In the event of a new infectious disease outbreak, mathematical and simulation models are commonly used to inform policy by evaluating which control strategies will minimize the impact of the epidemic. In the early stages of such outbreaks, substantial parameter uncertainty may limit the ability of models to provide accurate predictions, and policymakers do not have the luxury of waiting for data to alleviate this state of uncertainty. For policymakers, however, it is the selection of the optimal control intervention in the face of uncertainty, rather than accuracy of model predictions, that is the measure of success that counts. We simulate the process of real-time decision-making by fitting an epidemic model to observed, spatially-explicit, infection data at weekly intervals throughout two historical outbreaks of foot-and-mouth disease, UK in 2001 and Miyazaki, Japan in 2010, and compare forward simulations of the impact of switching to an alternative control intervention at the time point in question. These are compared to policy recommendations generated in hindsight using data from the entire outbreak, thereby comparing the best we could have done at the time with the best we could have done in retrospect. Our results show that the control policy that would have been chosen using all the data is also identified from an early stage in an outbreak using only the available data, despite high variability in projections of epidemic size. Critically, we find that it is an improved understanding of the locations of infected farms, rather than improved estimates of transmission parameters, that drives improved prediction of the relative performance of control interventions. However, the ability to estimate undetected infectious premises is a function of uncertainty in the transmission parameters. Here, we demonstrate the need for both real-time model fitting and generating projections to evaluate alternative control interventions throughout an outbreak. Our results highlight the use of using models at outbreak onset to inform policy and the importance of state-dependent interventions that adapt in response to additional information throughout an outbreak.

Wide-area live migration of virtual machines (VMs) is a key to advanced cloud federation, allowing dynamic and transparent load balancing among data centers. Although Mobile IPv6 (MIPv6) provides strong network infrastructure for mobile nodes, there still exists a missing link to the achievement of MIPv6-based VM migration. Real-world IaaS datacenters require guest-transparent and flexible tunneling mechanisms, which are not provided by existing MIPv6 programs. In this paper, we propose a guest-transparent MIPv6 tunneling mechanism (Kagemusha), that performs Client MIPv6 signaling and tunneling on a host operating system. No MIPv6 program is required to be installed into a guest operating system. The proposed system is fully compatible with existing home agents. It basically works with most virtual machine monitors, including Qemu/KVM and Xen. We have developed the first proof-of-concept prototype of the proposed mechanism. Our experiments showed that our prototype system successfully created MIPv6 tunnels with existing home agents. Its performance overhead was negligible for normal use cases. We also confirmed that the prototype system successfully supported live migration, transparently achieving continuous network reachability for migrated VMs. The downtime of migration increased only by several hundred milliseconds.

The present paper describes the cross calibration of the Remote Sensing Instrument (RSI) onboard Formosat-2 using the Advanced Spaceborne Thermal Emission and Reflection Radiometer (ASTER) onboard Terra as a reference, which has been continuously calibrated by means of the onboard and vicarious calibration methods. The data integration system for multi-satellite sensor databases on the Global Earth Observation Grid (GEO Grid) is used in order to find pairs of images acquired by both satellite optical sensors over the radiometric calibration sites on the same days. Radiative transfer simulations that consider different imaging conditions using the Second Simulation of a Satellite Signal in the Solar Spectrum (6S) code are performed based on the Moderate-resolution Imaging Spectroradiometer (MODIS) atmosphere and land products, and the optimum methodology for this cross calibration is discussed under the assumption of no ground-based measurements. The derived calibration coefficients are normalized by the values of preflight calibration and are compared with the results of in-flight cross calibration by the Centre National d'Études Spatiales (CNES) and vicarious calibration described in our previous paper. The average degradations of sensor sensitivity since preflight calibration until 2009 are estimated to be 10% (Band2), 11% (Band3), and 8% (Band4). The derived long-term degradation trends are almost consistent with the results of our vicarious calibration within the precision. The cross-calibration methodology used in the present paper facilitates the in-flight radiometric calibration of satellite optical sensors.

