MemXCT: Memory-centric X-ray CT reconstruction with massive parallelization

Mert Hidayetolu, Tekin Biçer, Simon Garcia De Gonzalo, Bin Ren, Doa Gürsoy, Rajkumar Kettimuthu, Ian T. Foster, Wen Mei W. Hwu

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Abstract

X-ray computed tomography (XCT)is used regularly at synchrotron light sources to study the internal morphology of materials at high resolution. However, experimental constraints, such as radiation sensitivity, can result in noisy or undersampled measurements. Further, depending on the resolution, sample size and data acquisition rates, the resulting noisy dataset can be terabyte-scale. Advanced iterative reconstruction techniques can produce high-quality images from noisy measurements, but their computational requirements have made their use exception rather than the rule. We propose here a novel memory-centric approach that avoids redundant computations at the expense of additional memory complexity. We develop a system, MemXCT, that uses an optimized SpMV implementation with two-level pseudo-Hilbert ordering and multi-stage input buffering. We evaluate MemXCT on various supercomputer architectures incolving KNL and GPU. MemXCT can reconstruct a large (11K×11K) mouse brain tomogram in ∼10 seconds using 4096 KNL nodes (256K cores), the largest iterative reconstruction achieved in near-real time.

Original languageEnglish (US)
Title of host publicationProceedings of SC 2019
Subtitle of host publicationThe International Conference for High Performance Computing, Networking, Storage and Analysis
PublisherIEEE Computer Society
ISBN (Electronic)9781450362290
DOIs
StatePublished - Nov 17 2019
Event2019 International Conference for High Performance Computing, Networking, Storage and Analysis, SC 2019 - Denver, United States
Duration: Nov 17 2019Nov 22 2019

Publication series

NameInternational Conference for High Performance Computing, Networking, Storage and Analysis, SC
ISSN (Print)2167-4329
ISSN (Electronic)2167-4337

Conference

Conference2019 International Conference for High Performance Computing, Networking, Storage and Analysis, SC 2019
CountryUnited States
CityDenver
Period11/17/1911/22/19

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ASJC Scopus subject areas

  • Computer Networks and Communications
  • Computer Science Applications
  • Hardware and Architecture
  • Software

Cite this

Hidayetolu, M., Biçer, T., De Gonzalo, S. G., Ren, B., Gürsoy, D., Kettimuthu, R., Foster, I. T., & Hwu, W. M. W. (2019). MemXCT: Memory-centric X-ray CT reconstruction with massive parallelization. In Proceedings of SC 2019: The International Conference for High Performance Computing, Networking, Storage and Analysis [a85] (International Conference for High Performance Computing, Networking, Storage and Analysis, SC). IEEE Computer Society. https://doi.org/10.1145/3295500.3356220