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1.
The influences of the operating system and system-specific effects on application performance are increasingly important considerations
in high performance computing. OS kernel measurement is key to understanding the performance influences and the interrelationship
of system and user-level performance factors. The KTAU (Kernel TAU) methodology and Linux-based framework provides parallel
kernel performance measurement from both a kernel-wide and process-centric perspective. The first characterizes overall aggregate kernel performance for the entire system. The second characterizes
kernel performance when it runs in the context of a particular process. KTAU extends the TAU performance system with kernel-level
monitoring, while leveraging TAU’s measurement and analysis capabilities. We explain the rational and motivations behind our
approach, describe the KTAU design and implementation, and show working examples on multiple platforms demonstrating the versatility
of KTAU in integrated system/application monitoring.
相似文献
Alan MorrisEmail: |
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A key point in the analysis of dynamical models of biological systems is to handle systems of relatively high dimensions.
In the present paper we propose a method to hierarchically organize a certain type of piecewise affine (PWA) differential
systems. This specific class of systems has been extensively studied for the past few years, as it provides a good framework
to model gene regulatory networks. The method, shown on several examples, allows a qualitative analysis of the asymptotic
behavior of a PWA system, decomposing it into several smaller subsystems. This technique, based on the well-known strongly
connected components decomposition, is not new. However, its adaptation to the non-smooth PWA differential equations turns
out to be quite relevant because of the strong discrete structure underlying these equations. Its biological relevance is
shown on a 7-dimensional PWA system modeling the gene network responsible for the carbon starvation response in Escherichia coli.
相似文献
Laurent Tournier (Corresponding author)Email: |
Jean-Luc GouzéEmail: |
6.
Large-scale scientific computing applications frequently make use of closely-coupled distributed parallel components. The
performance of such applications is therefore dependent on the component parts and their interaction at run-time. This paper
describes a methodology for predictive performance modelling and evaluation of parallel applications composed of multiple
interacting components. In this paper, the fundamental steps and required operations involved in the modelling and evaluation
process are identified—including component decomposition, component model combination, M×N communication modelling, dataflow analysis and overall performance evaluation. A case study is presented to illustrate the
modelling process and the methodology is verified through experimental analysis.
相似文献
Stephen A. JarvisEmail: |
7.
We develop a formal framework for the optimal allocation of limited resources that includes and clarifies the interplay between
individual optimization and the resulting effects at the population level. As an example, in regard to the evolution of sexual
recombination, the paradox of the twofold cost of sex is avoided by distinguishing between the evolution of recombination
and the subsequent emergence and stability of different mating types as a result of individual optimization within a population
that benefits from recombination.
相似文献
John PepperEmail: |
8.
Sub-Antarctic Marion Island has had a permanent research station for 50 years and the islands Wandering Albatrosses have been intensively studied for 20 years. The reactions of breeding birds to approaches by a human on foot were recorded. Three response variables were calculated: intensity of vocal reaction (IVR), intensity of non-vocal reaction (INR) and overall response index (ORI). At 5 m from the nest, twice as many birds stood and/or vocalised as at 15 m. Nearest neighbour distance, age and gender did not explain individual variability of responses. Study colony birds had higher IVR scores than non-study colony birds; birds at colonies closest to the station had the highest ORI scores. A better breeding record was associated with lower IVR and ORI scores, but a causative relationship remains to be demonstrated. A minimum viewing distance of 25 m is recommended for breeding Wandering Albatrosses.
相似文献
Marienne S. de VilliersEmail: Fax: +27-21-6503434 |
John CooperEmail: |
Peter G. RyanEmail: |
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We present two computational models (i) long-range horizontal connections and the nonlinear effect in V1 and (ii) the filling-in
process at the blind spot. Both models are obtained deductively from standard regularization theory to show that physiological
evidence of V1 and V2 neural properties is essential for efficient image processing. We stress that the engineering approach
should be imported to understand visual systems computationally, even though this approach usually ignores physiological evidence
and the target is neither neurons nor the brain.
相似文献
Shunji SatohEmail: |
11.
One of the distinct characteristics of computing platforms shared by multiple users such as a cluster and a computational
grid is heterogeneity on each computer and/or among computers. Temporal heterogeneity refers to variation, along the time
dimension, of computing power available for a task on a computer, and spatial heterogeneity represents the variation among
computers. In minimizing the average parallel execution time of a target task on a spatially heterogeneous computing system, it is not optimal to distribute the target task linearly proportional
to the average computing powers available on computers. In this paper, effects of the temporal and spatial heterogeneity on
performance of a target task have been analyzed in terms of the mean and standard deviation of parallel execution time. Based
on the analysis results, an approach to load balancing for minimizing the average parallel execution time of a target task
is described. The proposed approach whose validity has been verified through simulation considers temporal and spatial heterogeneities
in addition to the average computing power on each computer.
相似文献
Soo-Young Lee (Corresponding author)Email: |
12.
