9363851
Design, Implementation, and Performance Evaluation of a Detection-Based Adaptive Block Replacement Scheme
A new buffer replacement scheme, called DEAR (detection-based adaptive replacement), is presented for effective caching of disk blocks in the operating system. The proposed DEAR scheme automatically detects block reference patterns of applications and applies different replacement policies to different applications depending on the detected reference pattern. The detection is made by a periodic process and is based on the relationship between block attribute values, such as backward distance and frequency gathered in a period, and the forward distance observed in the next period. This paper also describes an implementation and performance measurement of the DEAR scheme in FreeBSD. The results from performance measurements of several real applications show that, compared with the LRU scheme, the proposed scheme reduces the number of disk I/Os by up to 51 percent, and the response time by up to 35 percent in the case of single application executions. For multiple application executions, the results show that the proposed scheme reduces the number of disk I/Os by up to 20 percent and the overall response time by up to 18 percent.
5741653
Batch Verification with DSA-Type Digital Signatures for Ubiquitous Computing
We propose a new method for verifying bad signature in a batch instance of DSA-type digital signatures when there is one bad signature in the batch. The proposed method can verify and identify a bad signature using two modular exponentiations and $n + 3\sqrt{n}/2$modular multiplications where n is the number of signatures in the batch instance. Simulation results show our method reduces considerably the number of modular multiplications compared with the existing methods.
16402463
Towards application/file-level characterization of block references: a case for fine-grained buffer management
Two contributions are made in this paper. First, we show that system level characterization of file block references is inadequate for maximizing buffer cache performance. We show that a finer-grained characterization approach is needed. Though application level characterization methods have been proposed, this is the first attempt, to the best of our knowledge, to consider file level characterizations. We propose an Application/File-level Characterization (AFC) scheme where we detect on-line the reference characteristics at the application level and then at the file level, if necessary. The results of this characterization are used to employ appropriate replacement policies in the buffer cache to maximize performance. The second contribution is in proposing an efficient and fair buffer allocation scheme. Application or file level resource management is infeasible unless there exists an allocation scheme that is efficient and fair. We propose the ΔHIT allocation scheme that takes away a block from the application/file where the removal results in the smallest reduction in the number of expected buffer cache hits. Both the AFC and ΔHIT schemes are on-line schemes that detect and allocate as applications execute. Experiments using trace-driven simulations show that substantial performance improvements can be made. For single application executions the hit ratio increased an average of 13 percentage points compared to the LRU policy, with a maximum increase of 59 percentage points, while for multiple application executions, the increase is an average of 12 percentage points, with a maximum of 32 percentage points for the workloads considered.
20405083
GAME: A simple and efficient whole genome alignment method using maximal exact match filtering
In this paper, we present a simple and efficient whole genome alignment method using maximal exact match (MEM). The major problem with the use of MEM anchor is that the number of hits in non-homologous regions increases exponentially when shorter MEM anchors are used to detect more homologous regions. To deal with this problem, we have developed a fast and accurate anchor filtering scheme based on simple match extension with minimum percent identity and extension length criteria. Due to its simplicity and accuracy, all MEM anchors in a pair of genomes can be exhaustively tested and filtered. In addition, by incorporating the translation technique, the alignment quality and speed of our genome alignment algorithm have been further improved. As a result, our genome alignment algorithm, GAME (Genome Alignment by Match Extension), performs competitively over existing algorithms and can align large whole genomes, e.g., A. thaliana, without the requirement of typical large memory and parallel processors. This is shown using an experiment which compares the performance of BLAST, BLASTZ, PatternHunter, MUMmer and our algorithm in aligning all 45 pairs of 10 microbial genomes. The scalability of our algorithm is shown in another experiment where all pairs of five chromosomes in A. thaliana were compared.
926635
Escape analysis for Java
This paper presents a simple and efficient data flow algorithm for escape analysis of objects in Java programs to determine (i) if an object can be allocated on the stack; (ii) if an object is accessed only by a single thread during its lifetime, so that synchronization operations on that object can be removed. We introduce a new program abstraction for escape analysis, the connection graph, that is used to establish reachability relationships between objects and object references. We show that the connection graph can be summarized for each method such that the same summary information may be used effectively in different calling contexts. We present an interprocedural algorithm that uses the above property to efficiently compute the connection graph and identify the non-escaping objects for methods and threads. The experimental results, from a prototype implementation of our framework in the IBM High Performance Compiler for Java, are very promising. The percentage of objects that may be allocated on the stack exceeds 70% of all dynamically created objects in three out of the ten benchmarks (with a median of 19%), 11% to 92% of all lock operations are eliminated in those ten programs (with a median of 51%), and the overall execution time reduction ranges from 2% to 23% (with a median of 7%) on a 333 MHz PowerPC workstation with 128 MB memory.
16784503
PhyloDraw: a phylogenetic tree drawing system
UNLABELLED
PhyloDraw is a unified viewing tool for phylogenetic trees. PhyloDraw supports various kinds of multi-alignment formats (Dialign2, Clustal-W, Phylip format, NEXUS, MEGA, and pairwise distance matrix) and visualizes various kinds of tree diagrams, e.g. rectangular cladogram, slanted cladogram, phylogram, unrooted tree, and radial tree. By using several control parameters, users can easily and interactively manipulate the shape of phylogenetic trees. This program can export the final tree layout to BMP (bitmap image format) and PostScript.


AVAILABILITY
http://pearl.cs.pusan.ac.kr/phylodraw/


CONTACT
jhchoi@pearl.cs.pusan.ac.kr
5394476
Cross-Layer Analysis of Rate Adaptation, DCF and TCP in Multi-Rate WLANs
Wireless Internet access is facilitated by IEEE 802.11 WLANs that, in addition to realizing a specific form of CSMA/CA-distributed coordination function (DCF)- implement a range of performance enhancement features such as multi-rate adaptation that induce cross-layer protocol coupling. Recent works in empirical WLAN performance evaluation have shown that cross-layer interactions can be subtle, sometimes leading to unexpected outcomes. Two such instances are: significant throughput degradation (a bell-shaped throughput curve) resulting from automatic rate fallback (ARF) having difficulty distinguishing collision from channel noise, and scalable TCP performance over DCF that is able to curtail effective multiple access contention in the presence of many contending stations. The latter also mitigates the negative performance effect of ARF. In this paper, we present station-centric Markov chain models of WLAN cross-layer performance aimed at capturing complex interactions between ARF, DCF, and TCP. Our performance analyses may be viewed as multi-protocol extensions of Bianchi's IEEE 802.11 model that, despite significantly increased complexity, lead to tractable and accurate performance predictions due to modular coupling. Our results complement empirical and simulation-based findings, demonstrating the versatility and efficacy of station-centric Markov chain analysis for capturing cross-layer WLAN dynamics.
351981
Real-time Animation Technique for Flexible and Thin Objects
In this paper, we propose an e cient technique for the animation of exible thin objects. Massspring model was employed to represent the exible objects. Many techniques have used the mass-spring model to generate plausible animation of soft objects. The easiest approach to animation with mass-spring model is explicit Euler method, but the explicit Euler method has serious disadvantage that it su ers from `instability problem'. The implicit integration method is a possible solution to overcome the instability problem. However, the most critical aw of the implicit method is that it involves a large linear system. This paper presents a fast animation technique for mass-spring model with approximated implicit method. The proposed technique stably updates the state of n mass-points in O(n) time when the number of total springs are O(n). We also consider the interaction of the exible object and air in order to generate plausible results.