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Adagio 4.16 user s guide.

Adagio is a three-dimensional, implicit solid mechanics code with a versatile element library, nonlinear material models, and capabilities for modeling large deformation and contact. Adagio is a parallel code, and its nonlinear solver and contact capabilities enable scalable solutions of large problems. It is built on the SIERRA Framework [1, 2]. SIERRA provides a data management framework in a parallel computing environment that allows the addition of capabilities in a modular fashion. The Adagio 4.16 User's Guide provides information about the functionality in Adagio and the command structure required to access this functionality in a user input file. This document is divided into chapters based primarily on functionality. For example, the command structure related to the use of various element types is grouped in one chapter; descriptions of material models are grouped in another chapter. The input and usage of Adagio is similar to that of the code Presto [3]. Presto, like Adagio, is a solid mechanics code built on the SIERRA Framework. The primary difference between the two codes is that Presto uses explicit time integration for transient dynamics analysis, whereas Adagio is an implicit code. Because of the similarities in input and usage between Adagio and Presto, the user's guides for the two codes are structured in the same manner and share common material. (Once you have mastered the input structure for one code, it will be easy to master the syntax structure for the other code.) To maintain the commonality between the two user's guides, we have used a variety of techniques. For example, references to Presto may be found in the Adagio user's guide and vice versa, and the chapter order across the two guides is the same. On the other hand, each of the two user's guides is expressly tailored to the features of the specific code and documents the particular functionality for that code. For example, though both Presto and Adagio have contact functionality, the content of the chapter on contact in the two guides differs. Important references for both Adagio and Presto are given in the references section at the end of this chapter. Adagio was preceded by the codes JAC and JAS3D; JAC is described in Reference 4; JAS3D is described in Reference 5. Presto was preceded by the code Pronto3D. Pronto3D is described in References 6 and 7. Some of the fundamental nonlinear technology used by both Presto and Adagio are described in References 8, 9, and 10. Currently, both Presto and Adagio use the Exodus II database and the XDMF database; Exodus II is more commonly used than XDMF. (Other options may be added in the future.) The Exodus II database format is described in Reference 11, and the XDMF database format is described in Reference 12. Important information about contact is provided in the reference document for ACME [13]. ACME is a third-party library for contact. One of the key concepts for the command structure in the input file is a concept referred to as scope. A detailed explanation of scope is provided in Section 1.2. Most of the command lines in Chapter 2 are related to a certain scope rather than to some particular functionality.

97 MATHEMATICS AND COMPUTING↗

Interfacing with Legacy using Remote Method Invocation

The assignment described was enough to make a neophyte Java developer bolt for the door: provide a remote method for use by an applet which invokes a native method that wraps a function in an existing legacy library. The purpose of the remote method is to return an instance of a class object whose contents reflect the data structure returned by the legacy function. While embroiled in implementation, I would have spent the time wading through their JNI use group archive as well, but I couldn't seem to locate one. Subsequently, I made the decision to try to document my findings in order to assist others. Before we start on the class design, let's look at what the existing legacy code does. The C function to be called, Get-Legacy-Data, consists of two steps: an ASII file is read from the local disk and its contents are parsed into a Legacy_Type structure whose address is passed as an argument by the caller. The legacy code was compiled into a shared object library, legacy. so, using the IRIX 6.2 compiler and then loaded onto the Web server, a Silicon Graphics Indy station loaded with the IRIX 6.4 operating system. As far as the class design is concerned, the first thing required is a class to act as a template for the data structure returned by the legacy function. This class, JLegacy, declares a series of public instance variables which correspond to the members of Legacy_Type and provides a parameterless constructor. This constructor is never called, not even by the native method which allocates the object for return to the remote method. Next, the remote interface declaration for the remote object must be defined. In order for JLegacyRO to implement getJLegacy, JLegacyRO must interface with the existing legacy code through a native method, getn. getn is declared in the JLegacyRO class but implemented in C, just like the legacy code. getn returns a JLegacy instance and is declared static since its implementation is the same for all instances of the JLegacyRO class.

