Un modèle booléen pour l'énumération des siphons et des pièges minimaux dans les réseaux de Petri

International audiencePetri-nets are a simple formalism for modeling concurrent computation. Recently, they have emerged as a powerful tool for the modeling and analysis of biochemical reaction networks, bridging the gap between purely qualitative and quantitative models. These networks can be large and complex, which makes their study difficult and computationally challenging. In this paper, we focus on two structural properties of Petri-nets, siphons and traps, that bring us information about the persistence of some molecular species. We present two methods for enumerating all minimal siphons and traps of a Petri-net by iterating the resolution of a boolean model interpreted as either a SAT or a CLP(B) program. We compare the performance of these methods with a state-of-the-art dedicated algorithm of the Petri-net community. We show that the SAT and CLP(B) programs are both faster. We analyze why these programs perform so well on the models of the repository of biological models biomodels.net, and propose some hard instances for the problem of minimal siphons enumeration

PetriBaR: A MATLAB Toolbox for Petri Nets Implementing Basis Reachability Approaches

This paper presents a MATLAB toolbox, called PetriBaR, for the analysis and control of Petri nets. PetriBaR is a package of functions devoted to basic Petri net analysis (including the computation of T-invariants, siphons, reachability graph, etc.), monitor design, reachability analysis, state estimation, fault diagnosis, and opacity verification. In particular, the functions for reachability analysis, state estimation, fault diagnosis, and opacity verification exploit the construction of the Basis Reachability Graph to avoid the exhaustive enumeration of the reachable set, thus leading to significant advantages in terms of computational complexity. All functions of PetriBaR are introduced in detail clarifying the syntax to be used to run them. Finally, they are illustrated via a series of numerical examples. PetriBaR is available online for public access

Contributions to the deadlock problem in multithreaded software applications observed as Resource Allocation Systems

Desde el punto de vista de la competencia por recursos compartidos sucesivamente reutilizables, se dice que un sistema concurrente compuesto por procesos secuenciales está en situación de bloqueo si existe en él un conjunto de procesos que están indefinidamente esperando la liberación de ciertos recursos retenidos por miembros del mismo conjunto de procesos. En sistemas razonablemente complejos o distribuidos, establecer una política de asignación de recursos que sea libre de bloqueos puede ser un problema muy difícil de resolver de forma eficiente. En este sentido, los modelos formales, y particularmente las redes de Petri, se han ido afianzando como herramientas fructíferas que permiten abstraer el problema de asignación de recursos en este tipo de sistemas, con el fin de abordarlo analíticamente y proveer métodos eficientes para la correcta construcción o corrección de estos sistemas. En particular, la teoría estructural de redes de Petri se postula como un potente aliado para lidiar con el problema de la explosión de estados inherente a aquéllos. En este fértil contexto han florecido una serie de trabajos que defienden una propuesta metodológica de diseño orientada al estudio estructural y la correspondiente corrección física del problema de asignación de recursos en familias de sistemas muy significativas en determinados contextos de aplicación, como el de los Sistemas de Fabricación Flexible. Las clases de modelos de redes de Petri resultantes asumen ciertas restricciones, con significado físico en el contexto de aplicación para el que están destinadas, que alivian en buena medida la complejidad del problema. En la presente tesis, se intenta acercar ese tipo de aproximación metodológica al diseño de aplicaciones software multihilo libres de bloqueos. A tal efecto, se pone de manifiesto cómo aquellas restricciones procedentes del mundo de los Sistemas de Fabricación Flexible se muestran demasiado severas para aprehender la versatilidad inherente a los sistemas software en lo que respecta a la interacción de los procesos con los recursos compartidos. En particular, se han de resaltar dos necesidades de modelado fundamentales que obstaculizan la mera adopción de antiguas aproximaciones surgidas bajo el prisma de otros dominios: (1) la necesidad de soportar el anidamiento de bucles no desplegables en el interior de los procesos, y (2) la posible compartición de recursos no disponibles en el arranque del sistema pero que son creados o declarados por un proceso en ejecución. A resultas, se identifica una serie de requerimientos básicos para la definición de un tipo de modelos orientado al estudio de sistemas software multihilo y se presenta una clase de redes de Petri, llamada PC2R, que cumple dicha lista de requerimientos, manteniéndose a su vez respetuosa con la filosofía de diseño de anteriores subclases enfocadas a otros contextos de aplicación. Junto con la revisión e integración de anteriores resultados en el nuevo marco conceptual, se aborda el estudio de propiedades inherentes a los sistemas resultantes y su relación profunda con otros tipos de modelos, la confección de resultados y algoritmos eficientes para el análisis estructural de vivacidad en la nueva clase, así como la revisión y propuesta de métodos de resolución de los problemas de bloqueo adaptadas a las particularidades físicas del dominio de aplicación. Asimismo, se estudia la complejidad computacional de ciertas vertientes relacionadas con el problema de asignación de recursos en el nuevo contexto, así como la traslación de los resultados anteriormente mencionados sobre el dominio de la ingeniería de software multihilo, donde la nueva clase de redes permite afrontar problemas inabordables considerando el marco teórico y las herramientas suministradas para subclases anteriormente explotadas

Comparison and Evaluation of Deadlock Prevention Methods for Different Size Automated Manufacturing Systems

