New Algorithms for Position Heaps

We present several results about position heaps, a relatively new alternative to suffix trees and suffix arrays. First, we show that, if we limit the maximum length of patterns to be sought, then we can also limit the height of the heap and reduce the worst-case cost of insertions and deletions. Second, we show how to build a position heap in linear time independent of the size of the alphabet. Third, we show how to augment a position heap such that it supports access to the corresponding suffix array, and vice versa. Fourth, we introduce a variant of a position heap that can be simulated efficiently by a compressed suffix array with a linear number of extra bits

POSH: Paris OpenSHMEM: A High-Performance OpenSHMEM Implementation for Shared Memory Systems

In this paper we present the design and implementation of POSH, an Open-Source implementation of the OpenSHMEM standard. We present a model for its communications, and prove some properties on the memory model defined in the OpenSHMEM specification. We present some performance measurements of the communication library featured by POSH and compare them with an existing one-sided communication library. POSH can be downloaded from \url{http://www.lipn.fr/~coti/POSH}. % 9 - 67Comment: This is an extended version (featuring the full proofs) of a paper accepted at ICCS'1

Strengthened Lazy Heaps: Surpassing the Lower Bounds for Binary Heaps

Let $n$ denote the number of elements currently in a data structure. An in-place heap is stored in the first $n$ locations of an array, uses $O(1)$ extra space, and supports the operations: minimum, insert, and extract-min. We introduce an in-place heap, for which minimum and insert take $O(1)$ worst-case time, and extract-min takes $O(\lg{} n)$ worst-case time and involves at most $\lg{} n + O(1)$ element comparisons. The achieved bounds are optimal to within additive constant terms for the number of element comparisons. In particular, these bounds for both insert and extract-min -and the time bound for insert- surpass the corresponding lower bounds known for binary heaps, though our data structure is similar. In a binary heap, when viewed as a nearly complete binary tree, every node other than the root obeys the heap property, i.e. the element at a node is not smaller than that at its parent. To surpass the lower bound for extract-min, we reinforce a stronger property at the bottom levels of the heap that the element at any right child is not smaller than that at its left sibling. To surpass the lower bound for insert, we buffer insertions and allow $O(\lg^2{} n)$ nodes to violate heap order in relation to their parents

On the Impact of Memory Allocation on High-Performance Query Processing

Somewhat surprisingly, the behavior of analytical query engines is crucially affected by the dynamic memory allocator used. Memory allocators highly influence performance, scalability, memory efficiency and memory fairness to other processes. In this work, we provide the first comprehensive experimental analysis on the impact of memory allocation for high-performance query engines. We test five state-of-the-art dynamic memory allocators and discuss their strengths and weaknesses within our DBMS. The right allocator can increase the performance of TPC-DS (SF 100) by 2.7x on a 4-socket Intel Xeon server

A Bulk-Parallel Priority Queue in External Memory with STXXL

We propose the design and an implementation of a bulk-parallel external memory priority queue to take advantage of both shared-memory parallelism and high external memory transfer speeds to parallel disks. To achieve higher performance by decoupling item insertions and extractions, we offer two parallelization interfaces: one using "bulk" sequences, the other by defining "limit" items. In the design, we discuss how to parallelize insertions using multiple heaps, and how to calculate a dynamic prediction sequence to prefetch blocks and apply parallel multiway merge for extraction. Our experimental results show that in the selected benchmarks the priority queue reaches 75% of the full parallel I/O bandwidth of rotational disks and and 65% of SSDs, or the speed of sorting in external memory when bounded by computation.Comment: extended version of SEA'15 conference pape

Hollow Heaps

We introduce the hollow heap, a very simple data structure with the same amortized efficiency as the classical Fibonacci heap. All heap operations except delete and delete-min take $O(1)$ time, worst case as well as amortized; delete and delete-min take $O(\log n)$ amortized time on a heap of $n$ items. Hollow heaps are by far the simplest structure to achieve this. Hollow heaps combine two novel ideas: the use of lazy deletion and re-insertion to do decrease-key operations, and the use of a dag (directed acyclic graph) instead of a tree or set of trees to represent a heap. Lazy deletion produces hollow nodes (nodes without items), giving the data structure its name.Comment: 27 pages, 7 figures, preliminary version appeared in ICALP 201