A middleware independent grid workflow builder for scientific applications

Grid workflow authoring tools are typically specific to particular workflow engines built into Grid middleware, or are application specific and are designed to interact with specific software implementations. g-Eclipse is a middleware independent Grid workbench that aims to provide a unified abstraction of the Grid and includes a Grid workflow builder to allow users to author and deploy workflows to the Grid. This paper describes the g-Eclipse Workflow Builder and its implementations for two Grid middlewares, gLite and GRIA, and a case study utilizing the Workflow Builder in a Grid user's scientific workflow deployment.

Security, trust and privacy supported by context-aware middleware

Driven by new network and middleware technologies such as mobile broadband, near-field communication, and context awareness the so-called ambient lifestyle will foster innovative use cases in building automation, healthcare and agriculture. In the EU project Hydra1 highlevel security, trust and privacy concerns such as loss of control, profiling and surveillance are considered at the outset. At the end of this project the Hydra middleware development platform will have been designed so as to enable developers to realise secure ambient scenarios especially in the user domains of building automation, healthcare, and agriculture. This paper gives a short introduction to the Hydra project, its user domains and its approach to ensure security by design. Based on the results of a focus group analysis of the building automation domain typical threats are evaluated and their risks are assessed. Then, specific security requirements with respect to security, privacy, and trust are derived in order to incorporate them into the Hydra Security Meta Model. How concepts such as context security, semantic security, and virtualisation support the overall Hydra approach will be introduced and illustrated on the basis of a technical building automation scenario.

Styx grid services: lightweight middleware for efficient scientific workflows

The service-oriented approach to performing distributed scientific research is potentially very powerful but is not yet widely used in many scientific fields. This is partly due to the technical difficulties involved in creating services and workflows and the inefficiency of many workflow systems with regard to handling large datasets. We present the Styx Grid Service, a simple system that wraps command-line programs and allows them to be run over the Internet exactly as if they were local programs. Styx Grid Services are very easy to create and use and can be composed into powerful workflows with simple shell scripts or more sophisticated graphical tools. An important feature of the system is that data can be streamed directly from service to service, significantly increasing the efficiency of workflows that use large data volumes. The status and progress of Styx Grid Services can be monitored asynchronously using a mechanism that places very few demands on firewalls. We show how Styx Grid Services can interoperate with with Web Services and WS-Resources using suitable adapters.

Communication mechanisms and middleware for distributed video surveillance

A new generation of advanced surveillance systems is being conceived as a collection of multi-sensor components such as video, audio and mobile robots interacting in a cooperating manner to enhance situation awareness capabilities to assist surveillance personnel. The prominent issues that these systems face are: the improvement of existing intelligent video surveillance systems, the inclusion of wireless networks, the use of low power sensors, the design architecture, the communication between different components, the fusion of data emerging from different type of sensors, the location of personnel (providers and consumers) and the scalability of the system. This paper focuses on the aspects pertaining to real-time distributed architecture and scalability. For example, to meet real-time requirements, these systems need to process data streams in concurrent environments, designed by taking into account scheduling and synchronisation. The paper proposes a framework for the design of visual surveillance systems based on components derived from the principles of Real Time Networks/Data Oriented Requirements Implementation Scheme (RTN/DORIS). It also proposes the implementation of these components using the well-known middleware technology Common Object Request Broker Architecture (CORBA). Results using this architecture for video surveillance are presented through an implemented prototype.

Running climate models on grids using G-Rex

Compute grids are used widely in many areas of environmental science, but there has been limited uptake of grid computing by the climate modelling community, partly because the characteristics of many climate models make them difficult to use with popular grid middleware systems. In particular, climate models usually produce large volumes of output data, and running them also involves complicated workflows implemented as shell scripts. A new grid middleware system that is well suited to climate modelling applications is presented in this paper. Grid Remote Execution (G-Rex) allows climate models to be deployed as Web services on remote computer systems and then launched and controlled as if they were running on the user's own computer. Output from the model is transferred back to the user while the run is in progress to prevent it from accumulating on the remote system and to allow the user to monitor the model. G-Rex has a REST architectural style, featuring a Java client program that can easily be incorporated into existing scientific workflow scripts. Some technical details of G-Rex are presented, with examples of its use by climate modellers.

Grid Remote Execution (G-Rex) of Climate Models

G-Rex is light-weight Java middleware that allows scientific applications deployed on remote computer systems to be launched and controlled as if they are running on the user's own computer. G-Rex is particularly suited to ocean and climate modelling applications because output from the model is transferred back to the user while the run is in progress, which prevents the accumulation of large amounts of data on the remote cluster. The G-Rex server is a RESTful Web application that runs inside a servlet container on the remote system, and the client component is a Java command line program that can easily be incorporated into existing scientific work-flow scripts. The NEMO and POLCOMS ocean models have been deployed as G-Rex services in the NERC Cluster Grid, and G-Rex is the core grid middleware in the GCEP and GCOMS e-science projects.

