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At least 19 records

Locality-aware and load-balanced static task scheduling for MapReduce

Task scheduling for MapReduce jobs has been an active area of research with the objective of decreasing the amount of data transferred during the shuffle phase via exploiting data locality. In the literature, generally only the scheduling of reduce tasks is considered with the assumption that scheduling of map tasks is already determined by the input data placement. However, in cloud or HPC deployments of MapReduce, the input data is located in a remote storage and scheduling map tasks gains importance. Here, we propose models for simultaneous scheduling of map and reduce tasks in order to improve data locality and balance the processors’ loads in both map and reduce phases. Our approach is based on graph and hypergraph models which correctly encode the interactions between map and reduce tasks. Partitions produced by these models are decoded to schedule map and reduce tasks. A two-constraint formulation utilized in these models enables balancing processors’ loads in both map and reduce phases. The partitioning objective in the hypergraph models correctly encapsulates the minimization of data transfer when a local combine step is performed prior to shuffle, whereas the partitioning objective in the graph models achieve the same feat when a local combine is not performed. Here, we show the validity of our scheduling on the MapReduce parallelizations of two important kernel operations – sparse matrix–vector multiplication (SpMV) and generalized sparse matrix–matrix multiplication (SpGEMM) – that are widely encountered in big data analytics and scientific computations. Compared to random scheduling, our models lead to tremendous savings in data transfer by reducing data traffic from several hundreds of megabytes to just a few megabytes in the shuffle phase and consequently leading up to 2.6x and 4.2x speedup for SpMV and SpGEMM, respectively.

97 MATHEMATICS AND COMPUTING↗

Performance Model of MapReduce Iterative Applications for Hybrid Cloud Bursting

Hybrid cloud bursting (i.e., leasing temporary off-premise cloud resources to boost the overall capacity during peak utilization) can be a cost-effective way to deal with the increasing complexity of big data analytics, especially for iterative applications. However, the low throughput, high latency network link between the on-premise and off-premise resources (“weak link”) makes maintaining scalability difficult. While several data locality techniques have been designed for big data bursting on hybrid clouds, their effectiveness is difficult to estimate in advance. Yet such estimations are critical, because they help users decide whether the extra pay-as-you-go cost incurred by using the off-premise resources justifies the runtime speed-up. To this end, the current paper presents a performance model and methodology to estimate the runtime of iterative MapReduce applications in a hybrid cloud-bursting scenario. The paper focuses on the overhead incurred by the weak link at fine granularity, for both the map and the reduce phases. This approach enables high estimation accuracy, as demonstrated by extensive experiments at scale using a mix of real-world iterative MapReduce applications from standard big data benchmarking suites that cover a broad spectrum of data patterns. As a result, not only are the produced estimations accurate in absolute terms compared with experimental results, but they are also up to an order of magnitude more accurate than applying state-of-art estimation approaches originally designed for single-site MapReduce deployments.

97 MATHEMATICS AND COMPUTING↗

Preliminary Evaluation of MapReduce for High-Performance Climate Data Analysis

MapReduce is an approach to high-performance analytics that may be useful to data intensive problems in climate research. It offers an analysis paradigm that uses clusters of computers and combines distributed storage of large data sets with parallel computation. We are particularly interested in the potential of MapReduce to speed up basic operations common to a wide range of analyses. In order to evaluate this potential, we are prototyping a series of canonical MapReduce operations over a test suite of observational and climate simulation datasets. Our initial focus has been on averaging operations over arbitrary spatial and temporal extents within Modern Era Retrospective- Analysis for Research and Applications (MERRA) data. Preliminary results suggest this approach can improve efficiencies within data intensive analytic workflows.

Duffy, Daniel Q.↗

A Spatiotemporal Indexing Approach for Efficient Processing of Big Array-Based Climate Data with MapReduce

