Scalable Adaptive Mantle Convection Simulation on Petascale Supercomputers

Mantle convection is the principal control on the thermal and geological evolution of the Earth. Mantle convection modeling involves solution of the mass, momentum, and energy equations for a viscous, creeping, incompressible non-Newtonian fluid at high Rayleigh and Peclet numbers. Our goal is to conduct global mantle convection simulations that can resolve faulted plate boundaries, down to 1 km scales. However, uniform resolution at these scales would result in meshes with a trillion elements, which would elude even sustained petaflops supercomputers. Thus parallel adaptive mesh refinement and coarsening (AMR) is essential. We present RHEA, a new generation mantle convection code designed to scale to hundreds of thousands of cores. RHEA is built on ALPS, a parallel octree-based adaptive mesh finite element library that provides new distributed data structures and parallel algorithms for dynamic coarsening, refinement, rebalancing, and repartitioning of the mesh. ALPS currently supports low order continuous Lagrange elements, and arbitrary order discontinuous Galerkin spectral elements, on octree meshes. A forest-ofoctrees implementation permits nearly arbitrary geometries to be accommodated. Using TACC’s 579 teraflops Ranger supercomputer, we demonstrate excellent weak and strong scalability of parallel AMR on up to 62,464 cores for problems with up to 12.4 billion elements. With RHEA’s adaptive capabilities, we have been able to reduce the number of elements by over three orders of magnitude, thus enabling us to simulate large-scale mantle convection with finest local resolution of 1.5 km

Acute glycogen synthase kinase-3 inhibition modulates human cardiac conduction

Glycogen synthase kinase 3 (GSK-3) inhibition has emerged as a potential therapeutic target for several diseases, including cancer. However, the role for GSK-3 regulation of human cardiac electrophysiology remains ill-defined. We demonstrate that SB216763, a GSK-3 inhibitor, can acutely reduce conduction velocity in human cardiac slices. Combined computational modeling and experimental approaches provided mechanistic insight into GSK-3 inhibition-mediated changes, revealing that decreased sodium-channel conductance and tissue conductivity may underlie the observed phenotypes. Our study demonstrates that GSK-3 inhibition in human myocardium alters electrophysiology and may predispose to an arrhythmogenic substrate; therefore, monitoring for adverse arrhythmogenic events could be considered

Chamber-specific transcriptional responses in atrial fibrillation

Atrial fibrillation (AF) is the most common cardiac arrhythmia, yet the molecular signature of the vulnerable atrial substrate is not well understood. Here, we delineated a distinct transcriptional signature in right versus left atrial cardiomyocytes (CMs) at baseline and identified chamber-specific gene expression changes in patients with a history of AF in the setting of end-stage heart failure (AF+HF) that are not present in heart failure alone (HF). We observed that human left atrial (LA) CMs exhibited Notch pathway activation and increased ploidy in AF+HF but not in HF alone. Transient activation of Notch signaling within adult CMs in a murine genetic model is sufficient to increase ploidy in both atrial chambers. Notch activation within LA CMs generated a transcriptomic fingerprint resembling AF, with dysregulation of transcription factor and ion channel genes, including Pitx2, Tbx5, Kcnh2, Kcnq1, and Kcnip2. Notch activation also produced distinct cellular electrophysiologic responses in LA versus right atrial CMs, prolonging the action potential duration (APD) without altering the upstroke velocity in the left atrium and reducing the maximal upstroke velocity without altering the APD in the right atrium. Our results support a shared human/murine model of increased Notch pathway activity predisposing to AF

The Etree Library: A System for Manipulating Large Octrees on Disk

This report describes a library, called the etree library, that allows C programmers to manipulate large octrees stored on disk. Octrees are stored as a sequence of fixed sized octant records sorted by a locational code order that is equivalent to a preorder traversal of the tree and a Z-order traversal through the domain. The sorted records are indexed by a conventional file-resident B-tree index and queried using fixed-length locational code keys. A schema can be defined to make an etree portable across different platforms. The etree library provides functions for creating, modifying, and searching octrees, including efficient mechanisms for appending octants and iterating over octants in Z-order. The library is the foundation for a larger research effort aimed at enabling scientists and engineers to solve large physical simulations on their desktop systems by recasting the simulation process to work directly on large etrees stored on disk

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The etree library : a system for manipulating large octrees on disk

Abstract: "This report describes a library, called the etree library, that allows C programmers to manipulate large octrees stored on disk. Octrees are stored as a sequence of fixed sized octant records sorted by a locational code order that is equivalent to a preorder traversal of the tree and a Z-order traversal through the domain. The sorted records are indexed by a conventional file-resident B-tree index and queried using fixed-length locational code keys. A schema can be defined to make an etree portable across different platforms. The etree library provides functions for creating, modifying, and searching octrees, including efficient mechanisms for appending octants and iterating over octants in Z-order. The library is the foundation for a larger research effort aimed at enabling scientists and engineers to solve large physical simulations on their desktop systems by recasting the simulation process to work directly on large etrees stored on disk.

Efficient Query Processing on Unstructured Tetrahedral Meshes

Modern scientific applications consume massive volumes of data produced by computer simulations. Such applications require new data management capabilities in order to scale to terabyte-scale data volumes [25, 10]. The most common way to discretize the application domain is to decompose it into pyramids, forming an unstructured tetrahedral mesh. Modern simulations generate meshes of high resolution and precision, to be queried by a visualization or analysis tool. Tetrahedral meshes are extremely flexible and therefore vital to accurately model complex geometries, but also are difficult to index. To reduce query execution time, applications either use only subsets of the data or rely on different (less flexible) structures, thereby trading accuracy for speed. Thi