Teaching the Grid: Learning Distributed Computing with the M-grid Framework

A classic challenge within Computer Science is to distribute data and processes so as to take advantage of multiple computers tackling a single problem in a simultaneous and coordinated way. This situation arises in a number of different scenarios, including Grid computing which is a secure, service-based architecture for tackling massively parallel problems and creating virtual organizations. Although the Grid seems destined to be an important part of the future computing landscape, it is very difficult to learn how to use as real Grid software requires extensive setting up and complex security processes. M-grid mimics the core features of the Grid, in a much simpler way, enabling the rapid prototyping of distributed applications. We describe m-grid and explore how it may be used to teach foundation Grid computing skills at the Higher Education level and report some of our experiences of deploying it as an exercise within a programming course

A service-oriented architecture for scientific computing on cloud infrastructures

This paper describes a service-oriented architecture that eases the process of scientific application deployment and execution in IaaS Clouds, with a focus on High Throughput Computing applications. The system integrates i) a catalogue and repository of Virtual Machine Images, ii) an application deployment and configuration tool, iii) a meta-scheduler for job execution management and monitoring. The developed system significantly reduces the time required to port a scientific application to these computational environments. This is exemplified by a case study with a computationally intensive protein design application on both a private Cloud and a hybrid three-level infrastructure (Grid, private and public Cloud).The authors wish to thank the financial support received from the Generalitat Valenciana for the project GV/2012/076 and to the Ministerio de Econom´ıa y Competitividad for the project CodeCloud (TIN2010-17804)Moltó, G.; Calatrava Arroyo, A.; Hernández García, V. (2013). A service-oriented architecture for scientific computing on cloud infrastructures. En High Performance Computing for Computational Science - VECPAR 2012. Springer Verlag (Germany). 163-176. doi:10.1007/978-3-642-38718-0_18S163176Vaquero, L.M., Rodero-Merino, L., Caceres, J., Lindner, M.: A break in the clouds. ACM SIGCOMM Computer Communication Review 39(1), 50 (2008)Armbrust, M., Fox, A., Griffith, R., Joseph, A.: Above the clouds: A berkeley view of cloud computing. Technical report, UC Berkeley Reliable Adaptive Distributed Systems Laboratory (2009)Rehr, J., Vila, F., Gardner, J., Svec, L., Prange, M.: Scientific computing in the cloud. Computing in Science 99 (2010)Keahey, K., Figueiredo, R., Fortes, J., Freeman, T., Tsugawa, M.: Science Clouds: Early Experiences in Cloud Computing for Scientific Applications. In: Cloud Computing and its Applications (2008)Carrión, J.V., Moltó, G., De Alfonso, C., Caballer, M., Hernández, V.: A Generic Catalog and Repository Service for Virtual Machine Images. In: 2nd International ICST Conference on Cloud Computing (CloudComp 2010) (2010)Moltó, G., Hernández, V., Alonso, J.: A service-oriented WSRF-based architecture for metascheduling on computational Grids. Future Generation Computer Systems 24(4), 317–328 (2008)Krishnan, S., Clementi, L., Ren, J., Papadopoulos, P., Li, W.: Design and Evaluation of Opal2: A Toolkit for Scientific Software as a Service. In: 2009 IEEE Congress on Services (2009)Distributed Management Task Force (DMTF): The Open Virtualization Format Specification (Technical report)Raman, R., Livny, M., Solomon, M.: Matchmaking: Distributed Resource Management for High Throughput Computing. In: Proceedings of the Seventh IEEE International Symposium on High Performance Distributed Computing, pp. 28–31 (1998)Wei, J., Zhang, X., Ammons, G., Bala, V., Ning, P.: Managing security of virtual machine images in a cloud environment. ACM Press, New York (2009)Keahey, K., Freeman, T.: Contextualization: Providing One-Click Virtual Clusters. In: Fourth IEEE International Conference on eScience, pp. 301–308 (2008)Foster, I.: Globus toolkit version 4: Software for service-oriented systems. Journal of Computer Science and Technology 21(4), 513–520 (2006)Moltó, G., Suárez, M., Tortosa, P., Alonso, J.M., Hernández, V., Jaramillo, A.: Protein design based on parallel dimensional reduction. Journal of Chemical Information and Modeling 49(5), 1261–1271 (2009)Calatrava, A.: In: Use of Grid and Cloud Hybrid Infrastructures for Scientific Computing (M.Sc. Thesis in Spanish), Universitat Politècnica de València (2012)Keahey, K., Freeman, T., Lauret, J., Olson, D.: Virtual workspaces for scientific applications. Journal of Physics: Conference Series 78(1), 012038 (2007)Pallickara, S., Pierce, M., Dong, Q., Kong, C.: Enabling Large Scale Scientific Computations for Expressed Sequence Tag Sequencing over Grid and Cloud Computing Clusters. In: Eigth International Conference on Parallel Processing and Applied Mathematics (PPAM 2009), Citeseer (2009)Merzky, A., Stamou, K., Jha, S.: Application Level Interoperability between Clouds and Grids. In: 2009 Workshops at the Grid and Pervasive Computing Conference, pp. 143–150 (2009)Thain, D., Tannenbaum, T., Livny, M.: Distributed computing in practice: the Condor experience. Concurrency and Computation: Practice and Experience 17(2-4), 323–356 (2005)Simmhan, Y., van Ingen, C., Subramanian, G., Li, J.: Bridging the Gap between Desktop and the Cloud for eScience Applications. In: 2010 IEEE 3rd International Conference on Cloud Computing, pp. 474–481. IEEE (2010)Chappell, D.: Introducing windows azure. Technical report (2009

