Non-Volatile Memory Accelerated Geometric Multi-Scale Resolution Analysis

Andrew Wood, Moshik Hershcovitch, Daniel Waddington, Sarel Cohen, Meredith Wolf, Hongjun Suh, Weiyu Zong, Peter Chin

Research output: Chapter in Book/Report/Conference proceedingConference contributionpeer-review


Dimensionality reduction algorithms are standard tools in a researcher's toolbox. Dimensionality reduction algorithms are frequently used to augment downstream tasks such as machine learning, data science, and also are exploratory methods for understanding complex phenomena. For instance, dimensionality reduction is commonly used in Biology as well as Neuroscience to understand data collected from biological subjects. However, dimensionality reduction techniques are limited by the von-Neumann architectures that they execute on. Specifically, data intensive algorithms such as dimensionality reduction techniques often require fast, high capacity, persistent memory which historically hardware has been unable to provide at the same time. In this paper, we present a re-implementation of an existing dimensionality reduction technique called Geometric Multi-Scale Resolution Analysis (GMRA) which has been accelerated via novel persistent memory technology called Memory Centric Active Storage (MCAS). Our implementation uses a specialized version of MCAS called PyMM that provides native support for Python datatypes including NumPy arrays and PyTorch tensors. We compare our PyMM implementation against a DRAM implementation, and show that when data fits in DRAM, PyMM offers competitive runtimes. When data does not fit in DRAM, our PyMM implementation is still able to process the data.

Original languageEnglish
Title of host publication2021 IEEE High Performance Extreme Computing Conference, HPEC 2021
PublisherInstitute of Electrical and Electronics Engineers Inc.
ISBN (Electronic)9781665423694
StatePublished - 2021
Externally publishedYes
Event2021 IEEE High Performance Extreme Computing Conference, HPEC 2021 - Virtual, Online, United States
Duration: 20 Sep 202124 Sep 2021

Publication series

Name2021 IEEE High Performance Extreme Computing Conference, HPEC 2021


Conference2021 IEEE High Performance Extreme Computing Conference, HPEC 2021
Country/TerritoryUnited States
CityVirtual, Online


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