Performance Bounds for Synchronized Queueing Networks

Las redes de Petri estocásticas constituyen un modelo unificado de las diferentes extensiones de redes de colas con sincronizaciones existentes en la literatura, válido para el diseño y análisis de prestaciones de sistemas informáticos distribuidos. En este trabajo se proponen técnicas de cálculo de cotas superiores e inferiores de las prestaciones de redes de Petri estocásticas en estado estacionario. Las cotas obtenidas son calculables en tiempo polinómico en el tamaño del modelo, por medio de la resolución de ciertos problemas de programación lineal definidos a partir de la matriz de incidencia de la red (en este sentido, las técnicas desarrolladas pueden considerarse estructurales). Las cotas calculadas dependen sólamente de los valores medios de las variables aleatorias que describen la temporización del sistema, y son independientes de los momentos de mayor orden. Esta independencia de la forma de las distribuciones de probabilidad asociadas puede considerarse como una útil generalización de otros resultados existentes para distribuciones particulares, puesto que los momentos de orden superior son, habitualmente, desconocidos en la realidad y difíciles de estimar. Finalmente, las técnicas desarrolladas se aplican al análisis de diferentes ejemplos tomados de la literatura sobre sistemas informáticos distribuidos y sistemas de fabricación. ******* Product form queueing networks have long been used for the performance evaluation of computer systems. Their success has been due to their capability of naturally expressing sharing of resources and queueing, that are typical situations of traditional computer systems, as well as to their efficient solution algorithms, of polynomial complexity on the size of the model. Unfortunately, the introduction of synchronization constraints usually destroys the product form solution, so that general concurrent and distributed systems are not easily studied with this class of models. Petri nets have been proved specially adequate to model parallel and distributed systems. Moreover, they have a well-founded theory of analysis that allows to investigate a great number of qualitative properties of the system. In the original definition, Petri nets did not include the notion of time, and tried to model only the logical behaviour of systems by describing the causal relations existing among events. This approach showed its power in the specification and analysis of concurrent systems in a way independent of the concept of time. Nevertheless the introduction of a timing specification is essential if we want to use this class of models for the performance evaluation of distributed systems. One of the main problems in the actual use of timed and stochastic Petri net models for the quantitative evaluation of large systems is the explosion of the computational complexity of the analysis algorithms. In general, exact performance results are obtained from the numerical solution of a continuous time Markov chain, whose dimension is given by the size of the state space of the model. Structural computation of exact performance measures has been possible for some subclasses of nets such as those with state machine topology. These nets, under certain assumptions on the stochastic interpretation are isomorphic to Gordon and Newell's networks, in queueing theory terminology. In the general case, efficient methods for the derivation of performance measures are still needed. Two complementary approaches to the derivation of exact measures for the analysis of distributed systems are the utilization of approximation techniques and the computation of bounds. Approximate values for the performance parameters are in general more efficiently derived than the exact ones. On the other hand, "exactness" only exists in theory! In other words, numerical algorithms must be applied in practice for the computation of exact values, therefore making errors is inevitable. Performance bounds are useful in the preliminary phases of the design of a system, in which many parameters are not known accurately. Several alternatives for those parameters should be quickly evaluated, and rejected those that are clearly bad. Exact (and even approximate) solutions would be computationally very expensive. Bounds become useful in these instances since they usually require much less computation effort. The computation of upper and lower bounds for the steady-state performance of timed and stochastic Petri nets is considered in this work. In particular, we study the throughput of transitions, defined as the average number of firings per time unit. For this measure we try to compute upper and lower bounds in polynomial time on the size of the net model, by means of proper linear programming problems defined from the incidence matrix of the net (in this sense, we develop structural techniques). These bounds depend only on the mean values and not on the higher moments of the probability distribution functions of the random variables that describe the timing of the system. The independence of the probability distributions can be viewed as a useful generalization of the performance results, since higher moments of the delays are usually unknown for real cases, and difficult to estimate and assess. From a different perspective, the obtained results can be applied to the analysis of queueing networks extended with some synchronization schemes. Monoclass queueing networks can be mapped on stochastic Petri nets. On the other hand, stochastic Petri nets can be interpreted as monoclass queueing networks augmented with synchronization primitives. Concerning the presentation of this manuscript, it should be mentioned that chapter 1 has been written with the object of giving the reader an outline of the stochastic Petri net model: its definition, terminology, basic properties, and related concepts, together with its deep relation with other classic stochastic network models. Chapter 2 is devoted to the presentation of the net subclasses considered in the rest of the work. The classification presented here is quite different from the one which is usual in the framework of Petri nets. The reason lies on the fact that our classification criterion, the computability of visit ratios for transitions, is introduced for the first time in the field of stochastic Petri nets in this work. The significance of that criterion is based on the important role that the visit ratios play in the computation of upper and lower bounds for the performance of the models. Nevertheless, classical important net subclasses are identified here in terms of the computability of their visit ratios from different parameters of the model. Chapter 3 is concerned with the computation of reachable upper and lower bounds for the most restrictive subclass of those presented in chapter 2: marked graphs. The explanation of this fact is easy to understand. The more simple is the model the more accessible will be the techniques an ideas for the development of good results. Chapter 4 provides a generalization for live and bounded free choice nets of the results presented in the previous chapter. Quality of obtained bounds is similar to that for strongly connected marked graphs: throughput lower bounds are reachable for bounded nets while upper bounds are reachable for 1-bounded nets. Chapter 5 considers the extension to other net subclasses, like mono-T-semiflow nets, FRT-nets, totally open deterministic systems of sequential processes, and persistent nets. The results are of diverse colours. For mono-T-semiflow nets and, therefore, for general FRT-nets, it is not possible (so far) to obtain reachable throughput bounds. On the other hand, for bounded ordinary persistent nets, tight throughput upper bounds are derived. Moreover, in the case of totally open deterministic systems of sequential processes the exact steady-state performance measures can be computed in polynomial time on the net size. In chapter 6 bounds for other interesting performance measures are derived from throughput bounds and from classical queueing theory laws. After that, we explore the introduction of more information from the probability distribution functions of service times in order to improve the bounds. In particular, for Coxian service delay of transitions it is possible to improve the throughput upper bounds of previous chapters which held for more general forms of distribution functions. This improvement shows to be specially fruitful for live and bounded free choice nets. Chapter 7 is devoted to case studies. Several examples taken from literature in the fields of distributed computing systems and manufacturing systems are modelled by means of stochastic Petri nets and evaluated using the techniques developed in previous chapters. Finally, some concluding remarks and considerations on possible extensions of the work are presented