We are developing an efficient resource management system with aggressive virtual machine (VM) relocation among physical nodes in a data center. Existing live migration technology, however, requires a long time to change the execution host of a VM, it is difficult to optimize VM packing on physical nodes dynamically, corresponding to ever-changing resource usage. In this paper, we propose an advanced live migration mechanism enabling instantaneous relocation of VMs. To minimize the time needed for switching the execution host, memory pages are transferred after a VM resumes at a destination host. A special character device driver allows transparent memory page retrievals from a source host for the running VM at the destination. In comparison with related work, the proposed mechanism supports guest operating systems without any modifications to them (i.e, no special device drivers and programs are needed in VMs). It is implemented as a lightweight extension to KVM (Kernel-based Virtual Machine Monitor). It is not required to modify critical parts of the VMM code. Experiments were conducted using the SPECweb2005 benchmark. A running VM with heavily-loaded web servers was successfully relocated to a destination within one second. Temporal performance degradation after relocation was resolved by means of a precaching mechanism for memory pages. In addition, for memory intensive workloads, our migration mechanism moved all the states of a VM faster than existing migration technology.

IaaS (Infrastructure-as-a-Service) is an emerging concept of cloud computing, which allows users to obtain hardware resources from virtualized data centers. Although many commercial IaaS clouds have recently been launched, dynamic virtual machine (VM) migration is not possible among service providers; users are locked into a particular provider, and cannot transparently relocate their VMs to another one for the best cost-effectiveness. In this paper, we propose an advanced storage access mechanism that strongly supports live VM migration over WAN. It rapidly relocates VM disks between source and destination sites with the minimum impact on I/O performance. The proposed mechanism addresses I/O consistency of virtual disks before/after migration, which is the major issue regarding wide-area live migration. The proposed mechanism works as a storage server of a block-level storage I/O protocol (e.g.,iSCSI and NBD). Two key techniques (on-demand fetching and background copying) move on-line virtual disks among remote sites, transparently and efficiently. Our prototype system works perfectly for Xen and KVM without any modification to them. Experiments showed the prototype system also worked successfully for an emulated WAN environment.

The understanding of H diffusion in materials is pivotal to designing suitable processes. Though a nudged elastic band (NEB)+molecular dynamics (MD)/quantum mechanics (QM) algorithm has been developed to simulate H diffusion in materials by our group, it is often not computationally feasible for large-scale models on a conventional single system. We thus gridify the NEB+MD/QM algorithm on the top of an integrated framework developed by our group. A two days simulation on H diffusion in alumina has been successfully carried out over a trans-pacific grid infrastructure consisting of supercomputers provided by TeraGrid and AIST. In this paper, we describe the NEB+MD/QM algorithm, briefly introduce the framework middleware, present the grid enablement work, and report the techniques to achieve fault-tolerance and load-balance for sustainable simulation. We believe our experience is of benefit to both middleware developers and application users.

The authors have been leading the GEO Grid project since 2005. This project is primarily aiming at providing an e-Science infrastructure for the worldwide Earth Sciences community. The GEO Grid is designed to virtually integrate all relevant data as a VO-enabled service based on Grid technology, and as such, is accessible as a set of services. This kind of infrastructure is demanded not only by geoscience, but also by biology, high-energy physics, and astronomy. In particular, an integration of existing application-driven service specifications is needed by the application community. However, the specifications in the geoscience community, which are discussed in the open geospatial consortium (OGC), are usually implemented in GET and POST operations under HTTP. Thus, it is difficult to enforce the security framework of Grid technology to OGC services, because the Grid security framework require SOAP-based application protocols. Hence, we consider the architecture and an implementation method for enabling them. In this paper, we design a security framework of the GEO grid services based on the requirements from an example application scenario. These services comply with standardized specifications from both grid technologies and the geoscience community thereby achieving service harmonization. In order to achieve this framework, we implement a credential broker, called OGCProxy, which provides an access method that the user connect VO-enabled OGC services without any modifications of existing applications. We also implement a credential delegation for OGC services, which is impossible so far, to achieve complex chaining, such as cascading services, third party data transfer, applying high performance computing behind processing services, etc. As a result of this security framework, an application that uses a complex chaining of VO-enabled OGC services is available without any modifications.

