Novel parallelization of simulated annealing and Hooke & Jeeves search algorithms for multicore systems with application to complex fisheries stock assessment models

[Abstract] Estimating parameters of a statistical fisheries assessment model typically involves a comparison of disparate datasets to a forward simulation model through a likelihood function. In all but trivial cases the estimations of these models tend to be time-consuming due to issues related to multi-modality and non-linearity. This paper develops novel parallel implementations of popular search algorithms, applicable to expensive function calls typically encountered in fisheries stock assessment. It proposes two versions of both Simulated Annealing and Hooke & Jeeves optimization algorithms with the aim of fully utilizing the processing power of common multicore systems. The proposals have been tested on a 24-core server using three different input models. Results indicate that the parallel versions are able to take advantage of available resources without sacrificing the quality of the solution.Galicia. Consellería de Cultura, Educación e Ordenación Universitaria; R2014/04

Scaling Multidimensional Inference for Big Structured Data

In information technology, big data is a collection of data sets so large and complex that it becomes difficult to process using traditional data processing applications [151]. In a world of increasing sensor modalities, cheaper storage, and more data oriented questions, we are quickly passing the limits of tractable computations using traditional statistical analysis methods. Methods which often show great results on simple data have difficulties processing complicated multidimensional data. Accuracy alone can no longer justify unwarranted memory use and computational complexity. Improving the scaling properties of these methods for multidimensional data is the only way to make these methods relevant. In this work we explore methods for improving the scaling properties of parametric and nonparametric models. Namely, we focus on the structure of the data to lower the complexity of a specific family of problems. The two types of structures considered in this work are distributive optimization with separable constraints (Chapters 2-3), and scaling Gaussian processes for multidimensional lattice input (Chapters 4-5). By improving the scaling of these methods, we can expand their use to a wide range of applications which were previously intractable open the door to new research questions

Cross-Layer Rapid Prototyping and Synthesis of Application-Specific and Reconfigurable Many-accelerator Platforms

