Computing in Science & Engineering

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Updated: 2 years 22 weeks ago

Writing Fiction

Tue, 11/08/2016 - 15:43

Columnist Charles Day explores the Internet's role as a novelist's tool.

Risk-Based Software Development Practices for CREATE Multiphysics HPC Software Applications

Tue, 11/08/2016 - 15:43

The January/February 2016 issue of this magazine presented descriptions of the US Defense Department's Computational Research and Engineering Acquisition Tools and Environments (CREATE) program and the software engineering approach for managing its programmatic risks. This article describes the software engineering methodology deployed to manage the development risks faced by CREATE, that is, the risks arising in the product development cycle and environment. The approach here is similar to the one for the management of CREATE programmatic risks and is based on a set of shared development practices. The management of these risks is especially challenging in the environment of distributed teams developing physics-based, system-of-systems, high-performance computing software anchored in the three military departments. The CREATE experience provides a concrete example of successful implementation of best software engineering practices in a computational science and engineering milieu that has historically questioned the value of traditional software engineering wisdom and has resisted the adoption of plan-centered software engineering processes. It has allowed CREATE to adopt important software engineering practices such as use case-centered requirements management, use of pilot projects to align customer and developer expectations, continuous code integration of modular components, and scalable product support models, among others.

Risks

Tue, 11/08/2016 - 15:43

How do we address risks, perceived and actual, in scientific programming? How can we mitigate these from both a technical and a project management perspective?

Argonne Discovery Yields Self-Healing Diamond-Like Carbon

Tue, 11/08/2016 - 15:43

Large-scale reactive molecular dynamics simulations carried out on the US Department of Energy's IBM Blue Gene/Q Mira supercomputer at the Argonne Leadership Computing Facility, along with experiments conducted by researchers in Argonne's Energy Systems Division, enabled the design of a "self-healing" anti-wear coating that drastically reduces friction and related degradation in engines and moving machinery. Now, the computational work advanced for this purpose is being used to identify the friction-fighting potential of other catalysts.

NASA Computational Case Study: Golomb Rulers and Their Applications

Tue, 11/08/2016 - 15:43

In this case study, the author describes Golomb rulers, their properties, construction algorithms, and applications in astrophysics and Earth sciences.

Maximum Mechanics

Tue, 11/08/2016 - 15:41

Michael Jay Schilaci reviews Todd Keene Timberlake and J. Wilson Mixon, Jr.'s "Classical Mechanics with Maxima," declaring it an excellent resource for classical mechanics instructors and students alike.

Navy Enhanced Sierra Mechanics (NESM): Toolbox for Predicting Navy Shock and Damage

Tue, 11/08/2016 - 15:41

The US Navy is developing a new suite of computational mechanics tools (Navy Enhanced Sierra Mechanics) for the prediction of ship response, damage, and shock environments transmitted to vital systems during threat weapon encounters. NESM includes fully coupled Euler-Lagrange solvers tailored to ship shock/damage predictions. NESM is optimized to support high-performance computing architectures, providing the physics-based ship response/threat weapon damage predictions needed to support the design and assessment of highly survivable ships. NESM is being employed to support current Navy ship design and acquisition programs while being further developed for future Navy fleet needs.

Audience-Targeted Design Considerations for Effective Scientific Storytelling

Tue, 11/08/2016 - 15:41

An effective visualization must be carefully designed according to its purpose. This article describes three projects focused on scientific storytelling in a different domain area and for a different target audience. The authors describe the lessons learned working in each scientific field and the techniques used to tailor the visual narrative to a specific audience type. The three projects are a visualization of particle accelerator data designed for domain scientists, a presentation of new findings from the fusion community designed for nonexpert adults, and an interactive exhibit of phytoplankton populations tailored toward museum visitors, especially children. Special design decisions had to be made to handle the unique conditions of each scientific area as well as the given background knowledge of the target audience. By evaluating the effectiveness of each of method, the authors gain insight into which aspects become important in developing a visualization with maximum usability.

The Computational Research and Engineering Acquisition Tools and Environments (CREATE) Program, Part 2

Tue, 11/08/2016 - 15:41

The guest editors of this special issue describe five articles that make up the second part of a series describing US Department of Defense software engineering efforts.

A Call to Action to Prepare the High-Performance Computing Workforce

Tue, 11/08/2016 - 15:41

This article presents the challenges and opportunities for preparing current and future generations to advance research, scholarship, and education with high-performance computing.

First-Principles Physics-Based Rotorcraft Flowfield Simulation Using HPCMP CREATE-AV Helios

Tue, 11/08/2016 - 15:36

The flowfield around a helicopter's spinning rotor, whether in forward flight or hover, is difficult to model due to the presence of unsteady flow and strong vorticity. Unlike a fixed-wing aircraft, which leaves its deposited wake behind it, a helicopter flies completely within its own strong vortex wake system. In hover, the strong tip vortices coil beneath the rotor and significantly alter the rotor's aerodynamic performance. In forward flight, the rotor-vortex wake is swept back to the tail, causing unsteady flow that affects control and vibration. The underlying issue in modeling rotorcraft flowfields is the need to correctly account for the complex vortex wake produced by the rotor. This article outlines the historical progress of first-principles physics-based predictive tools, from early estimations to the current state-of-the-art coupled computational fluid dynamics models used today in the HPCMP CREATE-AV Helios code.

