of data and analysis required for effective cybersecurity command and control decisions far exceeds humans’ capacity to perform manually. We characterize the analysis problem as cyber situational understanding. The research presented to improve cyber situational understanding focuses on vulnerability analysis and threat intelligence. Regarding vulnerabilities, entities must analyze and plan work for between thousands and tens of thousands of software vulnerabilities annually. Entities heavily use network firewalls to limit vulnerability exposure. As a result, some of these vulnerabilities permit exposure to adversarial exploitation, whereas others are inaccessible and therefore present negligible risk of exploitation. Distinguishing between high and low risk software vulnerabilities requires a deep understanding of the vulnerability, network firewall protection, and characteristics of the targeted device. This problem is solved by extracting network service features from vulnerability data features using both machine-learning and natural language processing. Then, the network firewall topology is parsed to determine which vulnerabilities are reachable by adversaries. Ultimately, a state-based safety analysis ascertains which vulnerabilities are unsafe. A related vulnerability analysis problem occurs in cybersecurity operations when associating an entity’s hardware and software assets to public vulnerability databases. Assets often reveal hardware and software through installation artifacts and network service identification, and entities store these artifacts in inventory databases. However, software and hardware vendors apply a standard Common Platform Enumeration (CPE) naming convention when publicly reporting vulnerabilities. Associating these two datasets often requires many hours to days of manual inspection. The proposed solution automates the mapping approach of human analysts using fuzzy matching techniques, natural language processing, and, ultimately, machine learning to present a small set of recommendations for mapping the two datasets. The result significantly reduces human analysis time and reduces the occurrence of false positives in vulnerability notifications. Finally, cyber threat intelligence (CTI) requires associating cyber observable artifacts, such as IP addresses, URIs, and file hashes, with cyber threat tactics, techniques, and procedures. Unfortunately, most CTI data is compartmentalized across multiple organizations and cannot be shared due to the legal and reputational risk with cyber threat being associated with the entity. The approach to solving this problem inovlves using a distributed ledger with anonymous token spending and authentication. This allows a consortium of semi-trusted entities to share the workload of curating CTI for a threat sharing community’s cooperative benefit.

Huff, Philip↗

AP-Cloud: Adaptive Particle-in-Cloud method for optimal solutions to Vlasov–Poisson equation

We propose a new adaptive Particle-in-Cloud (AP-Cloud) method for obtaining optimal numerical solutions to the Vlasov–Poisson equation. Unlike the traditional particle-in-cell (PIC) method, which is commonly used for solving this problem, the AP-Cloud adaptively selects computational nodes or particles to deliver higher accuracy and efficiency when the particle distribution is highly non-uniform. Unlike other adaptive techniques for PIC, our method balances the errors in PDE discretization and Monte Carlo integration, and discretizes the differential operators using a generalized finite difference (GFD) method based on a weighted least square formulation. As a result, AP-Cloud is independent of the geometric shapes of computational domains and is free of artificial parameters. Efficient and robust implementation is achieved through an octree data structure with 2:1 balance. We analyze the accuracy and convergence order of AP-Cloud theoretically, and verify the method using an electrostatic problem of a particle beam with halo. Simulation results show that the AP-Cloud method is substantially more accurate and faster than the traditional PIC, and it is free of artificial forces that are typical for some adaptive PIC techniques.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Mathematics: The Tao of Data Science

The two pieces, "Ten Research Challenge Areas in Data Science" by Jeannette M. Wing and “Challenges and Opportunities in Statistics and Data Science: Ten Research Areas” by Xuming He and Xihong Lin, provide an impressively complete list of data science challenges from luminaries in the field of data science. They have done an extraordinary job, so this response offers a complementary viewpoint from a mathematical perspective and evangelizes advanced mathematics as a key tool for meeting the challenges they have laid out. Notably, we pick up the themes of scientific understanding of machine learning and deep learning, computational considerations such as cloud computing and scalability, balancing computational and statistical considerations, and inference with limited data. We propose that mathematics is an important key to establishing rigor in the field of data science and as such has an essential role to play in its future.

