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)
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