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At least 217 records · Page 12

Computational Model of the Modulation of Gene Expression Following DNA Damage

High linear energy transfer (LET) radiation, such as heavy ions or neutrons, has an increased biological effectiveness compared to X rays for gene mutation, genomic instability, and carcinogenesis. In the traditional paradigm, mutations or chromosomal aberrations are causative of late effects. However, in recent years experimental evidence has demonstrated the important role of the description of the modification of gene expression by radiation in understanding the mechanisms of radiation action. In this report, approaches are discussed to the mathematical description of mRNA and protein expression kinetics following DNA damage. Several hypotheses for models of radiation modulation of protein expression are discussed including possible non-linear processes that evolve from the linear dose responses that follow the initial DNA damage produced by radiation.

NASA Center JSC↗

Status and projections of the NAS program

NASA's Numerical Aerodynamic Simulation (NAS) Program has completed development of the initial operating configuration of the NAS Processing System Network (NPSN). This is the first milestone in the continuing and pathfinding effort to provide state-of-the-art supercomputing for aeronautics research and development. The NPSN, available to a nation-wide community of remote users, provides a uniform UNIX environment over a network of host computers ranging from the Cray-2 supercomputer to advanced scientific workstations. This system, coupled with a vendor-independent base of common user interface and network software, presents a new paradigm for supercomputing environments. Background leading to the NAS program, its programmatic goals and strategies, technical goals and objectives, and the development activities leading to the current NPSN configuration are presented. Program status, near-term plans, and plans for the next major milestone, the extended operating configuration, are also discussed.

Bailey, Frank R.↗

Using Big Data Technologies with Earth Science Data in HDF5: HDF5 Scalable Solutions

HDF5 (Hierarchical Data Format 5) is open-source, high-performance software that consists of an abstract data model, library, and fileformat used for storing and managing extremely large and/or complex data collections. NASA Earth Observing System (EOS) Data and Information Systems use HDF5 as an archival format to store remote sensing data from EOS satellites. HDF5 is also used to store other types of Geoscience and Strophysical data, e.g., seismic data and data from Low-Frequency Array (LOFAR) radio telescopes. Data stored in HDF5 has reached tens of petabytes and is growing at an accelerated rate.With the growing amout of HDF5 Earth Science data to analyze and process, scientists need to adopt big data technologies including new storage paradigms such as cloud and object storage. To run models and perform data analysis they also need to utilizied efficient and diverse ways to access data, from high-performance computing's (HPC) Message Passing Interface (MPI) I/O and deep memory hierarchies (DMH) to non-HPC frameworks such as Apache Hadoop, Spark, and Drill. The HDF Group continually works to enable usage of big data technologies in HDF software.

Knox, Larry↗

Aerodynamic sound of flow past an airfoil

The long term objective of this project is to develop a computational method for predicting the noise of turbulence-airfoil interactions, particularly at the trailing edge. We seek to obtain the energy-containing features of the turbulent boundary layers and the near-wake using Navier-Stokes Simulation (LES or DNS), and then to calculate the far-field acoustic characteristics by means of acoustic analogy theories, using the simulation data as acoustic source functions. Two distinct types of noise can be emitted from airfoil trailing edges. The first, a tonal or narrowband sound caused by vortex shedding, is normally associated with blunt trailing edges, high angles of attack, or laminar flow airfoils. The second source is of broadband nature arising from the aeroacoustic scattering of turbulent eddies by the trailing edge. Due to its importance to airframe noise, rotor and propeller noise, etc., trailing edge noise has been the subject of extensive theoretical (e.g. Crighton & Leppington 1971; Howe 1978) as well as experimental investigations (e.g. Brooks & Hodgson 1981; Blake & Gershfeld 1988). A number of challenges exist concerning acoustic analogy based noise computations. These include the elimination of spurious sound caused by vortices crossing permeable computational boundaries in the wake, the treatment of noncompact source regions, and the accurate description of wave reflection by the solid surface and scattering near the edge. In addition, accurate turbulence statistics in the flow field are required for the evaluation of acoustic source functions. Major efforts to date have been focused on the first two challenges. To this end, a paradigm problem of laminar vortex shedding, generated by a two dimensional, uniform stream past a NACA0012 airfoil, is used to address the relevant numerical issues. Under the low Mach number approximation, the near-field flow quantities are obtained by solving the incompressible Navier-Stokes equations numerically at chord Reynolds number of 104. The far-field noise is computed using Curle's extension to the Lighthill analogy (Curle 1955). An effective method for separating the physical noise source from spurious boundary contributions is developed. This allows an accurate evaluation of the Reynolds stress volume quadrupoles, in addition to the more readily computable surface dipoles due to the unsteady lift and drag. The effect of noncompact source distribution on the far-field sound is assessed using an efficient integration scheme for the Curle integral, with full account of retarded-time variations. The numerical results confirm in quantitative terms that the far-field sound is dominated by the surface pressure dipoles at low Mach number. The techniques developed are applicable to a wide range of flows, including jets and mixing layers, where the Reynolds stress quadrupoles play a prominent or even dominant role in the overall sound generation.

