Message Passing Interface (MPI) is a standard library interface for writing parallel programs. The MPI specification is broadly used for solving engineering and scientific problems on parallel computers, and MPICH2 is a popular MPI implementation developed at Argonne National Laboratory. The scalability of MPI implementations is very important for building high performance parallel computing applications. The initial TCP (Transmission Control Protocol) network module developed for Nemesis communication sub-system in the MPICH2 library, however, was not scalable in how it established connections: pairwise connections between all of an application's processes were established during the initialization of the application (the library call to MPI_Init), regardless of whether the connections were eventually needed or not. In this work, we have developed a new TCP network module for Nemesis that establishes connections on-demand. The on-demand connection establishment scheme is designed to improve the scalability of the TCP network module in MPICH2 library, aiming to reduce the initialization time and the use of operating system resources of MPI applications. Our performance benchmark results show that MPI_Init in the on-demand connection establishment scheme becomes a fast constant time operation, and the additional cost of establishing connections later is negligible. The on-demand connection establishment between two processes, especially when two processes attempt to connect to each other simultaneously, is a complex task due to race-conditions and thus prone to hard-to-reproduce defects. To assure ourselves of the correctness of the TCP network module, we modeled its design using the SPIN model checker, and verified safety and liveness properties stated as Linear Temporal Logic claims.

This thesis establishes formal equational properties of multi-stage calculi and related proof techniques that support analyses of staged programs. A key promise of staging is to make programs efficient without destroying clarity, thereby reducing the likelihood of bugs. However, few publications rigorously verify that their staged programs indeed behave as intended. In fact, little is known about how staged programs can be verified, or what correctness issues staging introduces. To solve this problem, I show a reduction of the correctness of a staged program to that of an unstaged program. This reduction not only clarifies the effects of staging on program behavior but also eases verification, as unstaged programs are more susceptible to existing reasoning techniques. I also demonstrate that important single-stage reasoning techniques apply to staged programs. These techniques are useful for establishing side conditions for the reduction and for discovering or validating further reasoning principles. / NSF grant CCF-0747431

Functional verification is a critical problem facing the semiconductor industry: hardware designs are extremely complex and highly optimized, and even a single bug in deployed systems can cost more than $10 billion. We focus on the verification of pipelining, a key optimization that appears extensively in hardware systems such as microprocessors, multicore systems, and cache coherence protocols. Existing techniques for verifying pipelined machines either consume excessive amounts of time, effort, and resources, or are not applicable at the bit-level, the level of abstraction at which commercial systems are designed and functionally verified. We present a highly automated, efficient, compositional, and scalable refinement-based approach for the verification of bit-level pipelined machines. Our contributions include: (1) A complete compositional reasoning framework based on refinement. Our notion of refinement guarantees that pipelined machines satisfy the same safety and liveness properties as their instruction set architectures. In addition, our compositional framework can be used to decompose correctness proofs into smaller, more manageable pieces, leading to drastic reductions in verification times and a high-degree of scalability. (2) The development of ACL2-SMT, a verification system that integrates the popular ACL2 theorem prover (winner of the 2005 ACM Software System Award) with decision procedures. ACL2-SMT allows us to seamlessly take advantage of the two main approaches to hardware verification: theorem proving and decision procedures. (3) A proof methodology based on our compositional reasoning framework and ACL2-SMT that allows us to reduce the bit-level verification problem to a sequence of highly automated proof steps. (4) A collection of general-purpose refinement maps, functions that relate pipelined machine states to instruction set architecture states. These refinement maps provide more flexibility and lead to increased verification efficiency. The effectiveness of our approach is demonstrated by verifying various pipelined machine models, including a bit-level, Intel XScale inspired processor that implements 593 instructions and includes features such as branch prediction, precise exceptions, and predicated instruction execution.

