Poster (After Call)

FZJ-2020-00115

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png NUMA-Awareness as a Plug-In

Morgenstern, L. (Corresponding author)FZJ* ; Haensel, D.FZJ* ; Beckmann, A.FZJ* ; Kabadshow, I.FZJ*

2019

Please use a persistent id in citations: http://hdl.handle.net/2128/23823

Abstract: Molecular dynamics (MD) has become a vital research method in biochemistry and materials science. GROMACS aims do develop a flexible and unified tool-box in the field of MD simulations. In MD, the fast multipole method (FMM) is used to compute all pairwise long-range interactions between N particles in time O(N). To tackle exascale, MD applications – as well as several other HPCapplications – have to target strong scaling. To meet the according requirements such as synchronization- and latency-awareness, software needs to adopt to specific hardware properties such ascaching and non-uniform memory access (NUMA). This poster shows how we added NUMA-awareness to our C++ tasking framework for fine-grained parallelism with an FMM as use case. However, the poster has an emphasis on separation of concerns through software architecture since the representation of NUMA in software is not only relevant for the FMM but should be reusable by similar applications.

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Contributing Institute(s):

1. Jülich Supercomputing Center (JSC)

Research Program(s):

1. 511 - Computational Science and Mathematical Methods (POF3-511) (POF3-511)
2. PhD no Grant - Doktorand ohne besondere Förderung (PHD-NO-GRANT-20170405) (PHD-NO-GRANT-20170405)

Appears in the scientific report 2019

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Database coverage:

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