Dynamic steering of HPC scientific workflows: A survey

The field of scientific workflow management systems has grown significantly as applications start using them successfully. In 2007, several active researchers in scientific workflow developments presented the challenges for the state of the art in workflow technologies at that time. Many issues have been addressed, but one of them named ‘dynamic workflows and user steering’ remains with many open problems despite the contributions presented in the recent years. This article surveys the early and current efforts in this topic and proposes a taxonomy to identify the main concepts related to addressing issues in dynamic steering of high performance computing (HPC) in scientific workflows. The main concepts are related to putting the human-in-the-loop of the workflow lifecycle, involving user support in real-time monitoring, notification, analysis and interference by adapting the workflow execution at runtime.     

Boosting gLite with cloud augmented volunteer computing

The paper details the result of the EU FP7 EDGI project focusing on the cloud developments and usability improvements. Volunteer desktop grids, like BOINC, are designed to handle millions of parameter sweep type jobs and millions of desktop machines as worker nodes. Seamless transfer of gLite jobs to desktop grids was already implemented by EDGI; however this huge number of DG resources could not be utilized efficiently due to slow completion time caused by unpredictable behavior of the volunteer resources. The paper details how clouds have been utilized to shorten completion time on the EDGeS@home volunteer desktop grid to boost the performance of the supported gLite VO and also details how this service can be exploited by the gLite user communities of EGI (European Grid Initiative) all over Europe.     

Neurological and Epigenetic Implications of Nutritional Deficiencies on Psychopathology: Conceptualization and Review of Evidence

In recent years, a role for epigenetic modifications in the pathophysiology of disease has received significant attention. Many studies are now beginning to explore the gene–environment interactions, which may mediate early-life exposure to risk factors, such as nutritional deficiencies and later development of behavioral problems in children and adults. In this paper, we review the current literature on the role of epigenetics in the development of psychopathology, with a specific focus on the potential for epigenetic modifications to link nutrition and brain development. We propose a conceptual framework whereby epigenetic modifications (e.g., DNA methylation) mediate the link between micro- and macro-nutrient deficiency early in life and brain dysfunction (e.g., structural aberration, neurotransmitter perturbation), which has been linked to development of behavior problems later on in life.     

Improving scenario decomposition algorithms for robust nonlinear model predictive control

This paper deals with the efficient computation of solutions of robust nonlinear model predictive control problems that are formulated using multi-stage stochastic programming via the generation of a scenario tree. Such a formulation makes it possible to consider explicitly the concept of recourse, which is inherent to any receding horizon approach, but it results in large-scale optimization problems. One possibility to solve these problems in an efficient manner is to decompose the large-scale optimization problem into several subproblems that are iteratively modified and repeatedly solved until a solution to the original problem is achieved. In this paper we review the most common methods used for such decomposition and apply them to solve robust nonlinear model predictive control problems in a distributed fashion. We also propose a novel method to reduce the number of iterations of the coordination algorithm needed for the decomposition methods to converge. The performance of the different approaches is evaluated in extensive simulation studies of two nonlinear case studies.     

Simplifying the powder metallurgy manufacturing process using soft computing tools

The tools of soft computing will aid the knowledge mining in predicting and classifying the properties of various parameters while designing the composite preforms in the manufacturing of Powder Metallurgy (P/M) Lab. In this paper, an integrated PRNET (PCA-Radial basis functional neural NET) model is proposed in different versions to select the relevant parameters for preparing composite preforms and to predict the deformation and strain hardening properties of Al–Fe composites. It reveals that the predictability of this model has been increased by 67.89% relatively from the conventional models. A new PR-filter is proposed by slightly modifying the conventional filters of RBFNN, which improves the power of PRNET even though raw data are highly non-linear, interrelated and noisy. Moreover, fixing the range of input parameters for classifying the properties of composite preforms can be automated by the Fuzzy logic. These types of models will avoid expensive experimentation and risky environment while preparing sintered composite preforms. Thus the manufacturing process of composites in P/M Lab will be simplified with minimum energy by the support of these soft-computing tools.     

Rules discovery in fuzzy classifier systems with PSO for scheduling in grid computational infrastructures

Particle swarm optimization (PSO) is a bio-inspired optimization strategy founded on the movement of particles within swarms. PSO can be encoded in a few lines in most programming languages, it uses only elementary mathematical operations, and it is not costly as regards memory demand and running time. This paper discusses the application of PSO to rules discovery in fuzzy classifier systems (FCSs) instead of the classical genetic approach and it proposes a new strategy, Knowledge Acquisition with Rules as Particles (KARP). In KARP approach every rule is encoded as a particle that moves in the space in order to cooperate in obtaining high quality rule bases and in this way, improving the knowledge and performance of the FCS. The proposed swarm-based strategy is evaluated in a well-known problem of practical importance nowadays where the integration of fuzzy systems is increasingly emerging due to the inherent uncertainty and dynamism of the environment: scheduling in grid distributed computational infrastructures. Simulation results are compared to those of classical genetic learning for fuzzy classifier systems and the greater accuracy and convergence speed of classifier discovery systems using KARP is shown.     

