From Physics Model to Results: An Optimizing Framework for Cross-Architecture Code Generation

Starting from a high-level problem description in terms of partial differential equations using abstract tensor notation, the Chemora framework discretizes, optimizes, and generates complete high performance codes for a wide range of compute architectures. Chemora extends the capabilities of Cactus, facilitating the usage of large-scale CPU/GPU systems in an efficient manner for complex applications, without low-level code tuning. Chemora achieves parallelism through MPI and multi-threading, combining OpenMP and CUDA. Optimizations include high-level code transformations, efficient loop traversal strategies, dynamically selected data and instruction cache usage strategies, and JIT compilation of GPU code tailored to the problem characteristics. The discretization is based on higher-order finite differences on multi-block domains. Chemora's capabilities are demonstrated by simulations of black hole collisions. This problem provides an acid test of the framework, as the Einstein equations contain hundreds of variables and thousands of terms.Comment: 18 pages, 4 figures, accepted for publication in Scientific Programmin

IllinoisGRMHD: An Open-Source, User-Friendly GRMHD Code for Dynamical Spacetimes

In the extreme violence of merger and mass accretion, compact objects like black holes and neutron stars are thought to launch some of the most luminous outbursts of electromagnetic and gravitational wave energy in the Universe. Modeling these systems realistically is a central problem in theoretical astrophysics, but has proven extremely challenging, requiring the development of numerical relativity codes that solve Einstein's equations for the spacetime, coupled to the equations of general relativistic (ideal) magnetohydrodynamics (GRMHD) for the magnetized fluids. Over the past decade, the Illinois Numerical Relativity (ILNR) Group's dynamical spacetime GRMHD code has proven itself as a robust and reliable tool for theoretical modeling of such GRMHD phenomena. However, the code was written "by experts and for experts" of the code, with a steep learning curve that would severely hinder community adoption if it were open-sourced. Here we present IllinoisGRMHD, which is an open-source, highly-extensible rewrite of the original closed-source GRMHD code of the ILNR Group. Reducing the learning curve was the primary focus of this rewrite, with the goal of facilitating community involvement in the code's use and development, as well as the minimization of human effort in generating new science. IllinoisGRMHD also saves computer time, generating roundoff-precision identical output to the original code on adaptive-mesh grids, but nearly twice as fast at scales of hundreds to thousands of cores.Comment: 37 pages, 6 figures, single column. Matches published versio

Supplementary report to the final report of the coral reef expert group: S7. Coral reef models as assessment and reporting tools for the Reef 2050 Integrated Monitoring and Reporting Program – a review

[Extract] The objective of this report is to review the existing models of temporal/spatial dynamics of coral communities available for the Great Barrier Reef (the Reef), with the specific aim at evaluating their strengths and weaknesses for the assessment and reporting of coral reef health within the Reef 2050 Integrated Monitoring and Reporting Program (RIMReP). Focusing on peer-reviewed articles available by 28 February 2018, we found that a variety of modeling approaches exists yet with different scope, level of complexity, and ability to represent the various processes driving the dynamics of coral populations. Tools available to model Reef coral population dynamics also vary in their capacity to capture the spatial heterogeneity of coral populations and their environment, the variability of disturbance impacts and the uncertainty around current reef state and possible future trajectory. The various characteristics and properties exhibited by coral reef models means they have different capacities to complement reef monitoring and assessment on the Reef. This review provides guidance for integrating a modeling component to RIMReP by identifying the modeling approaches that offer the strongest support to reef monitoring and management.An accessible copy of this report is not yet available from this repository, please contact [email protected] for more information

Plant structural complexity and mechanical defenses mediate predator-prey interactions in an odonate-bird system.

Habitat-forming species provide refuges for a variety of associating species; these refuges may mediate interactions between species differently depending on the functional traits of the habitat-forming species. We investigated refuge provisioning by plants with different functional traits for dragonfly and damselfly (Odonata: Anisoptera and Zygoptera) nymphs emerging from water bodies to molt into their adult stage. During this period, nymphs experience high levels of predation by birds. On the shores of a small pond, plants with mechanical defenses (e.g., thorns and prickles) and high structural complexity had higher abundances of odonate exuviae than nearby plants which lacked mechanical defenses and exhibited low structural complexity. To disentangle the relative effects of these two potentially important functional traits on nymph emergence-site preference and survival, we conducted two fully crossed factorial field experiments using artificial plants. Nymphs showed a strong preference for artificial plants with high structural complexity and to a lesser extent, mechanical defenses. Both functional traits increased nymph survival but through different mechanisms. We suggest that future investigations attempt to experimentally separate the elements contributing to structural complexity to elucidate the mechanistic underpinnings of refuge provisioning

Spartan Daily, October 25, 1949

Volume 38, Issue 14https://scholarworks.sjsu.edu/spartandaily/11281/thumbnail.jp

Spartan Daily, October 25, 1949

Volume 38, Issue 14https://scholarworks.sjsu.edu/spartandaily/11281/thumbnail.jp

Comparative mitochondrial and chloroplast genomics of a genetically distinct form of Sargassum contributing to recent “Golden Tides” in the Western Atlantic

© The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Ecology and Evolution 7 (2017): 516–525, doi:10.1002/ece3.2630.Over the past 5 years, massive accumulations of holopelagic species of the brown macroalga Sargassum in coastal areas of the Caribbean have created “golden tides” that threaten local biodiversity and trigger economic losses associated with beach deterioration and impact on fisheries and tourism. In 2015, the first report identifying the cause of these extreme events implicated a rare form of the holopelagic species Sargassum natans (form VIII). However, since the first mention of S. natans VIII in the 1930s, based solely on morphological characters, no molecular data have confirmed this identification. We generated full-length mitogenomes and partial chloroplast genomes of all representative holopelagic Sargassum species, S. fluitans III and S. natans I alongside the putatively rare S. natans VIII, to demonstrate small but consistent differences between S. natans I and VIII (7 bp differences out of the 34,727). Our comparative analyses also revealed that both S. natans I and S. natans VIII share a very close phylogenetic relationship with S. fluitans III (94- and 96-bp differences of 34,727). We designed novel primers that amplified regions of the cox2 and cox3 marker genes with consistent polymorphic sites that enabled differentiation between the two S. natans forms (I and VIII) from each other and both from S. fluitans III in over 150 Sargassum samples including those from the 2014 golden tide event. Despite remarkable gene synteny and sequence conservation, the three Sargassum forms differ in morphology, ecology, and distribution patterns, warranting more extensive interrogation of holopelagic Sargassum genomes as a whole.This work was supported by a US National Science Foundation (NSF) collaborative grant to LAA-Z (OCE-1155571) and ERZ (OCE-1155379), and an NSF TUES grant (DUE-1043468) to LAA-Z and ER