Apr 15 2019



Completed since last meeting (Apr 1 2019)

  • several fixes for 2019
  • BioExcel KPIs and risks for D6.2
  • more nbnxm and do_force cleanup
  • BioExcel D1.1 draft ready to pass to EB review later today
  • BioExcel D3.1 input made
  • GPU naming conventions updated
  • Decided computeGlobals should be the function, doComputeGlobals the boolean
  • gmx dump is now a proper module

Upcoming targets

  • iteration on BioExcel deliverables by April 30

Decisions needed

  • BioExcel@SLL meeting this week?

Progress since last meeting

  • Pure-GPU MD loop draft up - Artem
  • Constraints tests + GPU implementation - Artem, Mark
  • GPU bonded kernel fusion proposed #2818 - Szilard
  • New cuda redmine issues from Alan need feedback - Szilard, Artem, Mark
  • CUDA buffer ops patches - Szilard, Berk, Mark
  • patches preparing cryo-EM refinement module - Christian
  • patches using mdspan infrastructure - Christian
  • sketch for abstraction layer for external data input, put on hold for now - Joe, Mark, Christian, Erik
  • Planning for FEP meeting - Mark, Berk, Michael Shirts
  • Modular integrator feature branch available - Mark
  • Python API patches up (and feature branch available) - Joe, Mark
  • do_force improvements
    • PBC setup in force loop improvements - Szilard
  • BioExcel-2
    • periodic report - all * create WP1 tasks in ClickUp - Mark, Paul, Berk, Christian * iterate on WP1 UEDIN QM/MM CP2K benchmarks and reports
  • Topology data structure cleanup - Paul, depends on more cleanup
  • refactoring of module setup to prepare for more use of gmx::Options - Mark
  • WIP updates for proposed gmx::compat::optional + tests - Mark
  • migrating dump, check and mdrun to use gmx::Options (for gmxapi) - Mark

New items

  • Documentation built in docker infrastructure as test for docker infrastructure for continuous integration and testing, Joe
  • GPU-only medium term goals
    - what features does it support?
    - what is the performance behavior, where does it add most to performance
    - what is to be done to get into release

Stale items

  • Draft single-rank single-GPU MD schedules - Szilard, Berk, Artem
  • 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
  • Adopt clang-format #2107 - Berk