Calculating the medial axis of a CAD model by multi-CPU based parallel computation

Computational efficiency is still a great challenge for the generation of the Medial Axis (MA) for complicated CAD models. Current research mainly focuses on CPU-based MA generation methods. However, most of the methods emphasize using a single CPU. The highly-efficient methods based on parallel computing are still missing. In this study, a parallel method based on multi-CPU is proposed for the efficient MA generation of CAD models using distance dilation. By dividing the whole model into several parts for which MAs are calculated in parallel and then combined, computational efficiency can be greatly improved in theory and the computation time can be reduced nearly K times if K CPUs are used. Firstly, an adaptive division method is proposed to divide the voxelized model into blocks which have nearly the same number of voxels to balance the computational burden. Secondly, the local Euclidean Distance Transform (EDT) is calculated for each block based on the existing distance dilation method. Thirdly, the complete inter-dilation method is proposed to compute the influence between different blocks to get a global EDT for each block. Finally, each block generates a sub-MA separately and then all the generated MAs are combined to obtain the final MA. The last three processes can be efficiently conducted in parallel by using multiple CPUs. Several groups of experiments are conducted which demonstrate the good performance of the proposed methods in terms of efficiency.     

Application of integrated soft computing techniques for optimisation of hybrid CO2 laser–MIG welding process

In this paper, artificial neural networks (ANNs), genetic algorithm (GA), simulated annealing (SA) and Quasi Newton line search techniques have been combined to develop three integrated soft computing based models such as ANN–GA, ANN–SA and ANN–Quasi Newton for prediction modelling and optimisation of welding strength for hybrid CO₂ laser–MIG welded joints of aluminium alloy. Experimental dataset employed for the purpose has been generated through full factorial experimental design. Laser power, welding speeds and wires feed rate are considered as controllable input parameters. These soft computing models employ a trained ANN for calculation of objective function value and thereby eliminate the need of closed form objective function. Among 11 tested networks, the ANN with best prediction performance produces maximum percentage error of only 3.21%. During optimisation ANN–GA is found to show best performance with absolute percentage error of only 0.09% during experimental validation. Low value of percentage error indicates efficacy of models. Welding speed has been found as most influencing factor for welding strength.     

Usability of a cloud-based collaborative learning framework to improve learners’ experience

Computer-Supported Collaborative Learning (CSCL) is concerned with how Information and Communication Technology (ICT) might facilitate learning in groups which can be co-located or distributed over a network of computers such as Internet. CSCL supports effective learning by means of communication of ideas and information among learners, collaborative access of essential documents, and feedback from instructors and peers on learning activities. As the cloud technologies are increasingly becoming popular and collaborative learning is evolving, new directions for development of collaborative learning tools deployed on cloud are proposed. Development of such learning tools requires access to substantial data stored in the cloud. Ensuring efficient access to such data is hindered by the high latencies of wide-area networks underlying the cloud infrastructures. To improve learners’ experience by accelerating data access, important files can be replicated so a group of learners can access data from nearby locations. Since a cloud environment is highly dynamic, resource availability, network latency, and learner requests may change. In this paper, we present the advantages of collaborative learning and focus on the importance of data replication in the design of such a dynamic cloud-based system that a collaborative learning portal uses. To this end, we introduce a highly distributed replication technique that determines optimal data locations to improve access performance by minimizing replication overhead (access and update). The problem is formulated using dynamic programming. Experimental results demonstrate the usefulness of the proposed collaborative learning system used by institutions in geographically distributed locations.     

Unrelated toxin–antitoxin systems cooperate to induce persistence

Persisters are drug-tolerant bacteria that account for the majority of bacterial infections. They are not mutants, rather, they are slow-growing cells in an otherwise normally growing population. It is known that the frequency of persisters in a population is correlated with the number of toxin–antitoxin systems in the organism. Our previous work provided a mechanistic link between the two by showing how multiple toxin–antitoxin systems, which are present in nearly all bacteria, can cooperate to induce bistable toxin concentrations that result in a heterogeneous population of slow- and fast-growing cells. As such, the slow-growing persisters are a bet-hedging subpopulation maintained under normal conditions. For technical reasons, the model assumed that the kinetic parameters of the various toxin–antitoxin systems in the cell are identical, but experimental data indicate that they differ, sometimes dramatically. Thus, a critical question remains: whether toxin–antitoxin systems from the diverse families, often found together in a cell, with significantly different kinetics, can cooperate in a similar manner. Here, we characterize the interaction of toxin–antitoxin systems from many families that are unrelated and kinetically diverse, and identify the essential determinant for their cooperation. The generic architecture of toxin–antitoxin systems provides the potential for bistability, and our results show that even when they do not exhibit bistability alone, unrelated systems can be coupled by the growth rate to create a strongly bistable, hysteretic switch between normal (fast-growing) and persistent (slow-growing) states. Different combinations of kinetic parameters can produce similar toxic switching thresholds, and the proximity of the thresholds is the primary determinant of bistability. Stochastic fluctuations can spontaneously switch all of the toxin–antitoxin systems in a cell at once. The spontaneous switch creates a heterogeneous population of growing and non-growing cells, typical of persisters, that exist under normal conditions, rather than only as an induced response. The frequency of persisters in the population can be tuned for a particular environmental niche by mixing and matching unrelated systems via mutation, horizontal gene transfer and selection.