22,447 research outputs found
Predicting Intermediate Storage Performance for Workflow Applications
Configuring a storage system to better serve an application is a challenging
task complicated by a multidimensional, discrete configuration space and the
high cost of space exploration (e.g., by running the application with different
storage configurations). To enable selecting the best configuration in a
reasonable time, we design an end-to-end performance prediction mechanism that
estimates the turn-around time of an application using storage system under a
given configuration. This approach focuses on a generic object-based storage
system design, supports exploring the impact of optimizations targeting
workflow applications (e.g., various data placement schemes) in addition to
other, more traditional, configuration knobs (e.g., stripe size or replication
level), and models the system operation at data-chunk and control message
level.
This paper presents our experience to date with designing and using this
prediction mechanism. We evaluate this mechanism using micro- as well as
synthetic benchmarks mimicking real workflow applications, and a real
application.. A preliminary evaluation shows that we are on a good track to
meet our objectives: it can scale to model a workflow application run on an
entire cluster while offering an over 200x speedup factor (normalized by
resource) compared to running the actual application, and can achieve, in the
limited number of scenarios we study, a prediction accuracy that enables
identifying the best storage system configuration
A Taxonomy of Workflow Management Systems for Grid Computing
With the advent of Grid and application technologies, scientists and
engineers are building more and more complex applications to manage and process
large data sets, and execute scientific experiments on distributed resources.
Such application scenarios require means for composing and executing complex
workflows. Therefore, many efforts have been made towards the development of
workflow management systems for Grid computing. In this paper, we propose a
taxonomy that characterizes and classifies various approaches for building and
executing workflows on Grids. We also survey several representative Grid
workflow systems developed by various projects world-wide to demonstrate the
comprehensiveness of the taxonomy. The taxonomy not only highlights the design
and engineering similarities and differences of state-of-the-art in Grid
workflow systems, but also identifies the areas that need further research.Comment: 29 pages, 15 figure
Enhancing Energy Production with Exascale HPC Methods
High Performance Computing (HPC) resources have become the key actor for achieving more ambitious challenges in many disciplines. In this step beyond, an explosion on the available parallelism and the use of special purpose
processors are crucial. With such a goal, the HPC4E project applies new exascale HPC techniques to energy industry simulations, customizing them if necessary, and going beyond the state-of-the-art in the required HPC exascale
simulations for different energy sources. In this paper, a general overview of these methods is presented as well as some specific preliminary results.The research leading to these results has received funding from the European Union's Horizon 2020 Programme (2014-2020) under the HPC4E Project (www.hpc4e.eu), grant agreement n° 689772, the Spanish Ministry of
Economy and Competitiveness under the CODEC2 project (TIN2015-63562-R), and
from the Brazilian Ministry of Science, Technology and Innovation through Rede
Nacional de Pesquisa (RNP). Computer time on Endeavour cluster is provided by the
Intel Corporation, which enabled us to obtain the presented experimental results in
uncertainty quantification in seismic imagingPostprint (author's final draft
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
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
- …