BP – Refactor is going well. Test server will come online soon – We’d like you to use this to see if anything breaks. Test server will be “fresh”/will not contain existing outputs.
DD – I could set up a tracking board just for that server, and have some of the QCA dataset submissions go to the test server.
BP – I’d like for this server to be something like a continuously-deployed version from master.
Queue status
QCA Dataset Tracking board:
DD – Been working on PEPCONF. Ran it for about 1.5 weeks with dlc coordinates and reset=True. We’ve had about 2000 complete out of 7000 jobs. The rest are errored. Focusing on two “unknown” errors.
DD – Trying various ways to measure memory usage. None of them seem unreasonable.
TG – I got unknown errors for these two jobs. QCE/Psi4 notes
DD – Queue is emptying out. We’ve been chewing on some really large sets like Cerutti’s protein fragments, but they’re nearly done.
DD – There are some pending PRs that are close to submission. I’ll prioritize getting those in and following up with submitters. I also need to submit the pharma partner benchmarks sets.
JW – Will the new submission standards be changed to have dlc?
DD + TG – Yes. There’s a variant called default-dlc that can be used (since we’ll still want tric for multi-molecule submissions.
SB – I’d be interested in a more targeted set for WBOs.
DD – The queue should be totally open
SB and PB will sync up to prepare a cleaner WBO set.
TG – SB, there’s also a new set intended to study WBOs submitted by JM and Chris Bayly.
User questions
HP – Re: PEPCONF. You’re using DLC now for pepconf. Have you tried using other internal coordinate systems other than tric or dlc? (or cartesian coordinates)? Does the time per step change with choice of coordinates? That is, if each iteration takes more time, the saving might now be great overall.
DD – We haven’t checked this yes.
HP – The advantage of TRIC should be that it can converge faster.
(General) – OpenFF hasn't tried coordinate systems other than tric and dlc. In theory, the SCF convergence should be the expensive part, not the coordinate transformations/updates.
HP will with with DD on trying different solutions for PEPCONF issues.
HP – Regarding QCFractal’s built-in job deduplication. It will store and deduplicate job outputs, and also allow for importing jobs completed elsewhere.
BP – QCFractal only deduplicates on input – It looks at (program, method, bases, keywords, molecule), and will identify duplicates if those match. The molecule is stores as a QCSchema molecule (also referred to as a QCElemental molecule). This can store connectivity (with bond order).
PB – In pepconf, some runs were failing with SCF convergence werrrors because density didn’t converge. Trying out second-order methods worked pretty well. Would it be OK to use second-order SCF methods as a backup?
BP – I don’t see a problem with that, though QCA will see that as a different calculation.
PB – Second-order methods and damping helped a lot of our failures converge.
DD – We could have our datasets be something like a frankenstein of jobs run with slightly different settings.
JW – How does cost scale with second-order methods?
PB – Goes from N^4 to N^6
TG – Would be interested in finding a workflow/combination of settings that uses second-order when appropriate.
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