High Performance Network of PC Cluster Maestro

This paper presents a design, an architecture, and performance evaluation of high-performance network of PC cluster, called Maestro. Most networks of recent clusters have been organized based on WAN or LAN technology, due to their market availability. However, communication protocols and functions of such conventional networks are not optimal for parallel computing, which requires low latency and high bandwidth communication. In this paper, we propose two optimizations for high-performance communication: (1) transferring in burst as many packets as the receiving buffer accepts at once, and (2) having each hardware component pass one data unit to another in a pipelined manner. We have developed a network interface and a switch, which are composed of dedicated hardware modules to realize these optimizations. An implementatin of the message passing library developed on Maestro cluster is also described. Performance evaluation shows that the proposed optimizations can extract the potential performance of the physical layer efficiently and improve the performance in communication.     

An Effective Logical Cache for a Clustered LRC-Based DSM System

As local-area workstation networks are widely available, the idea of offering a software distributed shared memory (SDSM) system across interconnects of clusters is quite an attractive alternative for compute-intensive applications. However, the higher cost of sending a message over an inter-cluster link compared to an intra-cluster one can limit applications' performance on a multi-cluster SDSM system. In this paper, we present the extensions that we have added to the SDSM TreadMarks, which provides the lazy release consistency (LRC) memory model, in order to adapt it to a loosely-coupled cluster-based platform. We have implemented a logical per-cluster cache that exploits cluster locality. By accessing the cache of its cluster, a processor can share data previously requested by a second processor of its cluster, thereby, minimizing, the cost of inter-cluster communication.     

The Rutgers Computational Grid: A Distributed Linux PC Cluster

The Rutgers Computational Grid (RCG) project is aimed at providing high throughput performance to Rutgers university faculty and students. The RCG employs dual processor PCs, with Pentium II and III processors, as computational nodes, running the Linux RedHat operating system. The Load Sharing Facility (LSF) scheduling system from Platform Computing is used for job control and monitoring. The nodes are grouped into subclusters physically located in several departments and controlled by a single master node through LSF. The hardware and software used in RCG are described. Utilization and performance issues, including parallel performance, are discussed based on the experience of the first two years of RCG operation.     

Performance Analysis of a Myrinet-Based Cluster

In recent years, there has been a growing interest in the cluster system as an accepted form of supercomputing, due to its high performance at an affordable cost. This paper attempts to elaborate performance analysis of Myrinet-based cluster. The communication performance and effect of background load on parallel applications were analyzed. For point-to-point communication, it was found that an extension to the Hockney's model was required to estimate the performance. The proposed model suggested that there should be two ranges to be used for the performance metrics to cope with the cache effect. Moreover, based on the extension of the point-to-point communication model, the Xu and Hwang's model for collective communication performance was also extended. Results showed that our models can make better estimation of the communication performance than the previous models. Finally, the interference of other user processes to the cluster system is evaluated by using synthetic background load generation programs.     

An Equivalent Tree Network Methodology for Efficient Utilization of Front-Ends in Linear Network

In this paper, divisible load scheduling in a linear network of processors is presented. The cases of processing load originating at the boundary and also at the interior of the network are considered. An equivalent tree network for the given linear network is derived. Using this equivalent tree network, we prove all the results obtained in the earlier studies. The equivalent tree network methodology presented in this paper, is more general than the earlier results, because in this approach, we can solve the scheduling problem even in an hetrogeneous linear network. The earlier studies considered only homogeneous linear network.     

An Evaluation of Some Beowulf Clusters

We report the results of an evaluation project on three Beowulf type clusters. The purpose of this study was to assess both the performance of the clusters and the availability and quality of the software for cluster management and management of the available resources. This last goal could hardly be achieved because at the time this project was undertaken much of the management software was either very immature or not yet available. However, it was possible to assess the cluster performance both from the point of view of single program execution as well as with respect to throughput by loading the systems according to a predefined schedule via the available batch systems. To this end a set of application programs, ranging from astronomy to quantum chemistry, together with a synthetic benchmark were employed. From the results we wanted to derive answers about the viability of using cluster systems routinely in a multi-user environment with comparable maintenance cost and effort to that of an integrated parallel machine.     

