2021-09-08 BespokeFit meeting notes

Post-talk questions

• BSwope – Are you generating new torsion TYPES, or just refitting the torsions that you have?

  • JH – Can do either – Generate new torsion types OR refit torsions in the FF

  • DMobley – We generally recommend generating new types, since you could mess up the FF by messing with the existing torsion types.

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Notebook session questions

• TFox – Dispatching calculations to slurm?

  • JH – We’re working on dispatching local computation to QCEngine, which may be a bit better.

  • TF: really has been nice to use the approach taken in benchmarking for use of HPC resources

  • JH: yeah, this execution style is something we aim to support

• MMackey: kernel crashed for me; on Debian testing

  • JW: can follow up with you in chat on troubleshooting

• TFox - couldn’t get git clone to work; had to download zip file instead

  • JW: ah, we should have used the https link instead of the git link for clone; apologies

• CBannan - getting Errno Snowflake instance did not boot properly, try increasing the timeout on MacOS Catalina; restarting notebook also gives “There appear to be 5 leaked semaphore objects to clean up at shutdown”; ps aux | grep postgres after killing kernel gives nothing

  • DD: so looks like Snowflake is cleaning up its postgres instances, so not clear

• MMackey: from openff.toolkit.topology import Molecule kills the jupyter kernel

• Questions to fill time:

  • Has everyone managed to execute the notebook?

  • Will using Bespokefit always require a notebook to run? How much could usage be simplified/will it be wrapped in a CLI?

  • What if I want up to k6?

  • Could we pre-download QCA datasets and package them with the bespokefit code?

• KMeier: having issues with Snowflake, colleague wasn’t, however, so doesn’t appear to be systematic to our infrastructure

  • was not running into TFox’s issue with “Connection Refused”

• MMackey: would be nice if you could tell ForceBalance to not spit out color codes in the log output

• CBannon: wasn’t clear how long executor would run, so killed it

  • JW: takes about 20 minutes on my machine

  • CBannon: maybe adding a comment to that notebook that this cell will take a while would be helpful for users

• BSwope: just watched, may give this a shot later

• KMeier: thank you for putting together this tutorial/workshop; will give this more a play to see if I can get around issue, colleague didn’t have it so pretty confident

• CBannon: will give this more a play if have time; not the highest priority in my group right now, so have to squeeze it in

• BSwope: very impressive work!

• CBannon: indeed, great stuff here!

Next steps

• JH will incorporate CBannan’s comment suggestions and migrate the notebook to the bespokefit examples.

• JW will upload video+slides to Zenodo, ping Karmen to upload video to Youtube.

Open