Wang, Meng↗

NAS-current status and future plans

The Numerical Aerodynamic Simulation (NAS) has met its first major milestone, the NAS Processing System Network (NPSN) Initial Operating Configuration (IOC). The program has met its goal of providing a national supercomputer facility capable of greatly enhancing the Nation's research and development efforts. Furthermore, the program is fulfilling its pathfinder role by defining and implementing a paradigm for supercomputing system environments. The IOC is only the begining and the NAS Program will aggressively continue to develop and implement emerging supercomputer, communications, storage, and software technologies to strengthen computations as a critical element in supporting the Nation's leadership role in aeronautics.

Bailey, F. R.↗

Status and projections of the NAS Program

NASA's Numerical Aerodynamic Simulation (NAS) Program has completed development of the initial operating configuration of the NAS Processing System Network (NPSN). This is the first milestone in the continuing and pathfinding effort to provide state-of-the-art supercomputing for aeronautics research and development. The NPSN, available to a nation-wide community of remote users, provides a uniform UNIX environment over a network of host computers ranging from the new Cray-2 supercomputer to advanced scientific workstations. This system, coupled with a vendor-independent base of common user interface and network software, presents a new paradigm for supercomputing environments. Presented here is the background leading to the NAS Program, its programmatic goals and strategies, technical goals and objectives, and the development activities leading to the current NPSN configuration. Program status, near-term plans and plans for the next major milestone, the extended operating configuration, are also discussed.

Bailey, F. R.↗

Good Practices in Free-energy Calculations

As access to computational resources continues to increase, free-energy calculations have emerged as a powerful tool that can play a predictive role in drug design. Yet, in a number of instances, the reliability of these calculations can be improved significantly if a number of precepts, or good practices are followed. For the most part, the theory upon which these good practices rely has been known for many years, but often overlooked, or simply ignored. In other cases, the theoretical developments are too recent for their potential to be fully grasped and merged into popular platforms for the computation of free-energy differences. The current best practices for carrying out free-energy calculations will be reviewed demonstrating that, at little to no additional cost, free-energy estimates could be markedly improved and bounded by meaningful error estimates. In energy perturbation and nonequilibrium work methods, monitoring the probability distributions that underlie the transformation between the states of interest, performing the calculation bidirectionally, stratifying the reaction pathway and choosing the most appropriate paradigms and algorithms for transforming between states offer significant gains in both accuracy and precision. In thermodynamic integration and probability distribution (histogramming) methods, properly designed adaptive techniques yield nearly uniform sampling of the relevant degrees of freedom and, by doing so, could markedly improve efficiency and accuracy of free energy calculations without incurring any additional computational expense.

Pohorille, Andrew↗

Spaceflight Operations Services Grid (SOSG)

