Solving large-scale traveling salesman problems with parallel Branch-and-Cut

We introduce the implementation of a parallel Branch-and-Cut algorithm to solve large-scale traveling salesman problems. Rather than using the well-known models of homogeneous distribution and simple Master/Slave communication, we present a more sophisticated distribution that takes the advantage of several independent features of a Branch-and-Cut code. Computational results are reported for several instances of the TSPLIB

Virtual machine scheduling in dedicated computing clusters

Time-critical applications process a continuous stream of input data and have to meet specific timing constraints. A common approach to ensure that such an application satisfies its constraints is over-provisioning: The application is deployed in a dedicated cluster environment with enough processing power to achieve the target performance for every specified data input rate. This approach comes with a drawback: At times of decreased data input rates, the cluster resources are not fully utilized. A typical use case is the HLT-Chain application that processes physics data at runtime of the ALICE experiment at CERN. From a perspective of cost and efficiency it is desirable to exploit temporarily unused cluster resources. Existing approaches aim for that goal by running additional applications. These approaches, however, a) lack in flexibility to dynamically grant the time-critical application the resources it needs, b) are insufficient for isolating the time-critical application from harmful side-effects introduced by additional applications or c) are not general because application-specific interfaces are used. In this thesis, a software framework is presented that allows to exploit unused resources in a dedicated cluster without harming a time-critical application. Additional applications are hosted in Virtual Machines (VMs) and unused cluster resources are allocated to these VMs at runtime. In order to avoid resource bottlenecks, the resource usage of VMs is dynamically modified according to the needs of the time-critical application. For this purpose, a number of previously not combined methods is used. On a global level, appropriate VM manipulations like hot migration, suspend/resume and start/stop are determined by an informed search heuristic and applied at runtime. Locally on cluster nodes, a feedback-controlled adaption of VM resource usage is carried out in a decentralized manner. The employment of this framework allows to increase a cluster’s usage by running additional applications, while at the same time preventing negative impact towards a time-critical application. This capability of the framework is shown for the HLT-Chain application: In an empirical evaluation the cluster CPU usage is increased from 49% to 79%, additional results are computed and no negative effect towards the HLT-Chain application are observed

Virtual machine scheduling in dedicated computing clusters

Time-critical applications process a continuous stream of input data and have to meet specific timing constraints. A common approach to ensure that such an application satisfies its constraints is over-provisioning: The application is deployed in a dedicated cluster environment with enough processing power to achieve the target performance for every specified data input rate. This approach comes with a drawback: At times of decreased data input rates, the cluster resources are not fully utilized. A typical use case is the HLT-Chain application that processes physics data at runtime of the ALICE experiment at CERN. From a perspective of cost and efficiency it is desirable to exploit temporarily unused cluster resources. Existing approaches aim for that goal by running additional applications. These approaches, however, a) lack in flexibility to dynamically grant the time-critical application the resources it needs, b) are insufficient for isolating the time-critical application from harmful side-effects introduced by additional applications or c) are not general because application-specific interfaces are used. In this thesis, a software framework is presented that allows to exploit unused resources in a dedicated cluster without harming a time-critical application. Additional applications are hosted in Virtual Machines (VMs) and unused cluster resources are allocated to these VMs at runtime. In order to avoid resource bottlenecks, the resource usage of VMs is dynamically modified according to the needs of the time-critical application. For this purpose, a number of previously not combined methods is used. On a global level, appropriate VM manipulations like hot migration, suspend/resume and start/stop are determined by an informed search heuristic and applied at runtime. Locally on cluster nodes, a feedback-controlled adaption of VM resource usage is carried out in a decentralized manner. The employment of this framework allows to increase a cluster’s usage by running additional applications, while at the same time preventing negative impact towards a time-critical application. This capability of the framework is shown for the HLT-Chain application: In an empirical evaluation the cluster CPU usage is increased from 49% to 79%, additional results are computed and no negative effect towards the HLT-Chain application are observed

