2024-07-30 alchemiscale : user group meeting notes

alchemiscale.org

• user questions, issues, requests

  • JS – Working well so far. I’ve been occasionally hitting 200 simultaneous tasks. The FFT error went away.

    • DD – The problem that we were getting with CUDA 11.7 seems to be resolved now that we’re getting 11.8

  • IA – Once 0.5 comes out, we’ll submit a bunch of benchmarking and validation sets.

    • JS – Sounds good. We run everything on our own tag/resources so these shouldn’t compete

  • IA – Would be good to pin openmm version since there’s a little smoke we’re seeing between 8.0 and 8.1

    • DD – I’ll pin to latest (8.1.2)

• compute resources status

  • DD – We’ve got a bunch of ASAP jobs in flight. But plenty of resources available.

• current stack versions:

  • python 3.10

  • alchemiscale: 0.4.0

  • neo4j: 5.18

  • gufe: 0.9.5

  • openfe: 0.14.0

  • perses: protocol-neqcyc

  • openmmforcefields: 0.12.0

DD: alchemiscale release 0.5.0 imminent; milestone complete

• DD – the 0.5.0 release is mostly waiting on my testing, most code changes are in place.

• includes:

  • openfe + gufe 1.0 compatibility

  • Folding@Home compute support via alchemiscale-fah 0.1.0

  • feflow inclusion, drop of perses

• will be deployed on a new host, new database as api.alchemiscale.org with advance notice to users

  • current api.alchemiscale.org instance will be moved to api.legacy.alchemiscale.org, kept around for some time, but with no new compute provisioned

  • new stack versions:

    • python 3.11

    • alchemiscale: 0.5.0

    • alchemiscale-fah: 0.1.0

    • neo4j: 5.22

    • gufe: 1.0.0

    • openfe: 1.0.1

    • feflow: 0.1.0

    • openmmforcefields: 0.14.1

    • openmm: 8.1.2

  • JS – Latest OpenFF force field?

    • JW – openff-2.2.0

    • IP – What version of the force fields are we defaulting to? In feflow it’s 2.0.0.

    • IA – I think this is being overridden by GUFE…. Yeah, it’s listed as 2.1.1. But folks can manually specify this.

    • IP – Ok, we should keep this in mind.

  • IA – OpenFE is pinned to OpenFF >0.15, <0.16 - Anything we should be aware of?

    • MT – https://docs.openforcefield.org/projects/toolkit/en/stable/releasehistory.html#id1

    • JW – No major changes, I don’t think. I’d 4/10 prefer that you use the latest, but if you had a good reason not to, then it’s your call.

    • IA – Ok, I’ll talk to MH.

  • IP – I recommend you pin the pip install for feflow to the tag and not the main branch.

    • DD – Will you make a C-F package?

    • IP – Yes, planning to start work on that this afternoon.

  • IP – To test feflow release, we’ll be running a few jobs. I don’t know if we’ll have an alchemiscale instance forthis. But I’ll be making+uploading a notebook to do this testing, and I’ll be happy to share this.

    • IA – Many of us are meeting on Friday to discuss benchmarking stuff. If we’re running our big benchmarking anyway, we can fold in more variables. If folks want to volunteer to help, we’d appreciate that. It’ll be morning BST.

  • JS – I’m struggling with an alchemiscale thing right now, would love to chat with DD or IK about this.

    • DD – We can work on it here.