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Feb 11 2019

Apologies

  • Mark, Erik at BioExcel-1 final review

Completed since last meeting (Feb 4 2019)

  • updated BioExcel-1 WP1 final review presentation
  • Meeting with NVIDIA
  • fixed force-switch sign bug
  • fixed rerun with perturbed mass or bond length
  • removed per-interaction kernels (C and SIMD) from group scheme
  • integrated new bonded tests
  • released 2016.6 as special exception to "out of support" policy
  • added ssize operator for smoother signed/unsigned array index arithmetic
  • filenames no longer use hyphens
  • mdspan merged

Upcoming patch release 2019.1

Progress since last meeting

  • native CUDA in cmake problematic #2831 - no progress, Mark has ideas but not yet time
  • how to find libstdc++ for icc and clang #2842 - Mark, ready but needs follow up (Cray CC is broken already)
  • naming conventions for GROMACS module and file names #2839 - Mark to promulgate decision
  • nbnxm cleanup partly integrated, needs update review - Paul will continue here, Szilard as well
  • ask ORNL for testing help - Mark
  • using Redmine for project organization - Mark
  • Email gmx-developers about development feature flags - Mark
  • Follow up on NVIDIA meeting with notes on delivery items - Mark
  • review Prashanth's patch - Mark
  • review Sebastian's patch - Mark
  • BioExcel-2 WP1
    • MS2 TOC to be drafted - Mark * D1.1 TOC to be drafted - Mark * create tasks in ClickUp - Mark, Paul for himself
  • BioExcel-1 AWH benchmarking writeup - Berk
  • mdspan infrastructure - Christian
  • 3x3 matrix - Christian, needs some more review
  • Topology data structure cleanup - Paul, depends on more cleanup
  • Hackblocks cleanup - Paul, getting there, still some bugs to fix
  • Constraints tests + GPU implementation - Artem, Mark
  • High level GPU manager - Szilard, Artem, Mark
    • High level object for long-lived GPU objects (hack struct with void pointers) - Szilard
  • Prioritize other GPU infrastructure improvements - Szilard, Artem, Mark
  • Adopt clang-format #2107 - TODO
  • Port tests to source repo #1587 - Paul to review more of Davids changes
  • proposed gmx::compat::optional - Mark
  • regex improvements, pdb2gmx tests in Jenkins - Mark, Paul to rebase refactoring on top

New items

  • Make an update module - Artem, Mark
  • add work on SVE to plans?
  • Separate molecule output? - Magnus
  • First cut at new MD schedules - Mark
  • Discuss NVIDIA changes, better to start from clean re-implementation?