Three parallel algorithms for classical molecular dynamics are presented. The first assigns each processor a fixed subset of atoms; the second assigns each a fixed subset of inter-atomic forces to compute; the third assigns each a fixed spatial region. The algorithms are suitable for molecular dynamics models which can be difficult to parallelize efficiently—those with short-range forces where the neighbors of each atom change rapidly. They can be implemented on any distributed-memory parallel machine which allows for message-passing of data between independently executing processors. The algorithms are tested on a standard Lennard-Jones benchmark problem for system sizes ranging from 500 to 100,000,000 atoms on several parallel supercomputers--the nCUBE 2, Intel iPSC/860 and Paragon, and Cray T3D. Comparing the results to the fastest reported vectorized Cray Y-MP and C90 algorithm shows that the current generation of parallel machines is competitive with conventional vector supercomputers even for small problems. For large problems, the spatial algorithm achieves parallel efficiencies of 90% and a 1840-node Intel Paragon performs up to 165 faster than a single Cray C9O processor. Trade-offs between the three algorithms and guidelines for adapting them to more complex molecular dynamics simulations are also discussed.

Fast parallel algorithms for short-range molecular dynamics

I have developed "tennis elbow" from lugging this book around the past four weeks, but it is worth the pain, the effort, and the aspirin. It is also worth the (relatively speaking) bargain price. Including appendixes, this book contains 894 pages of text. The entire panorama of the neural sciences is surveyed and examined, and it is comprehensive in its scope, from genomes to social behaviors. The editors explicitly state that the book is designed as "an introductory text for students of biology, behavior, and medicine," but it is hard to imagine any audience, interested in any fragment of neuroscience at any level of sophistication, that would not enjoy this book. The editors have done a masterful job of weaving together the biologic, the behavioral, and the clinical sciences into a single tapestry in which everyone from the molecular biologist to the practicing psychiatrist can find and appreciate his or

Principles of Neural Science

Turing Lecture from the winners of the 2007 ACM A.M. Turing Award. In 1981, Edmund M. Clarke and E. Allen Emerson, working in the USA, and Joseph Sifakis working independently in France, authored seminal papers that founded what has become the highly successful field of model checking. This verification technology provides an algorithmic means of determining whether an abstract model---representing, for example, a hardware or software design---satisfies a formal specification expressed as a temporal logic (TL) formula. Moreover, if the property does not hold, the method identifies a counterexample execution that shows the source of the problem. The progression of model checking to the point where it can be successfully used for complex systems has required the development of sophisticated means of coping with what is known as the state explosion problem. Great strides have been made on this problem over the past 28 years by what is now a very large international research community. As a result many major hardware and software companies are beginning to use model checking in practice. Examples of its use include the verification of VLSI circuits, communication protocols, software device drivers, real-time embedded systems, and security algorithms. The work of Clarke, Emerson, and Sifakis continues to be central to the success of this research area. Their work over the years has led to the creation of new logics for specification, new verification algorithms, and surprising theoretical results. Model checking tools, created by both academic and industrial teams, have resulted in an entirely novel approach to verification and test case generation. This approach, for example, often enables engineers in the electronics industry to design complex systems with considerable assurance regarding the correctness of their initial designs. Model checking promises to have an even greater impact on the hardware and software industries in the future. ---Moshe Y. Vardi, Editor-in-Chief

Model checking

https://www.inf.ed.ac.uk/teaching/courses/seoc/2005_2006/resources/statecharts.pdf

Statecharts: A visual formalism for complex systems

https://cmi.ac.in/~madhavan/courses/verification-2011/alur-dill-tcs-94.pdf

A theory of timed automata

Model Checking

We give an efficient procedure for verifying that a finite-state concurrent system meets a specification expressed in a (propositional, branching-time) temporal logic. Our algorithm has complexity linear in both the size of the specification and the size of the global state graph for the concurrent system. We also show how this approach can be adapted to handle fairness. We argue that our technique can provide a practical alternative to manual proof construction or use of a mechanical theorem prover for verifying many finite-state concurrent systems. Experimental results show that state machines with several hundred states can be checked in a matter of seconds.

/pdf/automatic-verification-of-finite-state-concurrent-systems-20f8fq7qdh.pdf

Automatic verification of finite-state concurrent systems using temporal logic specifications

A general method that represents the state space symbolically instead of explicitly is described. The generality of the method comes from using a dialect of the mu-calculus as the primary specification language. A model-checking algorithm for mu-calculus formulas which uses R.E. Bryant's (1986) binary decision diagrams to represent relations and formulas symbolically is described. It is then shown how the novel mu-calculus model checking algorithm can be used to derive efficient decision procedures for CTL model checking, satisfiability of linear-time temporal logic formulas, strong and weak observational equivalence of finite transition systems, and language containment of finite omega -automata. This eliminates the need to describe complicated graph-traversal or nested fixed-point computations for each decision procedure. The authors illustrate the practicality of their approach to symbolic model checking by discussing how it can be used to verify a simple synchronous pipeline. >

/pdf/symbolic-model-checking-10-sup-20-states-and-beyond-16hrqmhgon.pdf

Symbolic model checking: 10/sup 20/ states and beyond

Symbolic Model Checking [3, 14] has proven to be a powerful technique for the verification of reactive systems. BDDs [2] have traditionally been used as a symbolic representation of the system. In this paper we show how boolean decision procedures, like Stalmarck's Method [16] or the Davis & Putnam Procedure [7], can replace BDDs. This new technique avoids the space blow up of BDDs, generates counterexamples much faster, and sometimes speeds up the verification. In addition, it produces counterexamples of minimal length. We introduce a bounded model checking procedure for LTL which reduces model checking to propositional satisfiability. We show that bounded LTL model checking can be done without a tableau construction. We have implemented a model checker BMC, based on bounded model checking, and preliminary results are presented.

/pdf/symbolic-model-checking-without-bdds-4ad2rvo6mm.pdf

Edmund M. Clarke

Papers

Model checking

Model Checking

Automatic verification of finite-state concurrent systems using temporal logic specifications

Symbolic model checking: 10/sup 20/ states and beyond

Symbolic Model Checking without BDDs