2020-04-27 Core developers meeting notes

Owned by Jeffrey Wagner
Last updated: Apr 27, 2020
3 min read

Date

Apr 27, 2020

Participants

  • @Jeffrey Wagner

  • @Matt Thompson

  • @David Dotson

  • @Trevor Gokey

  • @Jeffry Setiadi

  • @Simon Boothroyd

  • @Trevor Gokey

 

Trevor + Matt + Jeff should discuss vsite spec, how LJ interactions are specified

Updates

Matt:

  • System object

    • starting prototyping

    • finding that many things may already be implemented by QCS

    • best path forward may be to abandoning doing everything native in OpenBenchmark

    • functions that do things may call out to QCSubmit

  • visualization PR got merged

  • DD,JW,MT discussed and decided on release schedule for OFFtk

  • JW: perhaps MT should beat the drum?

JH:

  • QCSubmit

SB:

  • Nothing to report

JS:

  • added equilibration step to paprika; work on SDSC cluster deployment

JW:

  • put together talk

  • coordinated best practices workshop

  • marshalling resources for QCF

  • ultimately did not compute everything needed

    • some molecules were really large

    • not necessarily a bad thing, but would have liked them.

    • 500/5000 Hessians were pushing the limits, we got about 4500

  • caught up w/ Cerutti

    • was blocked generating SMARTS; used JH's code as template

    • check out SMIRNOFF channel for details

  • managed to get chargeincrementmodel handler implementation figured out

    • needs to put in more tests before eyes on it

TG:

  • started up HPC cluster with QCF

    • no more jobs left

  • virtual site implementation; working with JW closely to handle all use cases, change spec if needed

  • MT: are we tying to LJs for virtual sites? Are we planning to also handle virtual site masses?

    • we are tying vdWs

    • not handling virtual masses

JRG:

  • working with Ambertools on conda-forge, release soon

    • might have timeouts due to compilation time on Azure

  • benchmarking

    • working with JH on JSON data

    • need other forcefield data yet

DD:

  • Reviewed OFFtk #560 (merged)

  • Reviewed QCEngine #239

  • Did not review nistdataselection #69 (merged)

  • Productive working meeting with Chaya Stern, Josh Horton, Jeff Wagner, Jessica Maat, David Mobley on Torsion WBOs

  • Implementation mostly complete for Torsion WBOs; some detailed work required and tests this week

  • Near end of the week, want to move on to:

    • OFFEvaluator #226

    • OFFtk #477

Task distribution

  1. Elect new tasks

    1. Guide/example for making new parameterhandler / 8

    2. CHARMM-GUI integration – (debug parmed converting to CHARMM issue / 13

    3. Blog post about file formats and move to SDF / 8 doing, / 3 or 5 for reviewing

    4. Pick up release testing PR / 5

    5. Split tests into separate GH actions (OFFTK #561) / 5

    6. Fix CMILES master / 5

    7. Update infrastructure and set up cron jobs on “orphaned” software – CMILES/Fragmenter/Chemper/SMIRKY (Migration to GHA is separate)

    8. Open PRs to update CI to GHA in all OFF repos – Will do during devs week

    9. Make “Central Command” repo with just a readme, containing a table with detailed statuses

    10. Organize and publicize devs week / 5

    11. Update project infrastructure diagram / 13

https://docs.google.com/presentation/d/1XqZAr1rCJNkPpk97hpDAuwPKdr5HWpQkU2I0vyjV5GA/edit#slide=id.g5bfb4d4f85_1_8

  1. Review previous tasks

    1. Review new AmberTools RC / 3 – JW – Didn’t do

    2. Review QCEngine PR – 3 – DD – Complete

    3. Have FFs know which XML(s) they were loaded from / #477 / 5 implement / 2 review - DD/MT - Didn’t do

    4. DD – Opened OFFE #226, replacing internal attribute with attrs – looking at evaluator 0.2.0 release (a month or two out) / 13 – Didn’t do

    5. DD – Torsion WBOs / 21 – In progress

    6. Issue triage – 5 – MT, with JW as secondary – Done

    7. JW – Chargeincrement PR / 13 – Did some, down to 8

  2. Allocate effort to ongoing tasks

    1. TG – Virtualsite implementation/ 21

    2. MT (primary) QCA OpenMM energy evaluation / 21

    3. MT – System design / 13

    4. JW – Cerutti support / 3

    5. JW – QCFractal management / 3

    6. DD – QCArchive onboarding / 5

    7. JW – Organizational meetings / 5

    8. MT – Issue triage / 5

  3. Measure capacity

    1. TG – 21

    2. JW – 19

    3. DD – 44

    4. MT – 39

  4. Assign new tasks

    1. MT / JW – CHARMM-GUI integration – (debug parmed converting to CHARMM issue / 13 / 5

    2. JRG – Split tests into separate GH actions (OFFTK #561) / 5

    3. JRG – Plan decision checklist for all-repo GHA migration/ 5

    4. DD – Guide/example for making new parameterhandler / 8

    5. JW – Organize and publicize devs week / 5

    6. JW – Fix CMILES tests / update infrastructure / 8

    7. MT – Update infrastructure and set up cron jobs on “orphaned” software – Fragmenter/Chemper/SMIRKY (Migration to GHA is separate) / 8

    8. DD – Update project infrastructure diagram (fine to use tool other that GSlides) / 13

    9. MT – Make “Central Command” repo with just a readme, containing a table with detailed statuses (copy table from website, open new repo) – Could use jinja template to automate making rows / 5

  5. Measure capacity

    1. JW – 37

    2. DD – 65

    3. MT – 65

    4. JRG – 10

    5. TG – 21

  6. Plan for missing next week’s meeting due to annual workshop

    1. Maybe move to two-week cadence moving forward anyway

    2. will continue doing roundtable every week