97 MATHEMATICS AND COMPUTING↗

The Magellan Final Report on Cloud Computing

The goal of Magellan, a project funded through the U.S. Department of Energy (DOE) Office of Advanced Scientific Computing Research (ASCR), was to investigate the potential role of cloud computing in addressing the computing needs for the DOE Office of Science (SC), particularly related to serving the needs of mid- range computing and future data-intensive computing workloads. A set of research questions was formed to probe various aspects of cloud computing from performance, usability, and cost. To address these questions, a distributed testbed infrastructure was deployed at the Argonne Leadership Computing Facility (ALCF) and the National Energy Research Scientific Computing Center (NERSC). The testbed was designed to be flexible and capable enough to explore a variety of computing models and hardware design points in order to understand the impact for various scientific applications. During the project, the testbed also served as a valuable resource to application scientists. Applications from a diverse set of projects such as MG-RAST (a metagenomics analysis server), the Joint Genome Institute, the STAR experiment at the Relativistic Heavy Ion Collider, and the Laser Interferometer Gravitational Wave Observatory (LIGO), were used by the Magellan project for benchmarking within the cloud, but the project teams were also able to accomplish important production science utilizing the Magellan cloud resources.

97 MATHEMATICS AND COMPUTING↗

Time Sequence Machine Learning-Based Data Intrusion Detection for Smart Voltage Source Converter-Enabled Power Grid

Smart inverters of distributed energy resources can enable cloud computing, condition monitoring, result visualization, remote control, and peer-to-peer energy trading in advanced power systems. However, the advent of data injection attacks in the communication architecture can alter measurement characteristics of power grids and have devastating consequences. In this article, we propose a time sequence machine learning-based anomaly detection methodology for detecting cyber intrusion into control signal setpoints and dc voltage signal measurement bias of the voltage source converter (VSC) in wind generators. We first investigated the effects of four types of denial of service, tampering signal, and stealthy-type data intrusion attacks on smart VSCs and overall wind farms. We then proposed a novel time sequence machine learning-based intrusion detection framework that can be implemented to detect different cyberattacks in the VSCs. The performance of the proposed framework has been compared with that of autoencoder and clustering-based intrusion detection framework. The proposed framework was validated by using the IEEE 39 bus power system in the presence of four wind farms in different locations. Using several metrics for intrusion detection performance, we validated the effectiveness of the proposed framework.

42 ENGINEERING↗

Progress on the FabrIc for Frontier Experiments project at Fermilab

The FabrIc for Frontier Experiments (FIFE) project is an ambitious, major-impact initiative within the Fermilab Scientific Computing Division designed to lead the computing model for Fermilab experiments. FIFE is a collaborative effort between experimenters and computing professionals to design and develop integrated computing models for experiments of varying needs and infrastructure. The major focus of the FIFE project is the development, deployment, and integration of Open Science Grid solutions for high throughput computing, data management, database access and collaboration within experiment. To accomplish this goal, FIFE has developed workflows that utilize Open Science Grid sites along with dedicated and commercial cloud resources. The FIFE project has made significant progress integrating into experiment computing operations several services including new job submission services, software and reference data distribution through CVMFS repositories, flexible data transfer client, and access to opportunistic resources on the Open Science Grid. Hence, the progress with current experiments and plans for expansion with additional projects will be discussed. FIFE has taken a leading role in the definition of the computing model for Fermilab experiments, aided in the design of computing for experiments beyond Fermilab, and will continue to define the future direction of high throughput computing for future physics experiments worldwide

97 MATHEMATICS AND COMPUTING↗

MWR3C physical retrievals of precipitable water vapor and cloud liquid water path

The data set contains physical retrievals of PWV and cloud LWP retrieved from MWR3C measurements during the MAGIC campaign. Additional data used in the retrieval process include radiosondes and ceilometer. The retrieval is based on an optimal estimation technique that starts from a first guess and iteratively repeats the forward model calculations until a predefined convergence criterion is satisfied. The first guess is a vector of [PWV,LWP] from the neural network retrieval fields in the netcdf file. When convergence is achieved the 'a posteriori' covariance is computed and its square root is expressed in the file as the retrieval 1-sigma uncertainty. The closest radiosonde profile is used for the radiative transfer calculations and ceilometer data are used to constrain the cloud base height. The RMS error between the brightness temperatures is computed at the last iterations as a consistency check and is written in the last column of the output file.

54 ENVIRONMENTAL SCIENCES↗

Future Online Analysis Platform Workshop Report

Recent technology trends, such as the increasing focus on data management technologies and the emergence of sustainable on-demand computing and commercial cloud facilities provide initial steps and potential building blocks for creating such a compute facility. How do we fill the gap between what we have now and the capabilities we need to make the vision of an online data facility a reality? What research challenges need to be addressed – and can be addressed – in the coming 5-10 years? How should we adjust our vision if they are not solved? Is such a facility compatible with the existing and evolving exascale resources and/or how should they evolve to be compatible? How do “beyond Moore’s law” technologies enable advanced data analysis? Those are the challeges that the Future Platform workshop was organized to address. This report is organized as follows. Section 2 summarizes data challenges and patterns related to the exemplar use cases presented during the first half day of the workshop. Section 3 summarizes the requirements presented by those use cases as well as a synthesis of those requirements into a Future Platform definition achieved on the 3rd half day of the workshop (morning of the 2nd day). Section 4 includes area breakout reports from the areas on the 2nd half day of the workshop (afternoon of the 1st day). Finally Section 5 has a report on recommendation for building methodology and metrics. The report concludes in Section 6.