Howard, Scott M.↗

On Why It Is Impossible to Prove that the BDX90 Dispatcher Implements a Time-sharing System

The Software Implemented Fault Tolerance SIFT system, is written in PASCAL except for about a page of machine code. The SIFT system implements a small time sharing system in which PASCAL programs for separate application tasks are executed according to a schedule with real time constraints. The PASCAL language has no provision for handling the notion of an interrupt such as the B930 clock interrupt. The PASCAL language also lacks the notion of running a PASCAL subroutine for a given amount of time, suspending it, saving away the suspension, and later activating the suspension. Machine code was used to overcome these inadequacies of PASCAL. Code which handles clock interrupts and suspends processes is called a dispatcher. The time sharing/virtual machine idea is completely destroyed by the reconfiguration task. After termination of the reconfiguration task, the tasks run by the dispatcher have no relation to those run before reconfiguration. It is impossible to view the dispatcher as a time-sharing system implementing virtual BDX930s running concurrently when one process can wipe out the others.

Boyer, R. S.↗

MODTRAN3: An update and recent validations against airborne high resolution interferometer measurements

MODTRAN, the Moderate Resolution Atmospheric Radiance and Transmittance Model, encompasses all the capabilities of LOWTRAN 7, the widely used 20 cm(exp -1) resolution radiance code, but incorporates a much more sensitive molecular band model with 2 cm(exp -1) resolution. MODTRAN contains many important elements that other band model based radiative transfer codes do not incorporate. It shares with FASCODE: spherical geometry, single and multiple scattering default atmospheric profile descriptors (gases, aerosols, clouds, fogs, and rain), and molecular continua (H2O, CO2, O3, O2, N2). In addition, it can calculate the solar/lunar direct and scattered radiation. MODTRAN3 was released to the general public in November 1994. It has several important features that the previous version, MODTRAN2, does not have. Chloro-fluorocarbon (CFC) and related heavy molecules (whose spectroscopic properties first appear on the HITRAN92 data base as temperature-dependent cross sections) have been incorporated into pseudo-band models, with provision for using both default and user supplied profiles. The addition of SO2 and O2 in the UV, along with upgraded ozone Chappuis bands in the visible is also part of MODTRAN3. An improved multiple scattering algorithm, the DIScrete Ordinate Radiative Transfer (DISORT) has also been incorporated into MODTRAN3. MODTRAN is very fast: simple timing runs of MODTRAN3 vs. FASCOD3 show an improvement of more than a factor of 100 for a typical 500 cm(exp -1) spectral interval and comparable vertical layering. Speed is an important consideration in heating/cooling rates calculations, where a large number of radiative transfer calculations are needed. The MODTRAN3 used in this study is based on HITRAN92, but as mentioned, above, it will be upgraded to HITRAN94 upon its release at the end of 1994. MODTRAN has been adopted by: some researchers in the AVIRIS program as one radiative transfer code to derive surface reflectance from AVIRIS measurements. The accuracy of the code is very important because any errors in the radiative transfer calculation will directly translate into errors in the derived surface reflectance. In this paper, the new solar irradiance calculated by Kurucz, which is adopted in MODTRAN3, will be presented. Recent validations of MODTRAN3 with airborne high resolution interferometer measurements over ocean will be discussed. Good agreeement between model calculations and measurements was achieved.

Anderson, Gail P.↗

Snowmass Computational Frontier: Topical Group Report on Experimental Algorithm Parallelization

The substantial increase in data volume and complexity expected from future experiments will require significant investment to prepare experimental algorithms. These algorithms include physics object reconstruction, calibrations, and processing of observational data. In addition, the changing computing architecture landscape, which will be primarily composed of heterogeneous resources, will continue to pose major challenges with regard to algorithmic migration. Portable tools need to be developed that can be shared among the frontiers (e.g., for code execution on different platforms) and opportunities, such as forums or cross-experimental working groups, need to be provided where experiences and lessons learned can be shared between experiments and frontiers. At the same time, individual experiments also need to invest considerable resources to develop algorithms unique to their needs (e.g., for facilities dedicated to the experiment), and ensure that their specific algorithms will be able to efficiently exploit external heterogeneous computing facilities. Common software tools represent a cost-effective solution, providing ready-to-use software solutions as well as a platform for R&D work. These are particularly important for small experiments which typically do not have dedicated resources needed to face the challenges imposed by the evolving computing technologies. Workforce development is a key concern across frontiers and experiments, and additional support is needed to provide career opportunities for researchers working in the field of experimental algorithm development. Finally, cross-discipline collaborations going beyond high-energy physics are a key ingredient to address the challenges ahead and more support for such collaborations needs to be created. This report targets future experiments, observations and experimental algorithm development for the next 10-15 years.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Production Level CFD Code Acceleration for Hybrid Many-Core Architectures