To ensure large-scale and long-time (LSLT) applications to run smoothly in a dynamic and heterogeneous grid environment, we have designed and implemented a WSRF-based framework with which users can reserve resources and request on-demand computing resources. The framework can be architecturely divided into three tiers: the tier providing client-side reservation and allocation APIs, the tier for reservation brokerage and resource allocation, and the tier for backend services. The reservation API is implemented for making and releasing a reservation, as well as for showing available reservations. The allocation API is implemented to request, to check, and to release a resource in a convenient way. The middle tier is designed to hide the complexity of the underlying grid infrastructure, and implemented to provide several allocation algorithms. One of the main backend services is Maui-based reservation service at present. A portal to facilitate the resource management is also available. In this paper, we present the API specification, the architecture, and the implementation of this framework. We also show a detailed experimental example.

Abstract One of the greatest evolutions brought about by Grid technology is ‘Grid utility computing’, which utilizes various kinds of IT resources and applications across multiple organizations and enterprises, and integrates them into a comprehensive and valuable service. Since 2004, we proposed and have been developing the GridASP framework, which realizes Grid‐enabled application service providers (ASPs) in order to realize Grid utility computing. GridASP can bind application providers, resource providers, and service providers together and provide application execution services with security and anonymity to enterprise/science users. In this article, we report the conceptual idea of GridASP and the detail of the framework now being developed. Information on GridASP can be found at http://www.gridasp.org . Copyright © 2006 John Wiley & Sons, Ltd.

The Grid technologies have brought us a set of new concepts such as utility computing, service ondemand, and resource sharing in the business scene as well as many examples of new modes of science. Although for limited applications grids are able to provide production quality of services today, we are still looking for enablers to apply them to a much broader area of use cases. Populating the Internet for personal and business use, it is to say that the Internet technology changes our personal life and business environment in terms of our work style like SOHO, accelerating business speed by easy communication and handy tools, globalization dismissing geographical boundaries and professional borders. However achieving such flexibility and speed in the business, current monolithic IT infrastructure never meets the demand of high agility in business. We take the service oriented architecture (SOA) as one of the key technologies to bridge the gap, but without considering computing resources, SOA will not become a feasible solution. Co-designing SOA for a flexible service building model and IT utility model of payper-use to save TCO, it is the perfect match to produce a future IT infrastructure, that is to say e-Infrastructure."

We propose a reservation-based sustainable adaptive Grid supercomputing paradigm to enable tightly coupled computations of considerable scale (involving over 1,000 processors) and duration (over tens of continuous days) on a Grid of geographically distributed parallel supercomputers. The paradigm is demonstrated for an adaptive multiscale simulation application, in which accurate but compute-intensive quantum mechanical (QM) simulations are embedded within a classical molecular dynamics (Md) simulation only when and where high fidelity is required. Key technical innovations include: 1) an embedded divide-and-conquer algorithmic framework to maximally expose data and computation localities for enhanced scalability; 2) a buffered-cluster hybridization scheme to adaptively adjust MD/QM boundaries to maintain the model accuracy; and 3) a hybrid Grid remote procedure call (GridRPC) + message passing interface (MPI) Grid application framework to combine flexibility (adaptive resource allocation and migration), fault tolerance (automated fault recovery), and efficiency (scalable management of large computing resources). We have achieved an automated execution of multiscale MD/QM simulation on a Grid consisting of 6 supercomputer centers in Japan and the US (in total of 150 thousand processor-hours) for the dynamic simulation of implanted oxygen atoms in a silicon substrate, in which the number of processors changes dynamically on demand and resources are allocated and migrated dynamically according to both reservations and unexpected faults. The simulation results reveal a strong dependence of the oxygen penetration depth on the incident oxygen-beam position, which is useful information to further advance SIMOX (separation by implanted oxygen) technique to fabricate high speed and low power-consumption semiconductor devices.