Petri nets for systems and synthetic biology

We give a description of a Petri net-based framework for modelling and analysing biochemical pathways, which uni¯es the qualita- tive, stochastic and continuous paradigms. Each perspective adds its con- tribution to the understanding of the system, thus the three approaches do not compete, but complement each other. We illustrate our approach by applying it to an extended model of the three stage cascade, which forms the core of the ERK signal transduction pathway. Consequently our focus is on transient behaviour analysis. We demonstrate how quali- tative descriptions are abstractions over stochastic or continuous descrip- tions, and show that the stochastic and continuous models approximate each other. Although our framework is based on Petri nets, it can be applied more widely to other formalisms which are used to model and analyse biochemical networks

A Petri Net Tool for Software Performance Estimation Based on Upper Throughput Bounds

Functional and non-functional properties analysis (i.e., dependability, security, or performance) ensures that requirements are fulfilled during the design phase of software systems. However, the Unified Modelling Language (UML), standard de facto in industry for software systems modelling, is unsuitable for any kind of analysis but can be tailored for specific analysis purposes through profiling. For instance, the MARTE profile enables to annotate performance data within UML models that can be later transformed to formal models (e.g., Petri nets or Timed Automatas) for performance evaluation. A performance (or throughput) estimation in such models normally relies on a whole exploration of the state space, which becomes unfeasible for large systems. To overcome this issue upper throughput bounds are computed, which provide an approximation to the real system throughput with a good complexity-accuracy trade-off. This paper introduces a tool, named PeabraiN, that estimates the performance of software systems via their UML models. To do so, UML models are transformed to Petri nets where performance is estimated based on upper throughput bounds computation. PeabraiN also allows to compute other features on Petri nets, such as the computation of upper and lower marking place bounds, and to simulate using an approximate (continuous) method. We show the applicability of PeabraiN by evaluating the performance of a building closed circuit TV system

