Date of Award

9-1-2011

Document Type

Thesis (Ph.D.)

Department or Program

Department of Computer Science

First Advisor

Thomas H. Cormen

Abstract

Applications that operate on datasets which are too big to fit in main memory, known in the literature as external-memory or out-of-core applications, store their data on one or more disks. Several of these applications make multiple passes over the data, where each pass reads data from disk, operates on it, and writes data back to disk. Compared with an in-memory operation, a disk-I/O operation takes orders of magnitude (approx. 100,000 times) longer; that is, disk-I/O is a high-latency operation. Out-of-core algorithms often run on a distributed-memory cluster to take advantage of a cluster's computing power, memory, disk space, and bandwidth. By doing so, however, they introduce another high-latency operation: interprocessor communication. Efficient implementations of these algorithms access data in blocks to amortize the cost of a single data transfer over the disk or the network, and they introduce asynchrony to overlap high-latency operations and computations. FG, short for Asynchronous Buffered Computation Design and Engineering Framework Generator, is a programming framework that helps to mitigate latency in out-of-core programs that run on distributed-memory clusters. An FG program is composed of a pipeline of stages operating on buffers. FG runs the stages asynchronously so that stages performing high-latency operations can overlap their work with other stages. FG supplies the code to create a pipeline, synchronize the stages, and manage data buffers; the user provides a straightforward function, containing only synchronous calls, for each stage. In this thesis, we use FG to tackle latency and exploit the available parallelism in out-of-core and distributed-memory programs. We show how FG helps us design out-of-core programs and think about parallel computing in general using three instances: an out-of-core, distribution-based sorting program; an implementation of external-memory suffix arrays; and a scientific-computing application called the fast Gauss transform. FG's interaction with these real-world programs is symbiotic: FG enables efficient implementations of these programs, and the design of the first two of these programs pointed us toward further extensions for FG. Today's era of multicore machines compels us to harness all opportunities for parallelism that are available in a program, and so in the latter two applications, we combine FG's multithreading capabilities with the routines that OpenMP offers for in-core parallelism. In the fast Gauss transform application, we use this strategy to realize an up to 20-fold performance improvement compared with an alternate fast Gauss transform implementation. In addition, we use our experience with designing programs in FG to provide some suggestions for the next version of FG.

Comments

Originally posted in the Dartmouth College Computer Science Technical Report Series, number TR2011-706.

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