REU Site: Supercomputing Undergraduate Program in Maine (SuperMe)

This award, for a new Research Experience for Undergraduates (REU) site, builds a Supercomputing Undergraduate Program in Maine (SuperMe). This new site provides ten-week summer research experiences at the University of Maine (UMaine) for ten undergraduates each year for three years. With integrated expertise of ten faculty researchers from both computer systems and domain applications, SuperMe allows each undergraduate to conduct meaningful research, such as developing supercomputing techniques and tools, and solving cutting-edge research problems through parallel computing and scientific visualization. Besides being actively involved in research groups, students attend weekly seminars given by faculty mentors, formally report and present their research experiences and results, conduct field trips, and interact with ITEST, RET and GK-12 participants. SuperMe provides scientific exploration ranging from engineering to sciences with a coherent intellectual focus on supercomputing. It consists of four computer systems projects that aim to improve techniques in grid computing, parallel I/O data accesses, high-resolution scientific visualization and information security, and five computer modeling projects that utilize world-class supercomputing and visualization facilities housed at UMaine to perform large, complex simulation experiments and data analysis in different science domains. SuperMe provides a diversity of cutting-edge research opportunities to students from under-represented groups or from universities in rural areas with limited research opportunities. Through interacting directly with the participant of existing programs at UMaine, including ITEST, RET and GK-12, REU students disseminates their research results and experiences to middle and high school students and teachers. This site is co-funded by the Department of Defense in partnership with the NSF REU Site program

MPICH-G2: A Grid-Enabled Implementation of the Message Passing Interface

Application development for distributed computing "Grids" can benefit from tools that variously hide or enable application-level management of critical aspects of the heterogeneous environment. As part of an investigation of these issues, we have developed MPICH-G2, a Grid-enabled implementation of the Message Passing Interface (MPI) that allows a user to run MPI programs across multiple computers, at the same or different sites, using the same commands that would be used on a parallel computer. This library extends the Argonne MPICH implementation of MPI to use services provided by the Globus Toolkit for authentication, authorization, resource allocation, executable staging, and I/O, as well as for process creation, monitoring, and control. Various performance-critical operations, including startup and collective operations, are configured to exploit network topology information. The library also exploits MPI constructs for performance management; for example, the MPI communicator construct is used for application-level discovery of, and adaptation to, both network topology and network quality-of-service mechanisms. We describe the MPICH-G2 design and implementation, present performance results, and review application experiences, including record-setting distributed simulations.Comment: 20 pages, 8 figure