Running Climate Models On The NERC Cluster Grid Using G-Rex

Compute grids are used widely in many areas of environmental science, but there has been limited uptake of grid computing by the climate modelling community, partly because the characteristics of many climate models make them difficult to use with popular grid middleware systems. In particular, climate models usually produce large volumes of output data, and running them usually involves complicated workflows implemented as shell scripts. For example, NEMO (Smith et al. 2008) is a state-of-the-art ocean model that is used currently for operational ocean forecasting in France, and will soon be used in the UK for both ocean forecasting and climate modelling. On a typical modern cluster, a particular one year global ocean simulation at 1-degree resolution takes about three hours when running on 40 processors, and produces roughly 20 GB of output as 50000 separate files. 50-year simulations are common, during which the model is resubmitted as a new job after each year. Running NEMO relies on a set of complicated shell scripts and command utilities for data pre-processing and post-processing prior to job resubmission. Grid Remote Execution (G-Rex) is a pure Java grid middleware system that allows scientific applications to be deployed as Web services on remote computer systems, and then launched and controlled as if they are running on the user's own computer. Although G-Rex is general purpose middleware it has two key features that make it particularly suitable for remote execution of climate models: (1) Output from the model is transferred back to the user while the run is in progress to prevent it from accumulating on the remote system and to allow the user to monitor the model; (2) The client component is a command-line program that can easily be incorporated into existing model work-flow scripts. G-Rex has a REST (Fielding, 2000) architectural style, which allows client programs to be very simple and lightweight and allows users to interact with model runs using only a basic HTTP client (such as a Web browser or the curl utility) if they wish. This design also allows for new client interfaces to be developed in other programming languages with relatively little effort. The G-Rex server is a standard Web application that runs inside a servlet container such as Apache Tomcat and is therefore easy to install and maintain by system administrators. G-Rex is employed as the middleware for the NERC1 Cluster Grid, a small grid of HPC2 clusters belonging to collaborating NERC research institutes. Currently the NEMO (Smith et al. 2008) and POLCOMS (Holt et al, 2008) ocean models are installed, and there are plans to install the Hadley Centre’s HadCM3 model for use in the decadal climate prediction project GCEP (Haines et al., 2008). The science projects involving NEMO on the Grid have a particular focus on data assimilation (Smith et al. 2008), a technique that involves constraining model simulations with observations. The POLCOMS model will play an important part in the GCOMS project (Holt et al, 2008), which aims to simulate the world’s coastal oceans. A typical use of G-Rex by a scientist to run a climate model on the NERC Cluster Grid proceeds as follows :(1) The scientist prepares input files on his or her local machine. (2) Using information provided by the Grid’s Ganglia3 monitoring system, the scientist selects an appropriate compute resource. (3) The scientist runs the relevant workflow script on his or her local machine. This is unmodified except that calls to run the model (e.g. with “mpirun”) are simply replaced with calls to "GRexRun" (4) The G-Rex middleware automatically handles the uploading of input files to the remote resource, and the downloading of output files back to the user, including their deletion from the remote system, during the run. (5) The scientist monitors the output files, using familiar analysis and visualization tools on his or her own local machine. G-Rex is well suited to climate modelling because it addresses many of the middleware usability issues that have led to limited uptake of grid computing by climate scientists. It is a lightweight, low-impact and easy-to-install solution that is currently designed for use in relatively small grids such as the NERC Cluster Grid. A current topic of research is the use of G-Rex as an easy-to-use front-end to larger-scale Grid resources such as the UK National Grid service.

A management architecture for active networks

In this paper we present an architecture for network and applications management, which is based on the Active Networks paradigm and shows the advantages of network programmability. The stimulus to develop this architecture arises from an actual need to manage a cluster of active nodes, where it is often required to redeploy network assets and modify nodes connectivity. In our architecture, a remote front-end of the managing entity allows the operator to design new network topologies, to check the status of the nodes and to configure them. Moreover, the proposed framework allows to explore an active network, to monitor the active applications, to query each node and to install programmable traps. In order to take advantage of the Active Networks technology, we introduce active SNMP-like MIBs and agents, which are dynamic and programmable. The programmable management agents make tracing distributed applications a feasible task. We propose a general framework that can inter-operate with any active execution environment. In this framework, both the manager and the monitor front-ends communicate with an active node (the Active Network Access Point) through the XML language. A gateway service performs the translation of the queries from XML to an active packet language and injects the code in the network. We demonstrate the implementation of an active network gateway for PLAN (Packet Language for Active Networks) in a forty active nodes testbed. Finally, we discuss an application of the active management architecture to detect the causes of network failures by tracing network events in time.

