14211255
An Implementation Study of a Detection-Based Adaptive Block Replacement Scheme
In this paper, we propose a new adaptive buffer management scheme called DEAR (DEtection based Adaptive Replacement) that automatically detects the block reference patterns of applications and applies different replacement policies to different applications based on the detected reference pattern. The proposed DEAR scheme uses a periodic process. Detection is made by associating block attribute values such as backward distance and frequency gathered at the (i - 1)-th invocation with forward distances of blocks referenced between the (i - 1)-th and i-th invocations. We implemented the DEAR scheme in FreeBSD 2.2.5 and measured its performance using several real applications. The results show that compared with the LRU buffer management scheme, the proposed scheme reduces the number of disk I/Os by up to 51% (with an average of 23%) and the response time by up to 35% (with an average of 12%) in the case of single application executions. For multiple applications, the proposed scheme reduces the number of disk I/Os by up to 20% (with an average of 12%) and the over-all response time by up to 18% (with an average of 8%).
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.
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.
10945598
An efficient merging algorithm for recovery and garbage collection in incremental checkpointing
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.
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.
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.
12480483
AlignScope: A Visual Mining Tool for Gene Team Finding with Whole Genome Alignment
One of the main issues in comparative genomics is the study of chromosomal gene order in one or more related species. Recently identifying sets of orthologous genes in several genomes has become getting important, since a cluster of similar genes helps us to predict the function of unknown genes. For this purpose, the whole genome alignment is usually used to determine horizontal gene transfer, gene duplication, and gene loss between two related genomes. Also it is well known that a novel visualization tool of the whole genome alignment would be very useful for understanding genome organization and the evolutionary process. In this paper, we propose a method for identifying and visualizing the alignment of the whole genome alignment, especially for detecting gene clusters between two aligned genomes. Since the current rigorous algorithm for finding gene clusters has strong and artificial constraints, they are not useful for coping with “noisy” alignments. We developed the system AlignScope to provide a simplified structure for genome alignment at any level, and also to help us to find gene clusters. In this experiment, we have tested AlignScope on several microbial genomes. Alignment is a procedure that compares two or more sequences by searching for a series of individual characters or character patterns that are in the same order in the sequences. This procedure assists in designating the functions of unknown proteins, determining the relatedness of organisms, and identifying structurally and functionally important elements and other useful functions. 9;12 Many widely divergent organisms are descended from a common ancestor through a process called evolution. The inheritance patterns and diversities of these organisms have significant information regarding the nature of small and large-scale evolutionary events. The complexity and the size of the genome make it difficult to analyze. Because the large amount of biological noises is present when visualizing genomes, it is not enough to simply draw the aligned pairs of various genomes. Therefore an alignment visualization tool needs to provide a method for viewing the global structure of whole genome alignment in a simplified form at any level of detail. Figure-1 clearly illustrates this problem. In Figure-1, the resolution of the snapshot is 800 by 600 pixels, so one pixel corresponds about 6000 bases of a given genome sequence. Currently there are several systems for visualizing the alignment of genomes. The NCBI Map Viewer 14 provides graphical displays of biological features on NCBI’s as
6230675
ARCS: an aggregated related column scoring scheme for aligned sequences
MOTIVATION
Biologists frequently align multiple biological sequences to determine consensus sequences and/or search for predominant residues and conserved regions. Particularly, determining conserved regions in an alignment is one of the most important activities. Since protein sequences are often several-hundred residues or longer, it is difficult to distinguish biologically important conserved regions (motifs or domains) from others. The widely used tools, Logos, Al2co, Confind, and the entropy-based method, often fail to highlight such regions. Thus a computational tool that can highlight biologically important regions accurately will be highly desired.


RESULTS
This paper presents a new scoring scheme ARCS (Aggregated Related Column Score) for aligned biological sequences. ARCS method considers not only the traditional character similarity measure but also column correlation. In an extensive experimental evaluation using 533 PROSITE patterns, ARCS is able to highlight the motif regions with up to 77.7% accuracy corresponding to the top three peaks.


AVAILABILITY
The source code is available on http://bio.informatics.indiana.edu/projects/arcs and http://goldengate.case.edu/projects/arcs
14118126
An efficient animation of wrinkled cloth with approximate implicit integration
This paper presents an efficient method for creating the animation of flexible objects. The mass-spring model was used to represent flexible objects. The easiest approach to creating animation with the mass-spring model is the explicit Euler method, but the method has a serious weakness in that it suffers from an instability problem. The implicit integration method is a possible solution, but a critical flaw of the implicit method is that it involves a large linear system. This paper presents an approximate implicit method for the mass-spring model. The proposed technique updates with stability the state of n mass points in O(n) time when the number of total springs is O(n). In order to increase the efficiency of simulation or reduce the numerical errors of the proposed approximate implicit method, the number of mass points must be as small as possible. However, coarse discretization with a small number of mass points generates an unrealistic appearance for a cloth model. By introducing a wrinkled cubic spline curve, we propose a new technique that generates realistic details of the cloth model, even though a small number of mass points are used for simulation.