On the Complexity of List Ranking in the Parallel External Memory Model

We study the problem of list ranking in the parallel external memory (PEM) model. We observe an interesting dual nature for the hardness of the problem due to limited information exchange among the processors about the structure of the list, on the one hand, and its close relationship to the problem of permuting data, which is known to be hard for the external memory models, on the other hand. By carefully defining the power of the computational model, we prove a permuting lower bound in the PEM model. Furthermore, we present a stronger \Omega(log^2 N) lower bound for a special variant of the problem and for a specific range of the model parameters, which takes us a step closer toward proving a non-trivial lower bound for the list ranking problem in the bulk-synchronous parallel (BSP) and MapReduce models. Finally, we also present an algorithm that is tight for a larger range of parameters of the model than in prior work

Integrating and Ranking Uncertain Scientific Data

Mediator-based data integration systems resolve exploratory queries by joining data elements across sources. In the presence of uncertainties, such multiple expansions can quickly lead to spurious connections and incorrect results. The BioRank project investigates formalisms for modeling uncertainty during scientific data integration and for ranking uncertain query results. Our motivating application is protein function prediction. In this paper we show that: (i) explicit modeling of uncertainties as probabilities increases our ability to predict less-known or previously unknown functions (though it does not improve predicting the well-known). This suggests that probabilistic uncertainty models offer utility for scientific knowledge discovery; (ii) small perturbations in the input probabilities tend to produce only minor changes in the quality of our result rankings. This suggests that our methods are robust against slight variations in the way uncertainties are transformed into probabilities; and (iii) several techniques allow us to evaluate our probabilistic rankings efficiently. This suggests that probabilistic query evaluation is not as hard for real-world problems as theory indicates

Modern Approaches to Exact Diagonalization and Selected Configuration Interaction with the Adaptive Sampling CI Method.

Recent advances in selected configuration interaction methods have made them competitive with the most accurate techniques available and, hence, creating an increasingly powerful tool for solving quantum Hamiltonians. In this work, we build on recent advances from the adaptive sampling configuration interaction (ASCI) algorithm. We show that a useful paradigm for generating efficient selected CI/exact diagonalization algorithms is driven by fast sorting algorithms, much in the same way iterative diagonalization is based on the paradigm of matrix vector multiplication. We present several new algorithms for all parts of performing a selected CI, which includes new ASCI search, dynamic bit masking, fast orbital rotations, fast diagonal matrix elements, and residue arrays. The ASCI search algorithm can be used in several different modes, which includes an integral driven search and a coefficient driven search. The algorithms presented here are fast and scalable, and we find that because they are built on fast sorting algorithms they are more efficient than all other approaches we considered. After introducing these techniques, we present ASCI results applied to a large range of systems and basis sets to demonstrate the types of simulations that can be practically treated at the full-CI level with modern methods and hardware, presenting double- and triple-ζ benchmark data for the G1 data set. The largest of these calculations is Si2H6 which is a simulation of 34 electrons in 152 orbitals. We also present some preliminary results for fast deterministic perturbation theory simulations that use hash functions to maintain high efficiency for treating large basis sets

Toward Contention Analysis for Parallel Executing Real-Time Tasks

In measurement-based probabilistic timing analysis, the execution conditions imposed to tasks as measurement scenarios, have a strong impact to the worst-case execution time estimates. The scenarios and their effects on the task execution behavior have to be deeply investigated. The aim has to be to identify and to guarantee the scenarios that lead to the maximum measurements, i.e. the worst-case scenarios, and use them to assure the worst-case execution time estimates. We propose a contention analysis in order to identify the worst contentions that a task can suffer from concurrent executions. The work focuses on the interferences on shared resources (cache memories and memory buses) from parallel executions in multi-core real-time systems. Our approach consists of searching for possible task contenders for parallel executions, modeling their contentiousness, and classifying the measurement scenarios accordingly. We identify the most contentious ones and their worst-case effects on task execution times. The measurement-based probabilistic timing analysis is then used to verify the analysis proposed, qualify the scenarios with contentiousness, and compare them. A parallel execution simulator for multi-core real-time system is developed and used for validating our framework. The framework applies heuristics and assumptions that simplify the system behavior. It represents a first step for developing a complete approach which would be able to guarantee the worst-case behavior

Best of Two Local Models: Local Centralized and Local Distributed Algorithms

We consider two models of computation: centralized local algorithms and local distributed algorithms. Algorithms in one model are adapted to the other model to obtain improved algorithms. Distributed vertex coloring is employed to design improved centralized local algorithms for: maximal independent set, maximal matching, and an approximation scheme for maximum (weighted) matching over bounded degree graphs. The improvement is threefold: the algorithms are deterministic, stateless, and the number of probes grows polynomially in $\log^* n$, where $n$ is the number of vertices of the input graph. The recursive centralized local improvement technique by Nguyen and Onak~\cite{onak2008} is employed to obtain an improved distributed approximation scheme for maximum (weighted) matching. The improvement is twofold: we reduce the number of rounds from $O(\log n)$ to $O(\log^*n)$ for a wide range of instances and, our algorithms are deterministic rather than randomized

The Hardness of Finding Linear Ranking Functions for Lasso Programs

Finding whether a linear-constraint loop has a linear ranking function is an important key to understanding the loop behavior, proving its termination and establishing iteration bounds. If no preconditions are provided, the decision problem is known to be in coNP when variables range over the integers and in PTIME for the rational numbers, or real numbers. Here we show that deciding whether a linear-constraint loop with a precondition, specifically with partially-specified input, has a linear ranking function is EXPSPACE-hard over the integers, and PSPACE-hard over the rationals. The precise complexity of these decision problems is yet unknown. The EXPSPACE lower bound is derived from the reachability problem for Petri nets (equivalently, Vector Addition Systems), and possibly indicates an even stronger lower bound (subject to open problems in VAS theory). The lower bound for the rationals follows from a novel simulation of Boolean programs. Lower bounds are also given for the problem of deciding if a linear ranking-function supported by a particular form of inductive invariant exists. For loops over integers, the problem is PSPACE-hard for convex polyhedral invariants and EXPSPACE-hard for downward-closed sets of natural numbers as invariants.Comment: In Proceedings GandALF 2014, arXiv:1408.5560. I thank the organizers of the Dagstuhl Seminar 14141, "Reachability Problems for Infinite-State Systems", for the opportunity to present an early draft of this wor

CCL: a portable and tunable collective communication library for scalable parallel computers

A collective communication library for parallel computers includes frequently used operations such as broadcast, reduce, scatter, gather, concatenate, synchronize, and shift. Such a library provides users with a convenient programming interface, efficient communication operations, and the advantage of portability. A library of this nature, the Collective Communication Library (CCL), intended for the line of scalable parallel computer products by IBM, has been designed. CCL is part of the parallel application programming interface of the recently announced IBM 9076 Scalable POWERparallel System 1 (SP1). In this paper, we examine several issues related to the functionality, correctness, and performance of a portable collective communication library while focusing on three novel aspects in the design and implementation of CCL: 1) the introduction of process groups, 2) the definition of semantics that ensures correctness, and 3) the design of new and tunable algorithms based on a realistic point-to-point communication model