GridMate: A Portable Simulation Environment for Large-Scale Adaptive Scientific Applications

In this paper we present an innovative decentralized dynamic resource scheduling solution of large scale application workflows onto distributed, heterogeneous grid environments. The presented resource allocation solution aims to optimize large-scale scientific application workflows by efficiently and effectively mapping and scheduling them onto grid resources. The proposed solution is part of a framework that aims to help scientists easily deploy large-scale scientific workflow applications from a wide-range of research fields. The decentralized architecture, together with the scheduling policies and fault management being proposed in this paper, are specifically designed to optimize the scheduling management for workflows in case of a wide range of grid environment. In order to demonstrate the validity and performance of the presented scheduling solution we propose using modeling and simulation techniques. For that we present the characteristics of a generic simulator that includes all the necessary components to help in evaluating a wide-range of scheduling procedures, such as the ones presented in this, in the context of large-scale heterogeneous grid environment.

The aim of this thesis is to design and implement a new Grid Resource Management methodology, where non-massive resources owners would be able to share their resources and integrate human collaboration across multiple domains regardless of network technology, operative platform or administrative domain.<br/>This thesis proposes a distributed and heuristic policy-based resource management architecture for large-scale Grids. The resource management architecture proposed herein is composed of four main building blocs: services management, resource discovery and monitoring, resource scheduling and jobs allocation and activation. The Grid Services Management (GSM) and Jobs Allocation and Activation (JAA) are supported by means of a Policy-based Grid Resource Management Architecture (PbGRMA). This architecture is able to identify service needs arising from diverse sources during the deployment and management of Grid Services, such as requirements demanded by customers, applications and network conditions. Afterwards, the PbGRMA merges these requirements into deployment policies for the corresponding Grid Services. The Grid Resource Discovery and Monitoring (GRDM) is supported by the introduction of the SNMP-based Balanced Load Monitoring Agents for Resource Scheduling (SBLOMARS), in which network and computational resources are monitored by distributed agents. This allows for a flexible, heterogeneous and scalable monitoring system. The Grid Resource Scheduling (GRS) is based on the Balanced Load Multi-Constrained Resource Scheduler (BLOMERS). This heuristic scheduler represents an alternate way of solving the inherent NP-hard problem for resource scheduling in large-scale distributed networks by means of the implementation of a Genetic Algorithm.<br/>Finally, based on the outcome of both the GRDM and GRS, the PbGRMA allocates the corresponding Grid Services by means of its interfaces with Globus ToolKit Middleware and Unix-based CLI commands along of any large-scale Grid Infrastructure. <br/>The synergy obtained by these components allows Grid administrators to exploit the available resources with predetermined levels of Quality of Service (QoS), reducing computational costs and makespan in resource scheduling while ensuring that the resource load is balanced throughout the Grid. The makespan of a schedule is the time required for all jobs to be processed when no one job could be interrupted during its execution and each node can perform at most one operation at any time.<br/>This new approach has been successfully tested in a real large-scale scenario such as Grid5000. The results presented along this Thesis show that our general solution is a reliable, flexible and scalable architecture to deploy and manage Grid Services in large-scale Grid Infrastructures. Moreover, the substitution of the heuristic algorithm approach used into the Grid Resource Scheduling (GRS) phase by other non-heuristics selection algorithms could make our solution useful in smaller Grid Infrastructures.

A Scheduler based on Resource Competition for Parameter Sweep Workflow

Many current international scientific projects are based on large scale applications that are both computationally complex and require the management of large amounts of distributed data. Grid computing is fast emerging as the solution to the problems posed by these applications. To evaluate the impact of resource optimisation algorithms, simulation of the Grid environment can be used to achieve important performance results before any algorithms are deployed on the Grid. In this paper, we study the effects of various job scheduling and data replication strategies and compare them in a variety of Grid scenarios using several performance metrics. We use the Grid simulator \textsf{OptorSim} , and base our simulations on a world-wide Grid testbed for data intensive high energy physics experiments. Our results show that scheduling algorithms which take into account both the file access cost of jobs and the workload of computing resources are the most effective at optimising computing and storage resources as well as improving the job throughput. The results also show that, in most cases, the economy-based replication strategies which we have developed improve the Grid performance under changing network loads.