This paper presents middleware enabling mutual and equal transfer of computing power between individuals, as in the original idea behind P2P, while also supporting large-scale distributed computation utilizing heterogeneous PCs. This goal is strongly supported by a network overlay over which peers can communicate with each other directly and bidirectionally. We made use of a general-purpose P2P library, JXTA, supporting the common requirements of P2P software, including network overlay. Other features of the P2P library, such as ad-hoc self-organization, discovery and grouping of peers, also support our middleware efficiently. In this paper, we propose and evaluate an application of those P2P concepts to virtual resource transfer and parallel computation with aggregated resources. However, such a P2P library imposes a certain amount of overhead on the middleware in terms of communication performance. Measured communication performance and throughput of an application program shows the feasibility of the application of P2P concepts. The middleware achieves 100 /spl times/ 10/sup 6/ bps communication performance and over a 20 fold increase in speed with 32 computers, even though the granularity of workunits is as fine as less than a second.

A full electron calculation for the photosynthetic reaction center of Rhodopseudomonas viridis was performed by using the fragment molecular orbital (FMO) method on a massive cluster computer. The target system contains 20,581 atoms and 77,754 electrons, which was divided into 1,398 fragments. According to the FMO prescription, the calculations of the fragments and pairs of the fragments were conducted to obtain the electronic state of the system. The calculation at RHF/6-31G* level of theory took 72.5 hours with 600 CPUs. The CPUs were grouped into several workers, to which the calculations of the fragments were dispatched. An uneven CPU grouping, where two types of workers are generated, was shown to be efficient.

The National Research Grid Initiative (NAREGI) is one of the major Japanese national IT projects currently being conducted. NAREGI will cover the period 2003-2007, and collaboration among industry, academia, and the government will play a key role in its success. The Center for Grid Research and Development has been established as a center for R&D of high-performance, scalable grid middleware technologies, which are aimed at enabling major computing centers to host grids over high-speed networks to provide a future computational infrastructure for scientific and engineering research in the 21st century. As an example of utilizing such grid computing technologies, the Center for Application Research and Development is conducting research on leading-edge, grid-enabled nanoscience and nanotechnology simulation applications, which will lead to the discovery and development of new materials and next-generation nanodevices. These two centers are collaborating to establish daily research use of a multiteraflop grid testbed infrastructure, which will be built to demonstrate the advantages of grid technologies for future applications in all areas of science and engineering.

GNET-1 is a fully programmable network testbed. It provides functions such as wide area network emulation, network instrumentation, traffic shaping, and traffic generation at gigabit Ethernet wire speeds by programming the core FPGA. GNET-1 is a powerful tool for developing network-aware grid software. It is also a network monitoring and traffic-shaping tool that provides high-performance communication over wide area networks. This work describes several sample uses of GNET-1 and presents its architecture.

The Grid Datafarm (Gfarm) architecture is designed for global petascale data-intensive computing. It provides a global parallel filesystem with online petascale storage, scalable I/O bandwidth, and scalable parallel processing, and it can exploit local I/O in a grid of clusters with tens of thousands of nodes. Gfarm parallel I/O APIs and commands provide a single filesystem image and manipulate filesystem metadata consistently. Fault tolerance and load balancing are automatically managed by file duplication or recomputation using a command history log. Preliminary performance evaluation has shown scalable disk I/O and network bandwidth on 64 nodes of the Presto III Athlon cluster. The Gfarm parallel I/O write and read operations has achieved data transfer rates of 1.74 GB/s and 1.97 GB/s, respectively, using 64 cluster nodes. The Gfarm parallel file copy reached 443 MB/s with 23 parallel streams on the Myrinet 2000. The Gfarm architecture is expected to enable petascale data-intensive Grid computing with an I/O bandwidth scales to the TB/s range and scalable computational power.