Climate observations and model simulations are producing vast amounts of array-based spatiotemporal data. Efficient processing of these data is essential for assessing global challenges such as climate change, natural disasters, and diseases. This is challenging not only because of the large data volume, but also because of the intrinsic high-dimensional nature of geoscience data. To tackle this challenge, we propose a spatiotemporal indexing approach to efficiently manage and process big climate data with MapReduce in a highly scalable environment. Using this approach, big climate data are directly stored in a Hadoop Distributed File System in its original, native file format. A spatiotemporal index is built to bridge the logical array-based data model and the physical data layout, which enables fast data retrieval when performing spatiotemporal queries. Based on the index, a data-partitioning algorithm is applied to enable MapReduce to achieve high data locality, as well as balancing the workload. The proposed indexing approach is evaluated using the National Aeronautics and Space Administration (NASA) Modern-Era Retrospective Analysis for Research and Applications (MERRA) climate reanalysis dataset. The experimental results show that the index can significantly accelerate querying and processing (10 speedup compared to the baseline test using the same computing cluster), while keeping the index-to-data ratio small (0.0328). The applicability of the indexing approach is demonstrated by a climate anomaly detection deployed on a NASA Hadoop cluster. This approach is also able to support efficient processing of general array-based spatiotemporal data in various geoscience domains without special configuration on a Hadoop cluster.

big data↗

Distributed X-ray photon correlation spectroscopy data reduction using Hadoop MapReduce

Multi-speckle X-ray photon correlation spectroscopy (XPCS) is a powerful technique for characterizing the dynamic nature of complex materials over a range of time scales. XPCS has been successfully applied to study a wide range of systems. Recent developments in higher-frame-rate detectors, while aiding in the study of faster dynamical processes, creates large amounts of data that require parallel computational techniques to process in near real-time. Here, an implementation of the multi-tau and two-time autocorrelation algorithms using the Hadoop MapReduce framework for distributed computing is presented. In conclusion, the system scales well with regard to the increase in the data size, and has been serving the users of beamline 8-ID-I at the Advanced Photon Source for near real-time autocorrelations for the past five years.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Predicting Execution Times for Disk-based and In-Situ Parallel Data Analytics (Final Technical Report)

In recent years, there has been a significant amount of interests in in-situ analytics on simulation programs. For a variety of reasons, it is desirable to be able to predict the execution time of an analytics program. At the same time, frameworks such as MapReduce have become popular for scientific data analytics. This paper focuses on developing performance models for predicting execution time of parallel data analytics, with a special emphasis on in-situ analytics. We take two distinct approach towards performance prediction. We first expand SKOPE (a SKeleton framewOrk for Performance Exploration) with performance models for disk data read, cache performance, and page fault penalty. Second, an analytical performance model is also developed. We have evaluated our performance prediction framework as well as the analytical model on three hardware setups with well-known data mining algorithms implemented in three programming paradigms, MapReduce, MATE (a MapReduce-like parallel system with an alternate API for multi-core environments) and Smart (a MapReduce-like framework for in-situ analytics). Results show that our performance prediction framework along with the incorporated performance models are capable of accurately predicting execution times for parallel scientific analytics on different hardware setups.

97 MATHEMATICS AND COMPUTING↗

Fractal Dimension Calculation for Big Data Using Box Locality Index

The box-counting approach for fractal dimension calculation is scaled up for big data using a data structure named box locality index (BLI). The BLI is constructed as key-value pair style with the key (an integer array) indexing the location of a “box” (i.e., a gird cell on the multi-dimensional space embedding a given dataset) and the value counting the number of data points inside the box (called “box occupancy”). Compared with the traditionally used E-dim tree, the BLI avoids complex hierarchical structure and encodes only necessary information required by box-counting approach for fractal dimension calculation. Moreover, the key-value pair nature of BLI, together with the fact that the box occupancy is aggregatable, grants box-counting approach the needed scalability for fractal dimension calculation of big data using distributed computing techniques (e.g., MapReduce and Spark). Taking the advantage of the BLI, MapReduce and Spark methods for fractal dimension calculation of big data are developed, which conduct box-counting for each grid level as a cascade of MapReduce/Spark jobs in a bottom-up fashion. In an empirical validation, the MapReduce and Spark methods demonstrated good effectiveness and efficiency in fractal calculation of a big synthetic dataset. In summary, this work provides an efficient solution for the estimation of intrinsic dimension of big data that is essential for many machine learning methods and data analytics.

