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Storing and manipulating environmental big data with JASMIN
JASMIN is a super-data-cluster designed to provide
a high-performance high-volume data analysis environment for
the UK environmental science community. Thus far JASMIN
has been used primarily by the atmospheric science and earth
observation communities, both to support their direct scientific workflow, and the curation of data products in the STFC Centre for Environmental Data Archival (CEDA). Initial JASMIN configuration and first experiences are reported here. Useful improvements in scientific workflow are presented. It is clear from the explosive growth in stored data and use that there was a pent up demand for a suitable big-data analysis environment.
This demand is not yet satisfied, in part because JASMIN does not yet have enough compute, the storage is fully allocated, and not all software needs are met. Plans to address these constraints are introduced
Distributed Computing in a Pandemic: A Review of Technologies Available for Tackling COVID-19
The current COVID-19 global pandemic caused by the SARS-CoV-2 betacoronavirus
has resulted in over a million deaths and is having a grave socio-economic
impact, hence there is an urgency to find solutions to key research challenges.
Much of this COVID-19 research depends on distributed computing. In this
article, I review distributed architectures -- various types of clusters, grids
and clouds -- that can be leveraged to perform these tasks at scale, at
high-throughput, with a high degree of parallelism, and which can also be used
to work collaboratively. High-performance computing (HPC) clusters will be used
to carry out much of this work. Several bigdata processing tasks used in
reducing the spread of SARS-CoV-2 require high-throughput approaches, and a
variety of tools, which Hadoop and Spark offer, even using commodity hardware.
Extremely large-scale COVID-19 research has also utilised some of the world's
fastest supercomputers, such as IBM's SUMMIT -- for ensemble docking
high-throughput screening against SARS-CoV-2 targets for drug-repurposing, and
high-throughput gene analysis -- and Sentinel, an XPE-Cray based system used to
explore natural products. Grid computing has facilitated the formation of the
world's first Exascale grid computer. This has accelerated COVID-19 research in
molecular dynamics simulations of SARS-CoV-2 spike protein interactions through
massively-parallel computation and was performed with over 1 million volunteer
computing devices using the Folding@home platform. Grids and clouds both can
also be used for international collaboration by enabling access to important
datasets and providing services that allow researchers to focus on research
rather than on time-consuming data-management tasks.Comment: 21 pages (15 excl. refs), 2 figures, 3 table
Stocator: A High Performance Object Store Connector for Spark
We present Stocator, a high performance object store connector for Apache
Spark, that takes advantage of object store semantics. Previous connectors have
assumed file system semantics, in particular, achieving fault tolerance and
allowing speculative execution by creating temporary files to avoid
interference between worker threads executing the same task and then renaming
these files. Rename is not a native object store operation; not only is it not
atomic, but it is implemented using a costly copy operation and a delete.
Instead our connector leverages the inherent atomicity of object creation, and
by avoiding the rename paradigm it greatly decreases the number of operations
on the object store as well as enabling a much simpler approach to dealing with
the eventually consistent semantics typical of object stores. We have
implemented Stocator and shared it in open source. Performance testing shows
that it is as much as 18 times faster for write intensive workloads and
performs as much as 30 times fewer operations on the object store than the
legacy Hadoop connectors, reducing costs both for the client and the object
storage service provider
An Approach to Ad hoc Cloud Computing
We consider how underused computing resources within an enterprise may be
harnessed to improve utilization and create an elastic computing
infrastructure. Most current cloud provision involves a data center model, in
which clusters of machines are dedicated to running cloud infrastructure
software. We propose an additional model, the ad hoc cloud, in which
infrastructure software is distributed over resources harvested from machines
already in existence within an enterprise. In contrast to the data center cloud
model, resource levels are not established a priori, nor are resources
dedicated exclusively to the cloud while in use. A participating machine is not
dedicated to the cloud, but has some other primary purpose such as running
interactive processes for a particular user. We outline the major
implementation challenges and one approach to tackling them
Virtual Cluster Management for Analysis of Geographically Distributed and Immovable Data
Thesis (Ph.D.) - Indiana University, Informatics and Computing, 2015Scenarios exist in the era of Big Data where computational analysis needs to utilize widely distributed and remote compute clusters, especially when the data sources are sensitive or extremely large, and thus unable to move. A large dataset in Malaysia could be ecologically sensitive, for instance, and unable to be moved outside the country boundaries. Controlling an analysis experiment in this virtual cluster setting can be difficult on multiple levels: with setup and control, with managing behavior of the virtual cluster, and with interoperability issues across the compute clusters. Further, datasets can be distributed among clusters, or even across data centers, so that it becomes critical to utilize data locality information to optimize the performance of data-intensive jobs. Finally, datasets are increasingly sensitive and tied to certain administrative boundaries, though once the data has been processed, the aggregated or statistical result can be shared across the boundaries. This dissertation addresses management and control of a widely distributed virtual cluster having sensitive or otherwise immovable data sets through a controller. The Virtual Cluster Controller (VCC) gives control back to the researcher. It creates virtual clusters across multiple cloud platforms. In recognition of sensitive data, it can establish a single network overlay over widely distributed clusters. We define a novel class of data, notably immovable data that we call "pinned data", where the data is treated as a first-class citizen instead of being moved to where needed. We draw from our earlier work with a hierarchical data processing model, Hierarchical MapReduce (HMR), to process geographically distributed data, some of which are pinned data. The applications implemented in HMR use extended MapReduce model where computations are expressed as three functions: Map, Reduce, and GlobalReduce. Further, by facilitating information sharing among resources, applications, and data, the overall performance is improved. Experimental results show that the overhead of VCC is minimum. The HMR outperforms traditional MapReduce model while processing a particular class of applications. The evaluations also show that information sharing between resources and application through the VCC shortens the hierarchical data processing time, as well satisfying the constraints on the pinned data
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