Decentralized load balancing for highly irregular search problems

In this paper, we present a distributed computing framework for problems characterized by a highly irregular search tree, whereby no reliable workload prediction is available. The framework is based on a peer-to-peer computing environment and dynamic load balancing. The system allows for dynamic resource aggregation, does not depend on any specific meta-computing middleware and is suitable for large-scale, multi-domain, heterogeneous environments, such as computational Grids. Dynamic load balancing policies based on global statistics are known to provide optimal load balancing performance, while randomized techniques provide high scalability. The proposed method combines both advantages and adopts distributed job-pools and a randomized polling technique. The framework has been successfully adopted in a parallel search algorithm for subgraph mining and evaluated on a molecular compounds dataset. The parallel application has shown good calability and close-to linear speedup in a distributed network of workstations.

High throughput profile-profile based fold recognition for the entire human proteome

BACKGROUND: In order to maintain the most comprehensive structural annotation databases we must carry out regular updates for each proteome using the latest profile-profile fold recognition methods. The ability to carry out these updates on demand is necessary to keep pace with the regular updates of sequence and structure databases. Providing the highest quality structural models requires the most intensive profile-profile fold recognition methods running with the very latest available sequence databases and fold libraries. However, running these methods on such a regular basis for every sequenced proteome requires large amounts of processing power.In this paper we describe and benchmark the JYDE (Job Yield Distribution Environment) system, which is a meta-scheduler designed to work above cluster schedulers, such as Sun Grid Engine (SGE) or Condor. We demonstrate the ability of JYDE to distribute the load of genomic-scale fold recognition across multiple independent Grid domains. We use the most recent profile-profile version of our mGenTHREADER software in order to annotate the latest version of the Human proteome against the latest sequence and structure databases in as short a time as possible. RESULTS: We show that our JYDE system is able to scale to large numbers of intensive fold recognition jobs running across several independent computer clusters. Using our JYDE system we have been able to annotate 99.9% of the protein sequences within the Human proteome in less than 24 hours, by harnessing over 500 CPUs from 3 independent Grid domains. CONCLUSION: This study clearly demonstrates the feasibility of carrying out on demand high quality structural annotations for the proteomes of major eukaryotic organisms. Specifically, we have shown that it is now possible to provide complete regular updates of profile-profile based fold recognition models for entire eukaryotic proteomes, through the use of Grid middleware such as JYDE.

Building a biodiversity GRID

In the BiodiversityWorld project we are building a GRID to support scientific biodiversity-related research. The requirements associated with such a GRID are somewhat different from other GRIDs, and this has influenced the architecture that we have developed. In this paper we outline these requirements, most notably the need to interoperate over a diverse set of legacy databases and applications in an environment that supports effective resource discovery and use of these resources in complex workflows. Our architecture provides an invocation model that is usable over a wide range of resource types and underlying GRID middleware. However, there is a trade-off between the flexibility provided by our architecture and its performance. We discuss how this affects the inclusion of computationally intensive applications and applications that are highly interactive; we also consider the broader issue of interoperation with other GRIDs.

Parallel and distributed computing with Java

The Java language first came to public attention in 1995. Within a year, it was being speculated that Java may be a good language for parallel and distributed computing. Its core features, including being objected oriented and platform independence, as well as having built-in network support and threads, has encouraged this view. Today, Java is being used in almost every type of computer-based system, ranging from sensor networks to high performance computing platforms, and from enterprise applications through to complex research-based.simulations. In this paper the key features that make Java a good language for parallel and distributed computing are first discussed. Two Java-based middleware systems, namely MPJ Express, an MPI-like Java messaging system, and Tycho, a wide-area asynchronous messaging framework with an integrated virtual registry are then discussed. The paper concludes by highlighting the advantages of using Java as middleware to support distributed applications.

Towards semantic resolution of security in ambient environments

Driven by new network and middleware technologies such as mobile broadband, near-field communication, and context awareness the so-called ambient lifestyle will foster innovative use cases in different domains. In the EU project Hydra high-level security, trust and privacy concerns such as loss of control, profiling and surveillance are considered at the outset. At the end of this project the. Hydra middleware development platform will have been designed so as to enable developers to realise secure ambient scenarios. This paper gives a short introduction to the Hydra project and its approach to ensure security by design. Based on the results of a focus group analysis of the user domain "building automation" typical threats are evaluated and their risks are assessed. Then, specific security requirements with respect to security, privacy, and trust are derived in order to incorporate them into the Hydra Security Meta-Model. How concepts such as context, semantic resolution of security, and virtualisation support the overall Hydra approach will be introduced and illustrated on the basis of it technical building automation scenario.