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Maintenance of Maywood Laboratory Operations Support During Contractor Transition and Replacement of the Project Databases - 16329

In December 2013, Cabrera Services (Cabrera) executed transition of the FUSRAP Maywood Superfund Site remediation project operations, including an on-site accredited environmental lab, from a large business that had established technology infrastructure in place for over a decade which required updating to support the expected remediation scope and client needs. As of November 2015, Cabrera has shipped over 116,000 yd{sup 3} of contaminated soil to disposal facilities. During the transition, the USACE FUSRAP Maywood Laboratory (UFML) continued to support project operations, providing the expected timely and reliable results and maintaining their New Jersey Department of Environmental Protection certification for all parameters of concern, while having to cope with new challenges and additional tasks having the potential to disrupt the laboratory's ability to support project operations. This case study examines the challenges with maintaining a certified radiochemistry laboratory and an aggressive remediation schedule during a period of prime contractor transition which included a complete IT infrastructure overhaul, and conversion of the existing Microsoft Access laboratory database and project Electronic Data Management System (EDMS) to a customized commercial solution. Challenges: I. Procurement of a new database subcontractor and working closely with them to achieve the following: a. Migration of all environmental (including radiological, chemical, and quality control), health and safety, and spatial data as well as reports, queries, and analytical instrument software processes from a MS Access data management system to a SQL server system; and b. Verification that the functionality and data integrity of the databases remained intact. II. The onsite laboratory was changed over to a new onsite network and the following tasks were completed with little or no interruption to site operations by January 10, 2014: i. Installation of new instrument personal computers (PCs) and making them fully operational; ii. Configuration of the lab domain and server to host the LIMS (replaced all servers/domain/workstations with Windows 7 and Server 2012 machines). iii. Networking of the laboratory building into the rest of the project site via fiber optic cabling across the site. iv. Upgrade of the wide area network (WAN) data connection to high-speed Fiber Optic service; v. Upgrade of the telephones into voice over internet protocol (VOIP) phones. vi. Splitting of the database into front ends and a centralized back-end hosted on the new server to allow simultaneous access for fixes and improvements. III. Phone service interruption; phone systems were operational by January 10, 2014. Additional Tasks: I. Revision of the USACE FUSRAP Maywood Laboratory (UFML) Quality Systems Manual Rev. 1 Submitted 01/16/14; II. Writing of the Uniform Federal Policy Quality Assurance Project Plan Rev. 1 (UFP-QAPP) submitted 1/21/14. This document replaced the prior project data quality plan, the Chemical Data Quality Management Plan. III. Support of USACE communications to the New Jersey Department of Environmental Protection (NJDEP) on lab management and personnel transition to Cabrera. This work was important since it ensured a smooth transition and shows how critical project records infrastructure such as databases, can be upgraded with minimal interruption of project support. Such work may provide benefit to other similar projects, especially long term projects where database infrastructure upgrades may be beneficial in terms of improved efficiencies in data recording and transfer, and improved security in data storage. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

Collaborative Research: Performance Retargeting of Instrumentation, Measurement, and Analysis Technologies for Exascale Computing: the PRIMA-X Project -- Final Technical Report

The PRIMA-X (Performance Retargeting of Instrumentation, Measurement, and Analysis Technologies for Exascale Computing) project was a collaborative research effort between the University of Oregon (UO) (Malony, PI) and the German Research School for Simulation Sciences GmbH (Wolf, PI) originally, later changed to the Technical University of Darmstadt. Our project aims addressed five areas -- scalability, dynamism, heterogeneity, locality, energy -- that present challenges to performance measurement systems at exascale, with emphasis placed on the first three. In essence, the general goal of the project was to prototype new technologies for performance measurement, analysis, and tuning on future exascale-enable computer systems. Each institution followed its research agena, with periodic coordination and sharing of ideas and results. After the 3-year funding, the PRIMA-X grant was extended beyond the 3-year period at no cost until the end of August 2018. This is the final technical report on the University of Oregon's progress during the entire project scope. Our main focus was to address the PRIMA-X challenges both through technological advancements in the TAU Performance System and their application, as well as prototypes developed in association with other exascale-directed research efforts (prior to the Exascale Computing Project (ECP)). Progress in Years 1 and 2 are summarized and our achievements in Year 3 (plus the extension) are discussed in more detail. This includes specific efforts on power, runtime systems, and monitoring infrastructure.

97 MATHEMATICS AND COMPUTING↗

Resonant Ultrasound Spectroscopy

New measurement techniques are central to the advancement of science. One emerging strategy, made possible today by the accessibility of powerful personal computers, is the development of instrumentation that requires massive computational power to produce otherwise unobtainable results. RUS is an example.

