2024-11-11 Science team meeting

Project updates

BW

• Past week

  • Wrapping up PRs (QCSubmit fix, etc)

  • Resubmitted hessian dataset

  • Monitoring QCA workers

    • MLPepper ran in 2 days

    • Lipid maps is going slowly as it’s not split by size – the resource requirements vary. Also, scaling deployment > 60 workers means everything crashes

  • yammbs PR

  • Benchmarks

    • PR openers upload:

      • a yaml file with config

      • Optionally, a FF file

    • Things we could review:

      • CSV files that get committed to repo

        • Human input: check they got uploaded

        • LW: can script generate plots for you?

        • BW: that’s possible

      • Zenodo submission (which is now on production OpenFF)

        • Note: YDS doesn’t publish entry. To review Zenodo, you need to be able to log into Zenodo.

        • Someone needs to review and hit publish, to include DOI, to include in PR.

        • BW: picturing DOI as a line in a README

    • AMI: is the idea to review before the run starts or after it ends?

      • BW: afterwards – there’s not a whole lot to review before the run. Just the yaml file and maybe an FF.

      • AMI: there’s not that much an external person could review afterwards either, other than checking the CSVs are there. Don’t really see downside to requiring a review

      • BW: just worried about best practices. Also need write permissions to trigger bot.

      •  

• Next week

  • More benchmarks

  • QCA workers

  • Split up second lipidmaps dataset

    • Separate PRs into the same directory

  • Organometallics dataset

  • yammbs PR(s)

  • YDS

    • Update scripts with plots

    • Publish Zenodo entry and merge PR

    • Which FFs?

      • 1.3.1

      • 2.0

      • 2.1

      • 2.2.1

      • experimental FFs

Project

updates

AMI

• Past week

  • mamba issues

  • DDX errors

    • looked into functional group breakdown

    • Also resubmitted same dataset without diffuse functions. No errors.

  • NAGL2 optimization dataset planning

    • Decided to do geom opts at usual level of theory

    • BP: can do 2.5-5 TB dataset. “Let’s see how well we can handle it”. “no problem” to do up to 1 TB.

    • AMI: 5 confs/mol would be ~2.5 TB. 5 TB would be 10 conformers. 2 confs/mol would be 1 TB.

    • LW: aim for 5 conf/mol

  • Follow up on standards document

  •  

• Next week

  • NAGL2 optimization dataset

  • Hessian DSs

  • (Freeze phosphate angle refit?)

  • (NAGL2 testing dataset--examine exisiting coverage and maybe setup opts)

  • Finish standards

LW

• Past week:

  • Working with various Kubernetes issues

  • Troubleshooting packmol

  • Collaborations and admin

• Next week:

  • Protein projects