Performance analysis and optimization of the JOREK code for many-core CPUs

This report investigates the performance of the JOREK code on the Intel Knights Landing and Skylake processor architectures. The OpenMP scaling of the matrix construction part of the code was analyzed and improved synchronization methods were implemented. A new switch was implemented to control the number of threads used for the linear equation solver independently from other parts of the code. The matrix construction subroutine was vectorized, and the data locality was also improved. These steps led to a factor of two speedup for the matrix construction

Bioink properties before, during and after 3D bioprinting

Bioprinting is a process based on additive manufacturing from materials containing living cells. These materials, often referred to as bioink, are based on cytocompatible hydrogel precursor formulations, which gel in a manner compatible with different bioprinting approaches. The bioink properties before, during and after gelation are essential for its printability, comprising such features as achievable structural resolution, shape fidelity and cell survival. However, it is the final properties of the matured bioprinted tissue construct that are crucial for the end application. During tissue formation these properties are influenced by the amount of cells present in the construct, their proliferation, migration and interaction with the material. A calibrated computational framework is able to predict the tissue development and maturation and to optimize the bioprinting input parameters such as the starting material, the initial cell loading and the construct geometry. In this contribution relevant bioink properties are reviewed and discussed on the example of most popular bioprinting approaches. The effect of cells on hydrogel processing and vice versa is highlighted. Furthermore, numerical approaches were reviewed and implemented for depicting the cellular mechanics within the hydrogel as well as for prediction of mechanical properties to achieve the desired hydrogel construct considering cell density, distribution and material-cell interaction

Differential Hoare Logics and Refinement Calculi for Hybrid Systems with Isabelle/HOL

We present simple new Hoare logics and refinement calculi for hybrid systems in the style of differential dynamic logic. (Refinement) Kleene algebra with tests is used for reasoning about the program structure and generating verification conditions at this level. Lenses capture hybrid program stores in a generic algebraic way. The approach has been formalised with the Isabelle/HOL proof assistant. A number of examples explains the workflow with the resulting verification components

A consistent foundation for Isabelle/HOL

The interactive theorem prover Isabelle/HOL is based on well understood Higher-Order Logic (HOL), which is widely believed to be consistent (and provably consistent in set theory by a standard semantic argument). However, Isabelle/HOL brings its own personal touch to HOL: overloaded constant definitions, used to achieve Haskell-like type classes in the user space. These features are a delight for the users, but unfortunately are not easy to get right as an extension of HOL—they have a history of inconsistent behavior. It has been an open question under which criteria overloaded constant definitions and type definitions can be combined together while still guaranteeing consistency. This paper presents a solution to this problem: non-overlapping definitions and termination of the definition-dependency relation (tracked not only through constants but also through types) ensures relative consistency of Isabelle/HOL

From types to sets by local type definitions in higher-order logic

Types in Higher-Order Logic (HOL) are naturally interpreted as nonempty sets—this intuition is reflected in the type definition rule for the HOL-based systems (including Isabelle/HOL), where a new type can be defined whenever a nonempty set is exhibited. However, in HOL this definition mechanism cannot be applied inside proof contexts. We propose a more expressive type definition rule that addresses the limitation and we prove its soundness. This higher expressive power opens the opportunity for a HOL tool that relativizes type-based statements to more flexible set-based variants in a principled way. We also address particularities of Isabelle/HOL and show how to perform the relativization in the presence of type classes

Pain shared, pain halved? Cooperation as a coping strategy for innovation barriers

The paper analyses the relationship between the perception of barriers to innovation and the firm’s propensity to cooperate to mitigate their effect. First, we look at whether cooperation with research organizations or private firms is associated with experiencing different types of barriers, for example, financial constraints, lack of human capital or uncertain market demand. Second, we test whether experiencing several types of barriers simultaneously has a super-modular effect on the propensity to cooperate tout court, and the choice of cooperation partner. We find that having to face a single, specific constraint leads to firms ‘sharing the pain’ with cooperation partners—both research organization and other firms. However, the results of a super-modularity test show that having to cope with different barriers is a deterrent to establishing cooperation agreements, especially when firms lack finance, adequate skills and information on technology or markets. The paper adds to the innovation literature by identifying the factors associated with firms’ coping with different barriers by applying a selective cooperation strategy

