Improving peer connectivity in wide-area overlays of virtual workstations

Self-configuring virtual networks rely on structured P2P routing to provide seamless connectivity among nodes through overlay routing of virtual IP packets, support decentralized hole-punching to establish bi-directional communication links among nodes behind network address translators, and dynamic configuration of virtual IP addresses. Our experiences with deployments of virtual networks in support of wide-area overlays of virtual workstations (WOWs) reveal that connectivity constraints imposed by symmetric NATs and by Internet route outages often hinder P2P overlay structure maintenance and routability, subsequently limiting the ability of WOWs to deliver high-throughput computing through aggregation of resources in different domains. In this paper, we describe and evaluate two novel approaches which are generally applicable and fully decentralized, and show that they improve routability of structured P2P networks in such connectivity constrained environments: (1) a fault-tolerant routing algorithm based on simulated annealing from optimization theory, and (2) tunneling of connections between adjacent nodes (in the P2P identifier space) over common neighbors when direct communication is not possible. Simulation-based analyses show that (1) when pairs of nodes only have 70% chance of being able to communicate directly, the described approaches improve all-to-all routability of the network from 90% to 99%, and (2) even when only 70% of the nodes are behind NATs that include symmetric NATs, these techniques improve the all-to-all connectivity of the network from less than 95% to more than 99%. We have implemented these techniques in the IP-over-P2P (IPOP) virtual network and have conducted experiments with a 180-node WOW Condor pool, demonstrating that, at 81% probability of establishing a pair-wise connection, annealing and tunneling combined allow all nodes to be connected to the pool, compared to only 160 nodes in the absence of these techniques.

Energy optimization schemes in cluster with virtual machines

Large scale clusters based on virtualization technologies have been widely used in many areas, including the data center and cloud computing environment. But how to save energy is a big challenge for building a “green cluster” recently. However, previous researches, including local approaches, which focus on saving the energy of the components in a single workstation without a global vision on the whole cluster, and cluster-wide energy saving techniques, which can only be applied to homogeneous workstations and specific applications, cannot solve the challenges. This paper describes the design and implementation of a novel scheme, called Magnet, that uses live migration of virtual machines to transfer load among the nodes on a multi-layer ring-based overlay. This scheme can reduce the power consumption greatly by regarding all the cluster nodes as a whole based on virtualization technologies. And, it can be applied to both the homogeneous and heterogeneous servers. Experimental measurements show that the new method can reduce the power consumption by 74.8% over base at most with certain adjustably acceptable overhead. The effectiveness and performance insights are also analytically verified.     

Power and environment aware control of Beowulf clusters

Beowulf clusters are now deployed worldwide, chiefly in support of scientific computing. Beowulf clusters yield high computing performance, yet they also pose several challenges: (1) heat-induced hardware failure makes large scale commodity clusters fail quite frequently and (2) cost effectiveness of the Beowulf cluster is challenged by the fact that it lacks means of adapting its power state according to varying work load. This paper addresses these issues by developing a Power and Environment Awareness Module (PEAM) for a Beowulf cluster. The busty nature of computation load in an academic environment inspired the implementation and analysis of a fixed timeout Dynamic Power Management (DPM) policy. Today it is common that many Beowulf clusters in academic environment are composed of older, recycled nodes that may lack of out-of-band management technologies, thus Advanced Configuration and Power Interface (ACPI) and Wake-on-LAN (WOL) technology is exploited to control the power state of cluster nodes. A data center environment monitoring system that uses Wireless Sensor Networks (WSN) technology is developed and deployed to realize environment awareness of the cluster. Our PEAM module has been implemented on our cluster at Purdue University, reducing the operational cost and increasing the reliability of the cluster by reducing heat generation and optimizing workload distribution in an environment aware manner.     

