Building an Evidence Library to Inform Exploration Medical System Design
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Dana R Levin↗
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Architectural Optimization of Digital Libraries
This work investigates performance and scaling issues relevant to large scale distributed digital libraries. Presently, performance and scaling studies focus on specific implementations of production or prototype digital libraries. Although useful information is gained to aid these designers and other researchers with insights to performance and scaling issues, the broader issues relevant to very large scale distributed libraries are not addressed. Specifically, no current studies look at the extreme or worst case possibilities in digital library implementations. A survey of digital library research issues is presented. Scaling and performance issues are mentioned frequently in the digital library literature but are generally not the focus of much of the current research. In this thesis a model for a Generic Distributed Digital Library (GDDL) and nine cases of typical user activities are defined. This model is used to facilitate some basic analysis of scaling issues. Specifically, the calculation of Internet traffic generated for different configurations of the study parameters and an estimate of the future bandwidth needed for a large scale distributed digital library implementation. This analysis demonstrates the potential impact a future distributed digital library implementation would have on the Internet traffic load and raises questions concerning the architecture decisions being made for future distributed digital library designs.
Biser, Aileen O.↗
Scare Tactics: Evaluating Problem Decompositions Using Failure Scenarios
Our interest is in the design of multi-agent problem-solving systems, which we refer to as composite systems. We have proposed an approach to composite system design by decomposition of problem statements. An automated assistant called Critter provides a library of reusable design transformations which allow a human analyst to search the space of decompositions for a problem. In this paper we describe a method for evaluating and critiquing problem decompositions generated by this search process. The method uses knowledge stored in the form of failure decompositions attached to design transformations. We suggest the benefits of our critiquing method by showing how it could re-derive steps of a published development example. We then identify several open issues for the method.
Helm, B. Robert↗
Challenges and Solutions for Leave-One-Out Biosensor Design in the Context of a Rugged Fitness Landscape
The leave-one-out (LOO) green fluorescent protein (GFP) approach to biosensor design combines computational protein design with split protein reconstitution. LOO-GFPs reversibly fold and gain fluorescence upon encountering the target peptide, which can be redefined by computational design of the LOO site. Such an approach can be used to create reusable biosensors for the early detection of emerging biological threats. Enlightening biophysical inferences for nine LOO-GFP biosensor libraries are presented, with target sequences from dengue, influenza, or HIV, replacing beta strands 7, 8, or 11. An initially low hit rate was traced to components of the energy function, manifesting in the over-rewarding of over-tight side chain packing. Also, screening by colony picking required a low library complexity, but designing a biosensor against a peptide of at least 12 residues requires a high-complexity library. This double-bind was solved using a “piecemeal” iterative design strategy. Also, designed LOO-GFPs fluoresced in the unbound state due to unwanted dimerization, but this was solved by fusing a fully functional prototype LOO-GFP to a fiber-forming protein, Drosophila ultrabithorax, creating a biosensor fiber. One influenza hemagglutinin biosensor is characterized here in detail, showing a shifted excitation/emission spectrum, a micromolar affinity for the target peptide, and an unexpected photo-switching ability.
Chemistry↗
Three-dimensional structure-guided evolution of a ribosome with tethered subunits
We report RNA-based macromolecular machines, such as the ribosome, have functional parts reliant on structural interactions spanning sequence-distant regions. These features limit evolutionary exploration of mutant libraries and confound three-dimensional structure-guided design. To address these challenges, we describe Evolink (evolution and linkage), a method that enables high-throughput evolution of sequence-distant regions in large macromolecular machines, and library design guided by computational RNA modeling to enable exploration of structurally stable designs. Using Evolink, we evolved a tethered ribosome with a 58% increased activity in orthogonal protein translation and a 97% improvement in doubling times in SQ171 cells compared to a previously developed tethered ribosome, and reveal new permissible sequences in a pair of ribosomal helices with previously explored biological function. The Evolink approach may enable enhanced engineering of macromolecular machines for new and improved functions for synthetic biology.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
(U) STATEMENT OF WORK, UCD RadHard Collaboration
The following subcontract engages UC Davis (UCD) to collaborate with Lawrence Livermore National Laboratory (LLNL) on the design and analysis of microelectronic circuits (macrocells). As part of the proposed statement of work UCD will be given access to information that is export controlled. Within this statement of work UCD is to acquire and install any applicable foundry PDK(s) and collaborate with LLNL on the design of new macrocells and assist in making improvements to existing macrocells as well as the design of ASICs using collections of macrocells. The intent is to increase the application space of the existing LLNL macrocell library and demonstrate the use of the macrocell library, including new designs, by making reference design ASICs.
42 ENGINEERING↗
Solar Energy Demonstration Project for Public Libraries
In this project, the South Hero Library Foundation purchased and installed a 39.95 kW DC roof-mounted solar array on the south-facing roof of the Worthen Library as well as on the south-facing roof of the neighboring 54 Community Lane building. This 94 panel array has a projected output of 39,950 kWh of power which will cover the Library’s annual power usage for heat and lighting. Any power overage will be distributed to other local organizations as designated by the Library. Library programming and added resources will be available to all patrons.