Grid Computing provides sharing of geographically distributed resources among large scale complex applications. Due to dynamic nature of resources in grid, there is a need of highly efficient job scheduling and resource management policies in grid. In this paper, a novel Grid Resource Scheduler (GRS) is proposed to effectively utilize the available resources in Grid. Proposed GRS contributes, an optimal job scheduling algorithm on Job Rank-Backfilling policy and a resource matching algorithm based on ranking of resources with best fit allocation model. Performance of GRS is measured by considering a web based BLAST algorithm -- a bioinformatics application -- . GRS aims in reducing; Make span of the job workflow and execution time of varied size jobs. The experimental results prove that proposed job scheduling and resource matching algorithms performs better when evaluated against widely used FCFS job scheduling and biggest free resource matching strategies.

Typical large-scale scientific applications periodically write checkpoint files to save the computational state throughout execution. Existing parallel file systems improve such write-only I/O patterns through the use of client-side file caching and write-behind strategies. In distributed environments where files are rarely accessed by more than one client concurrently, file caching has achieved significant success; however, in parallel applications where multiple clients manipulate a shared file, cache coherence control can serialize I/O. We have designed a thread based caching layer for the MPI I/O library, which adds a portable caching system closer to user applications so more information about the application's I/O patterns is available for better coherence control. We demonstrate the impact of our caching solution on parallel write performance with a comprehensive evaluation that includes a set of widely used I/O benchmarks and production application I/O kernels.

Efficient scheduling algorithm is one of the key factors in determining the performance of distributed memory machines. This paper presents an enhanced Search and Du plication Based Scheduling (SDBS) algorithm which car schedule Directed Acyclic Graphs (DA Gs) with variable execution time tasks. Since the DAGs are based on data dependencies of the tasks, the control dependencies are clustered within each node. If the node encapsulates a loop or an if-then-else kind of statement, then assuming the execution times to be fixed would not be appropriate. It is assumed in this paper that the execution time varies between two time estimates. The complexity of this scheduling algorithm is in 0(V 4- E), where V is the number of node,- and E is the number of edges in the task graph. This algo rithm is based on some realistic assumptions and generates an optimal time schedule. If the assumptions cannot be completely satisfied then the algorithm provides a schedule which is close to optimal. The performance in these cases has been obtained using extensive simulation work which indicate the closeness of the results.

Emerging petascale systems will have many hundreds of thousands of processors, but traditional task-level tracing tools already fail to scale to much smaller systems because the I/O backbones of these systems cannot handle the peak load offered by their cores. Complete event traces of all processes are thus infeasible. To retain the benefits of detailed performance measurement while reducing volume of collected data, we developed AMPL, a general-purpose toolkit that reduces data volume using stratified sampling. We adopt a scalable sampling strategy, since the sample size required to measure a system varies sub-linearly with process count. By grouping, or stratifying, processes that behave similarly, we can further reduce data overhead while also providing insight into an application's behavior. In this paper, we describe the AMPL toolkit and we report our experiences using it on large-scale scientific applications. We show that AMPL can successfully reduce the overhead of tracing scientific applications by an order of magnitude or more, and we show that our tool scales sub-linearly, so the improvement will be more dramatic on petascale machines. Finally, we illustrate the use of AMPL to monitor applications by performance-equivalent strata, and we show that this technique can allow for further reductions in trace data volume and traced execution time.

In this paper, we develop a fault tolerant job scheduling strategy in order to tolerate faults gracefully in an economy based grid environment. We propose a novel adaptive task checkpointing based fault tolerant job scheduling strategy for an economy based grid. The proposed strategy maintains a fault index of grid resources. It dynamically updates the fault index based on successful or unsuccessful completion of an assigned task. Whenever a grid resource broker has tasks to schedule on grid resources, it makes use of the fault index from the fault tolerant schedule manager in addition to using a time optimization heuristic. While scheduling a grid job on a grid resource, the resource broker uses fault index to apply different intensity of task checkpointing (inserting checkpoints in a task at different intervals). To simulate and evaluate the performance of the proposed strategy, this paper enhances the GridSim Toolkit-4.0 to exhibit fault tolerance related behavior. We also compare "checkpointing fault tolerant job scheduling strategy" with the well-known time optimization heuristic in an economy based grid environment. From the measured results, we conclude that even in the presence of faults, the proposed strategy effectively schedules grid jobs tolerating faults gracefully and executes more jobs successfully within the specified deadline and allotted budget. It also improves the overall execution time and minimizes the execution cost of grid jobs.