In this work, a novel graphics processing unit (GPU) distributed sharing model for hybrid many-core architectures is introduced and employed in the acceleration of a production-level computational fluid dynamics (CFD) code. The latest generation graphics hardware allows multiple processor cores to simultaneously share a single GPU through concurrent kernel execution. This feature has allowed the NASA FUN3D code to be accelerated in parallel with up to four processor cores sharing a single GPU. For codes to scale and fully use resources on these and the next generation machines, codes will need to employ some type of GPU sharing model, as presented in this work. Findings include the effects of GPU sharing on overall performance. A discussion of the inherent challenges that parallel unstructured CFD codes face in accelerator-based computing environments is included, with considerations for future generation architectures. This work was completed by the author in August 2010, and reflects the analysis and results of the time.

Duffy, Austen C.↗

Residual entanglement of accelerated fermions is useful

The non-vanishing residual entanglement, between the fermionic modes in the infinite acceleration limit, does not violate CHSH inequality, therefore it is not non-local. In this paper, we study the usefulness of the residual fermionic entanglement in single mode approximation and beyond single mode approximation. It is shown that there are some cases where the CHSH inequality is not violated by the residual entanglement, but the state is useful for quantum teleportation. Conditions for the violation of the CHSH inequality in terms of the “presence probability” of the particle in different Rindler regions are given for the state to be useful for teleportation and superdense coding. - Highlights: • Werner state is shared between an inertial observer and a uniformly accelerated one. • Single mode and beyond single mode approximation are considered. • Usefulness of residual entanglement in the infinite acceleration limit is studied. • The CHSH inequality and the quantum teleportation are used as a criterion. • Useful states for quantum information processing are found in the infinite acceleration.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Evaluation of hydrologic components of community land model 4 and bias identification

Runoff and soil moisture are two key components of the global hydrologic cycle that should be validated at local to global scales in Earth System Models (ESMs) used for climate projection. Here, we have evaluated the runoff and surface soil moisture output by the Community Climate System Model (CCSM) along with 8 other models from the Coupled Model Intercomparison Project (CMIP5) repository using satellite soil moisture observations and stream gauge corrected runoff products. A series of Community Land Model (CLM) runs forced by reanalysis and coupled model outputs was also performed to identify atmospheric drivers of biases and uncertainties in the CCSM. Results indicate that surface soil moisture simulations tend to be positively biased in high latitude areas by most selected CMIP5 models except CCSM, FGOALS, and BCC, which share similar land surface model code. With the exception of GISS, runoff simulations by all selected CMIP5 models were overestimated in mountain ranges and in most of the Arctic region. In general, positive biases in CCSM soil moisture and runoff due to precipitation input error were offset by negative biases induced by temperature input error. Excluding the impact from atmosphere modeling, the global mean of seasonal surface moisture oscillation was out of phase compared to observations in many years during 1985–2004. The CLM also underestimated runoff in the Amazon, central Africa, and south Asia, where soils all have high clay content. We hypothesize that lack of a macropore flow mechanism is partially responsible for this underestimation. However, runoff was overestimated in the areas covered by volcanic ash soils (i.e., Andisols), which might be associated with poor soil porosity representation in CLM. Finally, our results indicate that CCSM predictability of hydrology could be improved by addressing the compensating errors associated with precipitation and temperature and updating the CLM soil representation.

54 ENVIRONMENTAL SCIENCES↗

Reproducibility in materials informatics: lessons from ‘A general-purpose machine learning framework for predicting properties of inorganic materials’

The integration of machine learning techniques in materials discovery has become prominent in materials science research and has been accompanied by an increasing trend towards open data and open-source tools to propel the field. Despite the increasing usefulness and capabilities of these tools, developers neglecting to follow reproducible practices presents a significant barrier for other researchers looking to use or build upon their work. In this study, we investigate the challenges encountered while attempting to reproduce a section of the results presented in “A general-purpose machine learning framework for predicting properties of inorganic materials.” Our analysis identifies four major categories of challenges: (1) reporting software dependencies, (2) recording and sharing version logs, (3) sequential code organization, and (4) clarifying code references within the manuscript. The result is a proposed set of tangible action items for those aiming to make material informatics tools accessible to, and useful for the community.