In an effort to adapt existing space flight operations services to new emerging Grid technologies we are developing a Grid-based prototype space flight operations Grid. This prototype is based on the operational services being provided to the International Space Station's Payload operations located at the Marshall Space Flight Center, Alabama. The prototype services will be Grid or Web enabled and provided to four user communities through portal technology. Users will have the opportunity to assess the value and feasibility of Grid technologies to their specific areas or disciplines. In this presentation descriptions of the prototype development, User-based services, Grid-based services and status of the project will be presented. Expected benefits, findings and observations (if any) to date will also be discussed. The focus of the presentation will be on the project in general, status to date and future plans. The End-use services to be included in the prototype are voice, video, telemetry, commanding, collaboration tools and visualization among others. Security is addressed throughout the project and is being designed into the Grid technologies and standards development. The project is divided into three phases. Phase One establishes the baseline User-based services required for space flight operations listed above. Phase Two involves applying Gridlweb technologies to the User-based services and development of portals for access by users. Phase Three will allow NASA and end users to evaluate the services and determine the future of the technology as applied to space flight operational services. Although, Phase One, which includes the development of the quasi-operational User-based services of the prototype, development will be completed by March 2004, the application of Grid technologies to these services will have just begun. We will provide status of the Grid technologies to the individual User-based services. This effort will result in an extensible environment that incorporates existing and new spaceflight services into a standards-based framework providing current and future NASA programs with cost savings and new and evolvable methods to conduct science. This project will demonstrate how the use of new programming paradigms such as web and grid services can provide three significant benefits to the cost-effective delivery of spaceflight services. They will enable applications to operate more efficiently by being able to utilize pooled resources. They will also permit the reuse of common services to rapidly construct new and more powerful applications. Finally they will permit easy and secure access to services via a combination of grid and portal technology by a distributed user community consisting of NASA operations centers, scientists, the educational community and even the general population as outreach. The approach will be to deploy existing mission support applications such as the Telescience Resource Kit (TReK) and new applications under development, such as the Grid Video Distribution System (GViDS), together with existing grid applications and services such as high-performance computing and visualization services provided by NASA s Information Power Grid (IPG) in the MSFC s Payload Operations Integration Center (POIC) HOSC Annex. Once the initial applications have been moved to the grid, a process will begin to apply the new programming paradigms to integrate them where possible. For example, with GViDS, instead of viewing the Distribution service as an application that must run on a single node, the new approach is to build it such that it can be dispatched across a pool of resources in response to dynamic loads. To make this a reality, reusable services will be critical, such as a brokering service to locate appropriate resource within the pool. This brokering service can then be used by other applications such as the TReK. To expand further, if the GViDS application is constructed using a services-based mel, then other applications such as the Video Auditorium can then use GViDS as a service to easily incorporate these video streams into a collaborative conference. Finally, as these applications are re-factored into this new services-based paradigm, the construction of portals to integrate them will be a simple process. As a result, portals can be tailored to meet the requirements of specific user communities.

Bradford, Robert N.↗

Stereo vision for planetary rovers - Stochastic modeling to near real-time implementation

JPL has achieved the first autonomous cross-country robotic traverses to use stereo vision, with all computing onboard the vehicle. This paper describes the stereo vision system, including the underlying statistical model and the details of the implementation. It is argued that the overall approach provides a unifying paradigm for practical domain-independent stereo ranging.

Matthies, Larry↗

The Automated Instrumentation and Monitoring System (AIMS) reference manual

Whether a researcher is designing the 'next parallel programming paradigm,' another 'scalable multiprocessor' or investigating resource allocation algorithms for multiprocessors, a facility that enables parallel program execution to be captured and displayed is invaluable. Careful analysis of execution traces can help computer designers and software architects to uncover system behavior and to take advantage of specific application characteristics and hardware features. A software tool kit that facilitates performance evaluation of parallel applications on multiprocessors is described. The Automated Instrumentation and Monitoring System (AIMS) has four major software components: a source code instrumentor which automatically inserts active event recorders into the program's source code before compilation; a run time performance-monitoring library, which collects performance data; a trace file animation and analysis tool kit which reconstructs program execution from the trace file; and a trace post-processor which compensate for data collection overhead. Besides being used as prototype for developing new techniques for instrumenting, monitoring, and visualizing parallel program execution, AIMS is also being incorporated into the run-time environments of various hardware test beds to evaluate their impact on user productivity. Currently, AIMS instrumentors accept FORTRAN and C parallel programs written for Intel's NX operating system on the iPSC family of multi computers. A run-time performance-monitoring library for the iPSC/860 is included in this release. We plan to release monitors for other platforms (such as PVM and TMC's CM-5) in the near future. Performance data collected can be graphically displayed on workstations (e.g. Sun Sparc and SGI) supporting X-Windows (in particular, Xl IR5, Motif 1.1.3).

Yan, Jerry↗

The Automated Instrumentation and Monitoring System (AIMS): Design and Architecture

Whether a researcher is designing the 'next parallel programming paradigm', another 'scalable multiprocessor' or investigating resource allocation algorithms for multiprocessors, a facility that enables parallel program execution to be captured and displayed is invaluable. Careful analysis of such information can help computer and software architects to capture, and therefore, exploit behavioral variations among/within various parallel programs to take advantage of specific hardware characteristics. A software tool-set that facilitates performance evaluation of parallel applications on multiprocessors has been put together at NASA Ames Research Center under the sponsorship of NASA's High Performance Computing and Communications Program over the past five years. The Automated Instrumentation and Monitoring Systematic has three major software components: a source code instrumentor which automatically inserts active event recorders into program source code before compilation; a run-time performance monitoring library which collects performance data; and a visualization tool-set which reconstructs program execution based on the data collected. Besides being used as a prototype for developing new techniques for instrumenting, monitoring and presenting parallel program execution, AIMS is also being incorporated into the run-time environments of various hardware testbeds to evaluate their impact on user productivity. Currently, the execution of FORTRAN and C programs on the Intel Paragon and PALM workstations can be automatically instrumented and monitored. Performance data thus collected can be displayed graphically on various workstations. The process of performance tuning with AIMS will be illustrated using various NAB Parallel Benchmarks. This report includes a description of the internal architecture of AIMS and a listing of the source code.

