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Software [clear filter]
Tuesday, July 19
 

10:30am EDT

SW: A Virtual Filesystem for On-demand Processing of Multi-dimensional Datasets
Diverse areas of science and engineering are increasingly driven by high-throughput automated data capture and analysis. Modern acquisition technologies, used in many scientific applications (e.g., astronomy, physics, materials science, geology, biology, and engineering) and often running at gigabyte per second data rates, quickly generate terabyte to petabyte datasets that must be stored, shared, processed and analyzed at similar rates. The largest datasets are often multidimensional, such as volumetric and time series data derived from various types of image capture. Cost-effective and timely processing of these data requires system and software architectures that incorporate on-the-fly processing to minimize I/O traffic and avoid latency limitations. In this paper we present the Virtual Volume File System, a new approach to on-demand processing with file system semantics, combining these principles into a versatile and powerful data pipeline for dealing with some of the largest 3D volumetric datasets. We give an example of how we have started to use this approach in our work with massive electron microscopy image stacks. We end with a short discussion of current and future challenges.


Tuesday July 19, 2016 10:30am - 11:00am EDT
Brickell

11:00am EDT

SW: An Architecture for Automatic Deployment of Brown Dog Services At Scale into Diverse Computing Infrastructures
Brown Dog is an extensible data cyberinfrastructure, that provides a set of extensible and distributed data conversion and metadata extraction services to enable access and search within unstructured, un-curated and inaccessible research data across different domains of sciences and social science, which ultimately aids in supporting reproducibility of results. We envision that Brown Dog, as a data cyberinfrastructure, is an essential service in a comprehensive cyberinfrastructure which includes data services, high performance computing services and more that would enable scholarly research in a variety of disciplines that today is not yet possible. Brown Dog focuses on four initial use cases, specifically, addressing the conversion and extraction needs in the research areas of ecology, civil and environmental engineering, library and information science, and use by the general public. In this paper, we describe an architecture that supports contribution of data transformation tools from users, and automatic deployment of the tools as Brown Dog services in diverse infrastructures such as cloud or high performance computing (HPC) based on user demands and load on the system. We also present results validating the performance of the initial implementation of Brown Dog.


Tuesday July 19, 2016 11:00am - 11:30am EDT
Brickell

11:30am EDT

SW: In-memory Integration of Existing Software Components for Parallel Adaptive Unstructured Mesh Workflows
Reliable mesh-based PDE simulations are needed to solve complex engineering problems. Mesh adaptivity can increase reliability by reducing discretization errors, but requires two or more software components to exchange information. Often, components exchange information by reading and writing a common file format. 
On massively parallel computers filesystem bandwidth is a critical performance bottleneck. Our data stream and component interface approaches avoid the filesystem bottleneck. In this paper we present the approaches and discuss their use within the PHASTA computational fluid dynamics solver and Albany Multiphysics framework. Information exchange performance results are reported on up to 2048 cores of a BlueGene/Q system.


Tuesday July 19, 2016 11:30am - 12:00pm EDT
Brickell