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DOE OSTI2025

PETSc/TAO Users Manual Revision 3.24

This manual describes the use of the Portable, Extensible Toolkit for Scientific Computation (PETSc) and the Toolkit for Advanced Optimization (TAO) for the numerical solution of partial differential equations (PDEs) and related problems on high-performance computers. PETSc/TAO is a suite of data structures and routines that provide the building blocks for implementing large-scale application codes on parallel (and serial) computers. PETSc uses the MPI standard for all distributed memory communication.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2026

PETSc/TAO Users Manual Revision 3.25

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗

DOE OSTI2025

Demonstration of Optimal Benchmark Selection Website and Validation of the q c Coverage Metric Using HEU-SOL-THERM-013-003 Experiment

In the work documented in this interim report, the experiment selection toolkit web site was demonstrated and q C coverage metric methodology was validated for IEU-MET-FAST-002-001, MIX-COMP-THERM 004-004, and HEU-SOL-THERM-013-003 experiments. 𝑞 𝐶 is an information-theoretic measure based on mutual information that quantifies the ability of candidate benchmark experiments to reduce the bias and uncertainty of a target criticality safety application. The metric and an accompanying open-source Python toolkit with a web-based interface were tested against a benchmark set of 425 experiments drawn from the International Criticality Safety Benchmark Evaluation Project Handbook. The interface is hosted at https://edim.covdef.com. It accepts sensitivity data files produced by the TSUNAMI-IP module of the SCALE code system and supports both (i) deterministic analysis using the ENDF/B-VII.0 covariance library and (ii) stochastic analysis based on user-supplied keff samples. Demonstrations on representative applications across a range of material composition, spectrum, and form show that q C -guided benchmark selection achieves greater uncertainty reduction with fewer experiments and yields more stable posterior bias and uncertainty estimates than traditional similarity coefficient ( c k )–based selection, while also capturing valuable low-ck experiments that one-to-one metrics overlook.

Abdel-khalik, Hany S. [Indiana Univ.-Purdue Univ. ↗

DOE OSTI2023

Impact of Aerodynamic Modeling Assumptions on Flutter Speeds of Vertical-Axis Wind Turbines

Theodorsen’s unsteady aerodynamic theory has been used extensively in flutter speed prediction of wind turbine blades. In this study, three key assumptions of Theodorsen theory (thin airfoil, flat wake, and small angle of attack) have been revisited, and all three assumptions have been addressed in combination to obtain new lift and moment equations that are subsequently applied in flutter calculations for full-scale vertical-axis wind turbine (VAWT) rotors, not just of an individual airfoil or blade. Furthermore, edgewise aerodynamics terms are added to the lift and moment equations to include their effects on flutter speeds. The newly obtained equations were implemented in the OWENS (Offshore Wind ENergy Simulation) toolkit, which is an FEM (Finite Element Method)-based toolkit for aeroelastic analysis of VAWTs. The effect of modifying each of these assumptions has been studied for the flutter RPM prediction of three primary modes of flutter of VAWTs: propeller, butterfly, and tower modes. For the land-based case, the most change was observed for the flutter RPM of the propeller mode, with a maximum increase of 2.62% for the two-bladed UTD 5 MW VAWT case. For the floating offshore case, the primary flutter modes (tower and platform pitch) were not significantly affected.

Engineering↗

DOE OSTI2026

Advances in genetic tools for metabolic engineering of non-conventional yeasts

Non-conventional yeasts are emerging as powerful alternatives to Saccharomyces cerevisiae for metabolic engineering, owing to their innate stress tolerance, broad substrate utilization, and distinctive metabolic capabilities. These attributes position them as promising chassis for producing biofuels, pharmaceuticals, and specialty chemicals. This review synthesizes recent advances in genetic toolkits for four such species—Pichia kudriavzevii (Issatchenkia orientalis), Starmerella bombicola, Debaryomyces hansenii, and Pachysolen tannophilus—highlighting progress across plasmid architectures (episomal and integrative), identification of autonomously replicating sequences and centromeric elements, and the development of safe-harbor genomic loci. We summarize promoter and terminator libraries enabling tunable expression, the expansion of auxotrophic and antifungal selection markers with recycling strategies, and the rapid adaptation of CRISPR-based systems (Cas9 and Cas12a) with optimized guide RNA expression, multiplex editing, and approaches that enhance homologous recombination (e.g., KU70/80 disruption). We also review landing-pad platforms for modular, repeated integrations and transposon-based tools (e.g., piggyBac) that facilitate multigene pathway assembly. Collectively, these innovations are accelerating design-build-test-learn cycles and enabling precise, scalable engineering of non-conventional yeasts. Remaining challenges—including limited species-specific episomal systems, variable transformation efficiencies, genome-stability concerns, and alternative codon usage—define clear priorities for future toolkit development. Together, these advances and open needs chart a path toward robust, sustainable biomanufacturing using diverse non-conventional yeast chassis.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2016