Fractal dimension, Intrinsic dimension, Box-counti↗

Hadoop for High-Performance Climate Analytics: Use Cases and Lessons Learned

Scientific data services are a critical aspect of the NASA Center for Climate Simulations mission (NCCS). Hadoop, via MapReduce, provides an approach to high-performance analytics that is proving to be useful to data intensive problems in climate research. It offers an analysis paradigm that uses clusters of computers and combines distributed storage of large data sets with parallel computation. The NCCS is particularly interested in the potential of Hadoop to speed up basic operations common to a wide range of analyses. In order to evaluate this potential, we prototyped a series of canonical MapReduce operations over a test suite of observational and climate simulation datasets. The initial focus was on averaging operations over arbitrary spatial and temporal extents within Modern Era Retrospective- Analysis for Research and Applications (MERRA) data. After preliminary results suggested that this approach improves efficiencies within data intensive analytic workflows, we invested in building a cyber infrastructure resource for developing a new generation of climate data analysis capabilities using Hadoop. This resource is focused on reducing the time spent in the preparation of reanalysis data used in data-model inter-comparison, a long sought goal of the climate community. This paper summarizes the related use cases and lessons learned.

analytics↗

Map reduce using coordination namespace hardware acceleration

A system and method for supporting data MapReduce operations in a tuple space/coordinated namespace (CNS) extended memory storage architecture. The system-wide CNS provides an efficient means for storing and communicating data generated by local processes running at the nodes, and coordinated to provide MapReduce operations in a multi-nodal system. A hardware accelerated mechanism supports map reduce sorting/shuffle operations and reduce operations according to an aggregate function. Local processes running at a node generate a tuple corresponding to data generated by a process, each tuple having a tuple name and tuple data value corresponding to the generated data. Each tuple is processed and stored at the node or another node, dependent upon its tuple name. Tuple records associated with a tuple name are accumulated at one or more nodes according to a linked list structure at each that is accessible via a hash table index pointer at the node.

Jacob, Philip↗

Rendezvous algorithms for large-scale modeling and simulation

Rendezvous algorithms encode a communication pattern that is useful when processors sending data do not know who the receiving processors should be, or vice versa. The idea is to define an intermediate decomposition where datums from different sending processors can ”rendezvous” to perform a computation, in a manner that both the senders and eventual receivers of the results can identify the appropriate rendezvous processor. Though they were originally designed for interpolating between overlaid grids with independent parallel decompositions (Plimpton et al., 2004), we have recently found rendezvous algorithms useful for a variety of operations in particle- or grid-based simulation codes when running large problems on large numbers of processors. In particular, we show they can perform well when a load-balanced intermediate decomposition is randomized and not spatial, requiring all-to-all communication to move data between processors. In this case rendezvous algorithms leverage the large bisection communication bandwidths which parallel machines provide. We describe how rendezvous algorithms work in a scientific computing context and give specific examples for molecular dynamics and Direct Simulation Monte Carlo codes which result in dramatic performance improvements versus simpler algorithms which do not scale as well. We explain how a generic rendezvous algorithm can be implemented, and also point out similarities with the MapReduce paradigm popularized by Google and Hadoop.

97 MATHEMATICS AND COMPUTING↗

Design-time performance modeling of compositional parallel programs

Performance models are powerful instruments for understanding the performance of parallel systems and uncovering their bottlenecks. Already during system design, performance models can help ponder alternative development options. However, creating a performance model – whether theoretically or empirically – for an entire application that does not exist yet is challenging. In this paper, we propose to generate performance models of full programs from performance models of their components using formal composition operators derived from parallel design patterns. As long as the design of the overall system follows such a pattern, its performance model can be predicted with reasonable accuracy without an actual implementation. In conclusion, we demonstrate our approach with design patterns of varying complexity, including pipeline, task pool, and eventually MapReduce, which is representative of a broad class of data-analytics applications.

97 MATHEMATICS AND COMPUTING↗

MERRA Analytic Services: Meeting the Big Data Challenges of Climate Science Through Cloud-enabled Climate Analytics-as-a-service