Technological advances of recent years laid the foundation consolidation of informatisationof society, impacting on economic, political, cultural and socialdimensions. At the peak of this realization, today, more and more everydaydevices are connected to the web, giving the term ”Internet of Things”. The futureholds the full connection and interaction of IT and communications systemsto the natural world, delimiting the transition to natural cyber systems and offeringmeta-services in the physical world, such as personalized medical care, autonomoustransportation, smart energy cities etc. . Outlining the necessities of this dynamicallyevolving market, computer engineers are required to implement computingplatforms that incorporate both increased systemic complexity and also cover awide range of meta-characteristics, such as the cost and design time, reliabilityand reuse, which are prescribed by a conflicting set of functional, technical andconstruction constraints. This thesis aims to address these design challenges bydeveloping methodologies and hardware/software co-design tools that enable therapid implementation and efficient synthesis of architectural solutions, which specifyoperating meta-features required by the modern market. Specifically, this thesispresents a) methodologies to accelerate the design flow for both reconfigurableand application-specific architectures, b) coarse-grain heterogeneous architecturaltemplates for processing and communication acceleration and c) efficient multiobjectivesynthesis techniques both at high abstraction level of programming andphysical silicon level.Regarding to the acceleration of the design flow, the proposed methodologyemploys virtual platforms in order to hide architectural details and drastically reducesimulation time. An extension of this framework introduces the systemicco-simulation using reconfigurable acceleration platforms as co-emulation intermediateplatforms. Thus, the development cycle of a hardware/software productis accelerated by moving from a vertical serial flow to a circular interactive loop.Moreover the simulation capabilities are enriched with efficient detection and correctiontechniques of design errors, as well as control methods of performancemetrics of the system according to the desired specifications, during all phasesof the system development. In orthogonal correlation with the aforementionedmethodological framework, a new architectural template is proposed, aiming atbridging the gap between design complexity and technological productivity usingspecialized hardware accelerators in heterogeneous systems-on-chip and networkon-chip platforms. It is presented a novel co-design methodology for the hardwareaccelerators and their respective programming software, including the tasks allocationto the available resources of the system/network. The introduced frameworkprovides implementation techniques for the accelerators, using either conventionalprogramming flows with hardware description language or abstract programmingmodel flows, using techniques from high-level synthesis. In any case, it is providedthe option of systemic measures optimization, such as the processing speed,the throughput, the reliability, the power consumption and the design silicon area.Finally, on addressing the increased complexity in design tools of reconfigurablesystems, there are proposed novel multi-objective optimization evolutionary algo-rithms which exploit the modern multicore processors and the coarse-grain natureof multithreaded programming environments (e.g. OpenMP) in order to reduce theplacement time, while by simultaneously grouping the applications based on theirintrinsic characteristics, the effectively explore the design space effectively.The efficiency of the proposed architectural templates, design tools and methodologyflows is evaluated in relation to the existing edge solutions with applicationsfrom typical computing domains, such as digital signal processing, multimedia andarithmetic complexity, as well as from systemic heterogeneous environments, suchas a computer vision system for autonomous robotic space navigation and manyacceleratorsystems for HPC and workstations/datacenters. The results strengthenthe belief of the author, that this thesis provides competitive expertise to addresscomplex modern - and projected future - design challenges.Οι τεχνολογικές εξελίξεις των τελευταίων ετών έθεσαν τα θεμέλια εδραίωσης της πληροφοριοποίησης της κοινωνίας, επιδρώντας σε οικονομικές,πολιτικές, πολιτιστικές και κοινωνικές διαστάσεις. Στο απόγειο αυτής τη ςπραγμάτωσης, σήμερα, ολοένα και περισσότερες καθημερινές συσκευές συνδέονται στο παγκόσμιο ιστό, αποδίδοντας τον όρο «Ίντερνετ των πραγμάτων».