14,691 research outputs found
MPI-Vector-IO: Parallel I/O and Partitioning for Geospatial Vector Data
In recent times, geospatial datasets are growing in terms of size, complexity and heterogeneity. High performance systems are needed to analyze such data to produce actionable insights in an efficient manner. For polygonal a.k.a vector datasets, operations such as I/O, data partitioning, communication, and load balancing becomes challenging in a cluster environment. In this work, we present MPI-Vector-IO 1 , a parallel I/O library that we have designed using MPI-IO specifically for partitioning and reading irregular vector data formats such as Well Known Text. It makes MPI aware of spatial data, spatial primitives and provides support for spatial data types embedded within collective computation and communication using MPI message-passing library. These abstractions along with parallel I/O support are useful for parallel Geographic Information System (GIS) application development on HPC platforms
Scalable Solutions for Automated Single Pulse Identification and Classification in Radio Astronomy
Data collection for scientific applications is increasing exponentially and
is forecasted to soon reach peta- and exabyte scales. Applications which
process and analyze scientific data must be scalable and focus on execution
performance to keep pace. In the field of radio astronomy, in addition to
increasingly large datasets, tasks such as the identification of transient
radio signals from extrasolar sources are computationally expensive. We present
a scalable approach to radio pulsar detection written in Scala that
parallelizes candidate identification to take advantage of in-memory task
processing using Apache Spark on a YARN distributed system. Furthermore, we
introduce a novel automated multiclass supervised machine learning technique
that we combine with feature selection to reduce the time required for
candidate classification. Experimental testing on a Beowulf cluster with 15
data nodes shows that the parallel implementation of the identification
algorithm offers a speedup of up to 5X that of a similar multithreaded
implementation. Further, we show that the combination of automated multiclass
classification and feature selection speeds up the execution performance of the
RandomForest machine learning algorithm by an average of 54% with less than a
2% average reduction in the algorithm's ability to correctly classify pulsars.
The generalizability of these results is demonstrated by using two real-world
radio astronomy data sets.Comment: In Proceedings of the 47th International Conference on Parallel
Processing (ICPP 2018). ACM, New York, NY, USA, Article 11, 11 page
A Survey on Array Storage, Query Languages, and Systems
Since scientific investigation is one of the most important providers of
massive amounts of ordered data, there is a renewed interest in array data
processing in the context of Big Data. To the best of our knowledge, a unified
resource that summarizes and analyzes array processing research over its long
existence is currently missing. In this survey, we provide a guide for past,
present, and future research in array processing. The survey is organized along
three main topics. Array storage discusses all the aspects related to array
partitioning into chunks. The identification of a reduced set of array
operators to form the foundation for an array query language is analyzed across
multiple such proposals. Lastly, we survey real systems for array processing.
The result is a thorough survey on array data storage and processing that
should be consulted by anyone interested in this research topic, independent of
experience level. The survey is not complete though. We greatly appreciate
pointers towards any work we might have forgotten to mention.Comment: 44 page
Shingle 2.0: generalising self-consistent and automated domain discretisation for multi-scale geophysical models
The approaches taken to describe and develop spatial discretisations of the
domains required for geophysical simulation models are commonly ad hoc, model
or application specific and under-documented. This is particularly acute for
simulation models that are flexible in their use of multi-scale, anisotropic,
fully unstructured meshes where a relatively large number of heterogeneous
parameters are required to constrain their full description. As a consequence,
it can be difficult to reproduce simulations, ensure a provenance in model data
handling and initialisation, and a challenge to conduct model intercomparisons
rigorously. This paper takes a novel approach to spatial discretisation,
considering it much like a numerical simulation model problem of its own. It
introduces a generalised, extensible, self-documenting approach to carefully
describe, and necessarily fully, the constraints over the heterogeneous
parameter space that determine how a domain is spatially discretised. This
additionally provides a method to accurately record these constraints, using
high-level natural language based abstractions, that enables full accounts of
provenance, sharing and distribution. Together with this description, a
generalised consistent approach to unstructured mesh generation for geophysical
models is developed, that is automated, robust and repeatable, quick-to-draft,
rigorously verified and consistent to the source data throughout. This
interprets the description above to execute a self-consistent spatial
discretisation process, which is automatically validated to expected discrete
characteristics and metrics.Comment: 18 pages, 10 figures, 1 table. Submitted for publication and under
revie
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
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
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