Flexible, wide-area storage for distributed systems using semantic cues

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 2009.This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections.Cataloged from student submitted PDF version of thesis.Includes bibliographical references (p. 81-87).There is a growing set of Internet-based services that are too big, or too important, to run at a single site. Examples include Web services for e-mail, video and image hosting, and social networking. Splitting such services over multiple sites can increase capacity, improve fault tolerance, and reduce network delays to clients. These services often need storage infrastructure to share data among the sites. This dissertation explores the use of a new file system (WheelFS) specifically designed to be the storage infrastructure for wide-area distributed services. WheelFS allows applications to adjust the semantics of their data via semantic cues, which provide application control over consistency, failure handling, and file and replica placement. This dissertation describes a particular set of semantic cues that reflect the specific challenges that storing data over the wide-area network entails: high-latency and low-bandwidth links, coupled with increased node and link failures, when compared to local-area networks. By augmenting a familiar POSIX interface with support for semantic cues, WheelFS provides a wide-area distributed storage system intended to help multi-site applications share data and gain fault tolerance, in the form of a distributed file system. Its design allows applications to adjust the tradeoff between prompt visibility of updates from other sites and the ability for sites to operate independently despite failures and long delays. WheelFS is implemented as a user-level file system and is deployed on PlanetLab and Emu-lab.(cont.) Six applications (an all-pairs-pings script, a distributed Web cache, an email service, large file distribution, distributed compilation, and protein sequence alignment software) demonstrate that WheelFS's file system interface simplifies construction of distributed applications by allowing reuse of existing software. These applications would perform poorly with the strict semantics implied by a traditional file system interface, but by providing cues to WheelFS they are able to achieve good performance. Measurements show that applications built on WheelFS deliver comparable performance to services such as CoralCDN and BitTorrent that use specialized wide-area storage systems.by Jeremy Andrew Stribling.Ph.D

Over Cite : a cooperative digital research library

Thesis (S.M.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 2005.Includes bibliographical references (leaves 47-50).CiteSeer is a well-known online resource for the computer science research community, allowing users to search and browse a large archive of research papers. Unfortunately, its current centralized incarnation is costly to run. Although members of the community would presumably be willing to donate hardware and bandwidth at their own sites to assist CiteSeer, the current architecture does not facilitate such distribution of resources. OverCite is a design for a new architecture for a distributed and cooperative research library based on a distributed hash table (DHT). The new architecture harnesses donated resources at many sites to provide document search and retrieval service to researchers worldwide. A preliminary evaluation of an initial OverCite prototype shows that it can service more queries per second than a centralized system, and that it increases total storage capacity by a factor of n/4 in a system of n nodes. OverCite can exploit these additional resources by supporting new features such as document alerts, and by scaling to larger data sets.by Jeremy Stribling.S.M

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

Optimizations for Locality-Aware Structured Peer-to-Peer Overlays

We present several optimizations aimed at improving the object location performance of locality-aware structured peer-to-peer overlays. We present simulation results that demonstrate the effectiveness of these optimizations in Tapestry, and discuss their usage of the overall storage resources of the system

Prototyping a DHT-Oriented Architecture

We attempt to decouple identity from location in Internet hosts. In our proposal, hosts receive flat identifiers in a large and sparse namespace, and an Internet-wide distributed hash table (DHT) acts as a resolver by mapping these flat identifiers to IP addresses in analogy with today's DNS. Unlike DNS names, the source and destination identifiers appear in packets, in a shim layer after the IP header. Our proposal would change all host software but leave the core routers untouched. The advantages of our proposal are: (1) the benefits of decoupling location from identity, which have been articulated elsewhere (see, for example, [16, 19]) and (2) enhanced middlebox functions. The paper's focus is the second of these two advantages