PROPERTIES OF CARBON–OXYGEN WHITE DWARFS FROM MONTE CARLO STELLAR MODELS

We investigate properties of carbon–oxygen white dwarfs with respect to the composite uncertainties in the reaction rates using the stellar evolution toolkit, Modules for Experiments in Stellar Astrophysics (MESA) and the probability density functions in the reaction rate library STARLIB. These are the first Monte Carlo stellar evolution studies that use complete stellar models. Focusing on 3 M{sub ⊙} models evolved from the pre main-sequence to the first thermal pulse, we survey the remnant core mass, composition, and structure properties as a function of 26 STARLIB reaction rates covering hydrogen and helium burning using a Principal Component Analysis and Spearman Rank-Order Correlation. Relative to the arithmetic mean value, we find the width of the 95% confidence interval to be ΔM{sub 1TP} ≈ 0.019 M{sub ⊙} for the core mass at the first thermal pulse, Δt{sub 1TP} ≈ 12.50 Myr for the age, Δlog(T{sub c}/K) ≈ 0.013 for the central temperature, Δlog(ρ{sub c}/g cm{sup −3}) ≈ 0.060 for the central density, ΔY{sub e,c} ≈ 2.6 × 10{sup −5} for the central electron fraction, ΔX{sub c}({sup 22}Ne) ≈ 5.8 × 10{sup −4}, ΔX{sub c}({sup 12}C) ≈ 0.392, and ΔX{sub c}({sup 16}O) ≈ 0.392. Uncertainties in the experimental {sup 12}C(α,γ){sup 16}O, triple-α, and {sup 14}N(p,γ){sup 15}O reaction rates dominate these variations. We also consider a grid of 1–6 M{sub ⊙} models evolved from the pre main-sequence to the final white dwarf to probe the sensitivity of the initial–final mass relation to experimental uncertainties in the hydrogen and helium reaction rates.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2017

Forward Modeling of Large-scale Structure: An Open-source Approach with Halotools

Here, we present the first stable release of Halotools (v0.2), a community-driven Python package designed to build and test models of the galaxy-halo connection. Halotools provides a modular platform for creating mock universes of galaxies starting from a catalog of dark matter halos obtained from a cosmological simulation. The package supports many of the common forms used to describe galaxy-halo models: the halo occupation distribution (HOD), the conditional luminosity function (CLF), abundance matching, and alternatives to these models that include effects such as environmental quenching or variable galaxy assembly bias. Satellite galaxies can be modeled to live in subhalos, or to follow custom number density profiles within their halos, including spatial and/or velocity bias with respect to the dark matter profile. Here, the package has an optimized toolkit to make mock observations on a synthetic galaxy population, including galaxy clustering, galaxy-galaxy lensing, galaxy group identification, RSD multipoles, void statistics, pairwise velocities and others, allowing direct comparison to observations. Halotools is object-oriented, enabling complex models to be built from a set of simple, interchangeable components, including those of your own creation.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2016

