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1.
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: |
2.
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: |
3.
Viraj Bhat Manish Parashar Hua Liu Nagarajan Kandasamy Mohit Khandekar Scott Klasky Sherif Abdelwahed 《Cluster computing》2007,10(4):365-383
Efficient and robust data streaming services are a critical requirement of emerging Grid applications, which are based on
seamless interactions and coupling between geographically distributed application components. Furthermore the dynamism of
Grid environments and applications requires that these services be able to continually manage and optimize their operation
based on system state and application requirements. This paper presents a design and implementation of such a self-managing
data-streaming service based on online control strategies. A Grid-based fusion workflow scenario is used to evaluate the service
and demonstrate its feasibility and performance.
相似文献
Sherif AbdelwahedEmail: |
4.
The integration of multiple predictors promises higher prediction accuracy than the accuracy that can be obtained with a single
predictor. The challenge is how to select the best predictor at any given moment. Traditionally, multiple predictors are run
in parallel and the one that generates the best result is selected for prediction. In this paper, we propose a novel approach
for predictor integration based on the learning of historical predictions. Compared with the traditional approach, it does
not require running all the predictors simultaneously. Instead, it uses classification algorithms such as k-Nearest Neighbor
(k-NN) and Bayesian classification and dimension reduction technique such as Principal Component Analysis (PCA) to forecast the best predictor for the workload under study based on the learning of historical predictions. Then only the
forecasted best predictor is run for prediction. Our experimental results show that it achieved 20.18% higher best predictor
forecasting accuracy than the cumulative MSE based predictor selection approach used in the popular Network Weather Service
system. In addition, it outperformed the observed most accurate single predictor in the pool for 44.23% of the performance
traces.
相似文献
Renato J. FigueiredoEmail: |
5.
6.
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: |
7.
Pete Beckman Kamil Iskra Kazutomo Yoshii Susan Coghlan Aroon Nataraj 《Cluster computing》2008,11(1):3-16
We investigate operating system noise, which we identify as one of the main reasons for a lack of synchronicity in parallel
applications. Using a microbenchmark, we measure the noise on several contemporary platforms and find that, even with a general-purpose
operating system, noise can be limited if certain precautions are taken. We then inject artificially generated noise into
a massively parallel system and measure its influence on the performance of collective operations. Our experiments indicate
that on extreme-scale platforms, the performance is correlated with the largest interruption to the application, even if the
probability of such an interruption on a single process is extremely small. We demonstrate that synchronizing the noise can
significantly reduce its negative influence.
相似文献
Aroon NatarajEmail: |
8.
The competitiveness of online algorithms is measured based on the correctness of the results produced and processing time
efficiency. Traditionally evolutionary algorithms are not favored in online paradigms because of the large number of iterations
involved in the algorithm which translates directly into processing time overhead. In this paper we describe MARS (Management
Architecture for Resource Services) online scheduling algorithm which uses Simulated Annealing and concepts from Tabu Search
to drastically decrease the processing time of the algorithm. The paper outlines the concepts behind MARS, the components
involved and scheduling methodology used. In addition we also identify the time consuming bottlenecks in the performance of
the system and how evolutionary algorithms help us soar past them.
相似文献
Hesham El-RewiniEmail: |
9.
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: |
10.
The capacity needs of online services are mainly determined by the volume of user loads. For large-scale distributed systems
running such services, it is quite difficult to match the capacities of various system components. In this paper, a novel
and systematic approach is proposed to profile services for resource optimization and capacity planning. We collect resource
consumption related measurements from various components across distributed systems and further search for constant relationships
between these measurements. If such relationships always hold under various workloads along time, we consider them as invariants
of the underlying system. After extracting many invariants from the system, given any volume of user loads, we can follow
these invariant relationships sequentially to estimate the capacity needs of individual components. By comparing the current
resource configurations against the estimated capacity needs, we can discover the weakest points that may deteriorate system
performance. Operators can consult such analytical results to optimize resource assignments and remove potential performance
bottlenecks. In this paper, we propose several algorithms to support capacity analysis and guide operator’s capacity planning
tasks. Our algorithms are evaluated with real systems and experimental results are also included to demonstrate the effectiveness
of our approach.
相似文献
Kenji YoshihiraEmail: |
11.
12.
Samer Al-Kiswany Abdullah Gharaibeh Elizeu Santos-Neto Matei Ripeanu 《Cluster computing》2009,12(2):123-140
Today Graphics Processing Units (GPUs) are a largely underexploited resource on existing desktops and a possible cost-effective
enhancement to high-performance systems. To date, most applications that exploit GPUs are specialized scientific applications.
Little attention has been paid to harnessing these highly-parallel devices to support more generic functionality at the operating
system or middleware level. This study starts from the hypothesis that generic middleware-level techniques that improve distributed
system reliability or performance (such as content addressing, erasure coding, or data similarity detection) can be significantly
accelerated using GPU support.
We take a first step towards validating this hypothesis and we design StoreGPU, a library that accelerates a number of hashing-based
middleware primitives popular in distributed storage system implementations. Our evaluation shows that StoreGPU enables up
twenty five fold performance gains on synthetic benchmarks as well as on a high-level application: the online similarity detection
between large data files.
相似文献
Matei RipeanuEmail: |
13.
14.
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: |
15.
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: |
16.
We present a technique that controls the peak power consumption of a high-density server by implementing a feedback controller
that uses precise, system-level power measurement to periodically select the highest performance state while keeping the system
within a fixed power constraint. A control theoretic methodology is applied to systematically design this control loop with
analytic assurances of system stability and controller performance, despite unpredictable workloads and running environments.
In a real server we are able to control power over a 1 second period to within 1 W and over an 8 second period to within 0.1 W.
Conventional servers respond to power supply constraint situations by using simple open-loop policies to set a safe performance
level in order to limit peak power consumption. We show that closed-loop control can provide higher performance under these
conditions and implement this technique on an IBM BladeCenter HS20 server. Experimental results demonstrate that closed-loop
control provides up to 82% higher application performance compared to open-loop control and up to 17% higher performance compared
to a widely used ad-hoc technique.
相似文献
Malcolm WareEmail: |
17.
Studies on the effects of a variety of exogenous and anthropogenic environmental factors, including endocrine disruptors,
heavy metals, UV light, high temperature, and others, on marine organisms have been presented at the 2nd Bilateral Seminar
Italy–Japan held in November 2006. Reports were discussed in order to reveal the current situation of marine ecosystems, aiming
at evaluation and prediction of environmental risks.
相似文献
V. MatrangaEmail: |
18.
Leslie P. Francis Margaret P. Battin Jay Jacobson Charles Smith 《Journal of bioethical inquiry》2009,6(2):187-195
Syndromic surveillance uses new ways of gathering data to identify possible disease outbreaks. Because syndromic surveillance
can be implemented to detect patterns before diseases are even identified, it poses novel problems for informed consent, patient
privacy and confidentiality, and risks of stigmatization. This paper analyzes these ethical issues from the viewpoint of the
patient as victim and vector. It concludes by pointing out that the new International Health Regulations fail to take full
account of the ethical challenges raised by syndromic surveillance.
相似文献
Leslie P. FrancisEmail: |
19.
20.
Roger Sansom 《Biology & philosophy》2008,23(4):475-491
I show that gene regulation networks are qualitatively consistent and therefore sufficiently similar to linearly seperable
connectionist networks to warrant that the connectionist framework be applied to gene regulation. On this view, natural selection
designs gene regulation networks to overcome the difficulty of development. I offer some general lessons about their evolvability
that can be learned by examining the generic features of connectionist networks.
相似文献
Roger SansomEmail: |