Localization algorithm in wireless sensor networks based on semi-supervised manifold learning and its application

Localization of mobile nodes in wireless sensor network gets more and more important, because many applications need to locate the source of incoming measurements as precise as possible. Many previous approaches to the location-estimation problem need know the theories and experiential signal propagation model and collect a large number of labeled samples. So, these approaches are coarse localization because of the inaccurate model, and to obtain such data requires great effort. In this paper, a semi-supervised manifold learning is used to estimate the locations of mobile nodes in a wireless sensor network. The algorithm is used to compute a subspace mapping function between the signal space and the physical space by using a small amount of labeled data and a large amount of unlabeled data. This mapping function can be used online to determine the location of mobile nodes in a sensor network based on the signals received. We use independent development nodes to setup the network in metallurgical industry environment, outdoor and indoor. Experimental results show that we can achieve a higher accuracy with much less calibration effort as compared with RADAR localization systems.     

Probabilistic Clustering of the Human Connectome Identifies Communities and Hubs

A fundamental assumption in neuroscience is that brain function is constrained by its structural properties. This motivates the idea that the brain can be parcellated into functionally coherent regions based on anatomical connectivity patterns that capture how different areas are interconnected. Several studies have successfully implemented this idea in humans using diffusion weighted MRI, allowing parcellation to be conducted in vivo. Two distinct approaches to connectivity-based parcellation can be identified. The first uses the connection profiles of brain regions as a feature vector, and groups brain regions with similar connection profiles together. Alternatively, one may adopt a network perspective that aims to identify clusters of brain regions that show dense within-cluster and sparse between-cluster connectivity. In this paper, we introduce a probabilistic model for connectivity-based parcellation that unifies both approaches. Using the model we are able to obtain a parcellation of the human brain whose clusters may adhere to either interpretation. We find that parts of the connectome consistently cluster as densely connected components, while other parts consistently result in clusters with similar connections. Interestingly, the densely connected components consist predominantly of major cortical areas, while the clusters with similar connection profiles consist of regions that have previously been identified as the ‘rich club’; regions known for their integrative role in connectivity. Furthermore, the probabilistic model allows quantification of the uncertainty in cluster assignments. We show that, while most clusters are clearly delineated, some regions are more difficult to assign. These results indicate that care should be taken when interpreting connectivity-based parcellations obtained using alternative deterministic procedures.     

Anatomical connectivity defines the organization of clusters of cortical areas in the macaque monkey and the cat

The number of different cortical structures in mammalian brains and the number of extrinsic fibres linking these regions are both large. As with any complex system, systematic analysis is required to draw reliable conclusions about the organization of the complex neural networks comprising these numerous elements. One aspect of organization that has long been suspected is that cortical networks are organized into 'streams' or 'systems'. Here we report computational analyses capable of showing whether clusters of strongly interconnected areas are aspects of the global organization of cortical systems in macaque and cat. We used two different approaches to analyse compilations of corticocortical connection data from the macaque and the cat. The first approach, optimal set analysis, employed an explicit definition of a neural 'system' or 'stream', which was based on differential connectivity. We defined a two-component cost function that described the cost of the global cluster arrangement of areas in terms of the areas' connectivity within and between candidate clusters. Optimal cluster arrangements of cortical areas were then selected computationally from the very many possible arrangements, using an evolutionary optimization algorithm. The second approach, non-parametric cluster analysis (NPCA), grouped cortical areas on the basis of their proximity in multidimensional scaling representations. We used non-metric multidimensional scaling to represent the cortical connectivity structures metrically in two and five dimensions. NPCA then analysed these representations to determine the nature of the clusters for a wide range of different cluster shape parameters. The results from both approaches largely agreed. They showed that macaque and cat cortices are organized into densely intra-connected clusters of areas, and identified the constituent members of the clusters. These clusters reflected functionally specialized sets of cortical areas, suggesting that structure and function are closely linked at this gross, systems level.     

