Page Comparison

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25 Sep 2020

Participants

• David Dotson

• Trevor Gokey

• Joshua Horton

• Simon Boothroyd

• Ben Pritchard

Goals

• New advancements

• New submissions

  • Protein Fragments TorsionDrives

  • Enamine REAL subset Optimization

  • Jessica Maat’s dataset

  • PhAlkEthOH dataset

• Upcoming infrastructure improvements

  • Psi4Harness error reporting fix QCEngine#266

  • STANDARDS-based versioning #137

  • Torchani changes - QCEngine release

  • Identifier support in QCElemental.Molecule?

• Upcoming science support

  • PCM-based implicit solvent pathway

  • ESPs and wavefunction storage

  • Uploading datasets calculated on private server

• Larger advances

  • Automated FF coverage gap identification, torsion prioritization, submission generation

  • Benchmarking (dashboard, etc.)

Discussion topics

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Item	Presenter	Notes
QCFractal release, QCArchive upgrade	Ben	QCFractal release on track for next week modify and regenerate tasks maybe have the ability to set defunct status changes the modify_tasks Considering upgrading Postgres 10 → 13 Reworking fractal interface is going to be a challenging task TG: We need to change some data where the status is incomplete but the data exists BP: The new modify_tasks will create new tasks, and this will allow the job to be restarted. The problem could be the underlying task was already deleted, and couldn’t restart. We should use the create task functionality on a debugging basis only There is some talk about QCSchema changes
Entry creation	Trevor	TG: Entries aren’t created until tasks are created dataset doesn’t show up until you call compute BP: One of many things that needs a rework
Protein Fragments	David	Need to go through constraints with fine-tooth comb
Enamine REAL	Trevor	Working on performance optimizations for QCSubmit to handle a dataset of this size
PhAlkEthOH dataset	Trevor	Small dataset that was used for initial fit finally getting into QCArchive useful sandbox to test typing schemes ~40k conformers (different from the conformers used in the original dataset)
STANDARDS-based versioning	Trevor	Coupled with QCSubmit development
QCEngine Release	Ben	QCEngine release coinciding with Fractal next week
QCElemental Identifiers	Trevor, Josh	TG: it is implemented, present JH: We pushed for using Identifiers for CHMILES early on, but because this isn’t necessarily stable information if the connectivity changes over the course of the optimization conclusion: we didn’t want to put information that was searchable and meant to reflect the molecule as is but could very well be inaccurate the compromise was to put this information into extras since that is free-form and not considered to be as much of a source of truth TG: is it possible to guess connectivity at every optimization step? or do we have a postprocessing step at the end that guesses connectivity after an optimization? The drawback to the current implementation in QCElemental is that it does not perceive bond order.
PCM calculations	Josh	Can do PCM calculations, need to restrict symmetry latest conda build for Mac! Just need to update QCSubmit with corresponding options
Data Access layer in service of future advancements	David, discussion	DD: value streams, upcoming needs a data access layer would need to meet SB: really agree with the approach; partial to fewer packages TG: agree, will be working on QCSubmit more to include extraction bits, make sure these line up with input standards JH: agree, and like this approach; have some minimal data access bits currently to support bespoke-workflow TG: have a lot of existing functions that I can put into QCSubmit
QCFractal managers		TG: Using a pre-empt queue causes a lot of jobs to be killed, which are sent back as ERRORS, and need to be restarted manually. Can this be detected and have those jobs automatically restarted? DD & BP: This will be challenging as the exceptions are adapter specific TG: Short term solution is a loop that scans the dataset from a client and restarting tasks with specific exception strings in the output

Action items

•  Ben Pritchard will prepare a QCFractal release for next week, with deployment to the public QCArchive instance
•  Trevor Gokey will prepare PhAlkEthOH dataset for QCSubmit submission into QCArchive
•  Joshua Horton will update QCSubmit with options needed to support PCM calculations with recent Psi4
•  David Dotson will create a prototype for Jessica Maat, Dominic Rufa’s requests as a PR to QCSubmit (followed discussion with Trevor)

Decisions