Recursive Algorithms for Distributed Forests of Octrees

The forest-of-octrees approach to parallel adaptive mesh refinement and coarsening (AMR) has recently been demonstrated in the context of a number of large-scale PDE-based applications. Although linear octrees, which store only leaf octants, have an underlying tree structure by definition, it is not often exploited in previously published mesh-related algorithms. This is because the branches are not explicitly stored, and because the topological relationships in meshes, such as the adjacency between cells, introduce dependencies that do not respect the octree hierarchy. In this work we combine hierarchical and topological relationships between octree branches to design efficient recursive algorithms. We present three important algorithms with recursive implementations. The first is a parallel search for leaves matching any of a set of multiple search criteria. The second is a ghost layer construction algorithm that handles arbitrarily refined octrees that are not covered by previous algorithms, which require a 2:1 condition between neighboring leaves. The third is a universal mesh topology iterator. This iterator visits every cell in a domain partition, as well as every interface (face, edge and corner) between these cells. The iterator calculates the local topological information for every interface that it visits, taking into account the nonconforming interfaces that increase the complexity of describing the local topology. To demonstrate the utility of the topology iterator, we use it to compute the numbering and encoding of higher-order $C^0$ nodal basis functions. We analyze the complexity of the new recursive algorithms theoretically, and assess their performance, both in terms of single-processor efficiency and in terms of parallel scalability, demonstrating good weak and strong scaling up to 458k cores of the JUQUEEN supercomputer.Comment: 35 pages, 15 figures, 3 table

Soft Contract Verification

Behavioral software contracts are a widely used mechanism for governing the flow of values between components. However, run-time monitoring and enforcement of contracts imposes significant overhead and delays discovery of faulty components to run-time. To overcome these issues, we present soft contract verification, which aims to statically prove either complete or partial contract correctness of components, written in an untyped, higher-order language with first-class contracts. Our approach uses higher-order symbolic execution, leveraging contracts as a source of symbolic values including unknown behavioral values, and employs an updatable heap of contract invariants to reason about flow-sensitive facts. We prove the symbolic execution soundly approximates the dynamic semantics and that verified programs can't be blamed. The approach is able to analyze first-class contracts, recursive data structures, unknown functions, and control-flow-sensitive refinements of values, which are all idiomatic in dynamic languages. It makes effective use of an off-the-shelf solver to decide problems without heavy encodings. The approach is competitive with a wide range of existing tools---including type systems, flow analyzers, and model checkers---on their own benchmarks.Comment: ICFP '14, September 1-6, 2014, Gothenburg, Swede

Nascent polypeptide chains exit the ribosome in the same relative position in both eucaryotes and procaryotes.

We located the polypeptide nascent chain as it leaves cytoplasmic ribosomes from the plant Lemna gibba by immune electron microscopy using antibodies against the small subunit of the enzyme ribulose-1,5-bisphosphate carboxylase. Similar studies with Escherichia coli ribosomes, using antibodies directed against the enzyme beta-galactosidase, show that the polypeptide nascent chain emerges in the same relative position in plants and bacteria. The eucaryotic ribosomal exit site is on the large subunit, approximately 75 A from the interface between subunits and nearly 160 A from the central protuberance, the presumed site for peptidyl transfer. This is the first functional site on both the eucaryotic and procaryotic ribosomes to be determined

Size-Change Termination as a Contract

Termination is an important but undecidable program property, which has led to a large body of work on static methods for conservatively predicting or enforcing termination. One such method is the size-change termination approach of Lee, Jones, and Ben-Amram, which operates in two phases: (1) abstract programs into "size-change graphs," and (2) check these graphs for the size-change property: the existence of paths that lead to infinite decreasing sequences. We transpose these two phases with an operational semantics that accounts for the run-time enforcement of the size-change property, postponing (or entirely avoiding) program abstraction. This choice has two key consequences: (1) size-change termination can be checked at run-time and (2) termination can be rephrased as a safety property analyzed using existing methods for systematic abstraction. We formulate run-time size-change checks as contracts in the style of Findler and Felleisen. The result compliments existing contracts that enforce partial correctness specifications to obtain contracts for total correctness. Our approach combines the robustness of the size-change principle for termination with the precise information available at run-time. It has tunable overhead and can check for nontermination without the conservativeness necessary in static checking. To obtain a sound and computable termination analysis, we apply existing abstract interpretation techniques directly to the operational semantics, avoiding the need for custom abstractions for termination. The resulting analyzer is competitive with with existing, purpose-built analyzers

Data and donuts

Multiple sessions held on: 3/8/17, 5/16/17.So you've taken the R basics session and you're ready to make publication quality graphs using R. This month's Data and Donuts will show you how to use the ggplot package in R. After this session, you will be able to create a variety of plot types, alter their aesthetics, and use facets to automate the creation of several graphs at once. Some experience with R is recommended but not required

Data and donuts

Multiple sessions held on: 5/10/17, 7/25/17, 5/15/18.This month's Data and Donuts will cover best practices for preparing your data for archiving. We will discuss how to properly describe your data so that others, or you from 5 years from now, will know what it is and how to use it, as well as appropriate places to store it. We'll also discuss options for repositories that will allow others to access your research data, including CSU's digital repository

Alien Registration- Tobin, Loren C. (Ashland, Aroostook County)

https://digitalmaine.com/alien_docs/27294/thumbnail.jp