WCA: A Weighted Clustering Algorithm for Mobile Ad Hoc Networks

In this paper, we propose an on-demand distributed clustering algorithm for multi-hop packet radio networks. These types of networks, also known as ad hoc networks, are dynamic in nature due to the mobility of nodes. The association and dissociation of nodes to and from clusters perturb the stability of the network topology, and hence a reconfiguration of the system is often unavoidable. However, it is vital to keep the topology stable as long as possible. The clusterheads, form a dominant set in the network, determine the topology and its stability. The proposed weight-based distributed clustering algorithm takes into consideration the ideal degree, transmission power, mobility, and battery power of mobile nodes. The time required to identify the clusterheads depends on the diameter of the underlying graph. We try to keep the number of nodes in a cluster around a pre-defined threshold to facilitate the optimal operation of the medium access control (MAC) protocol. The non-periodic procedure for clusterhead election is invoked on-demand, and is aimed to reduce the computation and communication costs. The clusterheads, operating in dual power mode, connects the clusters which help in routing messages from a node to any other node. We observe a trade-off between the uniformity of the load handled by the clusterheads and the connectivity of the network. Simulation experiments are conducted to evaluate the performance of our algorithm in terms of the number of clusterheads, reaffiliation frequency, and dominant set updates. Results show that our algorithm performs better than existing ones and is also tunable to different kinds of network conditions.     

Traffic-aware routing protocol for wireless sensor networks

In wireless sensor networks, when a sensor node detects events in the surrounding environment, the sensing period for learning detailed information is likely to be short. However, the short sensing cycle increases the data traffic of the sensor nodes in a routing path. Since the high traffic load causes a data queue overflow in the sensor nodes, important information about urgent events could be lost. In addition, since the battery energy of the sensor nodes is quickly exhausted, the entire lifetime of wireless sensor networks would be shortened. In this paper, to address these problem issues, a new routing protocol is proposed based on a lightweight genetic algorithm. In the proposed method, the sensor nodes are aware of the data traffic rate to monitor the network congestion. In addition, the fitness function is designed from both the average and the standard deviation of the traffic rates of sensor nodes. Based on dominant gene sets in a genetic algorithm, the proposed method selects suitable data forwarding sensor nodes to avoid heavy traffic congestion. In experiments, the proposed method demonstrates efficient data transmission due to much less queue overflow and supports fair data transmission for all sensor nodes. From the results, it is evident that the proposed method not only enhances the reliability of data transmission but also distributes the energy consumption across wireless sensor networks.     

Predictively booting nodes to minimize performance degradation of a power-aware web cluster

With the ever increasing trend of dynamic and static content web, clusters have been widely used for large-scale web servers to improve the system scalability. Dynamically switching the cluster nodes between different power states is one effective approach to save the energy in such clusters. Many research efforts have been invested in designing power-aware clusters by using this method. However, booting a cluster node from a low-power state to an active state takes a certain amount of time that depends on different configurations. This process incurs significant performance degradation. The existing work normally trades a certain amount of performance degradation for energy saving. This paper proposes a hybrid method to predict the number of requests per booting time of the web workloads. A power-aware web cluster scheduler is designed to divide the cluster nodes into an active group and a low-power group. The scheduler attempts to minimize the active group and maximize the low-power group, and boot the cluster nodes in the low-power group in advance to minimize/eliminate performance degradation by leveraging the prediction scheme. Furthermore, this paper integrates the power awareness into the conventional load balancers including Least Connections, Deficit Round Robin, and Skew. Comprehensive experiments are performed to explore the potential opportunities to minimize/eliminate the performance degradation of the power-aware web cluster.     

A new approach to the rapid determination of protein side chain conformations

Two efficient algorithms have been developed which allow amino acid side chain conformations to be optimized rapidly for a given peptide backbone conformation. Both these approaches are based on the assumption that each side chain can be represented by a small number of rotameric states. These states have been obtained by a dynamic cluster analysis of a large data base of known crystallographic structures. Successful applications of these algorithms to the prediction of known protein conformations are presented.     

Multi-Parametric Clustering for Sensor Node Coordination in Cognitive Wireless Sensor Networks

The deployment of wireless sensor networks for healthcare applications have been motivated and driven by the increasing demand for real-time monitoring of patients in hospital and large disaster response environments. A major challenge in developing such sensor networks is the need for coordinating a large number of randomly deployed sensor nodes. In this study, we propose a multi-parametric clustering scheme designed to aid in the coordination of sensor nodes within cognitive wireless sensor networks. In the proposed scheme, sensor nodes are clustered together based on similar network behaviour across multiple network parameters, such as channel availability, interference characteristics, and topological characteristics, followed by mechanisms for forming, joining and switching clusters. Extensive performance evaluation is conducted to study the impact on important factors such as clustering overhead, cluster joining estimation error, interference probability, as well as probability of reclustering. Results show that the proposed clustering scheme can be an excellent candidate for use in large scale cognitive wireless sensor network deployments with high dynamics.     