Analysis of signalling pathways using the prism model checker

We describe a new modelling and analysis approach for signal transduction networks in the presence of incomplete data. We illustrate the approach with an example, the RKIP inhibited ERK pathway [1]. Our models are based on high level descriptions of continuous time Markov chains: reactions are modelled as synchronous processes and concentrations are modelled by discrete, abstract quantities. The main advantage of our approach is that using a (continuous time) stochastic logic and the PRISM model checker, we can perform quantitative analysis of queries such as if a concentration reaches a certain level, will it remain at that level thereafter? We also perform standard simulations and compare our results with a traditional ordinary differential equation model. An interesting result is that for the example pathway, only a small number of discrete data values is required to render the simulations practically indistinguishable

An Evaluation Framework for Comparative Analysis of Generalized Stochastic Petri Net Simulation Techniques

Availability of a common, shared benchmark to provide repeatable, quantifiable, and comparable results is an added value for any scientific community. International consortia provide benchmarks in a wide range of domains, being normally used by industry, vendors, and researchers for evaluating their software products. In this regard, a benchmark of untimed Petri net models was developed to be used in a yearly software competition driven by the Petri net community. However, to the best of our knowledge there is not a similar benchmark to evaluate solution techniques for Petri nets with timing extensions. In this paper, we propose an evaluation framework for the comparative analysis of generalized stochastic Petri nets (GSPNs) simulation techniques. Although we focus on simulation techniques, our framework provides a baseline for a comparative analysis of different GSPN solvers (e.g., simulators, numerical solvers, or other techniques). The evaluation framework encompasses a set of 50 GSPN models including test cases and case studies from the literature, and a set of evaluation guidelines for the comparative analysis. In order to show the applicability of the proposed framework, we carry out a comparative analysis of steady-state simulators implemented in three academic software tools, namely, GreatSPN, PeabraiN, and TimeNET. The results allow us to validate the trustfulness of these academic software tools, as well as to point out potential problems and algorithmic optimization opportunities

Model Checking Markov Chains with Actions and State Labels

In the past, logics of several kinds have been proposed for reasoning about discrete- or continuous-time Markov chains. Most of these logics rely on either state labels (atomic propositions) or on transition labels (actions). However, in several applications it is useful to reason about both state-properties and action-sequences. For this purpose, we introduce the logic asCSL which provides powerful means to characterize execution paths of Markov chains with actions and state labels. asCSL can be regarded as an extension of the purely state-based logic asCSL (continuous stochastic logic). \ud In asCSL, path properties are characterized by regular expressions over actions and state-formulas. Thus, the truth value of path-formulas does not only depend on the available actions in a given time interval, but also on the validity of certain state formulas in intermediate states.\ud We compare the expressive power of CSL and asCSL and show that even the state-based fragment of asCSL is strictly more expressive than CSL if time intervals starting at zero are employed. Using an automaton-based technique, an asCSL formula and a Markov chain with actions and state labels are combined into a product Markov chain. For time intervals starting at zero we establish a reduction of the model checking problem for asCSL to CSL model checking on this product Markov chain. The usefulness of our approach is illustrated by through an elaborate model of a scalable cellular communication system for which several properties are formalized by means of asCSL-formulas, and checked using the new procedure

Perfomance Analysis and Resource Optimisation of Critical Systems Modelled by Petri Nets