Το μέλλον επιφυλάσσει την πλήρη σύνδεση και αλληλεπίδραση των συστημάτων πληροφορικής και επικοινωνιών με τον φυσικό κόσμο, οριοθετώντας τη μετάβαση στα συστήματα φυσικού κυβερνοχώρου και προσφέροντας μεταυπηρεσίες στον φυσικό κόσμο όπως προσωποποιημένη ιατρική περίθαλψη, αυτόνομες μετακινήσεις, έξυπνες ενεργειακά πόλεις κ.α. . Σκιαγραφώντας τις ανάγκες αυτής της δυναμικά εξελισσόμενης αγοράς, οι μηχανικοί υπολογιστών καλούνται να υλοποιήσουν υπολογιστικές πλατφόρμες που αφενός ενσωματώνουν αυξημένη συστημική πολυπλοκότητα και αφετέρου καλύπτουν ένα ευρύ φάσμα μεταχαρακτηριστικών, όπως λ.χ. το κόστος σχεδιασμού, ο χρόνος σχεδιασμού, η αξιοπιστία και η επαναχρησιμοποίηση, τα οποία προδιαγράφονται από ένα αντικρουόμενο σύνολο λειτουργικών, τεχνολογικών και κατασκευαστικών περιορισμών. Η παρούσα διατριβή στοχεύει στην αντιμετώπιση των παραπάνω σχεδιαστικών προκλήσεων, μέσω της ανάπτυξης μεθοδολογιών και εργαλείων συνσχεδίασης υλικού/λογισμικού που επιτρέπουν την ταχεία υλοποίηση καθώς και την αποδοτική σύνθεση αρχιτεκτονικών λύσεων, οι οποίες προδιαγράφουν τα μετα-χαρακτηριστικά λειτουργίας που απαιτεί η σύγχρονη αγορά. Συγκεκριμένα, στα πλαίσια αυτής της διατριβής, παρουσιάζονται α) μεθοδολογίες επιτάχυνσης της ροής σχεδιασμού τόσο για επαναδιαμορφούμενες όσο και για εξειδικευμένες αρχιτεκτονικές, β) ετερογενή αδρομερή αρχιτεκτονικά πρότυπα επιτάχυνσης επεξεργασίας και επικοινωνίας και γ) αποδοτικές τεχνικές πολυκριτηριακής σύνθεσης τόσο σε υψηλό αφαιρετικό επίπεδο προγραμματισμού,όσο και σε φυσικό επίπεδο πυριτίου.Αναφορικά προς την επιτάχυνση της ροής σχεδιασμού, προτείνεται μια μεθοδολογία που χρησιμοποιεί εικονικές πλατφόρμες, οι οποίες αφαιρώντας τις αρχιτεκτονικές λεπτομέρειες καταφέρνουν να μειώσουν σημαντικά το χρόνο εξομοίωσης. Παράλληλα, εισηγείται η συστημική συν-εξομοίωση με τη χρήση επαναδιαμορφούμενων πλατφορμών, ως μέσων επιτάχυνσης. Με αυτόν τον τρόπο, ο κύκλος ανάπτυξης ενός προϊόντος υλικού, μετατεθειμένος από την κάθετη σειριακή ροή σε έναν κυκλικό αλληλεπιδραστικό βρόγχο, καθίσταται ταχύτερος, ενώ οι δυνατότητες προσομοίωσης εμπλουτίζονται με αποδοτικότερες μεθόδους εντοπισμού και διόρθωσης σχεδιαστικών σφαλμάτων, καθώς και μεθόδους ελέγχου των μετρικών απόδοσης του συστήματος σε σχέση με τις επιθυμητές προδιαγραφές, σε όλες τις φάσεις ανάπτυξης του συστήματος. Σε ορθογώνια συνάφεια με το προαναφερθέν μεθοδολογικό πλαίσιο, προτείνονται νέα αρχιτεκτονικά πρότυπα που στοχεύουν στη γεφύρωση του χάσματος μεταξύ της σχεδιαστικής πολυπλοκότητας και της τεχνολογικής παραγωγικότητας, με τη χρήση συστημάτων εξειδικευμένων επιταχυντών υλικού σε ετερογενή συστήματα-σε-ψηφίδα καθώς και δίκτυα-σε-ψηφίδα. Παρουσιάζεται κατάλληλη μεθοδολογία συν-σχεδίασης των επιταχυντών υλικού και του λογισμικού προκειμένου να αποφασισθεί η κατανομή των εργασιών στους διαθέσιμους πόρους του συστήματος/δικτύου. Το μεθοδολογικό πλαίσιο προβλέπει την υλοποίηση των επιταχυντών είτε με συμβατικές μεθόδους προγραμματισμού σε γλώσσα περιγραφής υλικού είτε με αφαιρετικό προγραμματιστικό μοντέλο με τη χρήση τεχνικών υψηλού επιπέδου σύνθεσης. Σε κάθε περίπτωση, δίδεται η δυνατότητα στο σχεδιαστή για βελτιστοποίηση συστημικών μετρικών, όπως η ταχύτητα επεξεργασίας, η ρυθμαπόδοση, η αξιοπιστία, η κατανάλωση ενέργειας και η επιφάνεια πυριτίου του σχεδιασμού. Τέλος, προκειμένου να αντιμετωπισθεί η αυξημένη πολυπλοκότητα στα σχεδιαστικά εργαλεία επαναδιαμορφούμενων συστημάτων, προτείνονται νέοι εξελικτικοί αλγόριθμοι πολυκριτηριακής βελτιστοποίησης, οι οποίοι εκμεταλλευόμενοι τους σύγχρονους πολυπύρηνους επεξεργαστές και την αδρομερή φύση των πολυνηματικών περιβαλλόντων προγραμματισμού (π.χ. OpenMP), μειώνουν το χρόνο επίλυσης του προβλήματος της τοποθέτησης των λογικών πόρων σε φυσικούς,ενώ ταυτόχρονα, ομαδοποιώντας τις εφαρμογές βάση των εγγενών χαρακτηριστικών τους, διερευνούν αποτελεσματικότερα το χώρο σχεδίασης.Η αποδοτικότητά των προτεινόμενων αρχιτεκτονικών προτύπων και μεθοδολογιών επαληθεύτηκε σε σχέση με τις υφιστάμενες λύσεις αιχμής τόσο σε αυτοτελής εφαρμογές, όπως η ψηφιακή επεξεργασία σήματος, τα πολυμέσα και τα προβλήματα αριθμητικής πολυπλοκότητας, καθώς και σε συστημικά ετερογενή περιβάλλοντα, όπως ένα σύστημα όρασης υπολογιστών για αυτόνομα διαστημικά ρομποτικά οχήματα και ένα σύστημα πολλαπλών επιταχυντών υλικού για σταθμούς εργασίας και κέντρα δεδομένων, στοχεύοντας εφαρμογές υψηλής υπολογιστικής απόδοσης (HPC). Τα αποτελέσματα ενισχύουν την πεποίθηση του γράφοντα, ότι η παρούσα διατριβή παρέχει ανταγωνιστική τεχνογνωσία για την αντιμετώπιση των πολύπλοκων σύγχρονων και προβλεπόμενα μελλοντικών σχεδιαστικών προκλήσεων