The performance skeleton of an application is a short running program whose performance in any scenario reflects the performance
of the application it represents. Specifically, the execution time of the performance skeleton is a small fixed fraction of
the execution time of the corresponding application in any execution environment. Such a skeleton can be employed to quickly
estimate the performance of a large application under existing network and node sharing. This paper presents a framework for
automatic construction of performance skeletons of a specified execution time and evaluates their use in performance prediction
with CPU and network sharing. The approach is based on capturing the execution behavior of an application and automatically
generating a synthetic skeleton program that reflects that execution behavior. The paper demonstrates that performance skeletons
running for a few seconds can predict the application execution time fairly accurately. Relationship of skeleton execution
time, application characteristics, and nature of resource sharing, to accuracy of skeleton based performance prediction, is
analyzed in detail. The goal of this research is accurate performance estimation in heterogeneous and shared computational
grids.
相似文献
Jaspal Subhlok (Corresponding author)Email: |
13.
Machado RR Lima Filho ES Jardim DF Ferreira MA de Faria CG Duarte RS Lesche B 《European biophysics journal : EBJ》2008,38(1):111-119
An interferometer that measures the refractive index changes due to bacterial metabolism is described. The apparatus permits
simultaneous and real time measurement of bacterial growth in several samples of slowly growing mycobacteria. The error sources
are discussed and the sensitivity of the apparatus is tested. For the species Mycobacterium bovis BCG and M. smegmatis, a relation between refractive index change and bacterial concentration is determined experimentally and the time constant
of bacterial growth is measured.
相似文献
B. LescheEmail: |
14.
The recent contribution by Jarmila Kukalová-Peck on Hennigian phylogenetics and hexapod limb evolution is critically evaluated.
相似文献
Michael S. Engel (Corresponding author)Email: |
15.
Rapid prototyping of distributed systems can be achieved by integrating commercial off-the-shelf (COTS) components. With components
as the building blocks, it is important to predict the performance of the system based on the performance of individual components.
In this paper, performance prediction of a system consisting of a small number of components is investigated under different
inter-component communication patterns, and the number of threads provided by components. Based on the experimental results,
it can be inferred that the proposed composition rules provide a reasonably accurate prediction of the performance of a system
made out of these components.
相似文献
Barrett R. BryantEmail: |
16.
The interconnection network is one of the key architectural components in any parallel computer. The distribution of the traffic
injected into the network is among the factors that greatly influences network performance. The uniform traffic pattern has
been adopted in many existing network performance evaluation studies due to the tractability of the resulting analytical modelling
approach. However, many real applications exhibit non-uniform traffic patterns such as hot-spot traffic. K-ary n-cubes have been the mostly widely used in the implementation of practical parallel systems. Extensive research studies have
been conducted on the performance modelling and evaluation of these networks. Nonetheless, most of these studies have been
confined to uniform traffic distributions and have been based on software simulation. The present paper proposes a new stochastic
model to predict message latency in k-ary
n-cubes with deterministic routing in the presence of hot-spot traffic. The model has been validated through simulation experiments
and has shown a close agreement with simulation results.
相似文献
Geyong MinEmail: |
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Douglas Medin Norbert Ross Douglas Cox Scott Atran 《Human ecology: an interdisciplinary journal》2007,35(3):315-329
There is a continuing controversy over Native American fishing and hunting rights. We show that Native American (Menominee)
and European American fish experts have a common knowledge base and share values and attitudes associated with fishing practices
(though organized around different ethical principles). Nonetheless, perceived group differences are dramatic (especially European American perceptions of Native Americans). Cultural differences in models
of nature and associated inference processes appear to mediate these stereotypes and may hold the key to reducing intergroup
conflict over resources.
相似文献
Douglas MedinEmail: |
19.
Methanogens growing on C-1 substrates synthesize 2-carbon acetyl groups in the form of acetyl-CoA for carbon assimilation
using the multienzyme complex acetyl-CoA decarbonylase/synthase (ACDS) which contains five different subunits encoded within
an operon. In species growing on acetate ACDS also functions to cleave the acetate C-C bond for energy production by methanogenesis.
A number of species of Methanosarcina that are capable of growth on either C-1 compounds or acetate contain two separate ACDS operons, and questions have been
raised about whether or not these operons play separate roles in acetate synthesis and cleavage. Methanosarcina thermophila genomic DNA was analyzed for the presence of two ACDS operons by PCR amplifications with different primer pairs, restriction
enzyme analyses, DNA sequencing and Southern blot analyses. A single ACDS operon was identified and characterized, with no
evidence for more than one. MALDI mass spectrometric analyses were carried out on ACDS preparations from methanol- and acetate-grown
cells. Peptide fragmentation patterns showed that the same ACDS subunits were present regardless of growth conditions. The
evidence indicates that a single form of ACDS is used both for acetate cleavage during growth on acetate and for acetate synthesis
during growth on C-1 substrates.
Electronic Supplementary Material Supplementary material is available for this article at
相似文献
David A. Grahame (Corresponding author)Email: |
Edward DeMoll (Corresponding author)Email: |
20.
Peter Godfrey-Smith 《Biology & philosophy》2007,22(3):429-437
Jablonka and Lamb's claim that evolutionary biology is undergoing a ‘revolution’ is queried. But the very concept of revolutionary
change has uncertain application to a field organized in the manner of contemporary biology. The explanatory primacy of sequence
properties is also discussed.
相似文献
Peter Godfrey-SmithEmail: |