The Parallel Persistent Memory Model

We consider a parallel computational model that consists of $P$ processors, each with a fast local ephemeral memory of limited size, and sharing a large persistent memory. The model allows for each processor to fault with bounded probability, and possibly restart. On faulting all processor state and local ephemeral memory are lost, but the persistent memory remains. This model is motivated by upcoming non-volatile memories that are as fast as existing random access memory, are accessible at the granularity of cache lines, and have the capability of surviving power outages. It is further motivated by the observation that in large parallel systems, failure of processors and their caches is not unusual. Within the model we develop a framework for developing locality efficient parallel algorithms that are resilient to failures. There are several challenges, including the need to recover from failures, the desire to do this in an asynchronous setting (i.e., not blocking other processors when one fails), and the need for synchronization primitives that are robust to failures. We describe approaches to solve these challenges based on breaking computations into what we call capsules, which have certain properties, and developing a work-stealing scheduler that functions properly within the context of failures. The scheduler guarantees a time bound of $O(W/P_A + D(P/P_A) \lceil\log_{1/f} W\rceil)$ in expectation, where $W$ and $D$ are the work and depth of the computation (in the absence of failures), $P_A$ is the average number of processors available during the computation, and $f \le 1/2$ is the probability that a capsule fails. Within the model and using the proposed methods, we develop efficient algorithms for parallel sorting and other primitives.Comment: This paper is the full version of a paper at SPAA 2018 with the same nam

Theorem proving support in programming language semantics

We describe several views of the semantics of a simple programming language as formal documents in the calculus of inductive constructions that can be verified by the Coq proof system. Covered aspects are natural semantics, denotational semantics, axiomatic semantics, and abstract interpretation. Descriptions as recursive functions are also provided whenever suitable, thus yielding a a verification condition generator and a static analyser that can be run inside the theorem prover for use in reflective proofs. Extraction of an interpreter from the denotational semantics is also described. All different aspects are formally proved sound with respect to the natural semantics specification.Comment: Propos\'e pour publication dans l'ouvrage \`a la m\'emoire de Gilles Kah

Universality and programmability of quantum computers

Manin, Feynman, and Deutsch have viewed quantum computing as a kind of universal physical simulation procedure. Much of the writing about quantum logic circuits and quantum Turing machines has shown how these machines can simulate an arbitrary unitary transformation on a finite number of qubits. The problem of universality has been addressed most famously in a paper by Deutsch, and later by Bernstein and Vazirani as well as Kitaev and Solovay. The quantum logic circuit model, developed by Feynman and Deutsch, has been more prominent in the research literature than Deutsch's quantum Turing machines. Quantum Turing machines form a class closely related to deterministic and probabilistic Turing machines and one might hope to find a universal machine in this class. A universal machine is the basis of a notion of programmability. The extent to which universality has in fact been established by the pioneers in the field is examined and this key notion in theoretical computer science is scrutinised in quantum computing by distinguishing various connotations and concomitant results and problems.Comment: 17 pages, expands on arXiv:0705.3077v1 [quant-ph

Classical computing, quantum computing, and Shor's factoring algorithm

This is an expository talk written for the Bourbaki Seminar. After a brief introduction, Section 1 discusses in the categorical language the structure of the classical deterministic computations. Basic notions of complexity icluding the P/NP problem are reviewed. Section 2 introduces the notion of quantum parallelism and explains the main issues of quantum computing. Section 3 is devoted to four quantum subroutines: initialization, quantum computing of classical Boolean functions, quantum Fourier transform, and Grover's search algorithm. The central Section 4 explains Shor's factoring algorithm. Section 5 relates Kolmogorov's complexity to the spectral properties of computable function. Appendix contributes to the prehistory of quantum computing.Comment: 27 pp., no figures, amste

COMPUTER SIMULATION AND COMPUTABILITY OF BIOLOGICAL SYSTEMS

The ability to simulate a biological organism by employing a computer is related to the ability of the computer to calculate the behavior of such a dynamical system, or the "computability" of the system.* However, the two questions of computability and simulation are not equivalent. Since the question of computability can be given a precise answer in terms of recursive functions, automata theory and dynamical systems, it will be appropriate to consider it first. The more elusive question of adequate simulation of biological systems by a computer will be then addressed and a possible connection between the two answers given will be considered. A conjecture is formulated that suggests the possibility of employing an algebraic-topological, "quantum" computer (Baianu, 1971b) for analogous and symbolic simulations of biological systems that may include chaotic processes that are not, in genral, either recursively or digitally computable. Depending on the biological network being modelled, such as the Human Genome/Cell Interactome or a trillion-cell Cognitive Neural Network system, the appropriate logical structure for such simulations might be either the Quantum MV-Logic (QMV) discussed in recent publications (Chiara, 2004, and references cited therein)or Lukasiewicz Logic Algebras that were shown to be isomorphic to MV-logic algebras (Georgescu et al, 2001)

Parallel Construction of Wavelet Trees on Multicore Architectures

The wavelet tree has become a very useful data structure to efficiently represent and query large volumes of data in many different domains, from bioinformatics to geographic information systems. One problem with wavelet trees is their construction time. In this paper, we introduce two algorithms that reduce the time complexity of a wavelet tree's construction by taking advantage of nowadays ubiquitous multicore machines. Our first algorithm constructs all the levels of the wavelet in parallel in $O(n)$ time and $O(n\lg\sigma + \sigma\lg n)$ bits of working space, where $n$ is the size of the input sequence and $\sigma$ is the size of the alphabet. Our second algorithm constructs the wavelet tree in a domain-decomposition fashion, using our first algorithm in each segment, reaching $O(\lg n)$ time and $O(n\lg\sigma + p\sigma\lg n/\lg\sigma)$ bits of extra space, where $p$ is the number of available cores. Both algorithms are practical and report good speedup for large real datasets.Comment: This research has received funding from the European Union's Horizon 2020 research and innovation programme under the Marie Sk{\l}odowska-Curie Actions H2020-MSCA-RISE-2015 BIRDS GA No. 69094