Towards Optimal Application Mapping for Energy-Efficient Many-Core Platforms

Siirretty Doriast

Nanometric and sub-nanometric structural properties of complex functional materials by means of solid-state NMR techniques

This thesis is about the application of SSNMR techniques to the study of different kind of functional materials with the aim of shedding light on the correlations between the structural and dynamic properties on a nanometric and sub-nanometric scale and the functional behaviour. This thesis is articulated in seven chapters. Chapter 1 introduces the SSNMR framework, presenting the theoretical background necessary to the comprehension of the SSNMR studies described in Chapters 3-7. Chapter 2 contains an introduction to functional materials, particularly focusing on the correlations between “microscopic” properties and functional behaviour, and on the role of SSNMR in the study of these systems. Then, in the remaining Chapters, the most important SSNMR studies that I carried out during my PhD on different classes of functional materials are presented. Each chapter starts with a presentation of the materials investigated, along with the results obtained by other experimental techniques, if present. The presentation of the SSNMR results is supported by descriptions of the employed SSNMR techniques and methodologies, which were different for the different studies. Chapter 3 presents an example of the application of SSNMR to the study of a novel anion exchange membrane based on polymeric materials. The combination of 13C CP/MAS experiments with 1H T1 and T1ρ measurements allowed information on the phase and structural properties of both the polymeric matrix and the conductive functional groups to be obtained, so contributing a complete and detailed picture of the properties of the material to be achieved. In the study reported in Chapter 4, the phase and dynamic behaviour of polymeric luminescent indicators were investigated, with the final aim of identifying the processes, occurring at a molecular and/or supramolecular level, responsible for the luminescent response of these materials under heating. In this case, the analyses of on resonance 1H FIDs acquired at increasing temperatures was found to be a very powerful tool for investigating the phase transformations occurring in polymeric domains, providing both structural and dynamic information. In Chapter 5 a detailed characterization of the dynamic properties in polymeric photoactive materials for solar cells is presented. In particular, the simultaneous analysis of 1H and 13C T1 curves as functions of temperature through suitable theoretical models was used to achieve a detailed characterization of the motional processes occurring in the MHz regime. Chapters 6 and 7 deal with the application of advanced high-resolution SSNMR techniques to the measurements of 19F and 1H chemical shift anisotropies in crystalline materials containing both organic and inorganic components. In Chapter 6, a methodological approach for the measurement of 19F chemical shift anisotropy based on both the analysis of spinning sideband profiles and the use of two-dimensional recoupling experiments is presented, along with the results obtained on two reference samples. Finally, Chapter 7 contains the applications of the methods described in Chapter 6 to the structural chararacterization of different zirconium phosphonates

