Engineering Parallel String Sorting

We discuss how string sorting algorithms can be parallelized on modern multi-core shared memory machines. As a synthesis of the best sequential string sorting algorithms and successful parallel sorting algorithms for atomic objects, we first propose string sample sort. The algorithm makes effective use of the memory hierarchy, uses additional word level parallelism, and largely avoids branch mispredictions. Then we focus on NUMA architectures, and develop parallel multiway LCP-merge and -mergesort to reduce the number of random memory accesses to remote nodes. Additionally, we parallelize variants of multikey quicksort and radix sort that are also useful in certain situations. Comprehensive experiments on five current multi-core platforms are then reported and discussed. The experiments show that our implementations scale very well on real-world inputs and modern machines.Comment: 46 pages, extension of "Parallel String Sample Sort" arXiv:1305.115

Reordering Rows for Better Compression: Beyond the Lexicographic Order

Sorting database tables before compressing them improves the compression rate. Can we do better than the lexicographical order? For minimizing the number of runs in a run-length encoding compression scheme, the best approaches to row-ordering are derived from traveling salesman heuristics, although there is a significant trade-off between running time and compression. A new heuristic, Multiple Lists, which is a variant on Nearest Neighbor that trades off compression for a major running-time speedup, is a good option for very large tables. However, for some compression schemes, it is more important to generate long runs rather than few runs. For this case, another novel heuristic, Vortex, is promising. We find that we can improve run-length encoding up to a factor of 3 whereas we can improve prefix coding by up to 80%: these gains are on top of the gains due to lexicographically sorting the table. We prove that the new row reordering is optimal (within 10%) at minimizing the runs of identical values within columns, in a few cases.Comment: to appear in ACM TOD

An Elegant Algorithm for the Construction of Suffix Arrays

The suffix array is a data structure that finds numerous applications in string processing problems for both linguistic texts and biological data. It has been introduced as a memory efficient alternative for suffix trees. The suffix array consists of the sorted suffixes of a string. There are several linear time suffix array construction algorithms (SACAs) known in the literature. However, one of the fastest algorithms in practice has a worst case run time of $O(n^2)$. The problem of designing practically and theoretically efficient techniques remains open. In this paper we present an elegant algorithm for suffix array construction which takes linear time with high probability; the probability is on the space of all possible inputs. Our algorithm is one of the simplest of the known SACAs and it opens up a new dimension of suffix array construction that has not been explored until now. Our algorithm is easily parallelizable. We offer parallel implementations on various parallel models of computing. We prove a lemma on the $\ell$-mers of a random string which might find independent applications. We also present another algorithm that utilizes the above algorithm. This algorithm is called RadixSA and has a worst case run time of $O(n\log{n})$. RadixSA introduces an idea that may find independent applications as a speedup technique for other SACAs. An empirical comparison of RadixSA with other algorithms on various datasets reveals that our algorithm is one of the fastest algorithms to date. The C++ source code is freely available at http://www.engr.uconn.edu/~man09004/radixSA.zi

A GPU-enabled solver for time-constrained linear sum assignment problems

This paper deals with solving large instances of the Linear Sum Assignment Problems (LSAPs) under realtime constraints, using Graphical Processing Units (GPUs). The motivating scenario is an industrial application for P2P live streaming that is moderated by a central tracker that is periodically solving LSAP instances to optimize the connectivity of thousands of peers. However, our findings are generic enough to be applied in other contexts. Our main contribution is a parallel version of a heuristic algorithm called Deep Greedy Switching (DGS) on GPUs using the CUDA programming language. DGS sacrifices absolute optimality in favor of a substantial speedup in comparison to classical LSAP solvers like the Hungarian and auctioning methods. We show the modifications needed to parallelize the DGS algorithm and the performance gains of our approach compared to a sequential CPU-based implementation of DGS and a mixed CPU/GPU-based implementation of it

Configurable Strategies for Work-stealing

Work-stealing systems are typically oblivious to the nature of the tasks they are scheduling. For instance, they do not know or take into account how long a task will take to execute or how many subtasks it will spawn. Moreover, the actual task execution order is typically determined by the underlying task storage data structure, and cannot be changed. There are thus possibilities for optimizing task parallel executions by providing information on specific tasks and their preferred execution order to the scheduling system. We introduce scheduling strategies to enable applications to dynamically provide hints to the task-scheduling system on the nature of specific tasks. Scheduling strategies can be used to independently control both local task execution order as well as steal order. In contrast to conventional scheduling policies that are normally global in scope, strategies allow the scheduler to apply optimizations on individual tasks. This flexibility greatly improves composability as it allows the scheduler to apply different, specific scheduling choices for different parts of applications simultaneously. We present a number of benchmarks that highlight diverse, beneficial effects that can be achieved with scheduling strategies. Some benchmarks (branch-and-bound, single-source shortest path) show that prioritization of tasks can reduce the total amount of work compared to standard work-stealing execution order. For other benchmarks (triangle strip generation) qualitatively better results can be achieved in shorter time. Other optimizations, such as dynamic merging of tasks or stealing of half the work, instead of half the tasks, are also shown to improve performance. Composability is demonstrated by examples that combine different strategies, both within the same kernel (prefix sum) as well as when scheduling multiple kernels (prefix sum and unbalanced tree search)

Attribute Value Reordering For Efficient Hybrid OLAP

The normalization of a data cube is the ordering of the attribute values. For large multidimensional arrays where dense and sparse chunks are stored differently, proper normalization can lead to improved storage efficiency. We show that it is NP-hard to compute an optimal normalization even for 1x3 chunks, although we find an exact algorithm for 1x2 chunks. When dimensions are nearly statistically independent, we show that dimension-wise attribute frequency sorting is an optimal normalization and takes time O(d n log(n)) for data cubes of size n^d. When dimensions are not independent, we propose and evaluate several heuristics. The hybrid OLAP (HOLAP) storage mechanism is already 19%-30% more efficient than ROLAP, but normalization can improve it further by 9%-13% for a total gain of 29%-44% over ROLAP