Characterization of the binding properties of SIRT2 inhibitors with a N-(3-phenylpropenoyl)-glycine tryptamide backbone

SIRT2 inhibitors with a N-(3-phenylpropenoyl)-glycine tryptamide backbone were studied. This backbone has been developed in our group, and it is derived from a compound originally found by virtual screening. In addition, compounds with a smaller 3-phenylpropenoic acid tryptamide backbone were also included in the study. Binding modes for the new compounds and the previously reported compounds were analyzed with molecular modelling methods. The approach, which included a combination of molecular dynamics, molecular docking and cluster analysis, showed that certain docking poses were favourable despite the conformational variation in the target protein. The N-(3-phenylpropenoyl)-glycine tryptamide backbone is also a good backbone for SIRT2 inhibitors, and the series of compounds includes several potent SIRT2 inhibitors.     

Ecoinformatics using wireless sensor networks: An overview

Wireless sensor networks have the potential to become significant subsystems of ecological experiment. Sensor networks consist of large number of tiny sensor nodes, all of which have sensing capabilities. These networks allow coordinated signal detection, monitoring, and tracking to enable sensor nodes to simultaneously capture geographically distinct measurements. Sensor nodes do not require predetermined positioning making such networks especially useful for applications in remote, inhospitable environments. In this paper we have tried to see the various ecological experimental scenarios, and how wireless sensor networks can be used in that field. One of the most challenging bottlenecks in the usage of wireless sensor networks in large scale experiments is the energy constraint. Various routing protocols which have tried to optimize the energy usage are also studied in the paper.     

An Adaptive Complex Network Model for Brain Functional Networks

Brain functional networks are graph representations of activity in the brain, where the vertices represent anatomical regions and the edges their functional connectivity. These networks present a robust small world topological structure, characterized by highly integrated modules connected sparsely by long range links. Recent studies showed that other topological properties such as the degree distribution and the presence (or absence) of a hierarchical structure are not robust, and show different intriguing behaviors. In order to understand the basic ingredients necessary for the emergence of these complex network structures we present an adaptive complex network model for human brain functional networks. The microscopic units of the model are dynamical nodes that represent active regions of the brain, whose interaction gives rise to complex network structures. The links between the nodes are chosen following an adaptive algorithm that establishes connections between dynamical elements with similar internal states. We show that the model is able to describe topological characteristics of human brain networks obtained from functional magnetic resonance imaging studies. In particular, when the dynamical rules of the model allow for integrated processing over the entire network scale-free non-hierarchical networks with well defined communities emerge. On the other hand, when the dynamical rules restrict the information to a local neighborhood, communities cluster together into larger ones, giving rise to a hierarchical structure, with a truncated power law degree distribution.     

VPM tokens: virtual machine-aware power budgeting in datacenters

Power consumption and cooling overheads are becoming increasingly significant for enterprise datacenters, affecting overall costs and the ability to extend resource capacities. To help mitigate these issues, active power management technologies are being deployed aggressively, including power budgeting, which enables improved power provisioning and can address critical periods when power delivery or cooling capabilities are temporarily reduced. Given the use of virtualization to encapsulate application components into virtual machines (VMs), however, such power management capabilities must address the interplay between budgeting physical resources and the performance of the virtual machines used to run these applications. This paper proposes a set of management components and abstractions for use by software power budgeting policies. The key idea is to manage power from a VM-centric point of view, where the goal is to be aware of global utility tradeoffs between different virtual machines (and their applications) when maintaining power constraints for the physical hardware on which they run. Our approach to VM-aware power budgeting uses multiple distributed managers integrated into the VirtualPower Management (VPM) framework whose actions are coordinated via a new abstraction, termed VPM tokens. An implementation with the Xen hypervisor illustrates technical benefits of VPM tokens that include up to 43% improvements in global utility, highlighting the ability to dynamically improve cluster performance while still meeting power budgets. We also demonstrate how VirtualPower based budgeting technologies can be leveraged to improve datacenter efficiency in the context of cooling infrastructure management.

