PaPaS: A Portable, Lightweight, and Generic Framework for Parallel Parameter Studies

The current landscape of scientific research is widely based on modeling and simulation, typically with complexity in the simulation's flow of execution and parameterization properties. Execution flows are not necessarily straightforward since they may need multiple processing tasks and iterations. Furthermore, parameter and performance studies are common approaches used to characterize a simulation, often requiring traversal of a large parameter space. High-performance computers offer practical resources at the expense of users handling the setup, submission, and management of jobs. This work presents the design of PaPaS, a portable, lightweight, and generic workflow framework for conducting parallel parameter and performance studies. Workflows are defined using parameter files based on keyword-value pairs syntax, thus removing from the user the overhead of creating complex scripts to manage the workflow. A parameter set consists of any combination of environment variables, files, partial file contents, and command line arguments. PaPaS is being developed in Python 3 with support for distributed parallelization using SSH, batch systems, and C++ MPI. The PaPaS framework will run as user processes, and can be used in single/multi-node and multi-tenant computing systems. An example simulation using the BehaviorSpace tool from NetLogo and a matrix multiply using OpenMP are presented as parameter and performance studies, respectively. The results demonstrate that the PaPaS framework offers a simple method for defining and managing parameter studies, while increasing resource utilization.Comment: 8 pages, 6 figures, PEARC '18: Practice and Experience in Advanced Research Computing, July 22--26, 2018, Pittsburgh, PA, US

Cosmological Simulations on a Grid of Computers

The work presented in this paper aims at restricting the input parameter values of the semi-analytical model used in GALICS and MOMAF, so as to derive which parameters influence the most the results, e.g., star formation, feedback and halo recycling efficiencies, etc. Our approach is to proceed empirically: we run lots of simulations and derive the correct ranges of values. The computation time needed is so large, that we need to run on a grid of computers. Hence, we model GALICS and MOMAF execution time and output files size, and run the simulation using a grid middleware: DIET. All the complexity of accessing resources, scheduling simulations and managing data is harnessed by DIET and hidden behind a web portal accessible to the users.Comment: Accepted and Published in AIP Conference Proceedings 1241, 2010, pages 816-82

Many-Task Computing and Blue Waters

This report discusses many-task computing (MTC) generically and in the context of the proposed Blue Waters systems, which is planned to be the largest NSF-funded supercomputer when it begins production use in 2012. The aim of this report is to inform the BW project about MTC, including understanding aspects of MTC applications that can be used to characterize the domain and understanding the implications of these aspects to middleware and policies. Many MTC applications do not neatly fit the stereotypes of high-performance computing (HPC) or high-throughput computing (HTC) applications. Like HTC applications, by definition MTC applications are structured as graphs of discrete tasks, with explicit input and output dependencies forming the graph edges. However, MTC applications have significant features that distinguish them from typical HTC applications. In particular, different engineering constraints for hardware and software must be met in order to support these applications. HTC applications have traditionally run on platforms such as grids and clusters, through either workflow systems or parallel programming systems. MTC applications, in contrast, will often demand a short time to solution, may be communication intensive or data intensive, and may comprise very short tasks. Therefore, hardware and software for MTC must be engineered to support the additional communication and I/O and must minimize task dispatch overheads. The hardware of large-scale HPC systems, with its high degree of parallelism and support for intensive communication, is well suited for MTC applications. However, HPC systems often lack a dynamic resource-provisioning feature, are not ideal for task communication via the file system, and have an I/O system that is not optimized for MTC-style applications. Hence, additional software support is likely to be required to gain full benefit from the HPC hardware

Global Grids and Software Toolkits: A Study of Four Grid Middleware Technologies

Grid is an infrastructure that involves the integrated and collaborative use of computers, networks, databases and scientific instruments owned and managed by multiple organizations. Grid applications often involve large amounts of data and/or computing resources that require secure resource sharing across organizational boundaries. This makes Grid application management and deployment a complex undertaking. Grid middlewares provide users with seamless computing ability and uniform access to resources in the heterogeneous Grid environment. Several software toolkits and systems have been developed, most of which are results of academic research projects, all over the world. This chapter will focus on four of these middlewares--UNICORE, Globus, Legion and Gridbus. It also presents our implementation of a resource broker for UNICORE as this functionality was not supported in it. A comparison of these systems on the basis of the architecture, implementation model and several other features is included.Comment: 19 pages, 10 figure

High-Performance Cloud Computing: A View of Scientific Applications

Scientific computing often requires the availability of a massive number of computers for performing large scale experiments. Traditionally, these needs have been addressed by using high-performance computing solutions and installed facilities such as clusters and super computers, which are difficult to setup, maintain, and operate. Cloud computing provides scientists with a completely new model of utilizing the computing infrastructure. Compute resources, storage resources, as well as applications, can be dynamically provisioned (and integrated within the existing infrastructure) on a pay per use basis. These resources can be released when they are no more needed. Such services are often offered within the context of a Service Level Agreement (SLA), which ensure the desired Quality of Service (QoS). Aneka, an enterprise Cloud computing solution, harnesses the power of compute resources by relying on private and public Clouds and delivers to users the desired QoS. Its flexible and service based infrastructure supports multiple programming paradigms that make Aneka address a variety of different scenarios: from finance applications to computational science. As examples of scientific computing in the Cloud, we present a preliminary case study on using Aneka for the classification of gene expression data and the execution of fMRI brain imaging workflow.Comment: 13 pages, 9 figures, conference pape

Cloudbus Toolkit for Market-Oriented Cloud Computing

This keynote paper: (1) presents the 21st century vision of computing and identifies various IT paradigms promising to deliver computing as a utility; (2) defines the architecture for creating market-oriented Clouds and computing atmosphere by leveraging technologies such as virtual machines; (3) provides thoughts on market-based resource management strategies that encompass both customer-driven service management and computational risk management to sustain SLA-oriented resource allocation; (4) presents the work carried out as part of our new Cloud Computing initiative, called Cloudbus: (i) Aneka, a Platform as a Service software system containing SDK (Software Development Kit) for construction of Cloud applications and deployment on private or public Clouds, in addition to supporting market-oriented resource management; (ii) internetworking of Clouds for dynamic creation of federated computing environments for scaling of elastic applications; (iii) creation of 3rd party Cloud brokering services for building content delivery networks and e-Science applications and their deployment on capabilities of IaaS providers such as Amazon along with Grid mashups; (iv) CloudSim supporting modelling and simulation of Clouds for performance studies; (v) Energy Efficient Resource Allocation Mechanisms and Techniques for creation and management of Green Clouds; and (vi) pathways for future research.Comment: 21 pages, 6 figures, 2 tables, Conference pape

A Meta-Brokering Framework for Science Gateways

Recently scientific communities produce a growing number of computation-intensive applications, which calls for the interoperation of distributed infrastructures including Clouds, Grids and private clusters. The European SHIWA and ER-flow projects have enabled the combination of heterogeneous scientific workflows, and their execution in a large-scale system consisting of multiple Distributed Computing Infrastructures. One of the resource management challenges of these projects is called parameter study job scheduling. A parameter study job of a workflow generally has a large number of input files to be consumed by independent job instances. In this paper we propose a meta-brokering framework for science gateways to support the execution of such workflows. In order to cope with the high uncertainty and unpredictable load of the utilized distributed infrastructures, we introduce the so called resource priority services. These tools are capable of determining and dynamically updating priorities of the available infrastructures to be selected for job instances. Our evaluations show that this approach implies an efficient distribution of job instances among the available computing resources resulting in shorter makespan for parameter study workflows