38720222
Evaluation of the continuation bit in the Cyclic Pipeline Computer
Abstract The Cyclic Pipeline Computer (CPC) is a shared resource computer which shares its pipeline among multiple instruction streams to create distinct virtual processors. This effectively removes data dependencies which reduce the performance of highly pipelined computers. However, when executing unbalanced parallel programs, the CPC suffers from performance degradation due to synchronization overhead. In this paper we introduce a hardware extension called the continuation bit . The continuation bit controls the instruction issue and determines whether an instruction is issued from the same stream or the next stream. Simulations of various programs indicate that the continuation bit is able to balance the execution of parallel programs by exploiting instruction level parallelism.
1841047
Design and Implementation of Abstract Machine for Parallel Lisp Compilation
15634785
The performance model of SilkRoad - a multithreaded DSM system for clusters
Distributed Shared Memory (DSM) is a highly desirable programming model for cluster based computing. Even though a number of software DSMs have been developed with their performance evaluated, few of them have a theoretical performance model. In this paper, we propose and analyze the performance model of the software DSM of SilkRoad,, a multithreaded runtime system for cluster computing. SilkRoad is built on the Cilk system with an extended memory consistency model which we call RC/sub dag/ consistency: Extending Cilk's theoretical performance model, we show that with the RC/sub dag/ consistent DSM, the expected execution.time T/sub P/ of a partially strict multithreaded computation on P processors is O((T/sub 1/(Z, L) + N)/P + /spl mu/HT/sub /spl infin//), where T/sub 1/(Z, L) is the total work of computation, T/sub /spl infin// is the critical path, N is the number of lock acquisitions, /spl mu/ is the service time of a cache miss, and H is the height of memory: Finally, we present experimental evidence that verify the performance model.
18143878
Compiling Parallel Lisp for a Shared Memory Multiprocessor
There is a commonly held idea that although Lisp is a good language for prototyping and software development, it is often too inefcient to be useful in actual implementation. Advances in compiling Lisp have begun to change this notion. However, the situation is less clear in the case of parallel Lisp dialects. In this paper, we report on our experience in implementing a compiler for a parallel Lisp dialect we called BaLinda Lisp for a shared memory multiprocessor. For a class of problems, our compiler was able to achieve performances on Lisp programs that are near, if not equal to, their imperative (C) equivalents. However, on other problems, the situation is less than ideal. We investigate this phenomenum and outline the future challenges in realizing a production strength parallel Lisp compiler.
3457072
Using UML 2.0 for system level design of real time SoC platforms for stream processing
While enabling fast implementation and reconfiguration of stream applications, programmable stream processors expose issues of incompatibility and lack of adoption in existing stream modeling languages. To address them we describe a design approach in which specifications are captured in UML 2.0, and automatically translated into SystemC models consisting of simulators and synthesizable code under proper style constraints. As an application case, we explain real time stream processor specifications using new UML 2.0 notations. Then we expound how our translator generates SystemC models and includes additional hardware details. Verifications are made during UML execution as well as assertions in SystemC. The case study demonstrates the feasibility of fast specifications, modifications and generation of real time stream processor designs.
9691799
Targeted Data Prefetching
Given the increasing gap between processors and memory, prefetching data into cache becomes an important strategy for preventing the processor from being starved of data. The success of any data prefetching scheme depends on three factors: timeliness, accuracy and overhead. In most hardware prefetching mechanism, the focus has been on accuracy – ensuring that the predicted address do turn out to be demanded in a later part of the code. In this paper, we introduce a simple hardware prefetching mechanism that targets delinquent loads, i.e. loads that account for a large proportion of the load misses in an application. Our results show that our prefetch strategy can reduce up to 45% of stall cycles of benchmarks running on a simulated out-of-order superscalar processor with an overhead of 0.0005 prefetch per CPU cycle.
