7845091
A Hybrid Number System Processor with Geometric and Complex Arithmetic Capabilities
The architecture, design, and performance of a hybrid number system processor are described. The processor performs multiplication, division, square root, and square in the logarithmic number system (LNS) domain. However, the input, output, addition, and subtraction are all executed in the 32-b IEEE standard floating-point number system. With the LNS multiplier and pipelined architecture, the processor is able to perform the geometric and complex arithmetic very effectively. The processor is also shown to compare well to an existing 32-b floating-point DSP (digital signal processor) chip. For the same level of CMOS technology, the performance ratios between the hybrid number system and the floating-point processor are shown to be 6.4:1 and 8:1 for division and square root, respectively; for the complex FFT (fast Fourier transform) algorithm, the ratio is around 2:1. >
40872599
Timestamp consistency and trace-driven analysis for distributed parallel systems
A continuous stream of event data describing the progress of parallel program execution is realized for trace-driven analysis. Unfortunately, it is often the case that separate streams are produced independently by multiple processors in the system, and the logical order of events cannot be guaranteed due to discrepancy among local clocks. We present an integrated approach for timestamp consistency and performance analysis techniques for IBM SPn systems. The trace facility requires no source code modification, and can generate message passing and system events with minimal trace overhead. Trace-driven analysis tools are developed to extract useful information. Analysis results for NAS kernel benchmarks are reported.<<ETX>>
8015300
MPI programming environment for IBM SP1/SP2
In this paper we discuss an implementation of the message passing interface standard (MPI) for the IBM Scalable Power PARALLEL 1 and 2 (SP1, SP2). Key to a reliable and efficient implementation of a message passing library on these machines is the careful design of a UNIX-Socket like layer in the user space with controlled access to the communication adapters and with adequate recovery and flow control. The performance of this implementation is at the same level as the IBM-proprietary message passing library (MPL). We also show that in the IBM SP1 and SP2 we achieve integrated tracing ability, where both system events, such as context switches and page fault etc., and MPI related activities are traced, with minimal overhead to the application program, thus presenting application programmers the trace of all the events that ultimately affect efficiency of a parallel program.
463160
A Rule-Based Circuit Representation for Automated CMOS Design and Verification
A novel rule-based circuit representation is proposed to describe the connectivities of CMOS circuits at the transistor level. The unique feature of the rule-based representation is its ability to automate CMOS circuit design and verification. A precise symbolic description of the functionality of a transistor-level circuit can be derived based on a set of production rules in linear time. Automated synthesis and verification of CMOS logic circuits are demonstrated.
12615323
PIRSF: family classification system at the Protein Information Resource
The Protein Information Resource (PIR) is an integrated public resource of protein informatics. To facilitate the sensible propagation and standardization of protein annotation and the systematic detection of annotation errors, PIR has extended its superfamily concept and developed the SuperFamily (PIRSF) classification system. Based on the evolutionary relationships of whole proteins, this classification system allows annotation of both specific biological and generic biochemical functions. The system adopts a network structure for protein classification from superfamily to subfamily levels. Protein family members are homologous (sharing common ancestry) and homeomorphic (sharing full-length sequence similarity with common domain architecture). The PIRSF database consists of two data sets, preliminary clusters and curated families. The curated families include family name, protein membership, parent-child relationship, domain architecture, and optional description and bibliography. PIRSF is accessible from the website at http://pir.georgetown.edu/pirsf/ for report retrieval and sequence classification. The report presents family annotation, membership statistics, cross-references to other databases, graphical display of domain architecture, and links to multiple sequence alignments and phylogenetic trees for curated families. PIRSF can be utilized to analyze phylogenetic profiles, to reveal functional convergence and divergence, and to identify interesting relationships between homeomorphic families, domains and structural classes.
19852972
Distributed Instruction Set Computer Architecture
The Distributed Instruction Set Computer Architecture (DISC) is proposed as a fine-grained multiprocessing computer architecture. DISC uses a parallel instruction set and a distributed control mechanism to explore fine-grained, parallel processing in a multiple-functional-unit system. Multiple instructions are executed in parallel and/or out of order at the highest speed of n instructions/cycle, where n is the number of functional units. Based on this architecture, a hardware system is developed. Extensive studies were conducted on a behavioral DISC system model to investigate the performance level, the effect of program sizes, and the hardware utilization. Simulation showed that a DISC system incorporating 16 functional units can run 7.7 times faster than a single-functional-unit DISC system. >
15660415
On-the-fly sharing for streamed aggregation
Data streaming systems are becoming essential for monitoring applications such as financial analysis and network intrusion detection. These systems often have to process many similar but different queries over common data. Since executing each query separately can lead to significant scalability and performance problems, it is vital to share resources by exploiting similarities in the queries. In this paper we present ways to efficiently share streaming aggregate queries with differing periodic windows and arbitrary selection predicates. A major contribution is our sharing technique that does not require any up-front multiple query optimization. This is a significant departure from existing techniques that rely on complex static analyses of fixed query workloads. Our approach is particularly vital in streaming systems where queries can join and leave the system at any point. We present a detailed performance study that evaluates our strategies with an implementation and real data. In these experiments, our approach gives us as much as an order of magnitude performance improvement over the state of the art.
6353106
The Universal Protein Resource (UniProt): an expanding universe of protein information
The Universal Protein Resource (UniProt) provides a central resource on protein sequences and functional annotation with three database components, each addressing a key need in protein bioinformatics. The UniProt Knowledgebase (UniProtKB), comprising the manually annotated UniProtKB/Swiss-Prot section and the automatically annotated UniProtKB/TrEMBL section, is the preeminent storehouse of protein annotation. The extensive cross-references, functional and feature annotations and literature-based evidence attribution enable scientists to analyse proteins and query across databases. The UniProt Reference Clusters (UniRef) speed similarity searches via sequence space compression by merging sequences that are 100% (UniRef100), 90% (UniRef90) or 50% (UniRef50) identical. Finally, the UniProt Archive (UniParc) stores all publicly available protein sequences, containing the history of sequence data with links to the source databases. UniProt databases continue to grow in size and in availability of information. Recent and upcoming changes to database contents, formats, controlled vocabularies and services are described. New download availability includes all major releases of UniProtKB, sequence collections by taxonomic division and complete proteomes. A bibliography mapping service has been added, and an ID mapping service will be available soon. UniProt databases can be accessed online at or downloaded at .
5170715
Distributed Instruction Set Computer
The Distributed Instruction Set Computer, or DISC for short, is an experimental computer system for fine-grained parallel processing. DISC employs a new parallel instruction set, an Early Binding and Scheduling data tagging scheme, and a distributed control mechanism to explore a software dataflow control method in a multiple-functional-unit system. 
With "zero" system control overhead, multiple instructions are executed in parallel and/or out of order at the highest speed of n instructions/cycle, where n is the number of functional units. The quantitative simulation result indicates that a DISC system with 16 functional units can deliverer a maximal 7.7X performance speedup over a single-functional-unit system at the same clock speed. 
Exploring a new parallel instruction set and distributed control mechanism, DISC represents three major breakthroughs in the domain of fine-grained parallel processing: (1) Fast multiple instruction issuing mechanism; (2) Parallel and/or out-of-order execution; (3) Software dataflow control scheme.