Cyclone: A High-Performance Cluster-Based Web Server with Socket Cloning

With the ever-growing web traffic, cluster-based web server is becoming more and more important to the Internet's infrastructure. Making the best use of all the available resources in the cluster to achieve high performance is thus a significant research issue. In this paper, we introduce Cyclone, a cluster-based web server that can achieve nearly optimal throughput. Cyclone makes use of a novel network support mechanism called Socket Cloning (SC), together with the method of hot object replication, to obtain high performance. SC allows an opened socket to be moved efficiently between cluster nodes. With SC, the processing of HTTP requests can be migrated to the node that has a cached copy of the requested document, thus obviating the need for any cache transfer between cluster nodes. To achieve better load balancing, frequently accessed documents (hot objects) are replicated to other cluster nodes. Trace-driven benchmark tests using http_load show that Cyclone outperforms existing approaches and can achieve a throughput of 14575 requests/s (89.5 MBytes/s), which is 98% efficiency of the available network bandwidth, with eight web server nodes.     

NMR structure of the sea urchin (Strongylocentrotus purpuratus) metallothionein MTA.

The three-dimensional structure of [(113)Cd7]-metallothionein-A (MTA) of the sea urchin Strongylocentrotus purpuratus was determined by homonuclear(1)H NMR experiments and heteronuclear [(1)H, (113)Cd]-correlation spectroscopy. MTA is composed of two globular domains, an N-terminal four-metal domain of the amino acid residues 1 to 36 and a Cd4Cys11cluster, and a C-terminal three-metal domain including the amino acid residues 37 to 65 and a Cd3Cys9cluster. The structure resembles the known mammalian and crustacean metallothioneins, but has a significantly different connectivity pattern of the Cys-metal co-ordination bonds and concomitantly contains novel local folds of some polypeptide backbone segments. These differences can be related to variations of the Cys sequence positions and thus emphasize the special role of the cysteine residues in defining the structure of metallothioneins, both on the level of the domain architecture and the topology of the metal-thiolate clusters.     

Backbone cluster identification in proteins by a graph theoretical method

A graph theoretical algorithm has been developed to identify backbone clusters of residues in proteins. The identified clusters show protein sites with the highest degree of interactions. An adjacency matrix is constructed from the non-bonded connectivity information in proteins. The diagonalization of such a matrix yields eigenvalues and eigenvectors, which contain the information on clusters. In graph theory, distinct clusters can be obtained from the second lowest eigenvector components of the matrix. However, in an interconnected graph, all the points appear as one single cluster. We have developed a method of identifying highly interacting centers (clusters) in proteins by truncating the vector components of high eigenvalues. This paper presents in detail the method adopted for identifying backbone clusters and the application of the algorithm to families of proteins like RNase-A and globin. The objective of this study was to show the efficiency of the algorithm as well as to detect conserved or similar backbone packing regions in a particular protein family. Three clusters in topologically similar regions in the case of the RNase-A family and three clusters around the porphyrin ring in the globin family were observed. The predicted clusters are consistent with the features of the family of proteins such as the topology and packing density. The method can be applied to problems such as identification of domains and recognition of structural similarities in proteins.     

On an improved clustering algorithm based on node density for WSN routing protocol

To better collect data in context to balance energy consumption, wireless sensor networks (WSN) need to be divided into clusters. The division of clusters makes the network become a hierarchical organizational structure, which plays the role of balancing the network load and prolonging the life cycle of the system. In clustering routing algorithm, the pros and cons of clustering algorithm directly affect the result of cluster division. In this paper, an algorithm for selecting cluster heads based on node distribution density and allocating remaining nodes is proposed for the defects of cluster head random election and uneven clustering in the traditional LEACH protocol clustering algorithm in WSN. Experiments show that the algorithm can realize the rapid selection of cluster heads and division of clusters, which is effective for node clustering and is conducive to equalizing energy consumption.