14960694
Comparative analysis of gene sets in the gene ontology space under the multiple hypothesis testing framework
The gene ontology (GO) resource can be used as a powerful tool to uncover the properties shared among, and specific to, a list of genes produced by high-throughput functional genomics studies, such as microarray studies. In the comparative analysis of several gene lists, researchers maybe interested in knowing which GO terms are enriched in one list of genes but relatively depleted in another. Statistical tests such as Fisher's exact test or Chi-square test can be performed to search for such GO terms. However, because multiple GO terms are tested simultaneously, individual p-values from individual tests do not serve as good indicators for picking GO terms. Furthermore, these multiple tests are highly correlated, usual multiple testing procedures that work under an independence assumption are not applicable. In this paper we introduce a procedure, based on false discovery rate (FDR), to treat this correlated multiple testing problem. This procedure calculates a moderately conserved estimator of q-value for every GO term. We identify the GO terms with q-values that satisfy a desired level as the significant GO terms. This procedure has been implemented into the GoSurfer software. GoSurfer is a windows based graphical data mining tool. It is freely available at http://www.gosurfer.org.
4523050
Determination of Local Statistical Significance of Patterns in Markov Sequences with Application to Promoter Element Identification
High-level eukaryotic genomes present a particular challenge to the computational identification of transcription factor binding sites (TFBSs) because of their long noncoding regions and large numbers of repeat elements. This is evidenced by the noisy results generated by most current methods. In this paper, we present a p-value-based scoring scheme using probability generating functions to evaluate the statistical significance of potential TFBSs. Furthermore, we introduce the local genomic context into the model so that candidate sites are evaluated based both on their similarities to known binding sites and on their contrasts against their respective local genomic contexts. We demonstrate that our approach is advantageous in the prediction of myogenin and MEF2 binding sites in the human genome. We also apply LMM to large-scale human binding site sequences in situ and found that, compared to current popular methods, LMM analysis can reduce false positive errors by more than 50% without compromising sensitivity. This improvement will be of importance to any subsequent algorithm that aims to detect regulatory modules based on known PSSMs.
2377420
Cooperative-diversity slotted ALOHA
We propose a cooperative-diversity technique for ad hoc networks based on the decode-and-forward relaying strategy. We develop a MAC protocol based on slotted ALOHA that allows neighbors of a transmitter to act as relays and forward a packet toward its final destination when the transmission to the intended recipient fails. The proposed technique provides additional robustness against fading, packet collisions and radio mobility. Network simulations confirm that under heavy traffic conditions, in which every radio always has packets to send, the proposed cooperative-diversity slotted-ALOHA protocol can provide a higher one-hop and end-to-end throughput than the standard slotted-ALOHA protocol can. A similar advantage in end-to-end delay can be obtained when the traffic is light. As a result, the proposed cooperative-diversity ALOHA protocol can be used to improve these measures of quality of service (QoS) in ad hoc wireless networks
14390918
Effective program debugging based on execution slices and inter-block data dependency
Localizing a fault in program debugging is a complex and time-consuming process. In this paper we present a novel approach using execution slices and inter-block data dependency to effectively identify the locations of program faults. An execution slice with respect to a given test case is the set of code executed by this test, and two blocks are data dependent if one block contains a definition that is used by another block or vice versa. Not only can our approach reduce the search domain for program debugging, but also prioritize suspicious locations in the reduced domain based on their likelihood of containing faults. More specifically, we use multiple execution slices to prioritize the likelihood of a piece of code containing a specific fault. In addition, the likelihood also depends on whether this piece of code is data dependent on other suspicious code. A debugging tool, DESiD, was developed to support our method. A case study that shows the effectiveness of our method in locating faults on an application developed for the European Space Agency is also reported.
17757852
Predicting fault detection effectiveness
Regression methods are used to model software fault detection effectiveness in terms of several product and testing process measures. The relative importance of these product/process measures for predicting fault detection effectiveness is assessed for a specific data set. A substantial family of models is considered, specifically, the family of quadratic response surface models with two way interaction. Model selection is based on "leave one out at a time" cross validation using the predicted residual sum of squares (PRESS) criterion. Prediction intervals for fault detection effectiveness are used to generate prediction intervals for the number of residual faults conditioned on the observed number of discovered faults. High levels of assurance about measures like fault detection effectiveness (residual faults) require more than just high (low) predicted values, they also require that the prediction intervals have high lower (low upper) bounds.