20,480 research outputs found
A Taxonomy of Data Grids for Distributed Data Sharing, Management and Processing
Data Grids have been adopted as the platform for scientific communities that
need to share, access, transport, process and manage large data collections
distributed worldwide. They combine high-end computing technologies with
high-performance networking and wide-area storage management techniques. In
this paper, we discuss the key concepts behind Data Grids and compare them with
other data sharing and distribution paradigms such as content delivery
networks, peer-to-peer networks and distributed databases. We then provide
comprehensive taxonomies that cover various aspects of architecture, data
transportation, data replication and resource allocation and scheduling.
Finally, we map the proposed taxonomy to various Data Grid systems not only to
validate the taxonomy but also to identify areas for future exploration.
Through this taxonomy, we aim to categorise existing systems to better
understand their goals and their methodology. This would help evaluate their
applicability for solving similar problems. This taxonomy also provides a "gap
analysis" of this area through which researchers can potentially identify new
issues for investigation. Finally, we hope that the proposed taxonomy and
mapping also helps to provide an easy way for new practitioners to understand
this complex area of research.Comment: 46 pages, 16 figures, Technical Repor
A Tale of Two Data-Intensive Paradigms: Applications, Abstractions, and Architectures
Scientific problems that depend on processing large amounts of data require
overcoming challenges in multiple areas: managing large-scale data
distribution, co-placement and scheduling of data with compute resources, and
storing and transferring large volumes of data. We analyze the ecosystems of
the two prominent paradigms for data-intensive applications, hereafter referred
to as the high-performance computing and the Apache-Hadoop paradigm. We propose
a basis, common terminology and functional factors upon which to analyze the
two approaches of both paradigms. We discuss the concept of "Big Data Ogres"
and their facets as means of understanding and characterizing the most common
application workloads found across the two paradigms. We then discuss the
salient features of the two paradigms, and compare and contrast the two
approaches. Specifically, we examine common implementation/approaches of these
paradigms, shed light upon the reasons for their current "architecture" and
discuss some typical workloads that utilize them. In spite of the significant
software distinctions, we believe there is architectural similarity. We discuss
the potential integration of different implementations, across the different
levels and components. Our comparison progresses from a fully qualitative
examination of the two paradigms, to a semi-quantitative methodology. We use a
simple and broadly used Ogre (K-means clustering), characterize its performance
on a range of representative platforms, covering several implementations from
both paradigms. Our experiments provide an insight into the relative strengths
of the two paradigms. We propose that the set of Ogres will serve as a
benchmark to evaluate the two paradigms along different dimensions.Comment: 8 pages, 2 figure
Optimizing Splicing Junction Detection in Next Generation Sequencing Data on a Virtual-GRID Infrastructure
The new protocol for sequencing the messenger RNA in a cell, named RNA-seq produce millions of short sequence fragments. Next Generation Sequencing technology allows more accurate analysis but increase needs in term of computational resources. This paper describes the optimization of a RNA-seq analysis pipeline devoted to splicing variants detection, aimed at reducing computation time and providing a multi-user/multisample environment. This work brings two main contributions. First, we optimized a well-known algorithm called TopHat by parallelizing some sequential mapping steps. Second, we designed and implemented a hybrid virtual GRID infrastructure allowing to efficiently execute multiple instances of TopHat running on different samples or on behalf of different users, thus optimizing the overall execution time and enabling a flexible multi-user environmen
Grid Infrastructure for Domain Decomposition Methods in Computational ElectroMagnetics
The accurate and efficient solution of Maxwell's equation is the problem addressed by the scientific discipline called Computational ElectroMagnetics (CEM). Many macroscopic phenomena in a great number of fields are governed by this set of differential equations: electronic, geophysics, medical and biomedical technologies, virtual EM prototyping, besides the traditional antenna and propagation applications. Therefore, many efforts are focussed on the development of new and more efficient approach to solve Maxwell's equation. The interest in CEM applications is growing on. Several problems, hard to figure out few years ago, can now be easily addressed thanks to the reliability and flexibility of new technologies, together with the increased computational power. This technology evolution opens the possibility to address large and complex tasks. Many of these applications aim to simulate the electromagnetic behavior, for example in terms of input impedance and radiation pattern in antenna problems, or Radar Cross Section for scattering applications. Instead, problems, which solution requires high accuracy, need to implement full wave analysis techniques, e.g., virtual prototyping context, where the objective is to obtain reliable simulations in order to minimize measurement number, and as consequence their cost. Besides, other tasks require the analysis of complete structures (that include an high number of details) by directly simulating a CAD Model. This approach allows to relieve researcher of the burden of removing useless details, while maintaining the original complexity and taking into account all details. Unfortunately, this reduction implies: (a) high computational effort, due to the increased number of degrees of freedom, and (b) worsening of spectral properties of the linear system during complex analysis. The above considerations underline the needs to identify appropriate information technologies that ease solution achievement and fasten required elaborations. The authors analysis and expertise infer that Grid Computing techniques can be very useful to these purposes. Grids appear mainly in high performance computing environments. In this context, hundreds of off-the-shelf nodes are linked together and work in parallel to solve problems, that, previously, could be addressed sequentially or by using supercomputers. Grid Computing is a technique developed to elaborate enormous amounts of data and enables large-scale resource sharing to solve problem by exploiting distributed scenarios. The main advantage of Grid is due to parallel computing, indeed if a problem can be split in smaller tasks, that can be executed independently, its solution calculation fasten up considerably. To exploit this advantage, it is necessary to identify a technique able to split original electromagnetic task into a set of smaller subproblems. The Domain Decomposition (DD) technique, based on the block generation algorithm introduced in Matekovits et al. (2007) and Francavilla et al. (2011), perfectly addresses our requirements (see Section 3.4 for details). In this chapter, a Grid Computing infrastructure is presented. This architecture allows parallel block execution by distributing tasks to nodes that belong to the Grid. The set of nodes is composed by physical machines and virtualized ones. This feature enables great flexibility and increase available computational power. Furthermore, the presence of virtual nodes allows a full and efficient Grid usage, indeed the presented architecture can be used by different users that run different applications
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
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