97 MATHEMATICS AND COMPUTING↗

Development of an end state vision to implement digital monitoring in nuclear plants

Transitioning from an onsite Maintenance & Diagnostics Center to cloud-based services offers many new opportunities with computing power and storage, but also new challenges in terms of networking and security. This report will cover everything required for that transition including data processing and uploading to cloud services, feature selection, model creation, and result visualization for decision making. Although there are several other cloud-based services (e.g. Amazon Web Services and Google Cloud), this report explores Microsoft Azure to simplify nomenclature and maintain a consistent focus. Many of the services offered by Microsoft Azure are also available in the other cloud-based services, and their differences have been recorded in other literature. The Azure services most important to a nuclear power plant including networking & security, storage & databases, and Artificial Intelligence (AI) are reviewed here. Networking covers all aspects related to communication to Azure resources including security, privacy, and redundancy. Storage & databases includes data storage, upgrading, patching, backups, and monitoring. The AI services allows the user access to the machine learning (ML) techniques developed with Azure including automated ML, anomaly detection, computer vision, and natural language processing. This report summaries the features, capabilities, and challenges when using cloud-based services in a user-friendly manner.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

A hybrid computational strategy to address WGS variant analysis in >5000 samples

Abstract Background The decreasing costs of sequencing are driving the need for cost effective and real time variant calling of whole genome sequencing data. The scale of these projects are far beyond the capacity of typical computing resources available with most research labs. Other infrastructures like the cloud AWS environment and supercomputers also have limitations due to which large scale joint variant calling becomes infeasible, and infrastructure specific variant calling strategies either fail to scale up to large datasets or abandon joint calling strategies. Results We present a high throughput framework including multiple variant callers for single nucleotide variant (SNV) calling, which leverages hybrid computing infrastructure consisting of cloud AWS, supercomputers and local high performance computing infrastructures. We present a novel binning approach for large scale joint variant calling and imputation which can scale up to over 10,000 samples while producing SNV callsets with high sensitivity and specificity. As a proof of principle, we present results of analysis on Cohorts for Heart And Aging Research in Genomic Epidemiology (CHARGE) WGS freeze 3 dataset in which joint calling, imputation and phasing of over 5300 whole genome samples was produced in under 6 weeks using four state-of-the-art callers. The callers used were SNPTools, GATK-HaplotypeCaller, GATK-UnifiedGenotyper and GotCloud. We used Amazon AWS, a 4000-core in-house cluster at Baylor College of Medicine, IBM power PC Blue BioU at Rice and Rhea at Oak Ridge National Laboratory (ORNL) for the computation. AWS was used for joint calling of 180 TB of BAM files, and ORNL and Rice supercomputers were used for the imputation and phasing step. All other steps were carried out on the local compute cluster. The entire operation used 5.2 million core hours and only transferred a total of 6 TB of data across the platforms. Conclusions Even with increasing sizes of whole genome datasets, ensemble joint calling of SNVs for low coverage data can be accomplished in a scalable, cost effective and fast manner by using heterogeneous computing platforms without compromising on the quality of variants.

59 BASIC BIOLOGICAL SCIENCES↗

rabpro: global watershed boundaries, river elevation profiles, and catchment statistics

River and Basin Profiler (rabpro) is a Python package to delineate watersheds, extract river flowlines and elevation profiles, and compute watershed statistics for any location on the Earth’s surface. As fundamental hydrologically-relevant units of surface area, watersheds are areas of land that drain via aboveground pathways to the same location, or outlet. Delineations of watershed boundaries are typically performed on digital elevation models (DEMs) that represent surface elevations as gridded rasters. Depending on the resolution of the DEM and the size of the watershed, delineation may be very computationally expensive. With this in mind, we designed rabpro to provide user-friendly workflows to manage the complexity and computational expense of watershed calculations given an arbitrary coordinate pair. In addition to basic watershed delineation, rabpro will extract the elevation profile for a watershed’s mainchannel flowline. This enables the computation of river slope, which is a critical parameter in many hydrologic and geomorphologic models. Finally, rabpro provides a user-friendly wrapper around Google Earth Engine’s (GEE) Python API to enable cloud-computing of zonal watershed statistics and/or time-varying forcing data from hundreds of available datasets. Altogether, rabpro provides the ability to automate or semi-automate complex watershed analysis workflows across broad spatial extents.

