Page Comparison

Updates from MolSSI

Ben

• BP: We got hammered by a bunch of requests a little while ago (like 100/second) for entire datasets. So I blocked the IP temporarily and worked with DD to find the person in OpenFF and help them access it in a more healthy way.

• BP: storage utilization creeping up, likely due to more wavefunctions storage

  • do need to plan a next-gen solution

  • JW: what kind of proactive steps can we take for 6 months to a year

  • BP: this factors into our options at ARC (VT supercomputer center)

    • our networking solution is somewhat better than previous, but we don’t have full control of the host

  • BP: have some stopgap measures on storage I can take, but they are painful

    • DD: can some of the NIH supplement be used for capital expense?

      • BP: pretty sure no

    • JW: there may be in-kind support OpenFF can provide re: hardware

  • JW: where are the wavefunctions coming from?

    • DD+JH: coming from pubchem single-points sets (OpenMM sets), more coming

  • JW: need to track down if Peter+John have funding for their pubchem set that will drive storage needs

    • JH: looking at ~1M calculations with wavefunctions

  • JW: If this is just a matter of ordering 20TB of SSD storage then we can just go straight ahead with this.

  • DD: It’s not just a short-term question - 20TB may get us a solution in the short term, but we’ll want to do a more sustainable solution in the long term. Could look at options for continued supercomputer hosting, bare metal hosting in MolSSI office, or cloud hosting.

  • BP – If each wavefunction is ~1MB, and we do a million of them, then that’s a terabyte. If there’s 1000 basis functions, then that’s a bit high…

Compute

• DD – QM workers on lilac weren’t given time to clean up. Led to weird job statuses. I’ve opened an PR on QCFractal to mitigate this.

• JH – We still have QM workers running on newcastle. They timed out today so I’ve resubmitted them

• DD – Great. We may want to switch to XTB, but let’s discuss that later.

• CC – TSCC is running right now - One job with 8 workers. I can spin up more if needed.

  • DD – Feel free to spin up more. We’re making forward progress, but more resources would be great.

• DD – We have QM, ANI, and XTB workers on PRP.

• DD – With XTB, we have two datasets that are error cycling, and seem to have memory issues?

  • PB – I’m not sure whether it’s a memory issue. The error messages aren’t clear.

  • DD – Memory issues are my first guess, I wonder if they’re getting killed by the queue scheduler for having memory usage too high. My PRP workers have 32GB of memory.

  • PB – 32GB should be fine.

  • DD – JH, do I recall that newcastle was having memory issues with XTB workers?

  • JH – For us it was ANI workers having memory problems. I’ll switch these over to XTB

  • DD – Thanks. I’ll tag them as openff-xtb. Should be updated in a few hours.

• JW – Is it possible that xtb is just ignoring our memory limits?

  • DD + JH – We’re not sure whether XTB is passed the memory limit from QCEngine.

• DD – #223 had had error cycling turned off for a few days to see if the same jobs were killing the workers repeatedly. I’ll turn error cycling back on

New datasets

• JH will take over on Folmsburg Huchison test set

  Github link macro
  link https://github.com/openforcefield/qca-dataset-submission/pull/255

• Dipeptide 2-D TorsionDrives

  • Large number of errors (>4000) with return message None

  • Errors with brand field from PRP manager

  • Workers on TSCC have low error rate (<5%)

  • CC will deploy additional managers on TSCC

  • DD will debug errors for openff-tscc compute tag on PRP

• JH resolved compute issues with OpenMM solvated amino acid dataset

Psi4 update

• DD – Problem with basis sets deploying psi4 1.5, incompatibilities of qcelemental 0.24, qcengine 0.21 with qcfractal 0.15.7

• JH – I think we

• DD – So,

  • new psi4 needs new QCEl and QCEngine

  • but production QCFractal needs old QCEl and QCEngine

• DD – Can we confirm that the second point is true?

• BP – The intercompatibility isn’t too bad, it may just work.

• JH + PB – We could run it with the old versions of everything, just need to set wcombine=False

  • JH – The keyword probably isn’t harmful, so it’s be safest to BOTH update the workers and ALSO submit a dataset with the new keyword. But in a pinch, just resubmitting with the new keyword is a good solution.

  • PB – Agree.

• PB will modify the prepared PRs (like pubchem set 2) to have wcombine=False, and then submit them to make sure that they don’t have the problem. If that works, we’ll make a new submission for the dipeptides which also has the updated keywords.

• PB – We’ll want to be careful with this, this is 100k records so it’ll be a bit wasteful if it is still broken

• DD – Is there any other reason that we should update to Psi4 1.5?

  • (General) – There’s no big motivating need for this.

• DD – Do we know if there’s a fundamental incompatibility between Psi4 1.5 and the QC stack?

  • BP – I don’t expect that there’d be an issue but I need to test. The risk is that QCEngine may send back a schema that QCF doesn’t understand.

• DD will test the new versions against each other

User questions?

Science support?

• JH: new qcsubmit release out (0.3.0); solvated amino acids issue addressed

Infrastructure support

• JW: Matt is making forward progress on some upstream items that mostly just require technical solutions