GPU Computing for Parallel Local Search Metaheuristics

International audienceLocal search metaheuristics (LSMs) are efficient methods for solving complex problems in science and industry. They allow significantly to reduce the size of the search space to be explored and the search time. Nevertheless, the resolution time remains prohibitive when dealing with large problem instances. Therefore, the use of GPU-based massively parallel computing is a major complementary way to speed up the search. However, GPU computing for LSMs is rarely investigated in the literature. In this paper, we introduce a new guideline for the design and implementation of effective LSMs on GPU. Very efficient approaches are proposed for CPU-GPU data transfer optimization, thread control, mapping of neighboring solutions to GPU threads and memory management. These approaches have been experimented using four well-known combinatorial and continuous optimization problems and four GPU configurations. Compared to a CPU-based execution, accelerations up to x80 are reported for the large combinatorial problems and up to x240 for a continuous problem. Finally, extensive experiments demonstrate the strong potential of GPU-based LSMs compared to cluster or grid-based parallel architectures

Ant Colony Optimization

Ant Colony Optimization (ACO) is the best example of how studies aimed at understanding and modeling the behavior of ants and other social insects can provide inspiration for the development of computational algorithms for the solution of difficult mathematical problems. Introduced by Marco Dorigo in his PhD thesis (1992) and initially applied to the travelling salesman problem, the ACO field has experienced a tremendous growth, standing today as an important nature-inspired stochastic metaheuristic for hard optimization problems. This book presents state-of-the-art ACO methods and is divided into two parts: (I) Techniques, which includes parallel implementations, and (II) Applications, where recent contributions of ACO to diverse fields, such as traffic congestion and control, structural optimization, manufacturing, and genomics are presented

Probabilistic grid scheduling based on job statistics and monitoring information

This transfer thesis presents a novel, probabilistic approach to scheduling applications on computational Grids based on their historical behaviour, current state of the Grid and predictions of the future execution times and resource utilisation of such applications. The work lays a foundation for enabling a more intuitive, user-friendly and effective scheduling technique termed deadline scheduling. Initial work has established motivation and requirements for a more efficient Grid scheduler, able to adaptively handle dynamic nature of the Grid resources and submitted workload. Preliminary scheduler research identified the need for a detailed monitoring of Grid resources on the process level, and for a tool to simulate non-deterministic behaviour and statistical properties of Grid applications. A simulation tool, GridLoader, has been developed to enable modelling of application loads similar to a number of typical Grid applications. GridLoader is able to simulate CPU utilisation, memory allocation and network transfers according to limits set through command line parameters or a configuration file. Its specific strength is in achieving set resource utilisation targets in a probabilistic manner, thus creating a dynamic environment, suitable for testing the scheduler’s adaptability and its prediction algorithm. To enable highly granular monitoring of Grid applications, a monitoring framework based on the Ganglia Toolkit was developed and tested. The suite is able to collect resource usage information of individual Grid applications, integrate it into standard XML based information flow, provide visualisation through a Web portal, and export data into a format suitable for off-line analysis. The thesis also presents initial investigation of the utilisation of University College London Central Computing Cluster facility running Sun Grid Engine middleware. Feasibility of basic prediction concepts based on the historical information and process meta-data have been successfully established and possible scheduling improvements using such predictions identified. The thesis is structured as follows: Section 1 introduces Grid computing and its major concepts; Section 2 presents open research issues and specific focus of the author’s research; Section 3 gives a survey of the related literature, schedulers, monitoring tools and simulation packages; Section 4 presents the platform for author’s work – the Self-Organising Grid Resource management project; Sections 5 and 6 give detailed accounts of the monitoring framework and simulation tool developed; Section 7 presents the initial data analysis while Section 8.4 concludes the thesis with appendices and references