Online Data Structures in External Memory

The original publication is available at www.springerlink.comThe data sets for many of today's computer applications are too large to t within the computer's internal memory and must instead be stored on external storage devices such as disks. A major performance bottleneck can be the input/output communication (or I/O) between the external and internal memories. In this paper we discuss a variety of online data structures for external memory, some very old and some very new, such as hashing (for dictionaries), B-trees (for dictionaries and 1-D range search), bu er trees (for batched dynamic problems), interval trees with weight-balanced B-trees (for stabbing queries), priority search trees (for 3-sided 2-D range search), and R-trees and other spatial structures. We also discuss several open problems along the way

Low Space External Memory Construction of the Succinct Permuted Longest Common Prefix Array

The longest common prefix (LCP) array is a versatile auxiliary data structure in indexed string matching. It can be used to speed up searching using the suffix array (SA) and provides an implicit representation of the topology of an underlying suffix tree. The LCP array of a string of length $n$ can be represented as an array of length $n$ words, or, in the presence of the SA, as a bit vector of $2n$ bits plus asymptotically negligible support data structures. External memory construction algorithms for the LCP array have been proposed, but those proposed so far have a space requirement of $O(n)$ words (i.e. $O(n \log n)$ bits) in external memory. This space requirement is in some practical cases prohibitively expensive. We present an external memory algorithm for constructing the $2n$ bit version of the LCP array which uses $O(n \log \sigma)$ bits of additional space in external memory when given a (compressed) BWT with alphabet size $\sigma$ and a sampled inverse suffix array at sampling rate $O(\log n)$. This is often a significant space gain in practice where $\sigma$ is usually much smaller than $n$ or even constant. We also consider the case of computing succinct LCP arrays for circular strings

MKtree: generation and simulations

The problem to represent very complex systems has been studied by several authors, obtaining solutions based on different data structures. In this paper, a K dimensional tree (Multirresolution Kdtree, MKtree) is introduced. The MKtree represents a hierarchical subdivision of the scene objects that guarantees a minimum space overlap between node regions. MKtrees are useful for collision detection and for time-critical rendering in very large environments requiring external memory storage. Examples in ship design applications are described.Postprint (published version

What Does Dynamic Optimality Mean in External Memory?

A data structure A is said to be dynamically optimal over a class of data structures ? if A is constant-competitive with every data structure C ? ?. Much of the research on binary search trees in the past forty years has focused on studying dynamic optimality over the class of binary search trees that are modified via rotations (and indeed, the question of whether splay trees are dynamically optimal has gained notoriety as the so-called dynamic-optimality conjecture). Recently, researchers have extended this to consider dynamic optimality over certain classes of external-memory search trees. In particular, Demaine, Iacono, Koumoutsos, and Langerman propose a class of external-memory trees that support a notion of tree rotations, and then give an elegant data structure, called the Belga B-tree, that is within an O(log log N)-factor of being dynamically optimal over this class. In this paper, we revisit the question of how dynamic optimality should be defined in external memory. A defining characteristic of external-memory data structures is that there is a stark asymmetry between queries and inserts/updates/deletes: by making the former slightly asymptotically slower, one can make the latter significantly asymptotically faster (even allowing for operations with sub-constant amortized I/Os). This asymmetry makes it so that rotation-based search trees are not optimal (or even close to optimal) in insert/update/delete-heavy external-memory workloads. To study dynamic optimality for such workloads, one must consider a different class of data structures. The natural class of data structures to consider are what we call buffered-propagation trees. Such trees can adapt dynamically to the locality properties of an input sequence in order to optimize the interactions between different inserts/updates/deletes and queries. We also present a new form of beyond-worst-case analysis that allows for us to formally study a continuum between static and dynamic optimality. Finally, we give a novel data structure, called the J?llo Tree, that is statically optimal and that achieves dynamic optimality for a large natural class of inputs defined by our beyond-worst-case analysis

Predicting Memory Demands of BDD Operations using Maximum Graph Cuts (Extended Paper)

The BDD package Adiar manipulates Binary Decision Diagrams (BDDs) in external memory. This enables handling big BDDs, but the performance suffers when dealing with moderate-sized BDDs. This is mostly due to initializing expensive external memory data structures, even if their contents can fit entirely inside internal memory. The contents of these auxiliary data structures always correspond to a graph cut in an input or output BDD. Specifically, these cuts respect the levels of the BDD. We formalise the shape of these cuts and prove sound upper bounds on their maximum size for each BDD operation. We have implemented these upper bounds within Adiar. With these bounds, it can predict whether a faster internal memory variant of the auxiliary data structures can be used. In practice, this improves Adiar's running time across the board. Specifically for the moderate-sized BDDs, this results in an average reduction of the computation time by 86.1% (median of 89.7%). In some cases, the difference is even 99.9\%. When checking equivalence of hardware circuits from the EPFL Benchmark Suite, for one of the instances the time was decreased by 52 hours.Comment: 25 pages, 11 Figures, 2 Tables. Extended version of paper published at ATVA 202

Worst-Case Optimal Algorithms for Parallel Query Processing

In this paper, we study the communication complexity for the problem of computing a conjunctive query on a large database in a parallel setting with $p$ servers. In contrast to previous work, where upper and lower bounds on the communication were specified for particular structures of data (either data without skew, or data with specific types of skew), in this work we focus on worst-case analysis of the communication cost. The goal is to find worst-case optimal parallel algorithms, similar to the work of [18] for sequential algorithms. We first show that for a single round we can obtain an optimal worst-case algorithm. The optimal load for a conjunctive query $q$ when all relations have size equal to $M$ is $O(M/p^{1/\psi^*})$, where $\psi^*$ is a new query-related quantity called the edge quasi-packing number, which is different from both the edge packing number and edge cover number of the query hypergraph. For multiple rounds, we present algorithms that are optimal for several classes of queries. Finally, we show a surprising connection to the external memory model, which allows us to translate parallel algorithms to external memory algorithms. This technique allows us to recover (within a polylogarithmic factor) several recent results on the I/O complexity for computing join queries, and also obtain optimal algorithms for other classes of queries

I/O efficient bisimulation partitioning on very large directed acyclic graphs

In this paper we introduce the first efficient external-memory algorithm to compute the bisimilarity equivalence classes of a directed acyclic graph (DAG). DAGs are commonly used to model data in a wide variety of practical applications, ranging from XML documents and data provenance models, to web taxonomies and scientific workflows. In the study of efficient reasoning over massive graphs, the notion of node bisimilarity plays a central role. For example, grouping together bisimilar nodes in an XML data set is the first step in many sophisticated approaches to building indexing data structures for efficient XPath query evaluation. To date, however, only internal-memory bisimulation algorithms have been investigated. As the size of real-world DAG data sets often exceeds available main memory, storage in external memory becomes necessary. Hence, there is a practical need for an efficient approach to computing bisimulation in external memory. Our general algorithm has a worst-case IO-complexity of O(Sort(|N| + |E|)), where |N| and |E| are the numbers of nodes and edges, resp., in the data graph and Sort(n) is the number of accesses to external memory needed to sort an input of size n. We also study specializations of this algorithm to common variations of bisimulation for tree-structured XML data sets. We empirically verify efficient performance of the algorithms on graphs and XML documents having billions of nodes and edges, and find that the algorithms can process such graphs efficiently even when very limited internal memory is available. The proposed algorithms are simple enough for practical implementation and use, and open the door for further study of external-memory bisimulation algorithms. To this end, the full open-source C++ implementation has been made freely available