THE AGORA HIGH-RESOLUTION GALAXY SIMULATIONS COMPARISON PROJECT. II. ISOLATED DISK TEST

Using an isolated Milky Way-mass galaxy simulation, we compare results from nine state-of-the-art gravito-hydrodynamics codes widely used in the numerical community. We utilize the infrastructure we have built for the AGORA High-resolution Galaxy Simulations Comparison Project. This includes the common disk initial conditions, common physics models (e.g., radiative cooling and UV background by the standardized package Grackle) and common analysis toolkit yt, all of which are publicly available. Subgrid physics models such as Jeans pressure floor, star formation, supernova feedback energy, and metal production are carefully constrained across code platforms. With numerical accuracy that resolves the disk scale height, we find that the codes overall agree well with one another in many dimensions including: gas and stellar surface densities, rotation curves, velocity dispersions, density and temperature distribution functions, disk vertical heights, stellar clumps, star formation rates, and Kennicutt–Schmidt relations. Quantities such as velocity dispersions are very robust (agreement within a few tens of percent at all radii) while measures like newly formed stellar clump mass functions show more significant variation (difference by up to a factor of ∼3). Systematic differences exist, for example, between mesh-based and particle-based codes in the low-density region, and between more diffusive and less diffusive schemes in the high-density tail of the density distribution. Yet intrinsic code differences are generally small compared to the variations in numerical implementations of the common subgrid physics such as supernova feedback. Our experiment reassures that, if adequately designed in accordance with our proposed common parameters, results of a modern high-resolution galaxy formation simulation are more sensitive to input physics than to intrinsic differences in numerical schemes.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2022

CLASSY IV. Exploring UV Diagnostics of the Interstellar Medium in Local High- z Analogs at the Dawn of the JWST Era

The Cosmic Origins Spectrograph (COS) Legacy Archive Spectroscopic SurveY (CLASSY) provides the first high resolution spectral catalog of 45 local high-z analogs in the ultraviolet (UV; 1200–2000 Å) to investigate their stellar and gas properties. Here we present a toolkit of UV interstellar medium (ISM) diagnostics, analyzing the main emission lines of CLASSY spectra (N IV] λλ1483,87, C IV λλ1548,51, He IIλ1640, O III]λλ1661,6, Si III] λλ1883,92, C III] λ1907,9). Specifically, our aim is to provide accurate diagnostics for the reddening E(B - V), electron density n e , electron temperature T e , metallicity 12+log(O/H), and ionization parameter log(U), taking the different ISM ionization zones into account. We calibrate our UV toolkit using well-known optical diagnostics, analyzing archival optical spectra for all CLASSY targets. We find that UV density diagnostics estimate n e values that are ~1–2 dex higher (e.g., n e (C III] λλ1907,9) ~ 10 4 cm -3 ) than those inferred from their optical counterparts (e.g., n e ([S II]λλ6717,31) ~ 10 2 cm -3 ; n e ([Ar IV]λλ4714,41) ~ 10 3 cm -3 ). T e derived from the hybrid ratio [O III] λ1666/λ5007 proves to be reliable, implying differences in determining 12+log(O/H) compared to the optical counterpart O III] λ4363/[O III] λ5007 within ~ ±0.3 dex. We also investigate the relation between the stellar and gas E(B - V), finding consistent values at high specific star formation rates (sSFRs; log sSFR ≳ -8 yr -1 ), while at low sSFRs we confirmed an excess of dust attenuation in the gas. Finally, we investigate UV line ratios and equivalent widths to provide correlations with 12+log (O/H) and log(U), but note that there are degeneracies between the two. With this suite of UV-based diagnostics, we illustrate the pivotal role CLASSY plays in understanding the chemical and physical properties of high-z systems that JWST can observe in the rest-frame UV.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2018

sympl (v. 0.4.0) and climt (v. 0.15.3) – towards a flexible framework for building model hierarchies in Python

sympl (System for Modelling Planets) andclimt (Climate Modelling and Diagnostics Toolkit) are anattempt to rethink climate modelling frameworks from the ground up. The aimis to use expressive data structures available in the scientific Pythonecosystem along with best practices in software design to allow scientists toeasily and reliably combine model components to represent the climate systemat a desired level of complexity and to enable users to fully understandwhat the model is doing. sympl is a framework which formulates the model in terms of astate that gets evolved forward in time or modified within a specifictime by well-defined components. sympl's design facilitates buildingmodels that are self-documenting, are highly interoperable, and providefine-grained control over model components and behaviour. symplcomponents contain all relevant information about the input they expect andoutput that they provide. Components are designed to be easily interchanged,even when they rely on different units or array configurations.sympl provides basic functions and objects which could be used inany type of Earth system model. climt is an Earth system modelling toolkit that contains scientificcomponents built using sympl base objects. These include both purePython components and wrapped Fortran libraries. climt providesfunctionality requiring model-specific assumptions, such as stateinitialization and grid configuration. climt's programming interfacedesigned to be easy to use and thus appealing to a wide audience. Model building, configuration and execution are performed through a Pythonscript (or Jupyter Notebook), enabling researchers to build an end-to-endPython-based pipeline along with popular Python data analysis andvisualization tools.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2021

