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Computing in Science & Engineering http://www.computer.org Physics, medicine, astronomy -- these and other hard sciences share a common need for efficient algorithms, system software, and computer architecture to address large computational problems. And yet, useful advances in computational techniques that could benefit many researchers are rarely shared. To meet that need, Computing in Science & Engineering presents scientific and computational contributions in a clear and accessible format. en-us Mon, 3 Nov 2014 15:34:36 GMT http://csdl.computer.org/common/images/logos/cise.gif IEEE Computer Society List of recently published journal articles http://www.computer.org/cise PrePrint: Reproducible research as a community effort: Lessons from the Madagascar project http://doi.ieeecomputersociety.org/10.1109/MCSE.2014.94 Reproducible research is the discipline of attaching software code and data to publications, which enables the reader to reproduce, verify, and extend published computational experiments. Instead of being the responsibility of an individual author, computational reproducibility should become the responsibility of open-source scientific-software communities. A dedicated community effort can keep a body of computational research alive by actively maintaining its reproducibility The Madagascar open-source software project offers an example of such a community. http://doi.ieeecomputersociety.org/10.1109/MCSE.2014.94 PrePrint: High Performance Computing Modeling Advances Accelerator Science for High Energy Physics http://doi.ieeecomputersociety.org/10.1109/MCSE.2014.76 The development and optimization of particle accelerators are essential for advancing our understanding of the properties of matter, energy, and space-time. Particle accelerators are complex devices whose behavior involves many physical effects and scales. Therefore, advanced computational tools utilizing high-performance computing (HPC) are essential for accurately modeling them. In the past decade, the DOE SciDAC program has produced such accelerator-modeling tools, which have been employed to tackle some of the most difficult accelerator science problems. In this article we discuss the Synergia beam-dynamics framework and its applications to high-intensity particle accelerator physics. Synergia is a hybrid Python/C++ accelerator simulation package capable of handling the entire spectrum of beam dynamics simulations. We present the design principles, key physics and numerical models in Synergia and its performance on HPC platforms. Finally, we present the results of current Synergia applications for the Fermilab proton source chain upgrade, known as the Proton Improvement Plan. http://doi.ieeecomputersociety.org/10.1109/MCSE.2014.76 PrePrint: pF3D Simulations of Laser-Plasma Interactions in National Ignition Facility Experiments http://doi.ieeecomputersociety.org/10.1109/MCSE.2014.79 The laser-plasma interaction code pF3D is used to simulate laser-plasma interactions in National Ignition Facility experiments. The paper begins with a brief descriptions of NIF experiments. We then describe pF3D with a focus on the features that are needed to get good performance with up to a million processes. The scalability of message passing, disk I/O, and code steering are key issues when running at this scale and are discussed in detail. Scaling studies on IBM Blue Gene/L, Cray XE6, and IBM Blue Gene/Q systems are used as examples. The paper concludes with a comparison of the backscattered light measured in NIF experiments and computed in the pF3D simulation. http://doi.ieeecomputersociety.org/10.1109/MCSE.2014.79 PrePrint: XSEDE: accelerating scientific discovery http://doi.ieeecomputersociety.org/10.1109/MCSE.2014.80 Computing in science and engineering is now ubiquitous: digital technologies underpin, accelerate, and enable new, even transformational, research in all domains. Access to an array of integrated and well-supported high-end digital services is critical for the advancement of knowledge. Driven by community needs, XSEDE (Extreme Science and Engineering Discovery Environment) substantially enhances the productivity of a growing community of scholars, researchers, and engineers (which will be collectively referred to as "scientists" throughout this paper) through access to advanced digital services that support open research. XSEDE's integrated, comprehensive suite of advanced digital services federates with other high-end facilities and with campus-based resources, serving as the foundation for a national e-science infrastructure ecosystem. XSEDE's e-science infrastructure has tremendous potential for enabling new advancements in research and education. XSEDE's vision is a world of digitally enabled scholars, researchers, and engineers participating in multidisciplinary collaborations to tackle society's grand challenges. http://doi.ieeecomputersociety.org/10.1109/MCSE.2014.80 Issue: July-Aug. 2014 (Vol. 16 No.4) http://www.computer.org/csdl/mags/cs/2014/04/index.html Computing in Science & Engineering http://www.computer.org/portal/site/cise PrePrint: Scientific Discovery in Fusion Plasma Turbulence Simulations at Extreme Scale