Methodological Guidelines for Engineering Self-organization and Emergence

The ASCENS project deals with the design and development of complex self-adaptive systems, where self-organization is one of the possible means by which to achieve self-adaptation. However, to support the development of self-organising systems, one has to extensively re-situate their engineering from a software architectures and requirements point of view. In particular, in this chapter, we highlight the importance of the decomposition in components to go from the problem to the engineered solution. This leads us to explain and rationalise the following architectural strategy: designing by following the problem organisation. We discuss architectural advantages for development and documentation, and its coherence with existing methodological approaches to self-organisation, and we illustrate the approach with an example on the area of swarm robotics

Recent EUROfusion Achievements in Support of Computationally Demanding Multiscale Fusion Physics Simulations and Integrated Modeling

Integrated modeling (IM) of present experiments and future tokamak reactors requires the provision of computational resources and numerical tools capable of simulating multiscale spatial phenomena as well as fast transient events and relatively slow plasma evolution within a reasonably short computational time. Recent progress in the implementation of the new computational resources for fusion applications in Europe based on modern supercomputer technologies (supercomputer MARCONI-FUSION), in the optimization and speedup of the EU fusion-related first-principle codes, and in the development of a basis for physics codes/modules integration into a centrally maintained suite of IM tools achieved within the EUROfusion Consortium is presented. Physics phenomena that can now be reasonably modelled in various areas (core turbulence and magnetic reconnection, edge and scrape-off layer physics, radio-frequency heating and current drive, magnetohydrodynamic model, reflectometry simulations) following successful code optimizations and parallelization are briefly described. Development activities in support to IM are summarized. They include support to (1) the local deployment of the IM infrastructure and access to experimental data at various host sites, (2) the management of releases for sophisticated IM workflows involving a large number of components, and (3) the performance optimization of complex IM workflows.This work has been carried out within the framework of the EUROfusion Consortium and has received funding from the Euratom research and training programme 2014 to 2018 under grant agreement 633053. The views and opinions expressed herein do not necessarily reflect those of the European Commission or ITER.Peer ReviewedPostprint (published version

Microalgae Lipid Characterization

To meet the growing interest of utilizing microalgae biomass in the production of biofuels and nutraceutical and pharmaceutical lipids, we need suitable analytical methods and a comprehensive database for their lipid components. The objective of the present work was to demonstrate methodology and provide data on fatty acid composition, lipid class content and composition, characteristics of the unsaponifiables, and type of chlorophylls of five microalgae. Microalgae lipids were fractionated into TAG, FFA, and polar lipids using TLC, and the composition of fatty acids in total lipids and in each lipid class, hydrocarbons, and sterols were determined by GC-MS. Glyco- and phospholipids were profiled by LC/ESI-MS. Chlorophylls and their related metabolites were qualified by LC/APCI-MS. The melting and crystallization profiles of microalgae total lipids and their esters were analyzed by DSC to evaluate their potential biofuel applications. Significant differences and complexities of lipid composition among the algae tested were observed. The compositional information is valuable for strain selection, downstream biomass fractionation, and utilization

Technological diversification within UK’s small serial innovators

This paper investigates the determinants of technological diversification among UK’s small serial innovators (SSIs). Using a longitudinal study of 339 UK-based small businesses accounting for almost 7000 patents between 1990 and 2006, this study constitutes the first empirical examination of technological diversification among SMEs in the literature. Results demonstrate that technological diversification is not solely a large firm activity, challenging the dominant view that innovative SMEs are extremely focused and specialised players with little technological diversification. Our findings suggest a nonlinear (i.e. inverse-U-shaped) relationship between the level of technological opportunities in the environment and the SSIs’ degree of technological diversification. This points to a trade-off between processes of exploration and exploitation across increasingly volatile technology regimes. The paper also demonstrates that small firms with impactful innovations focus their innovative activity around similar technological capabilities while firms that have introduced platform technologies in the past are more likely to engage in technological diversification