Evaluation of properties over phylogenetic trees using stochastic logics

Background: Model checking has been recently introduced as an integrated framework for extracting information of the phylogenetic trees using temporal logics as a querying language, an extension of modal logics that imposes restrictions of a boolean formula along a path of events. The phylogenetic tree is considered a transition system modeling the evolution as a sequence of genomic mutations (we understand mutation as different ways that DNA can be changed), while this kind of logics are suitable for traversing it in a strict and exhaustive way. Given a biological property that we desire to inspect over the phylogeny, the verifier returns true if the specification is satisfied or a counterexample that falsifies it. However, this approach has been only considered over qualitative aspects of the phylogeny. Results: In this paper, we repair the limitations of the previous framework for including and handling quantitative information such as explicit time or probability. To this end, we apply current probabilistic continuous-time extensions of model checking to phylogenetics. We reinterpret a catalog of qualitative properties in a numerical way, and we also present new properties that couldn't be analyzed before. For instance, we obtain the likelihood of a tree topology according to a mutation model. As case of study, we analyze several phylogenies in order to obtain the maximum likelihood with the model checking tool PRISM. In addition, we have adapted the software for optimizing the computation of maximum likelihoods. Conclusions: We have shown that probabilistic model checking is a competitive framework for describing and analyzing quantitative properties over phylogenetic trees. This formalism adds soundness and readability to the definition of models and specifications. Besides, the existence of model checking tools hides the underlying technology, omitting the extension, upgrade, debugging and maintenance of a software tool to the biologists. A set of benchmarks justify the feasibility of our approach

FleXR: A System Enabling Flexibly Distributed Extended Reality

Extended reality (XR) applications require computationally demanding functionalities with low end-to-end latency and high throughput. To enable XR on commodity devices, a number of distributed systems solutions enable offloading of XR workloads on remote servers. However, they make a priori decisions regarding the offloaded functionalities based on assumptions about operating factors, and their benefits are restricted to specific deployment contexts. To realize the benefits of offloading in various distributed environments, we present a distributed stream processing system, FleXR, which is specialized for real-time and interactive workloads and enables flexible distributions of XR functionalities. In building FleXR, we identified and resolved several issues of presenting XR functionalities as distributed pipelines. FleXR provides a framework for flexible distribution of XR pipelines while streamlining development and deployment phases. We evaluate FleXR with three XR use cases in four different distribution scenarios. In the results, the best-case distribution scenario shows up to 50% less end-to-end latency and 3.9x pipeline throughput compared to alternatives.Comment: 11 pages, 11 figures, conference pape

CRN++ : molecular programming language

Synthetic biology is a rapidly emerging research area, with expected wide-ranging impact in biology, nanofabrication, and medicine. A key technical challenge lies in embedding computation in molecular contexts where electronic micro-controllers cannot be inserted. This necessitates effective representation of computation using molecular components. While previous work established the Turing-completeness of chemical reactions, defining representations that are faithful, efficient, and practical remains challenging. This work introduces CRN++, a new language for programming deterministic (mass-action) chemical kinetics to perform computation. We present its syntax and semantics, and build a compiler translating CRN++ programs into chemical reactions, thereby laying the foundation of a comprehensive framework for molecular programming. Our language addresses the key challenge of embedding familiar imperative constructs into a set of chemical reactions happening simultaneously and manipulating real-valued concentrations. Although some deviation from ideal output value cannot be avoided, we develop methods to minimize the error, and implement error analysis tools. We demonstrate the feasibility of using CRN++ on a suite of well-known algorithms for discrete and real-valued computation. CRN++ can be easily extended to support new commands or chemical reaction implementations, and thus provides a foundation for developing more robust and practical molecular programs.Electrical and Computer Engineerin

