2024-08-06 alchemiscale : dev group meeting notes

This meeting instance was canceled due to DD illness. Written dev status summary below:

• DD : Currently live testing alchemiscale-fah 0.1.0rc with alchemiscale 0.5.0rc using mskcc2 and dev.alchemiscale.org

  • worked through connectivity issues with @Mike Henry and @Hugo Macdermott-Opeskin

  • worked through FAH client issues on Iris with @Hugo Macdermott-Opeskin and @John Chodera

  • our work units generated by alchemiscale-fah successfully execute on FAH, but two issues we’re working through:

    • replays of ProtocolDAGs that previously failed always fail due to files being cleaned up too overzealously in shared space

      • working to rectify this in alchemiscale-fah

    • execution of FahNonEquilibriumCyclingProtocol Tasks bottlenecked by minimization being performed in the SetupUnit, which occurs on the host the compute service lives on

      • need to move minimization to FAH, performed within openmm-core

        • https://github.com/FoldingAtHome/openmm-core/issues/517

      • also need to make it possible to defer minimization from SetupUnit to CycleUnit in feflow.NonEquilibriumCyclingProtocol

        • https://github.com/choderalab/feflow/pull/60

• IK : Implementing user-defined policies for server-side errored Task restarts in alchemiscale

  • Testing is taking longer than expected to implement and is the main blocker to restart resolution

• DD + IK : we’ve also started design cycles for Strategys; will present on this in an upcoming dev meeting

Participants

Goals

• DD : alchemiscale roadmap

  • Q1 : complete “living networks” performance improvements

  • Q1 : Folding@Home compute services deployed in production

    • finish MVP, with integration test suite by 2024.03 2024.06

    • perform FAH tests with volunteers during 2024.04 2024.06 2024.07

      • public work server up by 2024.03.15 2024.06.11 2024.07.19 2024.07.31

      • confidential work server up by 2024.04.01 2024.07.01 2024.07.31 2024.08.16

  • Q2 Q3 : develop Strategy structure, initial implementations

    • aiming to begin design 6/26 7/10 7/24 sprint, followed by MVP development during July August

  • Q3 : enable automated Strategy execution by end of Q3, 2024 (2024.10.01) mid Q4, 2024 (2024.11.15)

• DD : alchemiscale.org website proposal:

• DD : proposal: reorganize alchemiscale project

  • migrate alchemiscale under OpenFreeEnergy Github org

  • create alchemiscale channel in OpenFE Slack

  • move working group meeting notes under OpenFE working group

• DD : proposal: deprecate use of anaconda.org environments:

  • remove references to them in docs

  • keep instructions to users to clone repository, checkout release tag, install prod client env from there

• alchemiscale development : new sprint spanning 8/7 - 8/19

  • architecture overview : https://drive.google.com/file/d/1ZA-zuqrhKSlYBEiAIqxwNaHXvgJdlOkT/view?usp=share_link

  • coordination board : alchemiscale : Phase 3 - Folding@Home, new features, optimizations, targeted refactors

Discussion topics

Action items

Decisions