54 ENVIRONMENTAL SCIENCES↗

The medical science DMZ: a network design pattern for data-intensive medical science

Abstract Objective We describe a detailed solution for maintaining high-capacity, data-intensive network flows (eg, 10, 40, 100 Gbps+) in a scientific, medical context while still adhering to security and privacy laws and regulations. Materials and Methods High-end networking, packet-filter firewalls, network intrusion-detection systems. Results We describe a “Medical Science DMZ” concept as an option for secure, high-volume transport of large, sensitive datasets between research institutions over national research networks, and give 3 detailed descriptions of implemented Medical Science DMZs. Discussion The exponentially increasing amounts of “omics” data, high-quality imaging, and other rapidly growing clinical datasets have resulted in the rise of biomedical research “Big Data.” The storage, analysis, and network resources required to process these data and integrate them into patient diagnoses and treatments have grown to scales that strain the capabilities of academic health centers. Some data are not generated locally and cannot be sustained locally, and shared data repositories such as those provided by the National Library of Medicine, the National Cancer Institute, and international partners such as the European Bioinformatics Institute are rapidly growing. The ability to store and compute using these data must therefore be addressed by a combination of local, national, and industry resources that exchange large datasets. Maintaining data-intensive flows that comply with the Health Insurance Portability and Accountability Act (HIPAA) and other regulations presents a new challenge for biomedical research. We describe a strategy that marries performance and security by borrowing from and redefining the concept of a Science DMZ, a framework that is used in physical sciences and engineering research to manage high-capacity data flows. Conclusion By implementing a Medical Science DMZ architecture, biomedical researchers can leverage the scale provided by high-performance computer and cloud storage facilities and national high-speed research networks while preserving privacy and meeting regulatory requirements.

Peisert, Sean↗

Moving small files in a networked environment

Globally distributed computing infrastructures, such as clouds and supercomputers, are currently used to manage data that is generated with an unprecedented speed from a variety of resources. Coping with this trend, the volume of data exchanged across distant sites increases substantially. To accelerate data transfer, high-speed networks are provided to connect remote sites. Most existing data movement solutions are optimized for moving large files. However, it is still challenging to transfer a large number of small files across networks. This disadvantage not only lowers data transfer performance, but also decreases overall system utilization. Here, we identify that moving small files is mainly constrained by degraded file system throughput, not just network performance as might be suspected. We have built a data transfer pipeline model to analyze the impact of small network I/O and storage I/O on data movement. Extending one of the widely used open source data movement solutions, GridFTP, we demonstrate several appropriate engineering approaches that mitigate the bottleneck and increase data transfer efficiency. We show optimizations that improve data transfer performance more than 5 times. In comparison to existing solutions, our approaches can save a significant amount of system resources for moving lots of small files.

97 MATHEMATICS AND COMPUTING↗

Simplifying Energy Efficiency for Homeowners - Results from a California Utility's Pilot Study of a Scalable Solution to Assess Retrofit and Solar Opportunities: Preprint

For homeowners, typical choices to reduce net energy use in their homes include: upgrading their home with a tailored efficiency retrofit or investing in roof-top solar. Determining the unique combination of these options that will provide the most cost-effective solution requires analysis for each home. This analysis needs to be presented in a simple and actionable way to homeowners. The solution should also be easily scalable to thousands of homes to enable utilities to better target efficiency program options and support solar installations. Sacramento Municipal Utility District (SMUD) piloted a new tool developed by Vistar Energy called XeroHome that automates the assessment of energy efficiency and solar opportunities in existing homes. XeroHome demonstrates an approach to using building energy modeling, energy use data analytics and homeowner engagement to identify and target energy efficiency opportunities at scale. XeroHome uses automation to build an EnergyPlus model for each home, based on information from public data sources such as property assessment records, building permit records, aerial/satellite photography, and template models derived from ResStock. Utilizing cloud computing, machine learning and optimization algorithms, energy upgrade packages are ranked by cost-effectiveness for each home and presented over an interactive web-portal. This paper discusses SMUD's pilot project using XeroHome to conduct analysis for 1,500 existing homes in Sacramento, CA. Development of XeroHome's advanced analytics capabilities are discussed in the context of applicability for utility programs.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