Scalable Proximity-Based Methods for Large-Scale Analysis of Atom Probe Data
Powered by recent advances in data acquisition technologies, today's state-of-the-art atom probe microscopes yield data sets with sizes ranging from a few million atoms to billions of atoms. Analysis of these atomic data sets within rea-sonable turnaround times is a pressing data analysis challenge for material scientists currently equipped with software systems that do not scale to these massive data sets. Here, we present the shared memory component of a larger ongoing effort to develop a multi-feature data analysis framework capable of analyzing atom probe data of all sizes and scales from desktop multicore machines to large-scale high-performance computing platforms with hybrid (shared and distributed memory) architectures. Our focus here is on a broad class of popular atom probe data analysis methods that rely on core time-consuming k-NN queries. We present a scalable, heuristic algorithm for k-NN queries using three-dimensional range trees. To demonstrate its efficacy, the k-NN algorithm is integrated with two use cases of atom probe data analysis methods and the resulting analysis times are shown to speedup by over 20X on a 32-core Cray XC40 node using workloads up to 8 million atoms, which is already beyond the at-scale capabilities of existing atom probe software. Using this k-NN algorithm, we also introduce a novel parameter estimation method for a class of cluster finding methods, called friends-of-friends (FoF) methods, to completely bypass their expensive pre-processing steps. In each case, we validate the results on a variety of control data sets.
- Research Organization:
- Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States)
- Sponsoring Organization:
- USDOE
- DOE Contract Number:
- AC05-00OR22725
- OSTI ID:
- 1651414
- Resource Relation:
- Conference: 25TH IEEE International Conference on High Performance Computing (HiPC) - Bangalore, , India - 12/17/2018 10:00:00 AM-12/20/2018 10:00:00 AM
- Country of Publication:
- United States
- Language:
- English
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