http://doi.ieeecomputersociety.org/10.1109/MCSE.2014.54 The primary goal of the extreme scale plasma turbulence studies described in this paper is to gain new insights on confinement scaling in magnetic fusion systems by using powerful, world-class supercomputers to carry out simulations with unprecedented resolution and temporal duration. New insights have been gained on the key question of how the turbulent transport of plasma particles and associated confinement scale from present generation devices to much larger ITER-size plasmas. In particular, new results from large-scale simulation studies have demonstrated that improvement in confinement as devices grow larger takes place far more gradually, and with significantly lower loss rates, than less-powerful computer simulations have indicated in research carried out over the past decade. http://doi.ieeecomputersociety.org/10.1109/MCSE.2014.54 PrePrint: Real-time Stochastic Optimization of Complex Energy Systems on High Performance Computers http://doi.ieeecomputersociety.org/10.1109/MCSE.2014.53 We present a scalable approach that computes in operationally-compatible time the energy dispatch under uncertainty for electrical power grid systems of realistic size with thousands of scenarios. We propose several algorithmic and implementation advances in our parallel solver PIPS-IPM for stochastic optimization problems. The new developments include a novel incomplete augmented multicore sparse factorization implemented within PARDISO linear solver and new multicore- and GPU-based dense matrix implementations. We also improve the interprocess communication on Cray XK7 and XC30 systems. PIPS-IPM is used to solve 24-hour horizon power grid problems with up to 1.95 billion decision variables and 1.94 billion constraints on Cray XK7 and Cray XC30, where we observe very good parallel efficiencies and solution times within a operationally defined time interval. To our knowledge, "real-time"-compatible performance on a broad range of architectures for this class of problems has not been possible prior to present work. http://doi.ieeecomputersociety.org/10.1109/MCSE.2014.53 PrePrint: Experiences from Leadership Computing in Simulations of Turbulent Fluid Flows http://doi.ieeecomputersociety.org/10.1109/MCSE.2014.51 We performed a direct numerical simulation (DNS) of high Reynolds number turbulent channel flow to expand our understanding of wall-bounded turbulence. The nature of turbulent flows at high Reynolds leads to the need for leadership computing system. With Mira at Argonne Leadership Computing Facility, Argonne National Laboratory, we successfully achieved DNS at Reτ = 5200, and generated an approximately 120 TByte data set. To use Mira efficiently, we developed a new DNS code, PoongBack, including a new parallel 3D FFT kernel. The new code shows excellent scalability up to 786K cores. In this article, we summarize our code development and production simulation efforts, including parallel I/O. http://doi.ieeecomputersociety.org/10.1109/MCSE.2014.51 PrePrint: Large Scale Simulations of Sky Surveys http://doi.ieeecomputersociety.org/10.1109/MCSE.2014.49 Cosmological simulations aim to cover very large volumes typical of the observed Universe, containing many billions of galaxies. The simulations must obtain high accuracy predictions for a number of observables, as well as allow modeling of imperfectly understood astrophysical processes, such as those involved in galaxy formation. Modern simulations aim to maximally exploit the power of the largest supercomputers to produce synthetic skies in high-fidelity model universes that can then be compared to observations from deep, large-area, multi-wavelength cosmological surveys. In this paper, we describe the simulation and analysis chain used in our large-scale simulation campaigns, targeted at interpreting the results of observations to understand the properties of the dominant, yet mysterious, components of the Universe, dark matter and dark energy. http://doi.ieeecomputersociety.org/10.1109/MCSE.2014.49 PrePrint: Formal Verification of Gravity-induced Loss of Consciousness Monitoring System for Aircraft http://doi.ieeecomputersociety.org/10.1109/MCSE.2014.31 Military industry has developed many high-gravity maneuvering aircraft, such as high performance fighters and aerobatic aircrafts, which can maneuver beyond the acceleration tolerance limit of human being. Since this high-gravity maneuvering may cause pilots a loss of consciousness due to draining blood away from the brain, the Gravity-induced Loss of Consciousness (GLOC) is one of the main reasons for many high-gravity maneuvering aircraft accidents where many pilots have lost their lives. Therefore, many automatic GLOC monitoring systems have been proposed to prevent these accidents. However, it is not trivial to ensure the safety of the system by ordinary simulation or testing methods. In this paper, we present a novel approach to verify the GLOC monitoring system by using model checking technique. As a result of verification, we report a error case that the GLOC monitoring system misses, in which a pilot loses his consciousness after some intentional movements. http://doi.ieeecomputersociety.org/10.1109/MCSE.2014.31