47 OTHER INSTRUMENTATION↗

Algorithm-Driven Advances for Scientific CT Instruments: From model-based to deep learning-based approaches

Multiscale 3D characterization is widely used by materials scientists to further their understanding of the relationships between microscopic structure and macroscopic function. Scientific computed tomography (SCT) instruments are one of the most popular choices for 3D nondestructive characterization of materials at length scales ranging from the angstrom scale to the micron scale. These instruments typically have a source of radiation (such as electrons, X-rays, or neutrons) that interacts with the sample to be studied and a detector assembly to capture the result of this interaction (see Figure 1 ). A collection of such high-resolution measurements is made by reorienting the sample, which is mounted on a specially designed stage/holder after which reconstruction algorithms are used to produce the final 3D volume of interest. The specific choice of which instrument to use depends on the desired resolution and properties of the materials being imaged. Additionally, the end goal of SCT scans includes determining the morphology, chemical composition, or dynamic behavior of materials when subjected to external stimuli. In summary, SCT instruments are powerful tools that enable 3D characterization across multiple length scales and play a critical role in furthering the understanding of the structure–function relationships of different materials.

42 ENGINEERING↗

Hands-On Computer Science: The Array of Things Experimental Urban Instrument

Chicago's Array of Things (AoT) project is aptly described as a technology experiment or a "smart city" prototype. The concept of such an extensible "instrument" arose within a larger translational research vision applying computer science and engineering research for the multidimensional benefit of people and communities in cities. The AoT project hypothesized that wireless intelligent sensor networks could enable both quantitative social science and urban monitoring while also stimulating youth interest in science and technology. Successful deployment of such sensor networks could provide open data from urban measurements not only in support of diverse research questions-in environmental dynamics, urban architecture, engineering, and social sciences-but also informing community groups and city planners. Further, the AoT project and its successor SAGE project are a computer science and engineering experiment, but its success is inextricably tied to community engagement and experiential education. Simply put, community acceptance is a prerequisite to installing and testing the instrument.

97 MATHEMATICS AND COMPUTING↗

INTERSECT Architecture Specification: Use Case Design Patterns (V.0.9)

Connecting scientific instruments and robot-controlled laboratories with computing and data resources at the edge, the Cloud or the high-performance computing (HPC) center enables autonomous experiments, self-driving laboratories, smart manufacturing, and artificial intelligence (AI)-driven design, discovery and evaluation. The Self-driven Experiments for Science / Interconnected Science Ecosystem (INTERSECT) Open Architecture enables science breakthroughs using intelligent networked systems, instruments and facilities with a federated hardware/software architecture for the laboratory of the future. It relies on a novel approach, consisting of (1) science use case design patterns, (2) a system of systems architecture, and (3) a microservice architecture. This document introduces the science use case design patterns of the INTERSECT Architecture. It describes the overall background, the involved terminology and concepts, and the pattern format and classification. It further details the 12 defined patterns and provides insight into building solutions from these patterns. The document also describes the application of these patterns in the context of several INTERSECT autonomous laboratories. The target audience are computer, computational, instrument and domain science experts working in the field of autonomous experiments.

97 MATHEMATICS AND COMPUTING↗

Science Use Case Design Patterns for Autonomous Experiments

Connecting scientific instruments and robot-controlled laboratories with computing and data resources at the edge, the Cloud or the high-performance computing (HPC) center enables autonomous experiments, self-driving laboratories, smart manufacturing, and artificial intelligence (AI)-driven design, discovery and evaluation. The Self-driven Experiments for Science / Interconnected Science Ecosystem (INTERSECT) Open Architecture enables science breakthroughs using intelligent networked systems, instruments and facilities with a federated hardware/software architecture for the laboratory of the future. It relies on a novel approach, consisting of (1) science use case design patterns, (2) a system of systems architecture, and (3) a microservice architecture. This paper introduces the science use case design patterns of the INTERSECT Architecture. It describes the overall background, the involved terminology and concepts, and the pattern format and classification. It further offers an overview of the 12 defined patterns and 4 examples of patterns of 2 different pattern classes. It also provides insight into building solutions from these patterns. The target audience are computer, computational, instrument and domain science experts working in the field of autonomous experiments.

Engelmann, Christian↗

A Processing and Analytics System for Microscopy Data Workflows: The Pycroscopy Ecosystem of Packages

Major advancements in fields as diverse as biology and quantum computing have relied on a multitude of microscopy techniques. Despite the considerable proliferation of these instruments, significant bottlenecks remain in terms of processing, analysis, storage, and retrieval of the acquired datasets. Aside from lack of file standards, individual domain-specific analysis packages are often disjoint from the underlying datasets, and thus keeping track of analysis and processing steps remains tedious for the end-user, hampering reproducibility. Here, in this study, the pycroscopy ecosystem of packages is introduced, an open-source python-based ecosystem underpinned by a common data model. The data model, termed the N-dimensional spectral imaging data format, is realized in pycroscopy's sidpy package. This package is built on top of dask arrays, thus leveraging dask array attributes, but expanding them to accelerate microscopy relevant analysis and visualization. Several examples of the use of the pycroscopy ecosystem to create workflows for data ingestion and analysis of scanning transmission electron microscopy (STEM) and scanning probe microscopy data are shown. Adoption of such standardized routines will be critical to usher in the next generation of autonomous instruments where processing, computation, and meta-data storage will be critical to overall experimental operations.

