June 17 2019


Mark, Erik

Completed since last meeting (June 10 2019)

  • GPU bonded optimization (issue #2818, 'AMBER trick') - Private patch that fuses the bonded kernels submitted by Magnus.
  • Next 2019 release - done June 13.
  • Fix Python 3 on bs-nix-docs (Mark prepared a build job, Paul installed Python 3 on Windows slave).
  • PRACE Seasonal School June 10-13

Upcoming targets

  • Post-submit failing in complex.nbnxn-ljpme-LB-geometric (issue #2939) - Fix submitted, Berk will work more on this.
  • Half year plan meeting to discuss what should be attempted to merge into 2020 in June.
  • Lots of spamming accounts are created in Redmine.
  • Paul submitted a series of patches for in-memory tpr reading and writing. Review needed. Can we ran out of memory?

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
  • 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