GridRPC is a class of Grid middleware for scientific computing. Interoperability has been an important issue, because current GridRPC systems each employ its own protocol. Web services, where XML-based standards such as SOAP and WSDL are expected to see widespread use, could be the medium of interoperability; however it is not clear if 1) XML-based schemas have sufficient expressive power for GridRPC, and 2) whether performance could be made sufficient. Our experiments indicate that the use of such technologies are more promising. than previously reported. Although a naive implementation of SOAP-based GridRPC has severe performance overhead, application of a series of optimizations improves performance. However encoding of various features of GridRPC proved to be somewhat difficult due to WSDL limitations. The results show that GridRPC systems can be based on Web technologies, but there needs to be work to extend WSDL specifications, possibly impacting OGSA-based Grid services directions.

A fast message-passing library FMPL has been designed and developed to maximize communication performance by utilizing general architectural communication support such as remote memory operations, as well as to maximize total performance by eliminating dynamic communication overhead and overlapping communication and computation. FMPL provides a low-cost general-purpose point-to-point communication and collective communication such as broadcast, barrier synchronization and reduction. On a Hitachi SR8000, FMPL achieves an 8-byte latency of 12.8μsec., while MPI achieves 20μsec. FMPL is designed for building more highly functional message-passing libraries like BLACS as well as applications that need maximum performance.

Presents a performance evaluation of a wide-area cluster system based on a firewall-enabled Globus metacomputing toolkit. In order to establish communication links beyond the firewall, we have designed and implemented a resource manager called RMF (Resource Manager beyond the Firewall) and the Nexus Proxy, which relays TCP communication links beyond the firewall. In order to extend the Globus metacomputing toolkit to become firewall-enabled, we have built the Nexus Proxy into the Globus toolkit. We have built a firewall-enabled Globus-based wide-area cluster system in Japan and run some benchmarks on it. In this paper, we report various performance results, such as the communication bandwidth and latencies obtained, as well as application performance involving a tree search problem. In a wide-area environment, the communication latency through the Nexus Proxy is approximately six times larger when compared to that of direct communications. As the message size increases, however, the communication overhead caused by the Nexus Proxy can be negligible. We have developed a tree search problem using MPICH-G. We used a self-scheduling algorithm, which is considered to be suitable for a distributed heterogeneous metacomputing environment since it performs dynamic load balancing with low overhead. The performance results indicate that the communication overhead caused by the Nexus Proxy is not a severe problem in metacomputing environments.

Recent developments of global computing systems such as Ninf, NetSolve and Globus have opened up the opportunities for providing high-performance computing services over wide-area networks. However, most research focused on the individual architectural aspects of the system, or application deployment examples, instead of the necessary characteristics such systems should intrinsically satisfy, nor how such systems relate with each other. Our comparative study performs deployment of example applications of network-based libraries using Ninf, NetSolve, and CORBA systems. There, we discover that dedicated systems for global computing such as Ninf and NetSolve have management, programmability, and it does not suffer performance disadvantages over more generic distributed computing capabilities provided by CORBA. Such results indicate the advantage of dedicated global computing systems over general systems, stemming further basic research is necessary across multiple systems to identify the ideal software architectures for global computing.

MPl point-to-point communication is a basic operation, however it requires runtime-matching of send and receive that causes to reduce performance.This paper proposes a new approach to send messages by remote memory write without inquiring of the receiver under a communication pattern such that nonblocking receive is issued in advance.Basically, this approach makes it possible to gain low latency and high bandwidth as the hardware specification.MPI-EMX, our implementation of the MPI on the EM-X multiprocessor, achieves a zero-byte latency of 13.4 psec.and a maximum bandwidth of 31.4MB/s, which can compete with commercial MPPs.This approach to reduce communication latency is widely applicable to other systems and is quite a promising technique for achieving low latency and high bandwidth.

Ninflet is a Java-based global computing system that builds on our experiences with the Ninf system which facilitated RPC-based computing of numerical tasks in a wide-area network. The goal of Ninflet is to become a new generation of concurrent object-oriented systems which harness abundant idle computing powers, and also seamlessly integrate global as well as local network parallel computing. Ninflet is designed to make use of Java features to implement important features in global computing, such as resource allocation, inter-Ninflet communication, security, checkpointing, object migration, and easy server management via HTTP. © 1998 John Wiley & Sons, Ltd.