97 MATHEMATICS AND COMPUTING↗

QUBO formulations for training machine learning models

Abstract Training machine learning models on classical computers is usually a time and compute intensive process. With Moore’s law nearing its inevitable end and an ever-increasing demand for large-scale data analysis using machine learning, we must leverage non-conventional computing paradigms like quantum computing to train machine learning models efficiently. Adiabatic quantum computers can approximately solve NP-hard problems, such as the quadratic unconstrained binary optimization (QUBO), faster than classical computers. Since many machine learning problems are also NP-hard, we believe adiabatic quantum computers might be instrumental in training machine learning models efficiently in the post Moore’s law era. In order to solve problems on adiabatic quantum computers, they must be formulated as QUBO problems, which is very challenging. In this paper, we formulate the training problems of three machine learning models—linear regression, support vector machine (SVM) and balanced k-means clustering—as QUBO problems, making them conducive to be trained on adiabatic quantum computers. We also analyze the computational complexities of our formulations and compare them to corresponding state-of-the-art classical approaches. We show that the time and space complexities of our formulations are better (in case of SVM and balanced k-means clustering) or equivalent (in case of linear regression) to their classical counterparts.

97 MATHEMATICS AND COMPUTING↗

Carbon Monoxide Analyzer (CO-ANALYZER) Instrument Handbook

The N 2 O/CO analyzer uses LGR’s patented Off-axis ICOS technology, which employs a high-finesse optical cavity as the measurement cell. LGR’s technology has many proven advantages over conventional first-generation cavity ringdown spectroscopy (CRDS) techniques. In brief, since the laser beam does not have to be resonantly coupled to the measurement cell, precise beam alignment is not critical. Mentors can disassemble the cell for cleaning (CAREFULLY) the front surface mirrors. Analyzers are relatively inexpensive and inherently robust thermally and mechanically. In addition, since LGR’s technology can record reliable absorption spectra over a far wider range of optical depths (absorbance values) than CRDS, LGR analyzers provide measurements over a much wider range of mixing ratios (gas concentrations). The N 2 O/CO analyzer includes an internal computer that sends real-time data to the local instrument computer through its digital (RS-232) output.

47 OTHER INSTRUMENTATION↗

Performance Refactoring of Instrumentation, Measurement, and Analysis Technologies for Petascale Computing. The PRIMA Project

The growing number of cores provided by today’s high-­end computing systems present substantial challenges to application developers in their pursuit of parallel efficiency. To find the most effective optimization strategy, application developers need insight into the runtime behavior of their code. The University of Oregon (UO) and the Juelich Supercomputing Centre of Forschungszentrum Juelich (FZJ) develop the performance analysis tools TAU and Scalasca, respectively, which allow high-­performance computing (HPC) users to collect and analyze relevant performance data – even at very large scales. TAU and Scalasca are considered among the most advanced parallel performance systems available, and are used extensively across HPC centers in the U.S., Germany, and around the world. The TAU and Scalasca groups share a heritage of parallel performance tool research and partnership throughout the past fifteen years. Indeed, the close interactions of the two groups resulted in a cross-­fertilization of tool ideas and technologies that pushed TAU and Scalasca to what they are today. It also produced two performance systems with an increasing degree of functional overlap. While each tool has its specific analysis focus, the tools were implementing measurement infrastructures that were substantially similar. Because each tool provides complementary performance analysis, sharing of measurement results is valuable to provide the user with more facets to understand performance behavior. However, each measurement system was producing performance data in different formats, requiring data interoperability tools to be created. A common measurement and instrumentation system was needed to more closely integrate TAU and Scalasca and to avoid the duplication of development and maintenance effort. The PRIMA (Performance Refactoring of Instrumentation, Measurement, and Analysis) project was proposed over three years ago as a joint international effort between UO and FZJ to accomplish these objectives: (1) refactor TAU and Scalasca performance system components for core code sharing and (2) integrate TAU and Scalasca functionality through data interfaces, formats, and utilities. As presented in this report, the project has completed these goals. In addition to shared technical advances, the groups have worked to engage with users through application performance engineering and tools training. In this regard, the project benefits from the close interactions the teams have with national laboratories in the United States and Germany. We have also sought to enhance our interactions through joint tutorials and outreach. UO has become a member of the Virtual Institute of High-­Productivity Supercomputing (VI-­HPS) established by the Helmholtz Association of German Research Centres as a center of excellence, focusing on HPC tools for diagnosing programming errors and optimizing performance. UO and FZJ have conducted several VI-­HPS training activities together within the past three years.