14 SOLAR ENERGY↗
Do-It-Yourself: A Special Library's Approach to Creating Dynamic Web Pages Using Commercial Off-The-Shelf Applications
Many librarians may feel that dynamic Web pages are out of their reach, financially and technically. Yet we are reminded in library and Web design literature that static home pages are a thing of the past. This paper describes how librarians at the Institute for Defense Analyses (IDA) library developed a database-driven, dynamic intranet site using commercial off-the-shelf applications. Administrative issues include surveying a library users group for interest and needs evaluation; outlining metadata elements; and, committing resources from managing time to populate the database and training in Microsoft FrontPage and Web-to-database design. Technical issues covered include Microsoft Access database fundamentals, lessons learned in the Web-to-database process (including setting up Database Source Names (DSNs), redesigning queries to accommodate the Web interface, and understanding Access 97 query language vs. Standard Query Language (SQL)). This paper also offers tips on editing Active Server Pages (ASP) scripting to create desired results. A how-to annotated resource list closes out the paper.
Relational databases↗
Whole-building life-cycle analysis with a new GREET® tool: Embodied greenhouse gas emissions and payback period of a LEED-Certified library
Embodied greenhouse gas (GHG) emissions of building components and buildings operations need to be quantified to holistically address building sustainability. To evaluate embodied GHG emissions of buildings and to provide insights on building materials and building design decisions toward decarbonization, we have recently created a building life-cycle assessment (LCA) module in the widely used Greenhouse gases, Regulated Emissions, and Energy use in Technologies (GREET (R)) LCA model. We applied the GREET building LCA module to examine embodied GHG impacts and the payback period of a LEED (Leadership in Energy and Environmental Design) certified public library in Chicago, USA. We developed localized, detailed life-cycle inventories to address individual building materials used in the library. We expanded the LCA system boundary to include the mechanical, electrical, and plumbing system, as well as refrigerant impacts, which are often ignored in previous studies. Results show that the total embodied GHG emissions are approximately 817 metric tons, or approximately 538 kg/m 2 . Sensitivity analysis highlights the positive role of increasing the use of recycled materials for reducing embodied GHG emissions. Sensitivity analysis on embodied GHG emissions payback periods shows the need to benchmark the embodied and operational carbon performance of buildings for comparison to alternative building designs and sustainability practices. Furthermore, this analysis demonstrates that building LCA models, such as the GREET building LCA module, which addresses embodied and operational GHG emission impacts of whole buildings holistically, could empower building architects, technology developers, manufacturers, and general contractors to address embodied and operational impacts holistically for building sustainability.
32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗
Toward Resilient Heterogeneous Computing Workflow through Kokkos-DataSpaces Integration
With the growing number of applications designed for heterogeneous HPC devices, application programmers and users are finding it challenging to compose scalable workflows as ensembles of these applications, that are portable, performant and resilient. The Kokkos C++ library has been designed to simplify this cumbersome procedure by providing an intra-application uniform programming model and portable performance. However, assembling multiple Kokkos-enabled applications into a complex workflow is still a challenge. Although Kokkos enables a uniform programming model, the inter-application data exchange still remains a challenge from both performance and software development cost perspectives. In order to address this issue, we propose a Kokkos-DataSpaces Integration, with the goal of providing a virtual shared-space abstraction that can be accessed concurrently by all applications in an Kokkos workflow, thus extending Kokkos to support inter-application data exchange.
97 MATHEMATICS AND COMPUTING↗
Design and Performance of Kokkos Staging Space toward Scalable Resilient Application Couplings
With the growing number of applications designed for heterogeneous HPC devices, application programmers and users are finding it challenging to compose scalable workflows as ensembles of these applications, that are portable, performant and resilient. The Kokkos C++ library has been designed to simplify this cumbersome procedure by providing an intra-application uniform programming model and portable performance. However, assembling multiple Kokkos-enabled applications into a complex workflow is still a challenge. Although Kokkos enables a uniform programming model, the inter-application data exchange still remains a challenge from both performance and software development cost perspectives. In order to address this issue, we propose Kokkos data staging memory space, an extension of Kokkos' data abstraction (memory space) for heterogeneous computing systems. This new abstraction allows to express data on a virtual shared-space for multiple Kokkos applications, thus extending Kokkos to support inter-application data exchange to build an efficient application workflow. Additionally, we study the effectiveness of asynchronous data layout conversions for applications requiring different memory access patterns for the shared data. Our preliminary evaluation with a synthetic benchmark indicate the effectiveness of this conversion adapted to three different scenarios representing access frequency and use patterns of the shared data.
97 MATHEMATICS AND COMPUTING↗
Testing self-timed circuits using scan paths
Testing is an essential part of any digital system design and one that can be made much easier if testing is considered during the design process rather than after the system is complete. There are a number of techniques for integrating testability into system design, but many of these traditional testing methods used for synchronous circuits are not directly applicable to non-clocked asynchronous circuits. As a result, many asynchronous circuits do not employ design for testability techniques. A method of using the familiar model of scan paths modified to test self-timed systems are presented. Specifically, circuits designed using a library of self-timed modules to assemble systems with two-phase transition control and bundled data paths are considered. The method involves modifying these self-timed modules such that circuits designed from them have a built-in scan path.