Model checking is a formal verification technique which is widely used in different areas for automated verification and analysis. In this study, we applied a Model Checking method to a biological system. Firstly we constructed a single-cell, Boolean network model for the signaling pathways of apoptosis (programmed cell death) in lung cancers by combining the intrinsic and extrinsic Apoptosis pathways, p53 signaling pathway and p53 - DAP Kinase pathway in Lung cancers. We translated this model to the NuSMV input language. Then we converted known experimental results to CTL properties and checked the conformance of our model with respect to biological experimental results. We examined the dynamics of the apoptosis in lung cancer using NuSMV symbolic model checker and identified the relationship between apoptosis and lung cancer. Finally we generalized the whole process by introducing translation rules and CTL property patterns for biological queries so that model checking any signaling pathway can be automated.

<p>This work focuses on the usage of dominators in circuit graphs in order to reduce the complexity of synthesis and verification tasks. One of the contributions of this thesis is a new algorithm for computing multiple-vertex dominators in circuit graphs. Previous algorithms, based on single-vertex dominators suffer from their rare appearance in many circuits. The presented approach searches efficiently for multiple-vertex dominators in circuit graphs. It finds dominator relations, where algorithms for computing single-vertex dominators fail. Another contribution of this thesis is the application of dominators for combinational equivalence checking based on the arithmetic transform. Previous algorithms rely on representations providing an explicit or implicit disjoint function cover, which is usually excessive in memory requirements. The new algorithm allows a partitioned evaluation of the arithmetic transform directly on the circuit graph using dominator relations. The results show that the algorithm brings significant improvements in memory consumption for many benchmarks. Proper cuts are used in many areas of VLSI. They provide cut points, where a given problem can be split into two disjoint sub-problems. The algorithm proposed in this thesis efficiently detects proper cuts in a circuit graph and is based on a novel concept of a reduced dominator tree. The runtime of the algorithm is less than 0.4 seconds for the largest benchmark circuit. The final contribution of this thesis is the application of the proper cut algorithm as a structural method to decompose a Boolean function, represented by a circuit graph. In combination with a functional approach, it outperforms previous methods, which rely on functional decomposition only.</p>

Model checking is the most effective means of verifying the correctness of asynchronous designs, and state space exploration is central to model checking. Although model checking can achieve very high verification coverage, the high degree of concurrency in asynchronous designs often leads to state explosion during state space exploration. To inhibit this explosion, our approach builds on the ideas of compositional verification. In our approach, a design modeled in a high level description is partitioned into a set of parallel components. Before state space exploration, each component is paired with an over-approximated environment to decouple it from the rest of the design. Then, a global state transition graph is constructed by reducing and incrementally composing component state transition graphs. We take great care during reduction and composition to preserve all failures found during the initial state space exploration of each component. To further reduce complexity, interface constraints are automatically derived for the over-approximated environment of each component. We prove that our approach is conservative in that false positive results are never produced. The effectiveness of our approach is demonstrated by the experimental results of several case studies showing that our approach can verify designs that cannot be handled by traditional at approaches. The experiments also show that constraints can reduce the size of the global state transition graph and prevent some false failures.

Mechanized theorem proving is a promising means of formally establishing facts about complex systems. However, in applying theorem proving methodologies to industrial-scale hardware and software systems, a large amount of user interaction is required in order to prove useful properties. In practice, the human user tasked with such a verification must gain a deep understanding of the system to be verified, and prove numerous lemmas in order to allow the theorem proving program to approach a proof of the desired fact. Furthermore, proofs that fail during this process are a source of confusion: the proof may either fail because the conjecture was false, or because the prover required more help from the user in order to reach the desired conclusion. We have implemented a symbolic execution framework inside the ACL2 theorem prover in order to help address these issues on certain problem domains. Our framework introduces a proof strategy that applies bit-level symbolic execution using BDDs to finite-domain problems. This proof strategy is a fully verified decision procedure for such problems, and on many useful problem domains its capacity vastly exceeds that of exhaustive testing. Our framework also produces counterexamples for conjectures that it determines to be false. Our framework seeks to reduce the amount of necessary user interaction in proving theorems about industrial-scale hardware and software systems. By increasing the automation available in the prover, we allow the user to complete useful proofs while understanding less of the detailed implementation of the system. Furthermore, by producing counterexamples for falsified conjectures, our framework reduces the time spent by the user in trying to determine why a proof failed. / text