Rapid increase in speed and availability of network of supercomputers is making high-performance global computing possible, including our Ninf system. However, critical issues regarding system performance characteristics in global computing have been little investigated, especially under multi-client, multi-site WAN settings. In order to investigate the feasibility of Ninf and similar systems, we conducted benchmarks under various LAN and WAN environments, and observed the following results: 1) Given sufficient communication bandwidth, Ninf performance quickly overtakes client local performance, 2) current supercomputers are sufficient platforms for supporting Ninf and similar systems in terms of performance and OS fault resiliency, 3) for a vector-parallel machine (Cray J90), employing optimized data-parallel library is a better choice compared to conventional task-parallel execution employed for non-numerical data servers, 4) computationally intensive tasks such as EP can readily be supported under the current Ninf infrastructure, and 5) for communication-intensive applications such as Linpack, server CPU utilization dominates LAN performance, while communication bandwidth dominates WAN performance, and furthermore, aggregate bandwidth could be sustained for multiple clients located at different Internet sites; as a result, distribution of multiple tasks to computing servers on different networks would be essential for achieving higher client-observed performance. Our results are not necessarily restricted to the Ninf system, but rather, would be applicable to other similar global computing systems.

Latency associated with memory accesses and process communications are one of the most difficult obstacles in constructing a practical massively parallel system. So far, two approaches to hide latencies have been proposed. They are prefetching and multi-threading. An instruction-level data-driven computer is an ideal test-bed for evaluating these latency hiding methods because prefetching and multi-threading are naturally implemented in an instruction-level data-driven computer as unfolding and concurrent execution of multiple contexts. This paper evaluates latency hiding methods on SIGMA-1, a dataflow supercomputer developed in Electrotechnical Laboratory. As a result of evaluation, these methods are effective to hide static latencies but not effective to hide dynamic latencies. Also, concurrent execution of multiple contexts is more effective than prefetching.

In order to achieve implementation control in a dataflow architecture, it is necessary to bring data streams under control and branch them in accord with prevailing conditions. This study suggests methodologies for modeling and formulating the control overhead of data streams. From these methodologies, techniques are derived to minimize overhead. In order to verify the practicality of these techniques, they were first applied to three representative Japanese dataflow architectures to show their basic ability to reduce overhead, and for further verification, they were next applied to several real applications to test their more specific abilities, as well as their value as techniques for optimizing compilation.

In the past, various computer languages aimed at users of dataflow computers have been designed and implemented.VAL, Id and SISAL are famous examples.One concept that is common to such languages is to maintain a sense of functionality by introducing a single assignment rule for all variables.DFCII, Dataflow C II, the language proposed here, is designed for writing practical application programs and system programs that must be executed in parallel on the SIGMA-1.It is the most important dataflow research

An iterative algorithm for generating all partitions of the set {1,…,n} is presented. An empirical test shows that the new algorithm is faster than the previously fastest algorithm recently proposed by Er on some computers, though the former is slower than the latter on a computer where fast recursive call is provided based on an RISC architecture.

Structure-flow processing is proposed as a novel scheme for handling data structures such as vectors in data-flow architecture. The main objective of structure-flow processing is to enhance the vector processing performance. In this scheme, the arrival of a data structure unrolls the control structure that processes the data structure itself. A high-level structure is an implementation mechanism of a structure-flow scheme on a practical data-flow computer. Since all the computation is executed by instruction-level data-flow architecture, scalar-level parallelism and function-level parallelism are also fully utilized by this scheme. The SIGMA-1 architecture that supports high-level structure processing is discussed. Performance measurements show that vector programs can be executed three to four times faster than by unfolding using scalar dataflow processing.>

A processing element and a structure element of data flow computer SIGMA-1 for scientific computations is now operational. The elements are evaluated for several benchmark programs. For efficient execution of loop constructs, the sticky token mechanism which holds loop invariants is evaluated and exhibits a remarkable effect. From the standpoint that performance of a single processor of a data flow computer must be comparable to that of a Von Neumann computer, comparison of both computers is discussed and improvement of the SIGMA-1 instruction set is proposed.