A Twenty-Year Analysis of Winds in California for Offshore Wind Energy Production Using WRF v4.1.2

Offshore wind resource characterization in the United States relies heavily on simulated winds from numerical weather prediction (NWP) models, given the lack of hub-height observations offshore. One such NWP data set used extensively by U.S. stakeholders is the Wind Integration National Dataset (WIND) Toolkit, a 7-year time-series data set produced in 2013 by the National Renewable Energy Laboratory. In this study, we present an update to that data set for offshore California that leverages recent advancements in NWP modeling capabilities and extends the period of record to a full 20 years. The data set predicts a significantly larger wind resource (0.25–1.75 m s-1 stronger), including in three Call Areas that the Bureau of Ocean Energy Management is considering for commercial activity. We conduct a set of yearlong simulations to study factors that contribute to this increase in the modeled wind resource. The largest impact arises from a change in the planetary boundary layer parameterization from the Yonsei University scheme to the Mellor-Yamada-Nakanishi-Niino scheme and their diverging wind profiles under stable stratification. Additionally, we conduct a refined wind resource assessment at the three Call Areas, characterizing distributions of wind speed, shear, veer, stability, frequency of wind droughts, and power production. We find that, depending on the attribute, the new data set can show substantial disagreement with the WIND Toolkit, thereby driving important changes in predicted power.

49 EE - Wind and Water Power Program - Wind (EE-4W↗

NASA NTRS1986

TAE Plus: A conceptual view of TAE in the space station era

The use of the Transportable Applications Executive (TAE) for prototyping user interfaces has been the prime force behind the new TAE research and development work. The Data Systems Technology Division at GSFC is developing prototypes of user interfaces for different functions involved in the operation, analysis and data communication of space station payloads. TAE is a valuable prototyping tool because it enables a developer to build an entire application user interface model and run it without writing a single line of application code. One force driving new development is the need to update TAE's user interface to support the latest interactive graphic device technology. The current TAE, TAE Classic, uses interface techniques designed for an 80x24 character monochrome alphanumeric terminal, but does not effectively utilize features such as windowing, graphics, color, and selection devices available on newer workstations. To meet our needs, development of a TAE Plus began in FY-86 and involves augmenting TAE with three different sets of tools: a user interface toolkit; an application toolkit; and run-time service subroutines. A phased approach is being used to develop TAE Plus. In the first phase, we have met the needs of the user community and provided some support for rapid prototyping by developing a TAE Facelift, which adds an enhanced TAE interface (with windowing, mouse interaction, pull-down menus, etc.) to a select set of graphic workstations. The TAE Facelift allows many new concepts to be tested quickly for feedback and performance. In the second phase, a fully-integrated user interface management system, TAE Plus, will be built that supports the separation of interface from application, with the concomitant ability to prototype and rapidly change interfaces. This robust functionality will support, in an integrated manner, an application's development cycle from the prototype step through to the fully operational system.

Szczur, Martha↗

NASA NTRS1988

The design of an intelligent human-computer interface for the test, control and monitor system

The graphical intelligence and assistance capabilities of a human-computer interface for the Test, Control, and Monitor System at Kennedy Space Center are explored. The report focuses on how a particular commercial off-the-shelf graphical software package, Data Views, can be used to produce tools that build widgets such as menus, text panels, graphs, icons, windows, and ultimately complete interfaces for monitoring data from an application; controlling an application by providing input data to it; and testing an application by both monitoring and controlling it. A complete set of tools for building interfaces is described in a manual for the TCMS toolkit. Simple tools create primitive widgets such as lines, rectangles and text strings. Intermediate level tools create pictographs from primitive widgets, and connect processes to either text strings or pictographs. Other tools create input objects; Data Views supports output objects directly, thus output objects are not considered. Finally, a set of utilities for executing, monitoring use, editing, and displaying the content of interfaces is included in the toolkit.