36 MATERIALS SCIENCE↗

SU-F-P-10: A Web-Based Radiation Safety Relational Database Module for Regulatory Compliance

Purpose: Maintaining compliance with Radioactive Materials Licenses is inherently a time-consuming task requiring focus and attention to detail. Staff tasked with these responsibilities, such as the Radiation Safety Officer and associated personnel must retain disparate records for eventual placement into one or more annual reports. Entering results and records in a relational database using a web browser as the interface, and storing that data in a cloud-based storage site, removes procedural barriers. The data becomes more adaptable for mining and sharing. Methods: Web-based code was written utilizing the web framework Django, written in Python. Additionally, the application utilizes JavaScript for front-end interaction, SQL, HTML and CSS. Quality assurance code testing is performed in a sequential style, and new code is only added after the successful testing of the previous goals. Separate sections of the module include data entry and analysis for audits, surveys, quality management, and continuous quality improvement. Data elements can be adapted for quarterly and annual reporting, and for immediate notification of user determined alarm settings. Results: Current advances are focusing on user interface issues, and determining the simplest manner by which to teach the user to build query forms. One solution has been to prepare library documents that a user can select or edit in place of creation a new document. Forms are being developed based upon Nuclear Regulatory Commission federal code, and will be expanded to include State Regulations. Conclusion: Establishing a secure website to act as the portal for data entry, storage and manipulation can lead to added efficiencies for a Radiation Safety Program. Access to multiple databases can lead to mining for big data programs, and for determining safety issues before they occur. Overcoming web programming challenges, a category that includes mathematical handling, is providing challenges that are being overcome.

61 RADIATION PROTECTION AND DOSIMETRY↗

SOX2-driven enhancer landscape defines the transcriptional architecture of retinogenesis

Retinal neurogenesis is mediated by the coordinated activities of a complex gene regulatory network (GRN) of transcription factors (TFs) in multipotent retinal progenitor cells (RPCs). How this GRN mechanistically guides neural competence remains poorly understood. In this study, we present integrated transcriptional, genetic and genomic analyses to uncover the regulatory mechanisms of SOX2, a key factor in establishing neural identity in RPCs. We show that SOX2 is preferentially enriched in the RPC-specific enhancer landscape associated with essential regulators of retinogenesis. Disruption of SOX2 expression impairs retinogenesis, marked by a selective loss of enhancer activity near genes essential for RPC proliferation and lineage specification. We identified the RPC transcription factor VSX2 as a binding partner for SOX2 and, together, SOX2 and VSX2 co-target a core, retina-specific chromatin repertoire characterized by enhanced TF binding and robust chromatin accessibility. This cooperative binding establishes a shared SOX2-VSX2 transcriptional code that promotes the expression of crucial regulators of neurogenesis while repressing the acquisition of alternative lineage cell fate. Our data illuminate fundamental biological insights on how transcription factors act in concert to drive chromatin-based genetic programs underlying retinal neural identity.

Chromatin↗

Terascale High-Fidelity Simulations of Turbulent Combustion with Detailed Chemistry

The TSTC project is a multi-university collaborative effort to develop a high-fidelity turbulent reacting flow simulation capability utilizing terascale, massively parallel computer technology. The main paradigm of our approach is direct numerical simulation (DNS) featuring highest temporal and spatial accuracy, allowing quantitative observations of the fine-scale physics found in turbulent reacting flows as well as providing a useful tool for development of sub-models needed in device-level simulations. The code named S3D, developed and shared with Chen and coworkers at Sandia National Laboratories, has been enhanced with new numerical algorithms and physical models to provide predictive capabilities for spray dynamics, combustion, and pollutant formation processes in turbulent combustion. Major accomplishments include improved characteristic boundary conditions, fundamental studies of auto-ignition in turbulent stratified reactant mixtures, flame-wall interaction, and turbulent flame extinction by water spray. The overarching scientific issue in our recent investigations is to characterize criticality phenomena (ignition/extinction) in turbulent combustion, thereby developing unified criteria to identify ignition and extinction conditions. The computational development under TSTC has enabled the recent large-scale 3D turbulent combustion simulations conducted at Sandia National Laboratories.

