32,273 research outputs found
Workflow environments for advanced cyberinfrastructure platforms
Progress in science is deeply bound to the effective use of high-performance computing infrastructures and to the efficient extraction of knowledge from vast amounts of data. Such data comes from different sources that follow a cycle composed of pre-processing steps for data curation and preparation for subsequent computing steps, and later analysis and analytics steps applied to the results. However, scientific workflows are currently fragmented in multiple components, with different processes for computing and data management, and with gaps in the viewpoints of the user profiles involved. Our vision is that future workflow environments and tools for the development of scientific workflows should follow a holistic approach, where both data and computing are integrated in a single flow built on simple, high-level interfaces. The topics of research that we propose involve novel ways to express the workflows that integrate the different data and compute processes, dynamic runtimes to support the execution of the workflows in complex and heterogeneous computing infrastructures in an efficient way, both in terms of performance and energy. These infrastructures include highly distributed resources, from sensors and instruments, and devices in the edge, to High-Performance Computing and Cloud computing resources. This paper presents our vision to develop these workflow environments and also the steps we are currently following to achieve it.This work has been supported by the Spanish Government (SEV2015-0493), by the Spanish Ministry of Science and Innovation (contract TIN2015-65316-P), by Generalitat de Catalunya (contract 2014-SGR-1051). Javier Conejero postdoctoral contract is co-financed by the Ministry of Economy and Competitiveness under Juan de la Cierva Formacion´ postdoctoral fellowship number FJCI-2015-24651. This work is supported by the H2020 mF2C project (730929) and the CLASS project (780622). The participation of Rosa M Badia in the BDEC2 meetings is supported by the EXDCI project (800957). The dislib library developments are partially funded under the project agreement between BSC and FUJITSU.Peer ReviewedPostprint (author's final draft
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
CERN openlab Whitepaper on Future IT Challenges in Scientific Research
This whitepaper describes the major IT challenges in scientific research at CERN and several other European and international research laboratories and projects. Each challenge is exemplified through a set of concrete use cases drawn from the requirements of large-scale scientific programs. The paper is based on contributions from many researchers and IT experts of the participating laboratories and also input from the existing CERN openlab industrial sponsors. The views expressed in this document are those of the individual contributors and do not necessarily reflect the view of their organisations and/or affiliates
BioWorkbench: A High-Performance Framework for Managing and Analyzing Bioinformatics Experiments
Advances in sequencing techniques have led to exponential growth in
biological data, demanding the development of large-scale bioinformatics
experiments. Because these experiments are computation- and data-intensive,
they require high-performance computing (HPC) techniques and can benefit from
specialized technologies such as Scientific Workflow Management Systems (SWfMS)
and databases. In this work, we present BioWorkbench, a framework for managing
and analyzing bioinformatics experiments. This framework automatically collects
provenance data, including both performance data from workflow execution and
data from the scientific domain of the workflow application. Provenance data
can be analyzed through a web application that abstracts a set of queries to
the provenance database, simplifying access to provenance information. We
evaluate BioWorkbench using three case studies: SwiftPhylo, a phylogenetic tree
assembly workflow; SwiftGECKO, a comparative genomics workflow; and RASflow, a
RASopathy analysis workflow. We analyze each workflow from both computational
and scientific domain perspectives, by using queries to a provenance and
annotation database. Some of these queries are available as a pre-built feature
of the BioWorkbench web application. Through the provenance data, we show that
the framework is scalable and achieves high-performance, reducing up to 98% of
the case studies execution time. We also show how the application of machine
learning techniques can enrich the analysis process
Next Generation Cloud Computing: New Trends and Research Directions
The landscape of cloud computing has significantly changed over the last
decade. Not only have more providers and service offerings crowded the space,
but also cloud infrastructure that was traditionally limited to single provider
data centers is now evolving. In this paper, we firstly discuss the changing
cloud infrastructure and consider the use of infrastructure from multiple
providers and the benefit of decentralising computing away from data centers.
These trends have resulted in the need for a variety of new computing
architectures that will be offered by future cloud infrastructure. These
architectures are anticipated to impact areas, such as connecting people and
devices, data-intensive computing, the service space and self-learning systems.
Finally, we lay out a roadmap of challenges that will need to be addressed for
realising the potential of next generation cloud systems.Comment: Accepted to Future Generation Computer Systems, 07 September 201
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