Shoaff, William D.↗

NASA NTRS1992

Update of GRASP/Ada reverse engineering tools for Ada

The GRASP/Ada project (Graphical Representations of Algorithms, Structures, and Processes for Ada) has successfully created and prototyped a new algorithmic level graphical representation of Ada software, the Control Structure Diagram (CSD). The primary impetus for creation of the CSD was to improve the comprehension efficiency of Ada software and, as a result, improve reliability and reduce costs. The emphasis was on the automatic generation of the CSD from Ada PDL or source code to support reverse engineering and maintenance. The CSD has the potential to replace traditional prettyprinted Ada source code. In Phase 1 of the GRASP/Ada project, the CSD graphical constructs were created and applied manually to several small Ada programs. A prototype (Version 1) was designed and implemented using FLEX and BISON running under VMS on a VAS 11-780. In Phase 2, the prototype was improved and ported to the Sun 4 platform under UNIX. A user interface was designed and partially implemented using the HP widget toolkit and the X Windows System. In Phase 3, the user interface was extensively reworked using the Athena widget toolkit and X Windows. The prototype was applied successfully to numerous Ada programs ranging in size from several hundred to several thousand lines of source code. Following Phase 3, the prototype was evaluated by software engineering students at Auburn University and then updated with significant enhancements to the user interface including editing capabilities. Version 3.2 of the prototype was prepared for limited distribution to facilitate further evaluation. The current prototype provides the capability for the user to generate CSD's from Ada PDL or source code in a reverse engineering as well as forward engineering mode with a level of flexibility suitable for practical application.

Cross, James H., II↗

NASA NTRS1993

Update of GRASP/Ada reverse engineering tools for Ada

The GRASP/Ada project (Graphical Representations of Algorithms, Structures, and Processes for Ada) successfully created and prototyped a new algorithmic level graphical representation for Ada software, the Control Structure Diagram (CSD). The primary impetus for creation of the CSD was to improve the comprehension efficiency of Ada software and, as a result, improve reliability and reduce costs. The emphasis was on the automatic generation of the CSD from Ada PDL or source code to support reverse engineering and maintenance. The CSD has the potential to replace traditional pretty printed Ada source code. In Phase 1 of the GRASP/Ada project, the CSD graphical constructs were created and applied manually to several small Ada programs. A prototype CSD generator (Version 1) was designed and implemented using FLEX and BISON running under VMS on a VAX 11-780. In Phase 2, the prototype was improved and ported to the Sun 4 platform under UNIX. A user interface was designed and partially implemented using the HP widget toolkit and the X Windows System. In Phase 3, the user interface was extensively reworked using the Athena widget toolkit and X Windows. The prototype was applied successfully to numerous Ada programs ranging in size from several hundred to several thousand lines of source code. Following Phase 3,e two update phases were completed. Update'92 focused on the initial analysis of evaluation data collected from software engineering students at Auburn University and the addition of significant enhancements to the user interface. Update'93 (the current update) focused on the statistical analysis of the data collected in the previous update and preparation of Version 3.4 of the prototype for limited distribution to facilitate further evaluation. The current prototype provides the capability for the user to generate CSD's from Ada PDL or source code in a reverse engineering as well as forward engineering mode with a level of flexibility suitable for practical application. An overview of the GRASP/Ada project with an emphasis on the current update is provided.

Cross, James H., II↗

NASA NTRS1993

Sounds of silence: How to animate virtual worlds with sound

Sounds are an integral and sometimes annoying part of our daily life. Virtual worlds which imitate natural environments gain a lot of authenticity from fast, high quality visualization combined with sound effects. Sounds help to increase the degree of immersion for human dwellers in imaginary worlds significantly. The virtual reality toolkit of IGD (Institute for Computer Graphics) features a broad range of standard visual and advanced real-time audio components which interpret an object-oriented definition of the scene. The virtual reality system 'Virtual Design' realized with the toolkit enables the designer of virtual worlds to create a true audiovisual environment. Several examples on video demonstrate the usage of the audio features in Virtual Design.