Un sistema crítico debe cumplir con su misión a pesar de la presencia de problemas de seguridad. Este tipo de sistemas se suele desplegar en entornos heterogéneos, donde pueden ser objeto de intentos de intrusión, robo de información confidencial u otro tipo de ataques. Los sistemas, en general, tienen que ser rediseñados después de que ocurra un incidente de seguridad, lo que puede conducir a consecuencias graves, como el enorme costo de reimplementar o reprogramar todo el sistema, así como las posibles pérdidas económicas. Así, la seguridad ha de ser concebida como una parte integral del desarrollo de sistemas y como una necesidad singular de lo que el sistema debe realizar (es decir, un requisito no funcional del sistema). Así pues, al diseñar sistemas críticos es fundamental estudiar los ataques que se pueden producir y planificar cómo reaccionar frente a ellos, con el fin de mantener el cumplimiento de requerimientos funcionales y no funcionales del sistema. A pesar de que los problemas de seguridad se consideren, también es necesario tener en cuenta los costes incurridos para garantizar un determinado nivel de seguridad en sistemas críticos. De hecho, los costes de seguridad puede ser un factor muy relevante ya que puede abarcar diferentes dimensiones, como el presupuesto, el rendimiento y la fiabilidad. Muchos de estos sistemas críticos que incorporan técnicas de tolerancia a fallos (sistemas FT) para hacer frente a las cuestiones de seguridad son sistemas complejos, que utilizan recursos que pueden estar comprometidos (es decir, pueden fallar) por la activación de los fallos y/o errores provocados por posibles ataques. Estos sistemas pueden ser modelados como sistemas de eventos discretos donde los recursos son compartidos, también llamados sistemas de asignación de recursos. Esta tesis se centra en los sistemas FT con recursos compartidos modelados mediante redes de Petri (Petri nets, PN). Estos sistemas son generalmente tan grandes que el cálculo exacto de su rendimiento se convierte en una tarea de cálculo muy compleja, debido al problema de la explosión del espacio de estados. Como resultado de ello, una tarea que requiere una exploración exhaustiva en el espacio de estados es incomputable (en un plazo prudencial) para sistemas grandes. Las principales aportaciones de esta tesis son tres. Primero, se ofrecen diferentes modelos, usando el Lenguaje Unificado de Modelado (Unified Modelling Language, UML) y las redes de Petri, que ayudan a incorporar las cuestiones de seguridad y tolerancia a fallos en primer plano durante la fase de diseño de los sistemas, permitiendo así, por ejemplo, el análisis del compromiso entre seguridad y rendimiento. En segundo lugar, se proporcionan varios algoritmos para calcular el rendimiento (también bajo condiciones de fallo) mediante el cálculo de cotas de rendimiento superiores, evitando así el problema de la explosión del espacio de estados. Por último, se proporcionan algoritmos para calcular cómo compensar la degradación de rendimiento que se produce ante una situación inesperada en un sistema con tolerancia a fallos

Model-driven development of data intensive applications over cloud resources

The proliferation of sensors over the last years has generated large amounts of raw data, forming data streams that need to be processed. In many cases, cloud resources are used for such processing, exploiting their flexibility, but these sensor streaming applications often need to support operational and control actions that have real-time and low-latency requirements that go beyond the cost effective and flexible solutions supported by existing cloud frameworks, such as Apache Kafka, Apache Spark Streaming, or Map-Reduce Streams. In this paper, we describe a model-driven and stepwise refinement methodological approach for streaming applications executed over clouds. The central role is assigned to a set of Petri Net models for specifying functional and non-functional requirements. They support model reuse, and a way to combine formal analysis, simulation, and approximate computation of minimal and maximal boundaries of non-functional requirements when the problem is either mathematically or computationally intractable. We show how our proposal can assist developers in their design and implementation decisions from a performance perspective. Our methodology allows to conduct performance analysis: The methodology is intended for all the engineering process stages, and we can (i) analyse how it can be mapped onto cloud resources, and (ii) obtain key performance indicators, including throughput or economic cost, so that developers are assisted in their development tasks and in their decision taking. In order to illustrate our approach, we make use of the pipelined wavefront array