Climate science is a Big Data domain that is experiencing unprecedented growth. In our efforts to address the Big Data challenges of climate science, we are moving toward a notion of Climate Analytics-as-a-Service (CAaaS). We focus on analytics, because it is the knowledge gained from our interactions with Big Data that ultimately produce societal benefits. We focus on CAaaS because we believe it provides a useful way of thinking about the problem: a specialization of the concept of business process-as-a-service, which is an evolving extension of IaaS, PaaS, and SaaS enabled by Cloud Computing. Within this framework, Cloud Computing plays an important role; however, we it see it as only one element in a constellation of capabilities that are essential to delivering climate analytics as a service. These elements are essential because in the aggregate they lead to generativity, a capacity for self-assembly that we feel is the key to solving many of the Big Data challenges in this domain. MERRA Analytic Services (MERRAAS) is an example of cloud-enabled CAaaS built on this principle. MERRAAS enables MapReduce analytics over NASAs Modern-Era Retrospective Analysis for Research and Applications (MERRA) data collection. The MERRA reanalysis integrates observational data with numerical models to produce a global temporally and spatially consistent synthesis of 26 key climate variables. It represents a type of data product that is of growing importance to scientists doing climate change research and a wide range of decision support applications. MERRAAS brings together the following generative elements in a full, end-to-end demonstration of CAaaS capabilities: (1) high-performance, data proximal analytics, (2) scalable data management, (3) software appliance virtualization, (4) adaptive analytics, and (5) a domain-harmonized API. The effectiveness of MERRAAS has been demonstrated in several applications. In our experience, Cloud Computing lowers the barriers and risk to organizational change, fosters innovation and experimentation, facilitates technology transfer, and provides the agility required to meet our customers' increasing and changing needs. Cloud Computing is providing a new tier in the data services stack that helps connect earthbound, enterprise-level data and computational resources to new customers and new mobility-driven applications and modes of work. For climate science, Cloud Computing's capacity to engage communities in the construction of new capabilies is perhaps the most important link between Cloud Computing and Big Data.

Data Analytics↗

Leveraging the Cloud for Robust and Efficient Lunar Image Processing

The Lunar Mapping and Modeling Project (LMMP) is tasked to aggregate lunar data, from the Apollo era to the latest instruments on the LRO spacecraft, into a central repository accessible by scientists and the general public. A critical function of this task is to provide users with the best solution for browsing the vast amounts of imagery available. The image files LMMP manages range from a few gigabytes to hundreds of gigabytes in size with new data arriving every day. Despite this ever-increasing amount of data, LMMP must make the data readily available in a timely manner for users to view and analyze. This is accomplished by tiling large images into smaller images using Hadoop, a distributed computing software platform implementation of the MapReduce framework, running on a small cluster of machines locally. Additionally, the software is implemented to use Amazon's Elastic Compute Cloud (EC2) facility. We also developed a hybrid solution to serve images to users by leveraging cloud storage using Amazon's Simple Storage Service (S3) for public data while keeping private information on our own data servers. By using Cloud Computing, we improve upon our local solution by reducing the need to manage our own hardware and computing infrastructure, thereby reducing costs. Further, by using a hybrid of local and cloud storage, we are able to provide data to our users more efficiently and securely. 12 This paper examines the use of a distributed approach with Hadoop to tile images, an approach that provides significant improvements in image processing time, from hours to minutes. This paper describes the constraints imposed on the solution and the resulting techniques developed for the hybrid solution of a customized Hadoop infrastructure over local and cloud resources in managing this ever-growing data set. It examines the performance trade-offs of using the more plentiful resources of the cloud, such as those provided by S3, against the bandwidth limitations such use encounters with remote resources. As part of this discussion this paper will outline some of the technologies employed, the reasons for their selection, the resulting performance metrics and the direction the project is headed based upon the demonstrated capabilities thus far.

Cloud Computing↗

MERRA/AS: The MERRA Analytic Services Project Interim Report

MERRA AS is a cyberinfrastructure resource that will combine iRODS-based Climate Data Server (CDS) capabilities with Coudera MapReduce to serve MERRA analytic products, store the MERRA reanalysis data collection in an HDFS to enable parallel, high-performance, storage-side data reductions, manage storage-side driver, mapper, reducer code sets and realized objects for users, and provide a library of commonly used spatiotemporal operations that can be composed to enable higher-order analyses.

MapReduce↗

Co-location Pattern Mining of Geosocial Data to Characterize Urban Functional Spaces

Spatial Co-location Pattern (SCP) mining continues to play a critical role in understanding the morphology of urban functional spaces of world cities. It requires a large amount of fine-granular data and computing efficiency to handle the combinatorial explosion of co-location patterns. To this end, this work has two main contributions - i) We showcase a novel approach to perform SCP mining to characterize intra-city scale structure of urban functionality or co-located activity patterns using geosocial Points-of-Interest (POI) vector data. ii) We present a generalized and optimized parallel/distributed SCP mining algorithm implemented on a Hadoop MapReduce system and demonstrate the utility of our approach using the city of Berlin (Germany) as an example. The SCPs tend to vary across Berlin's municipal boroughs and at different spatial scales. Our findings on Berlin's functional structure conform to existing urban geography models. Such a data-driven exploration of massive urban POIs using distributed computing is first of its kind and can help better understand the changing dynamics of urban functionality, as well as physical, and social network structure around the world.

