Concurrent Deterministic Skiplist and Other Data Structures

Skiplists are used in a variety of applications for storing data subject to order criteria. In this article we discuss the design, analysis and performance of a concurrent deterministic skip list on many-core NUMA nodes. We also evaluate the performance of a concurrent lock-free unbounded queue implementation and three implementations of multi-writer, multi-reader~(MWMR) hash tables and compare their performance with equivalent implementations from Intel's Thread Building Blocks~(TBB) library. We focus on strategies for memory management that reduce page faults and cache misses for the memory access patterns in these data structures. This paper proposes hierarchical usage of concurrent data structures in programs to improve memory latencies by reducing memory accesses from remote NUMA nodes

Bayesian modelling of latent Gaussian models featuring variable selection

PhD ThesisLatent Gaussian models are popular and versatile models for performing Bayesian inference. In many cases, these models will be analytically intractable creating a need for alternative inference methods. Integrated nested Laplace approximations (INLA) provides fast, deterministic inference of approximate posterior densities by exploiting sparsity in the latent structure of the model. Markov chain Monte Carlo (MCMC) is often used for Bayesian inference by sampling from a target posterior distribution. This suffers poor mixing when many variables are correlated, but careful reparameterisation or use of blocking methods can mitigate these issues. Blocking comes with additional computational overheads due to the matrix algebra involved; these costs can be limited by harnessing the same latent Markov structures and sparse precision matrix properties utilised by INLA, with particular attention paid to efficient matrix operations. We discuss how linear and latent Gaussian models can be constructed by combining methods for linear Gaussian models with Gaussian approximations. We then apply these ideas to a case study in detecting genetic epistasis between telomere defects and deletion of non-essential genes in Saccharomyces cerevisiae, for an experiment known as Quantitative Fitness Analysis (QFA). Bayesian variable selection is included to identify which gene deletions cause a genetic interaction. Previous Bayesian models have proven successful in detecting interactions but time-consuming due to the complexity of the model and poor mixing. Linear and latent Gaussian models are created to pursue more efficient inference over standard Gibbs samplers, but we find inference methods for latent Gaussian models can struggle with increasing dimension. We also investigate how the introduction of variable selection provides opportunities to reduce the dimension of the latent model structure for potentially faster inference. Finally, we discuss progress on a new follow-on experiment, Mini QFA, which attempts to find epistasis between telomere defects and a pair of gene deletions

Coûts de Synchronization dans les Programmes Parallèles et les Structures de Donnèes Simultanées

To use the computational power of modern computing machines, we have to deal with concurrent programs. Writing efficient concurrent programs is notoriously difficult, primarily due to the need of harnessing synchronization costs. In this thesis, we focus on synchronization costs in parallel programs and concurrent data structures.First, we present a novel granularity control technique for parallel programs designed for the dynamic multithreading environment. Then in the context of concurrent data structures, we consider the notion of concurrency-optimality and propose the first implementation of a concurrency-optimal binary search tree that, intuitively, accepts a concurrent schedule if and only if the schedule is correct. Also, we propose parallel combining, a technique that enables efficient implementations of concurrent data structures from their parallel batched counterparts. We validate the proposed techniques via experimental evaluations showing superior or comparable performance with respect to state-of-the-art algorithms.From a more formal perspective, we consider the phenomenon of helping in concurrent data structures. Intuitively, helping is observed when the order of some operation in a linearization is fixed by a step of another process. We show that no wait-free linearizable implementation of stack using read, write, compare&swap and fetch&add primitives can be help-free, correcting a mistake in an earlier proof by Censor-Hillel et al. Finally, we propose a simple way to analytically predict the throughput of data structures based on coarse-grained locking.Pour utiliser la puissance de calcul des ordinateurs modernes, nous devons écrire des programmes concurrents. L’écriture de programme concurrent efficace est notoirement difficile, principalement en raison de la nécessité de gérer les coûts de synchronization. Dans cette thèse, nous nous concentrons sur les coûts de synchronisation dans les programmes parallèles et les structures de données concurrentes.D’abord, nous présentons une nouvelle technique de contrôle de la granularité pour les programmes parallèles conçus pour un environnement de multi-threading dynamique. Ensuite, dans le contexte des structures de données concurrentes, nous considérons la notion d’optimalité de concurrence (concurrency-optimality) et proposons la première implémentation concurrence-optimal d’un arbre binaire de recherche qui, intuitivement, accepte un ordonnancement concurrent si et seulement si l’ordonnancement est correct. Nous proposons aussi la combinaison parallèle (parallel combining), une technique qui permet l’implémentation efficace des structures de données concurrences à partir de leur version parallèle par lots. Nous validons les techniques proposées par une évaluation expérimentale, qui montre des performances supérieures ou comparables à celles des algorithmes de l’état de l’art.Dans une perspective plus formelle, nous considérons le phénomène d’assistance (helping) dans des structures de données concurrentes. On observe un phénomène d’assistance quand l’ordre d’une opération d’un processus dans une trace linéarisée est fixée par une étape d’un autre processus. Nous montrons qu’aucune implémentation sans attente (wait-free) linéarisable d’une pile utilisant les primitives read, write, compare&swap et fetch&add ne peut être “sans assistance” (help-free), corrigeant une erreur dans une preuve antérieure de Censor-Hillel et al. Finalement, nous proposons une façon simple de prédire analytiquement le débit (throughput) des structures de données basées sur des verrous à gros grains