The advent of large-scale collaborative scientific applications has demonstrated the potential for broad scientific communities to pool globally distributed resources to produce unprecedented data acquisition, movement, and analysis. System resources including supercomputers, data repositories, computing facilities, network infrastructures, storage systems, and display devices have been increasingly deployed at national laboratories and academic institutes. These resources are typically shared by large communities of users over Internet or dedicated networks and hence exhibit an inherent dynamic nature in their availability, accessibility, capacity, and stability. Scientific applications using either experimental facilities or computation-based simulations with various physical, chemical, climatic, and biological models feature diverse scientific workflows as simple as linear pipelines or as complex as a directed acyclic graphs, which must be executed and supported over wide-area networks with massively distributed resources. Application users oftentimes need to manually configure their computing tasks over networks in an ad hoc manner, hence significantly limiting the productivity of scientists and constraining the utilization of resources. The success of these large-scale distributed applications requires a highly adaptive and massively scalable workflow platform that provides automated and optimized computing and networking services. This project is to design and develop a generic Scientific Workflow Automation and Management Platform (SWAMP), which contains a web-based user interface specially tailored for a target application, a set of user libraries, and several easy-to-use computing and networking toolkits for application scientists to conveniently assemble, execute, monitor, and control complex computing workflows in heterogeneous high-performance network environments. SWAMP will enable the automation and management of the entire process of scientific workflows with the convenience of a few mouse clicks while hiding the implementation and technical details from end users. Particularly, we will consider two types of applications with distinct performance requirements: data-centric and service-centric applications. For data-centric applications, the main workflow task involves large-volume data generation, catalog, storage, and movement typically from supercomputers or experimental facilities to a team of geographically distributed users; while for service-centric applications, the main focus of workflow is on data archiving, preprocessing, filtering, synthesis, visualization, and other application-specific analysis. We will conduct a comprehensive comparison of existing workflow systems and choose the best suited one with open-source code, a flexible system structure, and a large user base as the starting point for our development. Based on the chosen system, we will develop and integrate new components including a black box design of computing modules, performance monitoring and prediction, and workflow optimization and reconfiguration, which are missing from existing workflow systems. A modular design for separating specification, execution, and monitoring aspects will be adopted to establish a common generic infrastructure suited for a wide spectrum of science applications. We will further design and develop efficient workflow mapping and scheduling algorithms to optimize the workflow performance in terms of minimum end-to-end delay, maximum frame rate, and highest reliability. We will develop and demonstrate the SWAMP system in a local environment, the grid network, and the 100Gpbs Advanced Network Initiative (ANI) testbed. The demonstration will target scientific applications in climate modeling and high energy physics and the functions to be demonstrated include workflow deployment, execution, steering, and reconfiguration. Throughout the project period, we will work closely with the science communities in the fields of climate modeling and high energy physics including Spallation Neutron Source (SNS) and Large Hadron Collider (LHC) projects to mature the system for production use.

Grid computing provides a high performance computing platform to solve larger scale applications by coordinating and sharing computational power, data storage and network resources across dynamic and geographically dispersed organizations. Scheduling onto the Grid is NP-complete, so there is no best scheduling algorithm for all grid computing systems. An alternative is to select an appropriate scheduling algorithm to use in a given grid environment because of the characteristics of the tasks, machines and network connectivity. Job scheduling is one of the key research area in grid computing. The goal of scheduling is to achieve highest possible system throughput and to match the application need with the available computing resources. Motivation of this study is to encourage and help the amateur researcher in the field of grid computing, so that they can understand easily the concept of scheduling and can contribute in developing more efficient and practical scheduling algorithm. This will benefit interested researchers to carry out further work in this thrust area of research.

