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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.

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.

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