LIPIcs, Volume 261, ICALP 2023, Complete Volume

LIPIcs, Volume 261, ICALP 2023, Complete Volum

Development of a Pseudo Non-LTE model for Z-pinch simulations

Predicting the energetic and spectral characteristics of Z-pinch sources is a very delicate task. Z-pinch plasmas conditions are spread across a wide range of parameter space and often far from Local Thermodynamic Equilibrium (LTE). In addition, the increasing optical depth of the plasma at stagnation can have a strong influence on its own dynamics, suggesting that simultaneous solution of both the magnetohydrodynamic (MHD) and radiative response is required. Unfortunately, the estimation of the frequency and time dependent radiative properties of Z-pinches is computationally challenging and the recent improvements made to the parallel architecture of the 3D resistive Eulerian MHD code GORGON have only reinforced the strong emphasis already placed on optimizing the physics solvers used in Z-pinch simulations. To address these issues, we have developed a simple and fast pseudo NLTE code based on a Screened Hydrogenic Model (SHM) that can be run in-line with GORGON or as a post processing tool with synthetic spectra capabilities. Making use of a computationally inexpensive modification of the Saha equation, this highly optimized code has demonstrated a good ability to represent Non-LTE plasma conditions. In order to handle the amount of data generated by the spectral treatment of the billions of numerical cells constituting the simulation grids, an original data structure derived from a self-balancing binary search tree has been developed, enabling the use of Non-LTE DCA calculations in a large scale three dimensional environment for the first time. The implementation of this model is described in detail and comparisons with a commercial package are offered. Results from Z-pinch simulations performed with the new code are discussed and possible future improvements are presented

LIPIcs, Volume 248, ISAAC 2022, Complete Volume

LIPIcs, Volume 248, ISAAC 2022, Complete Volum

5th International Probabilistic Workshop: 28-29 November 2007, Ghent, Belgium

These are the proceedings of the 5th International Probabilistic Workshop. Even though the 5th anniversary of a conference might not be of such importance, it is quite interesting to note the development of this probabilistic conference. Originally, the series started as the 1st and 2nd Dresdner Probabilistic Symposium, which were launched to present research and applications mainly dealt with at Dresden University of Technology. Since then, the conference has grown to an internationally recognised conference dealing with research on and applications of probabilistic techniques, mainly in the field of structural engineering. Other topics have also been dealt with such as ship safety and natural hazards. Whereas the first conferences in Dresden included about 12 presentations each, the conference in Ghent has attracted nearly 30 presentations. Moving from Dresden to Vienna (University of Natural Resources and Applied Life Sciences) to Berlin (Federal Institute for Material Research and Testing) and then finally to Ghent, the conference has constantly evolved towards a truly international level. This can be seen by the language used. The first two conferences were entirely in the German language. During the conference in Berlin however, the change from the German to English language was especially apparent as some presentations were conducted in German and others in English. Now in Ghent all papers will be presented in English. Participants now, not only come from Europe, but also from other continents. Although the conference will move back to Germany again next year (2008) in Darmstadt, the international concept will remain, since so much work in the field of probabilistic safety evaluations is carried out internationally. In two years (2009) the conference will move to Delft, The Netherlands and probably in 2010 the conference will be held in Szczecin, Poland. Coming back to the present: the editors wish all participants a successful conference in Ghent