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Mar 18 2019

Apologies

Erik travelling, Szilard sick

Absent

Completed since last meeting (Mar 11 2019)

  • BioExcel WP1 activities (D1.1 draft progress, KPIs proposal progress)
  • merged GROMOS-in-GROMACS warning
  • more tests and memory cleanup in gmxpreprocess
  • 2 or 3 rebase-over-test-failures
  • more nbnxm cleanup
  • sandbox-puregpu gerrit feature branch available
  • progress cleaning up in sim_util
  • poked CSCS to stay current and contribute

Upcoming targets

Progress since last meeting

  • ORNL open to the idea of giving us access, resource for CI possibly available in future, but no suggestion from them of manpower just now - Mark to continue
  • patches preparing cryo-EM refinement module - Christian
  • patches using mdspan infrastructure - Christian
  • Planning for FEP meeting - Mark, Berk, Michael Shirts
  • Pure-GPU MD loop draft up - Artem
  • Modular integrator feature branch available - Mark
  • Python API patches up (and feature branch available) - Joe, Mark
  • New cuda redmine issues from Alan need feedback - Szilard, Artem, Mark
  • Constraints tests + GPU implementation - Artem, Mark
  • CUDA buffer ops patches - Szilard, Berk, Mark
  • do_force improvements
    • PBC setup in force loop improvements - Szilard
  • BioExcel-2 WP1
    • finalize D1.1 content for GROMACS * create tasks in ClickUp - Mark, Paul, Berk, Christian * iterate on KPIs proposal - Mark, Berk, Paul, Erik, Christian * iterate on UEDIN QM/MM CP2K benchmarks and reports
  • BioExcel-1 AWH benchmarking writeup - Berk
  • 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
  • GPU bonded kernel fusion proposed #2818 - Szilard
  • broken virial in SHAKE #2879 - Mark
  • migrated gmx dump to use gmx::Options - Mark
  • proposed gmx::compat::optional - Mark
  • migrating check and mdrun to use gmx::Options (for gmxapi) - Mark

New items

  • Draft single-rank single-GPU MD schedules - 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
  • CSCS CI testing help - Mark
  • Adopt clang-format #2107 - TODO
  • Make an update module - Mark, Artem