Lock-free Concurrent Data Structures

Concurrent data structures are the data sharing side of parallel programming. Data structures give the means to the program to store data, but also provide operations to the program to access and manipulate these data. These operations are implemented through algorithms that have to be efficient. In the sequential setting, data structures are crucially important for the performance of the respective computation. In the parallel programming setting, their importance becomes more crucial because of the increased use of data and resource sharing for utilizing parallelism. The first and main goal of this chapter is to provide a sufficient background and intuition to help the interested reader to navigate in the complex research area of lock-free data structures. The second goal is to offer the programmer familiarity to the subject that will allow her to use truly concurrent methods.Comment: To appear in "Programming Multi-core and Many-core Computing Systems", eds. S. Pllana and F. Xhafa, Wiley Series on Parallel and Distributed Computin

The Parallelism Motifs of Genomic Data Analysis

Genomic data sets are growing dramatically as the cost of sequencing continues to decline and small sequencing devices become available. Enormous community databases store and share this data with the research community, but some of these genomic data analysis problems require large scale computational platforms to meet both the memory and computational requirements. These applications differ from scientific simulations that dominate the workload on high end parallel systems today and place different requirements on programming support, software libraries, and parallel architectural design. For example, they involve irregular communication patterns such as asynchronous updates to shared data structures. We consider several problems in high performance genomics analysis, including alignment, profiling, clustering, and assembly for both single genomes and metagenomes. We identify some of the common computational patterns or motifs that help inform parallelization strategies and compare our motifs to some of the established lists, arguing that at least two key patterns, sorting and hashing, are missing

AT-GIS: highly parallel spatial query processing with associative transducers

Users in many domains, including urban planning, transportation, and environmental science want to execute analytical queries over continuously updated spatial datasets. Current solutions for largescale spatial query processing either rely on extensions to RDBMS, which entails expensive loading and indexing phases when the data changes, or distributed map/reduce frameworks, running on resource-hungry compute clusters. Both solutions struggle with the sequential bottleneck of parsing complex, hierarchical spatial data formats, which frequently dominates query execution time. Our goal is to fully exploit the parallelism offered by modern multicore CPUs for parsing and query execution, thus providing the performance of a cluster with the resources of a single machine. We describe AT-GIS, a highly-parallel spatial query processing system that scales linearly to a large number of CPU cores. ATGIS integrates the parsing and querying of spatial data using a new computational abstraction called associative transducers(ATs). ATs can form a single data-parallel pipeline for computation without requiring the spatial input data to be split into logically independent blocks. Using ATs, AT-GIS can execute, in parallel, spatial query operators on the raw input data in multiple formats, without any pre-processing. On a single 64-core machine, AT-GIS provides 3× the performance of an 8-node Hadoop cluster with 192 cores for containment queries, and 10× for aggregation queries

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

GraphX: Unifying Data-Parallel and Graph-Parallel Analytics

From social networks to language modeling, the growing scale and importance of graph data has driven the development of numerous new graph-parallel systems (e.g., Pregel, GraphLab). By restricting the computation that can be expressed and introducing new techniques to partition and distribute the graph, these systems can efficiently execute iterative graph algorithms orders of magnitude faster than more general data-parallel systems. However, the same restrictions that enable the performance gains also make it difficult to express many of the important stages in a typical graph-analytics pipeline: constructing the graph, modifying its structure, or expressing computation that spans multiple graphs. As a consequence, existing graph analytics pipelines compose graph-parallel and data-parallel systems using external storage systems, leading to extensive data movement and complicated programming model. To address these challenges we introduce GraphX, a distributed graph computation framework that unifies graph-parallel and data-parallel computation. GraphX provides a small, core set of graph-parallel operators expressive enough to implement the Pregel and PowerGraph abstractions, yet simple enough to be cast in relational algebra. GraphX uses a collection of query optimization techniques such as automatic join rewrites to efficiently implement these graph-parallel operators. We evaluate GraphX on real-world graphs and workloads and demonstrate that GraphX achieves comparable performance as specialized graph computation systems, while outperforming them in end-to-end graph pipelines. Moreover, GraphX achieves a balance between expressiveness, performance, and ease of use