Yan, Jerry C.↗

Self-consistent Quantum Iteratively Sparsified Hamiltonian Algorithm (SQuISH)

Due to coherence time limitations, reducing the resources required to run quantum algorithms and simulate physical systems on a quantum computer is crucial. With regards to Hamiltonian simulation, a significant effort has focused on building efficient algorithms using various factorizations and truncations, typically derived from the Hamiltonian alone. We introduce a new paradigm for improving Hamiltonian simulation and reducing the cost of ground state problems based on ideas recently developed for classical chemistry simulations. The key idea is that one can find efficient ways to reduce resources needed by quantum algorithms by making use of two key pieces of information: the Hamiltonian operator and an approximate ground state wavefunction. We refer to our algorithm as the self-consistent quantum iteratively sparsified Hamiltonian (SQuISH). By performing our scheme iteratively, one can drive SQuISH to create an accurate wavefunction using a truncated, resource-efficient Hamiltonian. By utilizing this more compact Hamiltonian, our algorithm provides an approach to reduce the gate complexity of ground state calculations on quantum hardware. As proof of principle, we implement SQuISH using configuration interaction for small molecules and coupled cluster for larger systems. Through our combination of approaches, we demonstrate how it performs on a range of systems, the largest of which would require more than 200 qubits to run on quantum hardware.

Diana Chamaki↗

Opus: A Coordination Language for Multidisciplinary Applications

Data parallel languages, such as High Performance fortran, can be successfully applied to a wide range of numerical applications. However, many advanced scientific and engineering applications are multidisciplinary and heterogeneous in nature, and thus do not fit well into the data parallel paradigm. In this paper we present Opus, a language designed to fill this gap. The central concept of Opus is a mechanism called ShareD Abstractions (SDA). An SDA can be used as a computation server, i.e., a locus of computational activity, or as a data repository for sharing data between asynchronous tasks. SDAs can be internally data parallel, providing support for the integration of data and task parallelism as well as nested task parallelism. They can thus be used to express multidisciplinary applications in a natural and efficient way. In this paper we describe the features of the language through a series of examples and give an overview of the runtime support required to implement these concepts in parallel and distributed environments.

Chapman, Barbara↗

Performance of OVERFLOW-D Applications based on Hybrid and MPI Paradigms on IBM Power4 System

This report briefly discusses our preliminary performance experiments with parallel versions of OVERFLOW-D applications. These applications are based on MPI and hybrid paradigms on the IBM Power4 system here at the NAS Division. This work is part of an effort to determine the suitability of the system and its parallel libraries (MPI/OpenMP) for specific scientific computing objectives.

Djomehri, M. Jahed↗

What Multilevel Parallel Programs do when you are not Watching: A Performance Analysis Case Study Comparing MPI/OpenMP, MLP, and Nested OpenMP

With the current trend in parallel computer architectures towards clusters of shared memory symmetric multi-processors, parallel programming techniques have evolved that support parallelism beyond a single level. When comparing the performance of applications based on different programming paradigms, it is important to differentiate between the influence of the programming model itself and other factors, such as implementation specific behavior of the operating system (OS) or architectural issues. Rewriting-a large scientific application in order to employ a new programming paradigms is usually a time consuming and error prone task. Before embarking on such an endeavor it is important to determine that there is really a gain that would not be possible with the current implementation. A detailed performance analysis is crucial to clarify these issues. The multilevel programming paradigms considered in this study are hybrid MPI/OpenMP, MLP, and nested OpenMP. The hybrid MPI/OpenMP approach is based on using MPI [7] for the coarse grained parallelization and OpenMP [9] for fine grained loop level parallelism. The MPI programming paradigm assumes a private address space for each process. Data is transferred by explicitly exchanging messages via calls to the MPI library. This model was originally designed for distributed memory architectures but is also suitable for shared memory systems. The second paradigm under consideration is MLP which was developed by Taft. The approach is similar to MPi/OpenMP, using a mix of coarse grain process level parallelization and loop level OpenMP parallelization. As it is the case with MPI, a private address space is assumed for each process. The MLP approach was developed for ccNUMA architectures and explicitly takes advantage of the availability of shared memory. A shared memory arena which is accessible by all processes is required. Communication is done by reading from and writing to the shared memory.

