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

Intermediate Palomar Transient Factory: Realtime Image Subtraction Pipeline

A fast-turnaround pipeline for realtime data reduction plays an essential role in discovering and permitting follow-up observations to young supernovae and fast-evolving transients in modern time-domain surveys. In this paper, we present the realtime image subtraction pipeline in the intermediate Palomar Transient Factory. By using high-performance computing, efficient database, and machine learning algorithms, this pipeline manages to reliably deliver transient candidates within ten minutes of images being taken. Our experience in using high performance computing resources to process big data in astronomy serves as a trailblazer to dealing with data from large-scale time-domain facilities in near future.Comment: 18 pages, 6 figures, accepted for publication in PAS

Gurret: Decentralized data management using subscription-based file attribute propagation

Research institutions and funding agencies are increasingly adopting open-data science, where data is freely available or available under some data sharing policy. In addition to making publication efforts easier, open data science also promotes collaborative work using data from various sources around the world. While the research datasets are often static and immutable, the metadata of a file can be ever-changing. For researchers who frequently work with metadata, accessing the latest version may be essential. However, this is not trivial in a distributed environment where multiple people access the same file. We hypothesize that the publisher subscriber model is a useful abstraction to achieve this system. To this, we present Gurret: a distributed system for open science that uses a publisher-subscriber based substrate to propagate metadata updates to client machines. Gurret offers a transparent system infrastructure that lets users subscribe to metadata, configure update frequencies, and define custom metadata to create data policies. Additionally, Gurret tracks information flow inside a filesystem container to prevent data leakage and policy violations. Our evaluations show that Gurret has minimal overhead for small to medium-sized files and that Gurret can support hundreds of custom metadata without losing transparency

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

Self-adaptive Grid Resource Monitoring and discovery

The Grid provides a novel platform where the scientific and engineering communities can share data and computation across multiple administrative domains. There are several key services that must be offered by Grid middleware; one of them being the Grid Information Service( GIS). A GIS is a Grid middleware component which maintains information about hardware, software, services and people participating in a virtual organisation( VO). There is an inherent need in these systems for the delivery of reliable performance. This thesis describes a number of approaches which detail the development and application of a suite of benchmarks for the prediction of the process of resource discovery and monitoring on the Grid. A series of experimental studies of the characterisation of performance using benchmarking, are carried out. Several novel predictive algorithms are presented and evaluated in terms of their predictive error. Furthermore, predictive methods are developed which describe the behaviour of MDS2 for a variable number of user requests. The MDS is also extended to include job information from a local scheduler; this information is queried using requests of greatly varying complexity. The response of the MDS to these queries is then assessed in terms of several performance metrics. The benchmarking of the dynamic nature of information within MDS3 which is based on the Open Grid Services Architecture (OGSA), and also the successor to MDS2, is also carried out. The performance of both the pull and push query mechanisms is analysed. GridAdapt (Self-adaptive Grid Resource Monitoring) is a new system that is proposed, built upon the Globus MDS3 benchmarking. It offers self-adaptation, autonomy and admission control at the Index Service, whilst ensuring that the MIDS is not overloaded and can meet its quality-of-service,f or example,i n terms of its average response time for servicing synchronous queries and the total number of queries returned per unit time

Federation of compute resources available to the German CMS community

The German CMS community (DCMS) as a whole can benefit from the various compute resources, available to its different institutes. While Grid-enabled and National Analysis Facility resources are usually shared within the community, local and recently enabled opportunistic resources like HPC centers and cloud resources are not. Furthermore, there is no shared submission infrastructure available. Via HTCondor\u27s [1] mechanisms to connect resource pools, several remote pools can be connected transparently to the users and therefore used more efficiently by a multitude of user groups. In addition to the statically provisioned resources, also dynamically allocated resources from external cloud providers as well as HPC centers can be integrated. However, the usage of such dynamically allocated resources gives rise to additional complexity. Constraints on access policies of the resources, as well as workflow necessities have to be taken care of. To maintain a well-defined and reliable runtime environment on each resource, virtualization and containerization technologies such as virtual machines, Docker, and Singularity, are used

Design considerations for workflow management systems use in production genomics research and the clinic

Abstract The changing landscape of genomics research and clinical practice has created a need for computational pipelines capable of efficiently orchestrating complex analysis stages while handling large volumes of data across heterogeneous computational environments. Workflow Management Systems (WfMSs) are the software components employed to fill this gap. This work provides an approach and systematic evaluation of key features of popular bioinformatics WfMSs in use today: Nextflow, CWL, and WDL and some of their executors, along with Swift/T, a workflow manager commonly used in high-scale physics applications. We employed two use cases: a variant-calling genomic pipeline and a scalability-testing framework, where both were run locally, on an HPC cluster, and in the cloud. This allowed for evaluation of those four WfMSs in terms of language expressiveness, modularity, scalability, robustness, reproducibility, interoperability, ease of development, along with adoption and usage in research labs and healthcare settings. This article is trying to answer, which WfMS should be chosen for a given bioinformatics application regardless of analysis type?. The choice of a given WfMS is a function of both its intrinsic language and engine features. Within bioinformatics, where analysts are a mix of dry and wet lab scientists, the choice is also governed by collaborations and adoption within large consortia and technical support provided by the WfMS team/community. As the community and its needs continue to evolve along with computational infrastructure, WfMSs will also evolve, especially those with permissive licenses that allow commercial use. In much the same way as the dataflow paradigm and containerization are now well understood to be very useful in bioinformatics applications, we will continue to see innovations of tools and utilities for other purposes, like big data technologies, interoperability, and provenance