El Fin

Tue, 11/08/2016 - 15:35

EIC George K. Thiruvathukal says farewell in his final "from the editors" message.

Development and Application of an Incompressible Strand Solver

Tue, 11/08/2016 - 15:35

Computational fluid dynamics (CFD) is an ever-increasing component of the naval design and analysis process. Most current high-fidelity CFD methods used by the US Navy require body-fitted volume grids, which are time-consuming and depend on seasoned engineers with significant grid generation experience. Automated grid generation using a strand gridding approach is a relatively new concept that could transform the role of higher fidelity CFD within the Navy's design and analysis process. The HPCMP CREATE-SH team seeks to expand the compressible strand solver under development as part of the HPCMP CREATE-AV effort to incompressible flow problems for applications of interest to the Navy. The completed incompressible strand solver would allow quicker turnaround time for experienced CFD engineers while allowing more naval architects to use higher fidelity CFD as a part of the overall design process. The incompressible strand solver is a new development of the HPCMP CREATE-SH Hydro team, and this work will demonstrate the solver on validation cases of naval interest.

HPCMP CREATE-SH Integrated Hydrodynamic Design Environment

Tue, 11/08/2016 - 15:35

The HPCMP CREATE-SH Integrated Hydrodynamic Design Environment (IHDE) is a workbench-like desktop application that integrates a suite of hull form design and analysis tools allowing a user to execute round-trip evaluations of hydrodynamic performance, including visualization, in a simplified and timely manner. Ship hull designers are able to assess ship performance in areas of resistance, seakeeping, hydrodynamic loads, and operability for several different mission types. The development plan calls for additional capabilities related to maneuvering performance and multi-objective optimization. The IHDE also includes an analysis tool validation engine, which provides the user with validation information by leveraging historical model test data for comparisons. The advantages of the IHDE include automated analysis preparation, automated grid generation, and integrated visualization. The IHDE has been used to support several Navy design studies and this paper describes the capabilities of IHDE and shows examples of typical workflow processes and sample analysis results.

Chemical Kinetics: A CS Perspective

Fri, 08/26/2016 - 13:39

Chemical kinetics has played a critical role in understanding phenomena such as global climate change and photochemical smog, and researchers use it to analyze chemical reactors and alternative fuels. When computing is applied to the development of detailed chemical kinetic models, it allows scientists to predict the behavior of these complex chemical systems. This overview discusses algorithmic techniques for mechanism generation, consistency and completeness verification, and mechanism reduction, as well as ongoing research trends.

Beyond the Third Dimension: Visualizing High-Dimensional Data with Projections

Fri, 08/26/2016 - 13:39

Multidimensional projections are an increasingly popular technique for visualizing large datasets containing observations having tens or even hundreds of dimensions. Compared to other techniques such as parallel coordinates, tables, and scatterplot matrices, they support tasks such as finding groups of related observations and outliers in simpler, more effective, ways. The authors discuss here the advantages of multidimensional projections, how to compute them, and recent advances that enhance them by visual explanatory techniques, so as to make them efficient and effective instruments that should be part of the toolkit of any scientist interested in high-dimensional data exploration.

Massive Computation for Understanding Core-Collapse Supernova Explosions

Fri, 08/26/2016 - 13:39

How do massive stars explode? Progress toward the answer is driven by increases in compute power. Petascale supercomputers are enabling detailed 3D simulations of core-collapse supernovae that are elucidating the role of fluid instabilities, turbulence, and magnetic field amplification in supernova engines.

Multiyear Simulation Study Provides Breakthrough in Membrane Protein Research

Fri, 08/26/2016 - 13:39

A research team based at the University of Chicago used supercomputing resources at the US Department of Energy's (DOE's) Argonne National Laboratory to gain a deep mechanistic view of a critical ATP-driven calcium pump. The team's recent discovery fills in essential information inaccessible to experimentalists, and potentially crucial to new therapeutic drug design.

Computers in Cars

Fri, 08/26/2016 - 13:30

Columnist Charles Day explores computation and cars.

The Feasibility of Amazon's Cloud Computing Platform for Parallel, GPU-Accelerated, Multiphase-Flow Simulations

Fri, 08/26/2016 - 13:30

The feasibility of running MPI-parallel, GPU-accelerated, multiphase flow simulations on Amazon's Elastic Compute Cloud (EC2) service is evaluated as an alternative computational resource. A cloud cluster on Amazon EC2 is compared to a conventional local high-performance computing cluster in terms of performance and cost. The steps necessary to set up a cloud cluster and acquire the appropriate hardware and software stacks are outlined. The incompressible multiphase flow solver is benchmarked on both cloud and local clusters by performing strong and weak scaling analyses. Amazon's EC2 service is competitive with the local cluster in a certain range of simulations, but there are some performance limitations, particularly in its GPU card performance and cluster network connection, which negatively impact the parallel simulations presented herein. Finally, Amazon's EC2 service is studied from an economic perspective and compared with a conventional local cluster.

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