33 ADVANCED PROPULSION SYSTEMS↗

Level-2 Milestone 5588: Deliver Strategic Plan and Initial Scalability Assessment by Advanced Architecture and Portability Specialists Team

This report documents the fact that the work in creating a strategic plan and beginning customer engagements has been completed. The description of milestone is: The newly formed advanced architecture and portability specialists (AAPS) team will develop a strategic plan to meet the goals of 1) sharing knowledge and experience with code teams to ensure that ASC codes run well on new architectures, and 2) supplying skilled computational scientists to put the strategy into practice. The plan will be delivered to ASC management in the first quarter. By the fourth quarter, the team will identify their first customers within PEM and IC, perform an initial assessment and scalability and performance bottleneck for next-generation architectures, and embed AAPS team members with customer code teams to assist with initial portability development within standalone kernels or proxy applications.

97 MATHEMATICS AND COMPUTING↗

Comparison of Auxenochlorella protothecoides and Chlorella spp. Chloroplast Genomes: Evidence for Endosymbiosis and Horizontal Virus-like Gene Transfer

Resequencing of the chloroplast genome (cpDNA) of Auxenochlorella protothecoides UTEX 25 was completed (GenBank Accession no. KC631634.1), revealing a genome size of 84,576 base pairs and 30.8% GC content, consistent with features reported for the previously sequenced A. protothecoides 0710, (GenBank Accession no. KC843975). The A. protothecoides UTEX 25 cpDNA encoded 78 predicted open reading frames, 32 tRNAs, and 4 rRNAs, making it smaller and more compact than the cpDNA genome of C. variabilis (124,579 bp) and C. vulgaris (150,613 bp). By comparison, the compact genome size of A. protothecoides was attributable primarily to a lower intergenic sequence content. The cpDNA coding regions of all known Chlorella species were found to be organized in conserved colinear blocks, with some rearrangements. The Auxenochlorella and Chlorella species genome structure and composition were similar, and of particular interest were genes influencing photosynthetic efficiency, i.e., chlorophyll synthesis and photosystem subunit I and II genes, consistent with other biofuel species of interest. Phylogenetic analysis revealed that Prototheca cutis is the closest known A. protothecoides relative, followed by members of the genus Chlorella. The cpDNA of A. protothecoides encodes 37 genes that are highly homologous to representative cyanobacteria species, including rrn16, rrn23, and psbA, corroborating a well-recognized symbiosis. Several putative coding regions were identified that shared high nucleotide sequence identity with virus-like sequences, suggestive of horizontal gene transfer. Despite these predictions, no corresponding transcripts were obtained by RT-PCR amplification, indicating they are unlikely to be expressed in the extant lineage.

59 BASIC BIOLOGICAL SCIENCES↗

DTS: Building custom, intelligent schedulers

DTS is a decision-theoretic scheduler, built on top of a flexible toolkit -- this paper focuses on how the toolkit might be reused in future NASA mission schedulers. The toolkit includes a user-customizable scheduling interface, and a 'Just-For-You' optimization engine. The customizable interface is built on two metaphors: objects and dynamic graphs. Objects help to structure problem specifications and related data, while dynamic graphs simplify the specification of graphical schedule editors (such as Gantt charts). The interface can be used with any 'back-end' scheduler, through dynamically-loaded code, interprocess communication, or a shared database. The 'Just-For-You' optimization engine includes user-specific utility functions, automatically compiled heuristic evaluations, and a postprocessing facility for enforcing scheduling policies. The optimization engine is based on BPS, the Bayesian Problem-Solver (1,2), which introduced a similar approach to solving single-agent and adversarial graph search problems.

