A domain-specific language and matrix-free stencil code for investigating electronic properties of Dirac and topological materials

We introduce PVSC-DTM (Parallel Vectorized Stencil Code for Dirac and Topological Materials), a library and code generator based on a domain-specific language tailored to implement the specific stencil-like algorithms that can describe Dirac and topological materials such as graphene and topological insulators in a matrix-free way. The generated hybrid-parallel (MPI+OpenMP) code is fully vectorized using Single Instruction Multiple Data (SIMD) extensions. It is significantly faster than matrix-based approaches on the node level and performs in accordance with the roofline model. We demonstrate the chip-level performance and distributed-memory scalability of basic building blocks such as sparse matrix-(multiple-) vector multiplication on modern multicore CPUs. As an application example, we use the PVSC-DTM scheme to (i) explore the scattering of a Dirac wave on an array of gate-defined quantum dots, to (ii) calculate a bunch of interior eigenvalues for strong topological insulators, and to (iii) discuss the photoemission spectra of a disordered Weyl semimetal.Comment: 16 pages, 2 tables, 11 figure

Selected Challenges From Spatial Statistics For Spatial Econometricians

Griffith and Paelinck (2011) present selected non-standard spatial statistics and spatial econometrics topics that address issues associated with spatial econometric methodology. This paper addresses the following challenges posed by spatial autocorrelation alluded to and/or derived from the spatial statistics topics of this book: the Gaussian random variable Jacobian term for massive datasets; topological features of georeferenced data; eigenvector spatial filtering-based georeferenced data generating mechanisms; and, interpreting random effects.Artykuł prezentuje wybrane, niestandardowe statystyki przestrzenne oraz zagadnienia ekonometrii przestrzennej. Rozważania teoretyczne koncentrują się na wyzwaniach wynikających z autokorelacji przestrzennej, nawiązując do pojęć Gaussowskiej zmiennej losowej, topologicznych cech danych georeferencyjnych, wektorów własnych, filtrów przestrzennych, georeferencyjnych mechanizmów generowania danych oraz interpretacji efektów losowych

Trace Spaces: an Efficient New Technique for State-Space Reduction

State-space reduction techniques, used primarily in model-checkers, all rely on the idea that some actions are independent, hence could be taken in any (respective) order while put in parallel, without changing the semantics. It is thus not necessary to consider all execution paths in the interleaving semantics of a concurrent program, but rather some equivalence classes. The purpose of this paper is to describe a new algorithm to compute such equivalence classes, and a representative per class, which is based on ideas originating in algebraic topology. We introduce a geometric semantics of concurrent languages, where programs are interpreted as directed topological spaces, and study its properties in order to devise an algorithm for computing dihomotopy classes of execution paths. In particular, our algorithm is able to compute a control-flow graph for concurrent programs, possibly containing loops, which is "as reduced as possible" in the sense that it generates traces modulo equivalence. A preliminary implementation was achieved, showing promising results towards efficient methods to analyze concurrent programs, with very promising results compared to partial-order reduction techniques

Evolutionary Approaches to Minimizing Network Coding Resources

We wish to minimize the resources used for network coding while achieving the desired throughput in a multicast scenario. We employ evolutionary approaches, based on a genetic algorithm, that avoid the computational complexity that makes the problem NP-hard. Our experiments show great improvements over the sub-optimal solutions of prior methods. Our new algorithms improve over our previously proposed algorithm in three ways. First, whereas the previous algorithm can be applied only to acyclic networks, our new method works also with networks with cycles. Second, we enrich the set of components used in the genetic algorithm, which improves the performance. Third, we develop a novel distributed framework. Combining distributed random network coding with our distributed optimization yields a network coding protocol where the resources used for coding are optimized in the setup phase by running our evolutionary algorithm at each node of the network. We demonstrate the effectiveness of our approach by carrying out simulations on a number of different sets of network topologies.Comment: 9 pages, 6 figures, accepted to the 26th Annual IEEE Conference on Computer Communications (INFOCOM 2007

Assessment of available anatomical characters for linking living mammals to fossil taxa in phylogenetic analyses

ORCID: 0000-0003-4919-8655© 2016 The Authors. Published by the Royal Society under the terms of the Creative Commons Attribution License http://creativecommons.org/licenses/by/4.0/, which permits unrestricted use, provided the original author and source are credited. The file attached is the published version of the article

A Linear Network Code Construction for General Integer Connections Based on the Constraint Satisfaction Problem

The problem of finding network codes for general connections is inherently difficult in capacity constrained networks. Resource minimization for general connections with network coding is further complicated. Existing methods for identifying solutions mainly rely on highly restricted classes of network codes, and are almost all centralized. In this paper, we introduce linear network mixing coefficients for code constructions of general connections that generalize random linear network coding (RLNC) for multicast connections. For such code constructions, we pose the problem of cost minimization for the subgraph involved in the coding solution and relate this minimization to a path-based Constraint Satisfaction Problem (CSP) and an edge-based CSP. While CSPs are NP-complete in general, we present a path-based probabilistic distributed algorithm and an edge-based probabilistic distributed algorithm with almost sure convergence in finite time by applying Communication Free Learning (CFL). Our approach allows fairly general coding across flows, guarantees no greater cost than routing, and shows a possible distributed implementation. Numerical results illustrate the performance improvement of our approach over existing methods.Comment: submitted to TON (conference version published at IEEE GLOBECOM 2015