Low Latency High Bandwidth Message Transfer Mechanisms for a Network Interface Plugged into a Memory Slot

The communication architecture of the DIMMnet-1 network interface based on MEMOnet is described. MEMOnet is a class of a network interface plugged into a memory slot. This paper proposes three message transfer mechanisms named atomic on-the-fly sending (AOTF), block on-the-fly sending (BOTF) and OTF receiving with selective address translation. The DIMMnet-1 prototype will have an ASIC named Martini, two banks of PC133 based SO-DIMM slots and an 8 Gbps full duplex optical link. The software overhead incurred to generate a message is only 1 CPU cycle and the estimated hardware delay is 105 ns using AOTF. The estimated hardware delay for receiving to on chip memory using OTF receiver is 90 ns. The estimated achievable sending bandwidth of DIMMnet-1 using BOTF is 984 MB/s which was observed in our experiments. This bandwidth is 7.4 times higher than the maximum bandwidth of PCI. This high performance is available even when simultaneous sending and receiving are executed on a cheap personal computer with DIMM slots. This paper also discribes the effects of BOTF for a PCI-based NIC.     

网络药理学与药物发现研究进展

将生物学网络与药物作用网络整合,分析药物在网络中与节点或网络模块的关系,由寻找单一靶点转向综合网络分析,就形成了网络药理学.通过系统生物学的研究方法进行网络药理学分析,能够在分子水平上更好的理解细胞以及器官的行为,加速药物靶点的确认以及发现新的生物标志物.这使得我们有可能系统地预测和解释药物的作用,优化药物设计,发现影响药物作用有效性和安全性的因素,从而设计多靶点药物或药物组合.本文综述了网络药理学的新近研究进展,介绍在生物学网络的各个层面上网络药理学的研究和应用,展望网络药理未来的发展方向,对药物发现具有重要意义.     

Configurable Network Processing for Mobile Agents on the Internet

This paper presents a framework for building and deploying protocols for migrating mobile agents over the Internet. The framework enables network protocols for agent migration to be naturally implemented within mobile agents and then dynamically deployed at remote hosts by migrating the agents that perform the protocols. It is built on a hierarchical mobile agent system, called MobileSpaces, and several protocols for migrating agents for managing cluster computing systems have been designed and implemented based on the framework. This paper describes the framework and its prototype implementation, which uses Java as both the implementation language and the protocol development language.     

Dynamic Neural Network Models of the Premotoneuronal Circuitry Controlling Wrist Movements in Primates

Dynamic recurrent neural networks were derived to simulate neuronal populations generating bidirectional wrist movements in the monkey. The models incorporate anatomical connections of cortical and rubral neurons, muscle afferents, segmental interneurons and motoneurons; they also incorporate the response profiles of four populations of neurons observed in behaving monkeys. The networks were derived by gradient descent algorithms to generate the eight characteristic patterns of motor unit activations observed during alternating flexion-extension wrist movements. The resulting model generated the appropriate input-output transforms and developed connection strengths resembling those in physiological pathways. We found that this network could be further trained to simulate additional tasks, such as experimentally observed reflex responses to limb perturbations that stretched or shortened the active muscles, and scaling of response amplitudes in proportion to inputs. In the final comprehensive network, motor units are driven by the combined activity of cortical, rubral, spinal and afferent units during step tracking and perturbations.The model displayed many emergent properties corresponding to physiological characteristics. The resulting neural network provides a working model of premotoneuronal circuitry and elucidates the neural mechanisms controlling motoneuron activity. It also predicts several features to be experimentally tested, for example the consequences of eliminating inhibitory connections in cortex and red nucleus. It also reveals that co-contraction can be achieved by simultaneous activation of the flexor and extensor circuits without invoking features specific to co-contraction.     

An Evaluation Model of Supply Chain Performances Using 5DBSC and LMBP Neural Network Algorithm

A high efficient Supply Chain (SC) would bring great benefits to an enterprise such as integrated resources, reduced logistics costs, improved logistics efficiency and high quality of overall level of services. So it is important to research various methods, performance indicator systems and technology for evaluating, monitoring, predicting and optimizing the performance of a SC. In this paper, the existing performance indicator systems and methods are discussed and evaluated. Various nature-inspired algorithms are reviewed and their applications for SC Performance Evaluation (PE) are discussed. Then, a model is proposed and developed using 5 Dimensional Balanced Scorecard (5DBSC) and LMBP (Levenberg-Marquardt Back Propagation) neural network for SC PE. A program is written using Matlab tool box to implement the model based on the practical values of the 14 indicators of 5DBSC of a given previous period. This model can be used to evaluate, predict and optimize the performance of a SC. The analysis results of a case study of a company show that the proposed model is valid, reliable and effective. The convergence speed is faster than that in the previous work.     