Experiences with porting and modelling wavefront algorithms on many-core architectures

We are currently investigating the viability of many-core architectures for the acceleration of wavefront applications and this report focuses on graphics processing units (GPUs) in particular. To this end, we have implemented NASA’s LU benchmark – a real world production-grade application – on GPUs employing NVIDIA’s Compute Unified Device Architecture (CUDA). This GPU implementation of the benchmark has been used to investigate the performance of a selection of GPUs, ranging from workstation-grade commodity GPUs to the HPC "Tesla” and "Fermi” GPUs. We have also compared the performance of the GPU solution at scale to that of traditional high perfor- mance computing (HPC) clusters based on a range of multi- core CPUs from a number of major vendors, including Intel (Nehalem), AMD (Opteron) and IBM (PowerPC). In previous work we have developed a predictive “plug-and-play” performance model of this class of application running on such clusters, in which CPUs communicate via the Message Passing Interface (MPI). By extending this model to also capture the performance behaviour of GPUs, we are able to: (1) comment on the effects that architectural changes will have on the performance of single-GPU solutions, and (2) make projections regarding the performance of multi-GPU solutions at larger scale

On Evaluating Commercial Cloud Services: A Systematic Review

Background: Cloud Computing is increasingly booming in industry with many competing providers and services. Accordingly, evaluation of commercial Cloud services is necessary. However, the existing evaluation studies are relatively chaotic. There exists tremendous confusion and gap between practices and theory about Cloud services evaluation. Aim: To facilitate relieving the aforementioned chaos, this work aims to synthesize the existing evaluation implementations to outline the state-of-the-practice and also identify research opportunities in Cloud services evaluation. Method: Based on a conceptual evaluation model comprising six steps, the Systematic Literature Review (SLR) method was employed to collect relevant evidence to investigate the Cloud services evaluation step by step. Results: This SLR identified 82 relevant evaluation studies. The overall data collected from these studies essentially represent the current practical landscape of implementing Cloud services evaluation, and in turn can be reused to facilitate future evaluation work. Conclusions: Evaluation of commercial Cloud services has become a world-wide research topic. Some of the findings of this SLR identify several research gaps in the area of Cloud services evaluation (e.g., the Elasticity and Security evaluation of commercial Cloud services could be a long-term challenge), while some other findings suggest the trend of applying commercial Cloud services (e.g., compared with PaaS, IaaS seems more suitable for customers and is particularly important in industry). This SLR study itself also confirms some previous experiences and reveals new Evidence-Based Software Engineering (EBSE) lessons

ParaFPGA 2011 : high performance computing with multiple FPGAs : design, methodology and applications

ParaFPGA 2011 marks the third mini-symposium devoted to the methodology, design and implementation of parallel applications using FPGAs. The focus of the contributions is mainly on organizing parallel applications in multiple FPGAs. This includes experiences from building a supercomputer with FPGAs, automatic and dedicated balancing of different tasks on heterogeneous FPGA constellations and designing optimal interconnects between collaborating FPGAs

Resource provisioning in Science Clouds: Requirements and challenges

Cloud computing has permeated into the information technology industry in the last few years, and it is emerging nowadays in scientific environments. Science user communities are demanding a broad range of computing power to satisfy the needs of high-performance applications, such as local clusters, high-performance computing systems, and computing grids. Different workloads are needed from different computational models, and the cloud is already considered as a promising paradigm. The scheduling and allocation of resources is always a challenging matter in any form of computation and clouds are not an exception. Science applications have unique features that differentiate their workloads, hence, their requirements have to be taken into consideration to be fulfilled when building a Science Cloud. This paper will discuss what are the main scheduling and resource allocation challenges for any Infrastructure as a Service provider supporting scientific applications