Title: Trace: a high-throughput tomographic reconstruction engine for large-scale datasets

Abstract

Abstract Background Modern synchrotron light sources and detectors produce data at such scale and complexity that large-scale computation is required to unleash their full power. One of the widely used imaging techniques that generates data at tens of gigabytes per second is computed tomography (CT). Although CT experiments result in rapid data generation, the analysis and reconstruction of the collected data may require hours or even days of computation time with a medium-sized workstation, which hinders the scientific progress that relies on the results of analysis. Methods We present Trace, a data-intensive computing engine that we have developed to enable high-performance implementation of iterative tomographic reconstruction algorithms for parallel computers. Trace provides fine-grained reconstruction of tomography datasets using both (thread-level) shared memory and (process-level) distributed memory parallelization. Trace utilizes a special data structure called replicated reconstruction object to maximize application performance. We also present the optimizations that we apply to the replicated reconstruction objects and evaluate them using tomography datasets collected at the Advanced Photon Source. Results Our experimental evaluations show that our optimizations and parallelization techniques can provide 158× speedup using 32 compute nodes (384 cores) over a single-core configuration and decrease the end-to-end processing time of a largemore » sinogram (with 4501 × 1 × 22,400 dimensions) from 12.5 h to <5 min per iteration. Conclusion The proposed tomographic reconstruction engine can efficiently process large-scale tomographic data using many compute nodes and minimize reconstruction times.« less

Authors:

Bicer, Tekin ;

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Gürsoy, Doğa; Andrade, Vincent De; Kettimuthu, Rajkumar; Scullin, William; Carlo, Francesco De; Foster, Ian T.

Publication Date:

Sat Jan 28 00:00:00 EST 2017

Research Org.:

Argonne National Laboratory (ANL), Argonne, IL (United States)

Sponsoring Org.:

USDOE Office of Science (SC), Advanced Scientific Computing Research (ASCR)

OSTI Identifier:

1344024

Alternate Identifier(s):

OSTI ID: 1375811

Grant/Contract Number:  

AC02-06CH11357

Resource Type:

Published Article

Journal Name:

Advanced Structural and Chemical Imaging

Additional Journal Information:

Journal Name: Advanced Structural and Chemical Imaging Journal Volume: 3 Journal Issue: 1; Journal ID: ISSN 2198-0926

Publisher:

Springer Science + Business Media

Country of Publication:

Germany

Language:

English

Subject:

97 MATHEMATICS AND COMPUTING; 46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND TECHNOLOGY; Big Data; High-Throughput; Reconstruction; Tomography