97 MATHEMATICS AND COMPUTING↗

Introduction to the Special Issue on Software Tools for Quantum Computing: Part 1

Quantum computing is emerging as a remarkable technology that offers the possibility of achieving major scientific breakthroughs in many areas. Here, by leveraging the unique features of quantum mechanics, quantum computers may be instrumental in advancing many areas, including science, energy, defense, medicine, and finance. This includes solving complex problems whose solution lies well beyond the capacity of contemporary and even future supercomputers that are based on conventional computing technologies. As a foundation for future generations of computing and information processing, quantum computing represents an exciting area for developing new ideas in computer science and computational engineering.

97 MATHEMATICS AND COMPUTING↗

Introduction to the Special Issue on Software Tools for Quantum Computing: Part 2

Quantum computing is emerging as a remarkable technology that offers the possibility of achieving major scientific breakthroughs in many areas. By leveraging the unique features of quantum mechanics, quantum computers may be instrumental in advancing many areas, including science, energy, defense, medicine, and finance. This includes solving complex problems whose solution lies well beyond the capacity of contemporary and even future supercomputers that are based on conventional computing technologies. As a foundation for future generations of computing and information processing, quantum computing represents an exciting area for developing new ideas in computer science and computational engineering.

97 MATHEMATICS AND COMPUTING↗

Development of high-availability ATCA/PCIe data acquisition instrumentation

Latest Fusion energy experiments envision a quasi-continuous operation regime. In consequence, the largest experimental devices, currently in development, specify high-availability (HA) requirements for the whole plant infrastructure. HA features enable the whole facility to perform seamlessly in the case of failure of any of its components, coping with the increasing duration of plasma discharges (steady-state) and assuring safety of equipment, people, environment and investment. IPFN developed a control and data acquisition system, aiming for fast control of advanced Fusion devices, which is thus required to provide such HA features. The system is based on in-house developed Advanced Telecommunication Computing Architecture (ATCA) instrumentation modules - IO blades and data switch blades, establishing a PCIe network on the ATCA shelf's back-plane. The data switch communicates to an external host computer through a PCIe data network. At the hardware management level, the system architecture takes advantage of ATCA native redundancy and hot swap specifications to implement fail-over substitution of IO or data switch blades. A redundant host scheme is also supported by the ATCA/PCIe platform. At the software level, PCIe provides implementation of hot plug services, which translate the hardware changes to the corresponding software/operating system devices. The paper presents how the ATCA and PCIe based system can be setup to perform with the desired degree of HA, thus being suitable for advanced Fusion control and data acquisition systems. (authors)

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Performance Refactoring of Instrumentation, Measurement, and Analysis Technologies for Petascale Computing: the PRIMA Project

The growing number of cores provided by today’s high-end computing systems present substantial challenges to application developers in their pursuit of parallel efficiency. To find the most effective optimization strategy, application developers need insight into the runtime behavior of their code. The University of Oregon (UO) and the Julich Supercomputing Centre of Forschungszentrum Julich (FZJ) developed the performance analysis tools TAU and Scalasca, respectively, which allow high-performance computing (HPC) users to collect and analyze relevant performance data – even at very large scales. TAU and Scalasca are considered among the most advanced parallel performance systems available, and are used extensively across HPC centers in the U.S., Germany, and around the world.

97 MATHEMATICS AND COMPUTING↗

aosco (01)

As of 5 August, 2015, Los Gatos Research (LGR) CO/H2O/N2O analyzer instruments (COANALYZERs) were deployed in the Atmospheric Radiation Measurement (ARM) Aerial Facility (AAF), the third ARM Mobile Facility (AMF3) Aerosol Observing System (AOS), Eastern North Atlantic (ENA) AOS, and Mobile AOS (MAOS-C). The N2O/CO analyzer uses LGR’s patented Off-axis ICOS technology, which employs a high-finesse optical cavity as the measurement cell. LGR’s technology has many proven advantages over conventional first-generation cavity ringdown spectroscopy (CRDS) techniques. In brief, since the laser beam does not have to be resonantly coupled to the measurement cell, precise beam alignment is not critical. Mentors can disassemble the cell for cleaning (CAREFULLY) the front surface mirrors. Analyzers are relatively inexpensive and inherently robust thermally and mechanically. In addition, since LGR’s technology can record reliable absorption spectra over a far wider range of optical depths (absorbance values) than CRDS, LGR analyzers provide measurements over a much wider range of mixing ratios (gas concentrations). The N2O/CO analyzer includes an internal computer that sends real-time data to the local instrument computer through its digital (RS-232) output.

54 ENVIRONMENTAL SCIENCES↗