Parallel software for lattice N=4 supersymmetric Yang--Mills theory

We present new parallel software, SUSY LATTICE, for lattice studies of four-dimensional $\mathcal N = 4$ supersymmetric Yang--Mills theory with gauge group SU(N). The lattice action is constructed to exactly preserve a single supersymmetry charge at non-zero lattice spacing, up to additional potential terms included to stabilize numerical simulations. The software evolved from the MILC code for lattice QCD, and retains a similar large-scale framework despite the different target theory. Many routines are adapted from an existing serial code, which SUSY LATTICE supersedes. This paper provides an overview of the new parallel software, summarizing the lattice system, describing the applications that are currently provided and explaining their basic workflow for non-experts in lattice gauge theory. We discuss the parallel performance of the code, and highlight some notable aspects of the documentation for those interested in contributing to its future development.Comment: Code available at https://github.com/daschaich/sus

Chaste: a test-driven approach to software development for biological modelling

Chaste (‘Cancer, heart and soft-tissue environment’) is a software library and a set of test suites for computational simulations in the domain of biology. Current functionality has arisen from modelling in the fields of cancer, cardiac physiology and soft-tissue mechanics. It is released under the LGPL 2.1 licence.\ud \ud Chaste has been developed using agile programming methods. The project began in 2005 when it was reasoned that the modelling of a variety of physiological phenomena required both a generic mathematical modelling framework, and a generic computational/simulation framework. The Chaste project evolved from the Integrative Biology (IB) e-Science Project, an inter-institutional project aimed at developing a suitable IT infrastructure to support physiome-level computational modelling, with a primary focus on cardiac and cancer modelling

Quantitative Analysis of Probabilistic Models of Software Product Lines with Statistical Model Checking

We investigate the suitability of statistical model checking techniques for analysing quantitative properties of software product line models with probabilistic aspects. For this purpose, we enrich the feature-oriented language FLan with action rates, which specify the likelihood of exhibiting particular behaviour or of installing features at a specific moment or in a specific order. The enriched language (called PFLan) allows us to specify models of software product lines with probabilistic configurations and behaviour, e.g. by considering a PFLan semantics based on discrete-time Markov chains. The Maude implementation of PFLan is combined with the distributed statistical model checker MultiVeStA to perform quantitative analyses of a simple product line case study. The presented analyses include the likelihood of certain behaviour of interest (e.g. product malfunctioning) and the expected average cost of products.Comment: In Proceedings FMSPLE 2015, arXiv:1504.0301

GHOST: Building blocks for high performance sparse linear algebra on heterogeneous systems

While many of the architectural details of future exascale-class high performance computer systems are still a matter of intense research, there appears to be a general consensus that they will be strongly heterogeneous, featuring "standard" as well as "accelerated" resources. Today, such resources are available as multicore processors, graphics processing units (GPUs), and other accelerators such as the Intel Xeon Phi. Any software infrastructure that claims usefulness for such environments must be able to meet their inherent challenges: massive multi-level parallelism, topology, asynchronicity, and abstraction. The "General, Hybrid, and Optimized Sparse Toolkit" (GHOST) is a collection of building blocks that targets algorithms dealing with sparse matrix representations on current and future large-scale systems. It implements the "MPI+X" paradigm, has a pure C interface, and provides hybrid-parallel numerical kernels, intelligent resource management, and truly heterogeneous parallelism for multicore CPUs, Nvidia GPUs, and the Intel Xeon Phi. We describe the details of its design with respect to the challenges posed by modern heterogeneous supercomputers and recent algorithmic developments. Implementation details which are indispensable for achieving high efficiency are pointed out and their necessity is justified by performance measurements or predictions based on performance models. The library code and several applications are available as open source. We also provide instructions on how to make use of GHOST in existing software packages, together with a case study which demonstrates the applicability and performance of GHOST as a component within a larger software stack.Comment: 32 pages, 11 figure

Towards the Formal Specification and Verification of Maple Programs

In this paper, we present our ongoing work and initial results on the formal specification and verification of MiniMaple (a substantial subset of Maple with slight extensions) programs. The main goal of our work is to find behavioral errors in such programs w.r.t. their specifications by static analysis. This task is more complex for widely used computer algebra languages like Maple as these are fundamentally different from classical languages: they support non-standard types of objects such as symbols, unevaluated expressions and polynomials and require abstract computer algebraic concepts and objects such as rings and orderings etc. As a starting point we have defined and formalized a syntax, semantics, type system and specification language for MiniMaple

Orbifold equivalence: structure and new examples

Orbifold equivalence is a notion of symmetry that does not rely on group actions. Among other applications, it leads to surprising connections between hitherto unrelated singularities. While the concept can be defined in a very general category-theoretic language, we focus on the most explicit setting in terms of matrix factorisations, where orbifold equivalences arise from defects with special properties. Examples are relatively difficult to construct, but we uncover some structural features that distinguish orbifold equivalences -- most notably a finite perturbation expansion. We use those properties to devise a search algorithm, then present some new examples including Arnold singularities.Comment: 34 pages, web-link to Singular code provide