Astheimer, Peter↗

NASA NTRS1994

Automated Instrumentation, Monitoring and Visualization of PVM Programs Using AIMS

We present views and analysis of the execution of several PVM codes for Computational Fluid Dynamics on a network of Sparcstations, including (a) NAS Parallel benchmarks CG and MG (White, Alund and Sunderam 1993); (b) a multi-partitioning algorithm for NAS Parallel Benchmark SP (Wijngaart 1993); and (c) an overset grid flowsolver (Smith 1993). These views and analysis were obtained using our Automated Instrumentation and Monitoring System (AIMS) version 3.0, a toolkit for debugging the performance of PVM programs. We will describe the architecture, operation and application of AIMS. The AIMS toolkit contains (a) Xinstrument, which can automatically instrument various computational and communication constructs in message-passing parallel programs; (b) Monitor, a library of run-time trace-collection routines; (c) VK (Visual Kernel), an execution-animation tool with source-code clickback; and (d) Tally, a tool for statistical analysis of execution profiles. Currently, Xinstrument can handle C and Fortran77 programs using PVM 3.2.x; Monitor has been implemented and tested on Sun 4 systems running SunOS 4.1.2; and VK uses X11R5 and Motif 1.2. Data and views obtained using AIMS clearly illustrate several characteristic features of executing parallel programs on networked workstations: (a) the impact of long message latencies; (b) the impact of multiprogramming overheads and associated load imbalance; (c) cache and virtual-memory effects; and (4significant skews between workstation clocks. Interestingly, AIMS can compensate for constant skew (zero drift) by calibrating the skew between a parent and its spawned children. In addition, AIMS' skew-compensation algorithm can adjust timestamps in a way that eliminates physically impossible communications (e.g., messages going backwards in time). Our current efforts are directed toward creating new views to explain the observed performance of PVM programs. Some of the features planned for the near future include: (a) ConfigView, showing the physical topology of the virtual machine, inferred using specially formatted IP (Internet Protocol) packets; and (b) LoadView, synchronous animation of PVM-program execution and resource-utilization patterns.

Mehra, Pankaj↗

NASA NTRS1994

Automated Instrumentation, Monitoring and Visualization of PVM Programs Using AIMS

We present views and analysis of the execution of several PVM (Parallel Virtual Machine) codes for Computational Fluid Dynamics on a networks of Sparcstations, including: (1) NAS Parallel Benchmarks CG and MG; (2) a multi-partitioning algorithm for NAS Parallel Benchmark SP; and (3) an overset grid flowsolver. These views and analysis were obtained using our Automated Instrumentation and Monitoring System (AIMS) version 3.0, a toolkit for debugging the performance of PVM programs. We will describe the architecture, operation and application of AIMS. The AIMS toolkit contains: (1) Xinstrument, which can automatically instrument various computational and communication constructs in message-passing parallel programs; (2) Monitor, a library of runtime trace-collection routines; (3) VK (Visual Kernel), an execution-animation tool with source-code clickback; and (4) Tally, a tool for statistical analysis of execution profiles. Currently, Xinstrument can handle C and Fortran 77 programs using PVM 3.2.x; Monitor has been implemented and tested on Sun 4 systems running SunOS 4.1.2; and VK uses XIIR5 and Motif 1.2. Data and views obtained using AIMS clearly illustrate several characteristic features of executing parallel programs on networked workstations: (1) the impact of long message latencies; (2) the impact of multiprogramming overheads and associated load imbalance; (3) cache and virtual-memory effects; and (4) significant skews between workstation clocks. Interestingly, AIMS can compensate for constant skew (zero drift) by calibrating the skew between a parent and its spawned children. In addition, AIMS' skew-compensation algorithm can adjust timestamps in a way that eliminates physically impossible communications (e.g., messages going backwards in time). Our current efforts are directed toward creating new views to explain the observed performance of PVM programs. Some of the features planned for the near future include: (1) ConfigView, showing the physical topology of the virtual machine, inferred using specially formatted IP (Internet Protocol) packets: and (2) LoadView, synchronous animation of PVM-program execution and resource-utilization patterns.

Mehra, Pankaj↗