Position analysis based on multi-affine formulations

Aplicat embargament des de la data de defensa fins el 31/5/2022The position analysis problem is a fundamental issue that underlies many problems in Robotics such as the inverse kinematics of serial robots, the forward kinematics of parallel robots, the coordinated manipulation of objects, the generation of valid grasps, the constraint-based object positioning, the simultaneous localization and map building, and the analysis of complex deployable structures. It also arises in other fields, such as in computer aided design, when the location of objects in a design is given in terms of geometric constrains, or in the conformational analysis of biomolecules. The ubiquity of this problem, has motivated an intense quest for methods able of tackling it. Up to now, efficient algorithms for the general problem have remained elusive and they are only available for particular cases. Moreover, the complexity of the problem has typically led to methods difficult to be implemented. Position analysis can be decomposed into two equally important steps: obtaining a set of closure equations, and solving them. This thesis deals with both of them to obtain a general, simple, and yet efficient solution method that we call the trapezoid method. The first step is addressed relying on dual quaternions. Although it has not been properly highlighted in the past, the use of dual quaternions permits expressing the closure condition of a kinematic loop involving only lower pairs as a system of multi-affine equations. In this thesis, this property is leveraged to introduce an interval-based method specially tailored for solving multi-affine systems. The proposed method is objectively simpler (in the sense that it is easier to understand and to implement) than previous methods based on general techniques such as interval Newton methods, conversions to Bernstein basis, or linear relaxations. Moreover, it relies on two simple operations, namely, linear interpolations and projections on coordinate planes, which can be executed with a high performance. The result is a method that accurately and efficiently bounds the valid solutions of the problem at hand. To further improve the accuracy, we propose the use of redundant, multi affine equations that are derived from the minimal set of equations describing the problem. To improve the efficiency, we introduce a variable elimination methodology that preserves the multi-affinity of the system of equations. The generality and the performance of the proposed trapezoid method are extensively evaluated on different kind of mechanisms, including spherical mechanisms, generic 6R and 7R loops, over-constrained systems, and multi-loop mechanisms. The proposed method is, in all cases, significantly faster than state of the art alternatives.El problema de l'anàlisi de posició és un tema fonamental que subjau a molts problemes de la robòtica, com ara la cinemàtica inversa de robots sèrie, la cinemàtica directa de robots paral·lels, la manipulació coordinada d'objectes, la generació de prensions vàlides amb mans robòtiques, el posicionament d'objectes basat en restriccions, la localització i la creació de mapes de forma simultània, i l'anàlisi d'estructures desplegables complexes. També sorgeix en altres camps, com ara en el disseny assistit per ordinador, quan la ubicació dels objectes en un disseny es dóna en termes de restriccions geomètriques o en l'anàlisi conformacional de biomolècules. La omnipresència d'aquest problema ha motivat una intensa recerca de mètodes capaços d'afrontar-lo. Fins al moment, els algoritmes eficients per al problema general han estat esquius i només estan disponibles per a casos particulars. A més, la complexitat del problema normalment ha conduït a mètodes difícils d'implementar. L'anàlisi de posició es pot descompondre en dos passos igualment importants: l'obtenció d'un sistema d'equacions de tancament i la resolució d'aquest sistema. Aquesta tesi tracta de tots dos passos per tal d'obtenir un mètode de solució general, senzill i alhora eficient que anomenem el mètode del trapezoide. El primer pas s'aborda utilitzant quaternions duals. Tot i que no ha estat suficientment destacat en el passat, l'ús de quaternions duals permet expressar la condició de tancament d'un bucle cinemàtic que impliqui només parells inferiors com a un sistema d'equacions multi-afins. En aquesta tesi s'aprofita aquesta propietat per introduir un mètode especialment dissenyat per resoldre sistemes multi-afins. El mètode proposat és objectivament més senzill (en el sentit que és més fàcil d'entendre i d'implementar) que els mètodes anteriors que utilitzen tècniques generals com ara els mètodes de Newton basats en intervals, les conversions a la base de Bernstein o les relaxacions lineals. A més, el mètode es basa en dues operacions simples, a saber, les interpolacions lineals i les projeccions en plans de coordenades, que es poden executar de forma molt eficient. El resultat és un mètode que acota amb precisió i eficiència les solucions vàlides del problema. Per millorar encara més la precisió, proposem l'ús d'equacions multi-afins redundants derivades del conjunt mínim d'equacions que descriuen el problema. Per altra banda, per millorar l'eficiència, introduïm un metodologia d'eliminació de variables que preserva la multi-afinitat del sistema d'equacions. La generalitat i el rendiment del mètode del trapezoide s'avalua extensivament en diferents tipus de mecanismes, inclosos els mecanismes esfèrics, bucles 6R i 7R genèrics, sistemes sobre-restringits i mecanismes de múltiples bucles. El mètode proposat és, en tots els casos, significativament més ràpid que els mètodes alternatius descrits en la literatura fins al moment.Postprint (published version

Towards description and optimization of abstract machines in an extension of prolog

Competitive abstract machines for Prolog are usually large, intricate, and incorpórate sophisticated optimizations. This makes them difñcult to code, optimize, and, especially, maintain and extend. This is partly due to the fact that efñciency considerations make it necessary to use low-level languages in their implementation. Writing the abstract machine (and ancillary code) in a higher-level language can help harness this inherent complexity. In this paper we show how the semantics of basic components of an efficient virtual machine for Prolog can be described using (a variant of) Prolog which retains much of its semantics. These descriptions are then compiled to C and assembled to build a complete bytecode emulator. Thanks to the high level of the language used and its closeness to Prolog the abstract machine descriptions can be manipulated using standard Prolog compilation and optimization techniques with relative ease. We also show how, by applying program transformations selectively, we obtain abstract machine implementations whose performance can match and even exceed that of highly-tuned, hand-crafted emulators