Project

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Mar 11 2019

Apologies

Joe travelling

Absent

Completed since last meeting (Mar 4 2019)

  • nbnxm bounding box cleanup
  • asked ORNL for testing help
  • new tests for pdb2gmx, editconf
  • much refactoring of gmxpreprocess (hackblocks is done)
  • rebase of x buffer ops patch over nbnxm changes
  • relaxed OpenCL gather kernel barrier on AMD
  • fixed Apple+OpenCL bug (kernel must have an argument!)

Progress since last meeting

  • New warning about GROMOS force field #2884 - Berk
  • Planning for FEP meeting - Mark, Berk, Michael Shirts
  • Constraints tests + GPU implementation - Artem, Mark
  • migrated gmx dump to use gmx::Options - Mark
  • GPU bonded kernel fusion proposed #2818 - Szilard
  • do_force improvements
    • PBC setup in force loop improvements - Szilard * expansion of PpForceWorkload - Szilard
  • proposed gmx::compat::optional - Mark
  • migrating check and mdrun to use gmx::Options (for gmxapi) - Mark
  • BioExcel-2 WP1
    • create tasks in ClickUp - Mark, Paul, Berk, Christian * iterate on KPIs proposal - Mark, Berk, Paul, Erik, Christian
  • BioExcel-1 AWH benchmarking writeup - Berk
  • patches preparing cryo-EM refinement module - Christian
  • patches using mdspan infrastructure - Christian
  • Topology data structure cleanup - Paul, depends on more cleanup
  • High level GPU manager - Szilard, Artem, Mark
    • High level object for long-lived GPU objects (hack struct with void pointers) - Szilard
  • lambda dynamics patches - Paul
  • analysis module outputadapter patches - Paul

New items

  • Draft single-rank single-GPU MD schedules - Mark
  • 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
  • using Redmine for project organization - Mark
  • Email gmx-developers about development feature flags - Mark
  • feature branches on gerrit - Mark
  • CSCS CI testing help - Mark
  • review Sebastian's patch - Mark
  • Adopt clang-format #2107 - TODO
  • Make an update module - Mark
  • how should we start using 3x3 matrix - Christian