Khoche, Ajay↗
Geometry Technology Module (GTM). Volume 1: Engineering description and utilization manual
The geometry technology module (GTM) is described as a system of computerized elements residing in the engineering design integration system library developed for the generation, manipulation, display, computation of mass properties, and data base management of panelled geometry. The GTM is composed of computer programs and associated data for performing configuration analysis on geometric shapes. The program can be operated in batch or demand mode and is designed for interactive use.
Reiners, S. J.↗
Distributed memory compiler design for sparse problems
A compiler and runtime support mechanism is described and demonstrated. The methods presented are capable of solving a wide range of sparse and unstructured problems in scientific computing. The compiler takes as input a FORTRAN 77 program enhanced with specifications for distributing data, and the compiler outputs a message passing program that runs on a distributed memory computer. The runtime support for this compiler is a library of primitives designed to efficiently support irregular patterns of distributed array accesses and irregular distributed array partitions. A variety of Intel iPSC/860 performance results obtained through the use of this compiler are presented.
Wu, Janet↗
Co-design for Particle Applications at Exascale
Co-design across the Exascale Computing Project (ECP) has been critical for both enabling science applications and bringing disparate communities together. Developing and porting applications to the various high-performance computing (HPC) architectures on pre-exascale and exascale computers has been quite challenging due to the diversity of hardware features and software stacks. The Co-design Center for Particle Applications (CoPA) has developed and enhanced the Cabana and PROGRESS/BML libraries to facilitate the creation of new particle applications, make existing particle applications exascale capable, and allow teams to explore new capabilities. Particle methods from atomistic, mesoscale, continuum, through cosmological scales have been built with Cabana, along with new possibilities for application coupling. Similarly, the PROGRESS/BML library has enabled quantum particle applications with linear algebra solvers to use advanced hardware. Across these CoPA-developed libraries, the co-design abstraction layer combines performance portability with math library support to facilitate separation of concerns and directly support science runs.
97 MATHEMATICS AND COMPUTING↗
A simulation model for wind energy storage systems. Volume 2: Operation manual
A comprehensive computer program (SIMWEST) developed for the modeling of wind energy/storage systems utilizing any combination of five types of storage (pumped hydro, battery, thermal, flywheel, and pneumatic) is described. Features of the program include: a precompiler which generates computer models (in FORTRAN) of complex wind source/storage/application systems, from user specifications using the respective library components; a program which provides the techno-economic system analysis with the respective I/O the integration of system dynamics, and the iteration for conveyance of variables; and capability to evaluate economic feasibility as well as general performance of wind energy systems. The SIMWEST operation manual is presented and the usage of the SIMWEST program and the design of the library components are described. A number of example simulations intended to familiarize the user with the program's operation is given along with a listing of each SIMWEST library subroutine.
Warren, A. W.↗
PETSc/TAO developments for GPU-based early exascale systems
The Portable Extensible Toolkit for Scientific Computation (PETSc) library provides scalable solvers for nonlinear time-dependent differential and algebraic equations and for numerical optimization via the Toolkit for Advanced Optimization (TAO). PETSc is used in dozens of scientific fields and is an important building block for many simulation codes. During the U.S. Department of Energy’s Exascale Computing Project, the PETSc team has made substantial efforts to enable efficient utilization of the massive fine-grain parallelism present within exascale compute nodes and to enable performance portability across exascale architectures. We recap some of the challenges that designers of numerical libraries face in such an endeavor, and then discuss the many developments we have made, which include the addition of new GPU backends, features supporting efficient on-device matrix assembly, better support for asynchronicity and GPU kernel concurrency, and new communication infrastructure. In conclusion, we evaluate the performance of these developments on some pre-exascale systems as well as the early exascale systems Frontier and Aurora, using compute kernel, communication layer, solver, and mini-application benchmark studies, and then close with a few observations drawn from our experiences on the tension between portable performance and other goals of numerical libraries.
Exascale Computing Project (ECP)↗
A Robust and Scalable Software Library for Parallel Adaptive Refinement on Unstructured Meshes
The design and implementation of Pyramid, a software library for performing parallel adaptive mesh refinement (PAMR) on unstructured meshes, is described. This software library can be easily used in a variety of unstructured parallel computational applications, including parallel finite element, parallel finite volume, and parallel visualization applications using triangular or tetrahedral meshes. The library contains a suite of well-designed and efficiently implemented modules that perform operations in a typical PAMR process. Among these are mesh quality control during successive parallel adaptive refinement (typically guided by a local-error estimator), parallel load-balancing, and parallel mesh partitioning using the ParMeTiS partitioner. The Pyramid library is implemented in Fortran 90 with an interface to the Message-Passing Interface (MPI) library, supporting code efficiency, modularity, and portability. An EM waveguide filter application, adaptively refined using the Pyramid library, is illustrated.
Lou, John Z.↗