Masrur, Arif↗

DECA: scalable XHMM exome copy-number variant calling with ADAM and Apache Spark

Abstract Background XHMM is a widely used tool for copy-number variant (CNV) discovery from whole exome sequencing data but can require hours to days to run for large cohorts. A more scalable implementation would reduce the need for specialized computational resources and enable increased exploration of the configuration parameter space to obtain the best possible results. Results DECA is a horizontally scalable implementation of the XHMM algorithm using the ADAM framework and Apache Spark that incorporates novel algorithmic optimizations to eliminate unneeded computation. DECA parallelizes XHMM on both multi-core shared memory computers and large shared-nothing Spark clusters. We performed CNV discovery from the read-depth matrix in 2535 exomes in 9.3 min on a 16-core workstation (35.3× speedup vs. XHMM), 12.7 min using 10 executor cores on a Spark cluster (18.8× speedup vs. XHMM), and 9.8 min using 32 executor cores on Amazon AWS’ Elastic MapReduce. We performed CNV discovery from the original BAM files in 292 min using 640 executor cores on a Spark cluster. Conclusions We describe DECA’s performance, our algorithmic and implementation enhancements to XHMM to obtain that performance, and our lessons learned porting a complex genome analysis application to ADAM and Spark. ADAM and Apache Spark are a performant and productive platform for implementing large-scale genome analyses, but efficiently utilizing large clusters can require algorithmic optimizations and careful attention to Spark’s configuration parameters.

Linderman, Michael D. (ORCID:0000000296437148)↗

A Magnetoencephalographic/Encephalographic (MEG/EEG) Brain-Computer Interface Driver for Interactive iOS Mobile Videogame Applications Utilizing the Hadoop Ecosystem, MongoDB, and Cassandra NoSQL Databases

In Phase I, we collected data on five subjects yielding over 90% positive performance in Magnetoencephalographic (MEG) mid-and post-movement activity. In addition, a driver was developed that substituted the actions of the Brain Computer Interface (BCI) as mouse button presses for real-time use in visual simulations. The process was interfaced to a flight visualization demonstration utilizing left or right brainwave thought movement, the user experiences, the aircraft turning in the chosen direction, or on iOS Mobile Warfighter Videogame application. The BCI’s data analytics of a subject’s MEG brain waves and flight visualization performance videogame analytics were stored and analyzed using the Hadoop Ecosystem as a quick retrieval data warehouse. In Phase II portion of the project involves the Emotiv Encephalographic (EEG) Wireless Brain–Computer interfaces (BCIs) allow for people to establish a novel communication channel between the human brain and a machine, in this case, an iOS Mobile Application(s). The EEG BCI utilizes advanced and novel machine learning algorithms, as well as the Spark Directed Acyclic Graph (DAG), Cassandra NoSQL database environment, and also the competitor NoSQL MongoDB database for housing BCI analytics of subject’s response and users’ intent illustrated for both MEG/EEG brainwave signal acquisition. The wireless EEG signals that were acquired from the OpenVibe and the Emotiv EPOC headset can be connected via Bluetooth to an iPhone utilizing a thin Client architecture. The use of NoSQL databases were chosen because of its schema-less architecture and Map Reduce computational paradigm algorithm for housing a user’s brain signals from each referencing sensor. Thus, in the near future, if multiple users are playing on an online network connection and an MEG/EEG sensor fails, or if the connection is lost from the smartphone and the webserver due to low battery power or failed data transmission, it will not nullify the NoSQL document-oriented (MongoDB) or column-oriented Cassandra databases. Additionally, NoSQL databases have fast querying and indexing methodologies, which are perfect for online game analytics and technology. In Phase II, we collected data on five MEG subjects, yielding over 90% positive performance on iOS Mobile Applications with Objective-C and C++, however on EEG signals utilized on three subjects with the Emotiv wireless headsets and (n < 10) subjects from the OpenVibe EEG database the Variational Bayesian Factor Analysis Algorithm (VBFA) yielded below 60% performance and we are currently pursuing extending the VBFA algorithm to work in the time-frequency domain referred to as VBFA-TF to enhance EEG performance in the near future. The novel usage of NoSQL databases, Cassandra and MongoDB, were the primary main enhancements of the BCI Phase II MEG/EEG brain signal data acquisition, queries, and rapid analytics, with MapReduce and Spark DAG demonstrating future implications for next generation biometric MEG/EEG NoSQL databases.

McClay, Wilbert↗