Hansson, Othar↗

Comparison of 250 MHz R10K Origin 2000 and 400 MHz Origin 2000 Using NAS Parallel Benchmarks

This report describes results of benchmark tests on Steger, a 250 MHz Origin 2000 system with R10K processors, currently installed at the NASA Ames National Advanced Supercomputing (NAS) facility. For comparison purposes, the tests were also run on Lomax, a 400 MHz Origin 2000 with R12K processors. The BT, LU, and SP application benchmarks in the NAS Parallel Benchmark Suite and the kernel benchmark FT were chosen to measure system performance. Having been written to measure performance on Computational Fluid Dynamics applications, these benchmarks are assumed appropriate to represent the NAS workload. Since the NAS runs both message passing (MPI) and shared-memory, compiler directive type codes, both MPI and OpenMP versions of the benchmarks were used. The MPI versions used were the latest official release of the NAS Parallel Benchmarks, version 2.3. The OpenMP versions used were PBN3b2, a beta version that is in the process of being released. NPB 2.3 and PBN3b2 are technically different benchmarks, and NPB results are not directly comparable to PBN results.

Turney, Raymond D.↗

Comparison of Origin 2000 and Origin 3000 Using NAS Parallel Benchmarks

This report describes results of benchmark tests on the Origin 3000 system currently being installed at the NASA Ames National Advanced Supercomputing facility. This machine will ultimately contain 1024 R14K processors. The first part of the system, installed in November, 2000 and named mendel, is an Origin 3000 with 128 R12K processors. For comparison purposes, the tests were also run on lomax, an Origin 2000 with R12K processors. The BT, LU, and SP application benchmarks in the NAS Parallel Benchmark Suite and the kernel benchmark FT were chosen to determine system performance and measure the impact of changes on the machine as it evolves. Having been written to measure performance on Computational Fluid Dynamics applications, these benchmarks are assumed appropriate to represent the NAS workload. Since the NAS runs both message passing (MPI) and shared-memory, compiler directive type codes, both MPI and OpenMP versions of the benchmarks were used. The MPI versions used were the latest official release of the NAS Parallel Benchmarks, version 2.3. The OpenMP versiqns used were PBN3b2, a beta version that is in the process of being released. NPB 2.3 and PBN 3b2 are technically different benchmarks, and NPB results are not directly comparable to PBN results.

Turney, Raymond D.↗

Large-Eddy Simulation Code Developed for Propulsion Applications

A large-eddy simulation (LES) code was developed at the NASA Glenn Research Center to provide more accurate and detailed computational analyses of propulsion flow fields. The accuracy of current computational fluid dynamics (CFD) methods is limited primarily by their inability to properly account for the turbulent motion present in virtually all propulsion flows. Because the efficiency and performance of a propulsion system are highly dependent on the details of this turbulent motion, it is critical for CFD to accurately model it. The LES code promises to give new CFD simulations an advantage over older methods by directly computing the large turbulent eddies, to correctly predict their effect on a propulsion system. Turbulent motion is a random, unsteady process whose behavior is difficult to predict through computer simulations. Current methods are based on Reynolds-Averaged Navier- Stokes (RANS) analyses that rely on models to represent the effect of turbulence within a flow field. The quality of the results depends on the quality of the model and its applicability to the type of flow field being studied. LES promises to be more accurate because it drastically reduces the amount of modeling necessary. It is the logical step toward improving turbulent flow predictions. In LES, the large-scale dominant turbulent motion is computed directly, leaving only the less significant small turbulent scales to be modeled. As part of the prediction, the LES method generates detailed information on the turbulence itself, providing important information for other applications, such as aeroacoustics. The LES code developed at Glenn for propulsion flow fields is being used to both analyze propulsion system components and test improved LES algorithms (subgrid-scale models, filters, and numerical schemes). The code solves the compressible Favre-filtered Navier- Stokes equations using an explicit fourth-order accurate numerical scheme, it incorporates a compressible form of Smagorinsky s model for the subgrid-scale turbulence, and it uses generalized curvilinear coordinates to allow analysis of a wide range of geometries. The code runs in parallel on shared memory multiprocessor computers and is written in Fortran 90 with dynamic memory allocation. A sample result for a Mach-1.4 round jet is presented in the figure. Instantaneous Mach number contours in several cross-planes downstream of the nozzle exit are shown, illustrating how an LES captures the large unsteady three-dimensional turbulent structures present in the jet.

DeBonis, James R.↗