An upgrade from dual-core to quad-core AMD processor on the Cray XT system at the Oak Ridge National Laboratory (ORNL) Leadership Computing Facility (LCF) has resulted in significant changes in the hardware and software stack, including a deeper memory hierarchy, SIMD instructions and a multi-core aware MPI library. In this paper, we evaluate impact of a subset of these key changes on large-scale scientific applications. We will provide insights into application tuning and optimization process and report on how different strategies yield varying rates of successes and failures across different application domains. For instance, we demonstrate that the vectorization instructions (SSE) provide a performance boost of as much as 50% on fusion and combustion applications. Moreover, we reveal how the resource contentions could limit the achievable performance and provide insights into how application could exploit Petascale XT5 system's hierarchical parallelism.

Today clusters of PCs are powerful computing platforms offering an inexpensive alternative to traditional supercomputers. Besides the low price, the major reason for the emergence of PC clusters is the availability of a wealth of public domain as well as important commercial software on top of the Linux operating system. Furthermore, a PC cluster can be built in a modular fashion enabling a potential customer to perfectly meet his requirements. For instance, the number of nodes, the node types, and the network can be chosen. In this note, experiences with an SCI-based Linux cluster installed at the Computing Center of Aachen University of Technology are reported. Timing results for two different applications, a two-dimensional fast Fourier transform and a molecular dynamics simulation, are presented. Our experiences demonstrate the importance of a fast network when dealing with large-scale scientific applications on a Linux cluster.

The increasing gap between processor cycle times and access times to storage devices makes it necessary to use powerful optimizations. This is especially true for applications in the parallel computing domain that frequently perform large amounts of file I/O. Collective I/O strategy that coordinates the processes to perform I/O on each other's behalf has demonstrated a significant performance improvement. This article proposes a new concept called Multicollective I/O (MCIO) that expands the collective I/O to allow data from multiple files to be requested in a single I/O request, in contrast to allowing only multiple segments for a single file to be specified together. MCIO considers multiple arrays simultaneously by having a more global view of the overall I/O behavior exhibited by parallel applications. This article shows that determining the optimal MCIO access pattern is an NP-complete problem, and proposes two different heuristics for the access pattern detection problem, also called the assignment problem. Both heuristics have been implemented within a runtime library, and tested using a large-scale scientific application. Our results show that MCIO outperforms collective I/O by as much as 87%. Our runtime library-based implementation can be used by application users as well as by optimizing compilers. Based on our results, we recommend that future library designers for I/O-intensive applications include MCIO in their suite of optimizations.

The Computational Grid[1] is a promising platform for running large-scale scientific applications. It provides a base software infrastructure that allows for the development of middleware aimed at deploying applications on Grid resources. The question is, how do you program it---in this regard, Network-Enabled Server (NES) paradigm, which enables Grid-based RPC, or GridRPC for short is a good candidate as a viable Grid middleware that offers a simple yet powerful programming paradigm for programming on the Grid. Several systems that facilitate whole or parts of the paradigm are already in existence, such as Neos[7], Netsolve[3], Nimrod/G[4], Ninf[2], and RCS[6], and we feel that pursuit of a common design in GridRPC, as had been done for MPI for message passing, will bring benefits of standardized programming model to the Grid world. This talk will introduce the NES/Grid RPC features, discuss early user experiences, and touch upon the Grid Data Farm project, based on Grid RPC, which involving processing Petabytes of collider accelerator data streaming over the Euro-Japanese link with thousands-node scale cluster possibly spread over several Japanese institutions. Compared to traditional RPC systems, such as CORBA, designed for applications that facilitate nonscientific applications, GridRPC systems offer features and capabilities that make it easy to program mediumto coarse-grained, task parallel applications that involve hundreds to thousands or more high-performance nodes, either concentrated as a tightly coupled cluster, or a set of them spread over a wide-area network. Such applications will often require handling of shipping megabytes of multidimensional array data in a user-transparent and efficient way, as well as requiring the support of RPC calls that range anywhere from 100s of milliseconds up to several days or even weeks. There are other necessary features of Grid RPC systems such as dynamic resource discovery, dynamic load balancing, fault tolerance, security (multisite authentication, delegation of authentication, adapting to multiple security policies, etc.), easy-to-use client/server management, firewall and private address considerations, remote large file and I/O support etc. These features are essentially what is needed for the Grid RPC systems to execute well on the Grid---features either missing or incomplete in traditional `closed world’ RPC systems ---and in fact are what are provided by lower level Grid substrates such as Condor[10], Globus[8], and Legion[9]. As such GridRPC systems either provide these features themselves, or builds upon the features provided by such substrates.