Ralph Butler

The Subsystems Approach to Genome Annotation and its Use in the Project to Annotate 1000 Genomes

The release of the 1000th complete microbial genome will occur in the next two to three years. In anticipation of this milestone, the Fellowship for Interpretation of Genomes (FIG) launched the Project to Annotate 1000 Genomes. The project is built around the principle that the key to improved accuracy in high-throughput annotation technology is to have experts annotate single subsystems over the complete collection of genomes, rather than having an annotation expert attempt to annotate all of the genes in a single genome. Using the subsystems approach, all of the genes implementing the subsystem are analyzed by an expert in that subsystem. An annotation environment was created where populated subsystems are curated and projected to new genomes. A portable notion of a populated subsystem was defined, and tools developed for exchanging and curating these objects. Tools were also developed to resolve conflicts between populated subsystems. The SEED is the first annotation environment that supports this model of annotation. Here, we describe the subsystem approach, and offer the first release of our growing library of populated subsystems. The initial release of data includes 180 177 distinct proteins with 2133 distinct functional roles. This data comes from 173 subsystems and 383 different organisms.

Monitors, messages, and clusters: the p4 parallel programming system

p4 is a portable library of C and Fortran subroutines for programming parallel computers. It is the current version of a system that has been in use since 1984. It includes features for explicit parallel programming of shared-memory machines, distributed-memory machines (including heterogeneous networks of workstations), and clusters, by which we mean shared-memory multiprocessors communicating via message passing. We discuss here the design goals, history, and system architecture of p4 and describe briefly a diverse collection of applications that have demonstrated the utility of p4.

A Scalable Process-Management Environment for Parallel Programs

We present a process management system for parallel programs such as those written using MPI. A primary goal of the system, which we call MPD (for multipurpose daemon), is to be scalable. By this we mean that startup of interactive parallel jobs comprising a thousand processes is quick, that signals can be quickly delivered to processes, and that stdin, stdout, and stderr are managed intuitively. Our primary target is parallel machines made up of clusters of SMPs, but the system is also useful in more tightly integrated environments. We describe how MPD enables much faster startup and better runtime management of MPICH jobs. We show how close control of stdio can support the easy implementation of a number of convenient system utilities, even a parallel debugger. MPD is implemented and freely distributed with MPICH.

Automated Reasoning Contributed to Mathematics and Logic

In this article, we present some results of our research focusing on the use of our newest automated reasoning program OTTER to prove theorems from Robbins algebra, equivalential calculus, implicational calculus, combinatory logic, and finite semigroups. Included among the results are answers to open questions and new shorter and less complex proofs to known theorems. To obtain these results, we relied upon our usual paradigm, which heavily emphasizes the role of demodulation, subsumption, set of support, weighting, paramodulation, hyperresolution, and UR-resolution. Our position is that all of these components are essential, even though we can shed little light on the relative importance of each, the coupling of the various components, and the metarules for making the most effective choices. Indeed, without these components, a program will too often offer inadequate control over the redundancy and irrelevancy of deduced information. We include experimental evidence to support our position, examples producing success when the paradigm is employed, and examples producing failure when it is not. In addition to providing evidence that automated reasoning has made contributions to both mathematics and logic, the theorems we discuss also serve nicely as challenge problems for testing the merits of a new idea or a new program and provide interesting examples for comparing different paradigms.

Components and interfaces of a process management system for parallel programs

Parallel jobs are different from sequential jobs and require a different type of process management. We present here a process management system for parallel programs such as those written using MPI. A primary goal of the system, which we call MPD (for multipurpose daemon), is to be scalable. By this we mean that startup of interactive parallel jobs comprising thousands of processes is quick, that signals can be quickly delivered to processes, and that stdin, stdout, and stderr are managed intuitively. Our primary target is parallel machines made up of clusters of SMPs, but the system is also useful in more tightly integrated environments. We describe how MPD enables much faster startup and better runtime management of parallel jobs. We show how close control of stdio can support the easy implementation of a number of convenient system utilities, even a parallel debugger. We describe a simple but general interface that can be used to separate any process manager from a parallel library, which we use to keep MPD separate from MPICH.

Introducing parallel processing at the undergraduate level

With multiprocessor computers becoming more readily available on college campuses and with the recent development of software tools to aid in the implementation of parallel algorithms, it is time for parallel processing to enter the undergraduate curriculum. In this paper we show how widely available tools combined with concepts learned in an operating systems course could be used to develop an upper level undergraduate course in parallel processing. A typical artificial intelligence search problem (N-queens) is implemented in C and exhibits almost linear speedups.

p4-Linda: a portable implementation of Linda

Facilities such as interprocess communication and protection of shared resources have been added to operating systems to support multiprogramming and have since been adapted to exploit explicit multiprocessing within the scope of two models: the shared-memory model and the distributed (message-passing) model. When multiprocessors (or networks of heterogeneous processors) are used for explicit parallelism, the difference between these models is exposed to the programmer. The p4 tool set was originally developed to buffer the programmer from synchronization issues while offering an added advantage in portability, however two models are often still needed to develop parallel algorithms. The authors provide two implementations of Linda in an attempt to support a single high-level programming model on top of the existing paradigms in order to provide a consistent semantics regardless of the underlying model. Lindas fundamental properties associated with generative communication eliminate the distinction between shared and distributed memory.<<ETX>>

CPVM: customizable portable virtual machines

We present our experiences with a customizable portable virtual machine (CPVM) environment that makes it possible for students and professors to develop a customized, fully loaded, fully functional virtual machine that they can run on any computer that has a USB port or an ftp client without compromising the host. We also make available to students and faculty a copy of a portable virtual machine which provides compilers, window managers, and IDEs as well as the virtual operating system. This copy is identical to the environment found in our labs. CPVM has allowed students to use their personal Windows computers as if they were the Linux machines in the lab without having to install Linux. It has also enabled professors to effectively take their office environments with them to remote locations such as conferences. CPVM is composed of free, open-source software, and is available via anonymous ftp.

An Interoperability Approach to System Software, Tools, and Libraries for Clusters

Systems software for clusters typically derives from a multiplicity of sources: the kernel itself, software associated with a particular distribution, site-specific purchased or open-source software, and assorted home-grown tools and procedures that attempt to glue everything together to meet the needs of the users and administrators of a particular cluster. Whether a cluster is a general-purpose resource serving multiple users or dedicated to a single application, getting everything to work together is a challenge. The challenge is partially met by special software distributions for clusters such as OSCAR or ROCKS. In this article, we discuss another approach (although it is not inconsistent with existing distributions), in which a small number of concepts are deployed to facilitate the customized integration of various software tools for cluster management, operation, and user jobs. The concepts include (1) a component approach to basic system software such as schedulers, queue managers, process managers, and monitors; (2) a software development kit for constructing networks of system software components, either from scratch or by wrapping “foreign” software, and (3) the use of explicit parallelism in building system tools for high performance. We illustrate this approach with a description of a mid-sized general-purpose cluster operated entirely by software built this way.

Formula databases for high-performance resolution/paramodulation systems

Over the past 25 years, researchers have written numerous deduction systems based on resolution and paramodulation. Of these systems, very few have been capable of generating and maintaining aformula database containing more than just a few thousand clauses. These few systems were used to explore mechanisms for rapidly extracting limited subsets of ‘relevant’ clauses. We have developed a simple, powerful deduction system that reflects some of the best of the ideas that have emerged from the research. This paper describes that deduction system and casts the idea in a form that makes them easily accessible to researchers wishing to write their own high-performance systems.