Jost, Gabriele↗

Efficient Parallelization of a Dynamic Unstructured Application on the Tera MTA

The success of parallel computing in solving real-life computationally-intensive problems relies on their efficient mapping and execution on large-scale multiprocessor architectures. Many important applications are both unstructured and dynamic in nature, making their efficient parallel implementation a daunting task. This paper presents the parallelization of a dynamic unstructured mesh adaptation algorithm using three popular programming paradigms on three leading supercomputers. We examine an MPI message-passing implementation on the Cray T3E and the SGI Origin2OOO, a shared-memory implementation using cache coherent nonuniform memory access (CC-NUMA) of the Origin2OOO, and a multi-threaded version on the newly-released Tera Multi-threaded Architecture (MTA). We compare several critical factors of this parallel code development, including runtime, scalability, programmability, and memory overhead. Our overall results demonstrate that multi-threaded systems offer tremendous potential for quickly and efficiently solving some of the most challenging real-life problems on parallel computers.

Oliker, Leonid↗

In-Time Safety Assessment & Risk Prediction for Unmanned Aerial Systems

One of the critical challenges in emerging autonomous systems is timely mitigation of hazards encountered during operation which may not be known or accounted for at the time of design. Efficient execution of unmanned systems therefore demands a paradigm shift from scheduled periodic maintenance to predictive risk analysis that includes condition-based-monitoring, real-time reliability assessment and hazard mitigation. Particularly, the state-of-health parameters needs to be computed at the component level, unit level as well as the integrated system level. While in the former two levels, the physics of health propagation may be based on underlying electro-mechanical properties, system level prognostics often relies on data-driven models. Further, uncertainty from model, measurements and input sources should be accurately quantified to generate meaningful prediction results that can be fed into reliable decision making processes. Finally, the expected risk and time to failure has to be computed based on the current state-of-health of the overall system. This talk presents a conceptual design of such an in-time safety assurance approach for unmanned aerial vehicles (UAV) operating at low altitudes near and over populated areas. Typical in-flight hazard incidents include unplanned detour, proximity to obstacles, mid-flight component faults, limited battery life and poor quality of GPS measurements. Safety assessment therefore comprises trajectory generation and re-plan, battery RUL computation, distributed fault diagnostics and uncertainty management of predicted trajectory based on GPS measurement noise. The entire monitoring framework will be demonstrated on simulated as well as real UAV flight experiments conducted at the NASA Langley Research Center. This tutorial will therefore guide the audience through a step-by-step tracking of an autonomous system with focus on in-time risk prediction in the presence of unforeseen hazards and uncertain environment.

diagnostics↗

Social Networking Adapted for Distributed Scientific Collaboration

Share is a social networking site with novel, specially designed feature sets to enable simultaneous remote collaboration and sharing of large data sets among scientists. The site will include not only the standard features found on popular consumer-oriented social networking sites such as Facebook and Myspace, but also a number of powerful tools to extend its functionality to a science collaboration site. A Virtual Observatory is a promising technology for making data accessible from various missions and instruments through a Web browser. Sci-Share augments services provided by Virtual Observatories by enabling distributed collaboration and sharing of downloaded and/or processed data among scientists. This will, in turn, increase science returns from NASA missions. Sci-Share also enables better utilization of NASA s high-performance computing resources by providing an easy and central mechanism to access and share large files on users space or those saved on mass storage. The most common means of remote scientific collaboration today remains the trio of e-mail for electronic communication, FTP for file sharing, and personalized Web sites for dissemination of papers and research results. Each of these tools has well-known limitations. Sci-Share transforms the social networking paradigm into a scientific collaboration environment by offering powerful tools for cooperative discourse and digital content sharing. Sci-Share differentiates itself by serving as an online repository for users digital content with the following unique features: a) Sharing of any file type, any size, from anywhere; b) Creation of projects and groups for controlled sharing; c) Module for sharing files on HPC (High Performance Computing) sites; d) Universal accessibility of staged files as embedded links on other sites (e.g. Facebook) and tools (e.g. e-mail); e) Drag-and-drop transfer of large files, replacing awkward e-mail attachments (and file size limitations); f) Enterprise-level data and messaging encryption; and g) Easy-to-use intuitive workflow.

Karimabadi, Homa↗