Growth Medium and Phosphorus Supply Affect Cluster Root Formation and Citrate Exudation by Lupinus albus Grown in a Sand/Solution Split-Root System

We examined cluster root formation and root exudation by white lupin (Lupinus albus L. cv. Kiev Mutant) in response to growth medium and phosphorus supply in a sand/solution split-root system. The split-root system consisted of a nutrient solution compartment and a siliceous sand compartment. Phosphorus was applied at 1 (low-P plants) or 50 (high-P plants) μM as KH₂PO₄ to the solution compartment and at 10, 50 or 250 mg P kg⁻¹ as hydroxyapatite (Ca-P) to the sand compartment. In contrast to the high-P plants, P concentration and P uptake in the low-P plants increased with increasing P supply to the sand compartment. The NaHCO₃-extractable P was lower in the rhizosphere of the low-P plants than the high-P ones. The proton extrusion rate by the solution-grown roots of the low-P plants was higher than that of the high-P plants at the early growth stage. For the low-P plants, the proportion of dry root biomass allocated to cluster roots was higher in the solution compartment than that in the sand compartment. The citrate exudation increased in the sand compartment and decreased in the solution compartment with time, showing a lack of synchronization in citrate exudation by two root halves grown in different media. The cluster root proportion and citrate exudation in both compartments decreased with increasing shoot P concentration. An additional experiment with no P added to either root compartment showed that the proportion of cluster roots was about 9% lower in the sand than solution compartments. The results suggest that cluster root formation and citrate exudation can be significantly affected by the root growth medium in addition to being regulated by shoot P status. More P can be exploited from sparingly available Ca-P by the low-P plants than the high-P ones due to greater citrate exudation under P deficiency.     

Population Dynamics Modelling in an Hierarchical Arborescent River Network: An Attempt with Salmo trutta

The balance between births and deaths in an age-structured population is strongly influenced by the spatial distribution of sub-populations. Our aim was to describe the demographic process of a fish population in an hierarchical dendritic river network, by taking into account the possible movements of individuals. We tried also to quantify the effect of river network changes (damming or channelling) on the global fish population dynamics. The Salmo trutta life pattern was taken as an example for.We proposed a model which includes the demographic and the migration processes, considering migration fast compared to demography. The population was divided into three age-classes and subdivided into fifteen spatial patches, thus having 45 state variables. Both processes were described by means of constant transfer coefficients, so we were dealing with a linear system of difference equations. The discrete case of the variable aggregation method allowed the study of the system through the dominant elements of a much simpler linear system with only three global variables: the total number of individuals in each age-class.From biological hypothesis on demographic and migratory parameters, we showed that the global population dynamics of fishes is well characterized in the reference river network, and that dams could have stronger effects on the global dynamics than channelling.     

Oral cavity gate of an entry into the Communication Network

For ages naso-oro-pharyngreal cavity was considered as gate of entry toliving organism for air and food. In recent years, however, the thoughtshave changed considerably. Several lines of evidence indicate that the oralcavity with adjacent cavities plays a pivotal role for the recognition ofsignals coming from the surrounding world. These signals in form of food,germs, poisonous substances are initially analyzed in oral cavity andmessages are distributed by a variety of communication pathways intopertinent parts of the body. All these diverse functions are performed byanatomical structures present in the naso-oro-pharyngreal cavity. Thefollowing article describes some of the functions discovered recently.     

Construction of a Bacterial Artificial Chromosome Library and Characterization of hrp/hrc Gene Cluster of Pseudomonas Syringae Pathovar tagetis LMG5090

Pseudomonas syringae pv. tagetis causes apical chlorosis of several plant species in the Asteraceae, including marigold. As a means to facilitate the isolation of pathogenicity genes and to characterize the genome of this bacterium, we have constructed a bacterial artificial chromosome library of P. syringae pv. tagetis strain LMG5090. The library consists of 1,536 clones with insert size ranging from 30 to 160 kb and an average size of 86 kb. Based upon colony hybridization, the BAC clone 420E23 containing the hrp/hrc gene cluster encoding the type III secretion system was identified from this library and subsequently shotgun sequenced. The hrp/hrc gene cluster of P. syringae pv. tagetis has a 23 kb sequence which contains 27 open reading frames. Comparative analysis of the hrp/hrc gene cluster of P. syringae pv. tagetis LMG5090, P. syringae pv. tomato DC3000, P. syringae pv. syringae B728a, and P. syringae pv. phaseolicola 1448A revealed that the entire hrp/hrc gene cluster of P. syringae pv. tagetis is conserved and identically arranged in all four pathovars     

改进GA-SVM在冠状动脉疾病诊断中的应用

改进的遗传算法（GA）自动优化支持向量机（SVM）参数,同步决策最优特征子集。新颖的分组多基因交叉技术保留了基因小组中的信息,而且允许后代继承更多的来自染色体的遗传信息。该算法促进可行解集中的高质量染色体信息交换,提高了解空间的搜索能力。实验结果说明：改进GA-SVM不仅可决策出与疾病相关的重要特征变量、优化SVM参数,而且可提升分类性能。与前馈BP神经网络及自适应模糊推理系统两种学习算法的比较表明,改进GA-SVM具有更好地表现。