Many tools have been developed to automatically verify security properties on cryptographic protocols. But until recently, most tools focused on trace properties (or reachability properties) such as authentication and secrecy. However, many security properties cannot be expressed as trace properties, but can be written as equivalence properties. Privacy, unlinkability, and strong secrecy are typical examples of equivalence properties. Intuitively, two protocols P, Q are equivalent if an adversary can not distinguish P from Q by interacting with these processes. In the literature, several notions of equivalence were studied, e.g. trace equivalence or a stronger one, observational equivalence. However, it is often very difficult to prove by hand any of these equivalences, hence the need for efficient and automatic tools. We first worked on an approach that rely on constraint solving techniques and that is well suited for bounded number of sessions. We provided a new algorithm for deciding the trace equivalence between processes that may contain negative tests and non-determinism. We applied our results on concrete examples such as anonymity of the Private Authentication protocol and the E-passport protocol. We also investigated composition results. More precisely, we focused on parallel composition under shared secrets. We showed that under certain conditions on the protocols, the privacy type properties are preserved under parallel composition and under shared secrets. We applied our result on the e-passport protocol. At last this work presents an extension of the automatic protocol verifier ProVerif in order to prove more observational equivalences. This extension have been implemented in ProVerif and allows us to automatically prove anonymity in the private authentication protocol.

With the development of digital networks, such as Internet, communication protocols are omnipresent. Digital devices have to interact with each other in order to perform the numerous and complex tasks we have come to expect as commonplace, such as using a mobile phone, sending or receiving electronic mail, making purchases online and so on. In such applications, security is important. For instance, in the case of an online purchase, the right amount of money has to be paid without leaking the buyer personal information to outside parties. Communication protocols are the rules that govern these interactions. In order to make sure that they guarantee a certainlevel of security, it is desirable to analyze them. Doing so manually or by testing them is not enough, as attacks can be quite subtle. Some protocols have been used for years before an attack was discovered. Because of their increasing ubiquity in many important applications, e.g. electronic commerce, a very important research challenge consists in developing methods and verification tools to increase our trust on security protocols, and so on the applications that rely on them. For example, more than 28 billion Euros were spent in France using Internet transactions, and the number is growing. Moreover, new types of protocols are continuously appearing in order to face new technological and societal challenges, e.g. electronic voting, electronic passport to name a few.

This thesis is about the formal verification and composition of security protocols, motivated by applications to electronic voting protocols. Chapters 3 to 5 concern the verification of security protocols while Chapter 6 concerns composition.We show in Chapter 3 how to reduce certain problems from a quotient term algebra to the free term algebra via the use of strongly complete sets of variants. We show that, when the quotient algebra is given by a convergent optimally reducing rewrite system, finite strongly complete sets of variants exist and are effectively computable.In Chapter 4, we show that static equivalence for (classes of) equational theories including subterm convergent equational theories, trapdoor commitment and blind signatures is decidable in polynomial time. We also provide an efficient implementation.In Chapter 5 we extend the previous decision procedure to handle trace equivalence. We use finite strongly complete sets of variants introduced in Chapter 3 to get rid of the equational theory and we model each protocol trace as a Horn theory which we solve using a refinement of resolution. Although we have not been able to prove that this procedure always terminates, we have implemented it and used it to provide the first automated proof of vote privacy of the FOO electronic voting protocol.In Chapter 6, we study composition of protocols. We show that two protocols that use arbitrary disjoint cryptographic primitives compose securely if they do not reveal or reuse any shared secret. We also show that a form of tagging is sufficient to provide disjointness in the case of a fixed set of cryptographic primitives.