In automated manufacturing systems (AMSs), deadlocks problems can arise due to limited shared resources. Petri nets are an effective tool to prevent deadlocks in AMSs. In this paper, a simulation based on existing deadlock prevention policies and different Petri net models are considered to explore whether a permissive liveness-enforcing Petri net supervisor can provide better time performance. The work of simulation is implemented as follows. (1) Assign the time to the controlled Petri net models, which leads to timed Petri nets. (2) Build the Petri net model using MATLAB software. (3) Run and simulate the model, and simulation results are analyzed to determine which existing policies are suitable for different systems. Siphons and iterative methods are used for deadlocks prevention. Finally, the computational results show that the selected deadlock policies may not imply high resource utilization and plant productivity, which have been shown theoretically in previous publications. However, for all selected AMSs, the iterative methods always lead to structurally and computationally complex liveness-enforcing net supervisors compared to the siphons methods. Moreover, they can provide better behavioral permissiveness than siphons methods for small systems. For large systems, a strict minimal siphon method leads to better behavioral permissiveness than the other methods

Towards Efficient Verification of Population Protocols

Population protocols are a well established model of computation by anonymous, identical finite state agents. A protocol is well-specified if from every initial configuration, all fair executions reach a common consensus. The central verification question for population protocols is the well-specification problem: deciding if a given protocol is well-specified. Esparza et al. have recently shown that this problem is decidable, but with very high complexity: it is at least as hard as the Petri net reachability problem, which is EXPSPACE-hard, and for which only algorithms of non-primitive recursive complexity are currently known. In this paper we introduce the class WS3 of well-specified strongly-silent protocols and we prove that it is suitable for automatic verification. More precisely, we show that WS3 has the same computational power as general well-specified protocols, and captures standard protocols from the literature. Moreover, we show that the membership problem for WS3 reduces to solving boolean combinations of linear constraints over N. This allowed us to develop the first software able to automatically prove well-specification for all of the infinitely many possible inputs.Comment: 29 pages, 1 figur

Graphical Conditions for Rate Independence in Chemical Reaction Networks

Chemical Reaction Networks (CRNs) provide a useful abstraction of molecular interaction networks in which molecular structures as well as mass conservation principles are abstracted away to focus on the main dynamical properties of the network structure. In their interpretation by ordinary differential equations, we say that a CRN with distinguished input and output species computes a positive real function $f : R+$\rightarrow$R+$, if for any initial concentration x of the input species, the concentration of the output molecular species stabilizes at concentration f (x). The Turing-completeness of that notion of chemical analog computation has been established by proving that any computable real function can be computed by a CRN over a finite set of molecular species. Rate-independent CRNs form a restricted class of CRNs of high practical value since they enjoy a form of absolute robustness in the sense that the result is completely independent of the reaction rates and depends solely on the input concentrations. The functions computed by rate-independent CRNs have been characterized mathematically as the set of piecewise linear functions from input species. However, this does not provide a mean to decide whether a given CRN is rate-independent. In this paper, we provide graphical conditions on the Petri Net structure of a CRN which entail the rate-independence property either for all species or for some output species. We show that in the curated part of the Biomodels repository, among the 590 reaction models tested, 2 reaction graphs were found to satisfy our rate-independence conditions for all species, 94 for some output species, among which 29 for some non-trivial output species. Our graphical conditions are based on a non-standard use of the Petri net notions of place-invariants and siphons which are computed by constraint programming techniques for efficiency reasons

Deadlock Prevention Policy with Behavioral Optimality or Suboptimality Achieved by the Redundancy Identification of Constraints and the Rearrangement of Monitors

This work develops an iterative deadlock prevention method for a special class of Petri nets that can well model a variety of flexible manufacturing systems. A deadlock detection technique, called mixed integer programming (MIP), is used to find a strict minimal siphon (SMS) in a plant model without a complete enumeration of siphons. The policy consists of two phases. At the first phase, SMSs are obtained by MIP technique iteratively and monitors are added to the complementary sets of the SMSs. For the possible existence of new siphons generated after the first phase, we add monitors with their output arcs first pointed to source transitions at the second phase to avoid new siphons generating and then rearrange the output arcs step by step on condition that liveness is preserved. In addition, an algorithm is proposed to remove the redundant constraints of the MIP problem in this paper. The policy improves the behavioral permissiveness of the resulting net and greatly enhances the structural simplicity of the supervisor. Theoretical analysis and experimental results verify the effectiveness of the proposed method

On the Enforcement of a Class of Nonlinear Constraints on Petri Nets

International audienceThis paper focuses on the enforcement of nonlinear constraints in Petri nets. First, a supervisory structure is proposed for a nonlinear constraint. The proposed structure consists of added places and transitions. It controls the transitions in the net to be controlled only but does not change its states since there is no arc between the added transitions and the places in the original net. Second, an integer linear programming model is proposed to transform a nonlinear constraint to a minimal number of conjunc-tive linear constraints that have the same control performance as the nonlinear one. By using a place invariant based method, the obtained linear constraints can be easily enforced by a set of control places. The control places consist to a supervisor that can enforce the given nonlinear constraint. On condition that the admissible markings space of a nonlinear constraint is non-convex, another integer linear programming model is developed to obtain a minimal number of constraints whose disjunctions are equivalent to the nonlinear constraint. Finally, a number of examples are provided to demonstrate the proposed approach