June 10 2019


Mark, Christian, Artem

Completed since last meeting (June 3 2019)

  • Preparations for PRACE seasonal school

Upcoming targets

  • Post-submit failing in complex.nbnxn-ljpme-LB-geometric (issue #2939) - Berk and Szilard are working more on this.
  • GPU bonded optimization (issue #2818, 'AMBER trick')
  • 2019.3 release planned for Friday.
  • Fix Python 3 on bs-nix-docs (Joe, Paul) - Might be easier to spin up new VM for this.
  • Lots of spamming accounts are created in Redmine - Needs fixing, but no solution present right now.

Progress since last meeting

  • Cryo EM finished and up to review - Christian
  • Enable static selection using selection syntax - Christian
  • BioExcel-2 MS6.2 user survey is planned during summer school - Christian
  • BioExcel-2 CSC workshops, all set up, applied for PRACE funding, no news yet - Christian
  • Extracting MPI setup from commrec setup, patches - needs review (Paul)
  • WIP of Docker+k8s documentation build, going forward but killed Marks PC - Mark
  • BioExcel-2 Sardinia summer school July. Deadline: June 17 - Christian & Mark
  • CUDA update/constrain unification patches waiting for review - Artem
  • CUDA buffer ops patches - Szilard, Artem
  • Constant pH code - working branch, code not very clean, nothing new for now - Berk, Paul
  • Topology data structure cleanup - review needed - Paul, Mark
  • Trajectory analysis output filters - Paul, Mark
  • Paul started to split up EnergyAnalysis framework
  • Paul started work on rewriting TPR IO to use serializer interface.
  • Berk has working branch for always using domain decomposition - L-BGFS minimizer does not work with this