What you should know about NAMD and charm++ but were hoping to ignore

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

Abstract

The biomolecular simulation program NAMD is used heavily at many HPC centers. Supporting NAMD users requires knowledge of the Charm++ parallel runtime system on which NAMD is built. Introduced in 1993, Charm++ supports message-driven, task-based, and other programming models and has demonstrated its portability across generations of architectures, interconnects, and operating systems. While Charm++ can use MPI as a portable communication layer, specialized high-performance layers are preferred for Cray, IBM, and InfiniBand networks and a new OFI layer supports Omni-Path. NAMD binaries using some specialized layers can be launched directly with mpiexec or its equivalent, or mpiexec can be called by the charmrun program to leverage system job-launch mechanisms. Charm++ supports multi-threaded parallelism within each process, with a single thread dedicated to communication and the rest for computation. The optimal balance between thread and process parallelism depends on the size of the simulation, features used, memory limitations, nodes count, and the core count and NUMA structure of each node. It is also important to enable the Charm++ built-in CPU affinity settings to bind worker and communication threads appropriately to processor cores. Appropriate execution configuration and CPU affinity settings are particularly non-intuitive on Intel KNL processors due to their high core counts and flat NUMA hierarchy. Rules and heuristics for default settings can provide good default performance in most cases and dramatically reduce the search space when optimizing for a specific simulation on particular machine. Upcoming Charm++ and NAMD releases will simplify and automate launch configuration and affinity settings.

Original languageEnglish (US)
Title of host publicationPractice and Experience in Advanced Research Computing 2018
Subtitle of host publicationSeamless Creativity, PEARC 2018
PublisherAssociation for Computing Machinery (ACM)
ISBN (Print)9781450364461
DOIs
StatePublished - Jul 22 2018
Event2018 Practice and Experience in Advanced Research Computing Conference: Seamless Creativity, PEARC 2018 - Pittsburgh, United States
Duration: Jul 22 2017Jul 26 2017

Publication series

NameACM International Conference Proceeding Series

Other

Other2018 Practice and Experience in Advanced Research Computing Conference: Seamless Creativity, PEARC 2018
CountryUnited States
CityPittsburgh
Period7/22/177/26/17

Keywords

  • Charm++
  • High-performance computing
  • Molecular dynamics
  • NAMD
  • Scientific software tuning
  • Structural biology
  • User support

ASJC Scopus subject areas

  • Software
  • Human-Computer Interaction
  • Computer Vision and Pattern Recognition
  • Computer Networks and Communications

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