From aade5e3d6fb3448ba4d5654cf56b251fc1651c4a Mon Sep 17 00:00:00 2001 From: Jammy2211 Date: Wed, 9 Sep 2026 17:18:28 -0400 Subject: [PATCH 1/2] cortex: activate ic50_workspace and submit graphical-ep phase 4 MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Phase 4 of the graphical-ep campaign (IC50 use case) is live on RAL. projects.yaml — the row described a project it could not actually read. Three fields were wrong, all now verified against the checkout and the cluster: * sync_verbs: [pull] -> the real 17-verb list. hpc/sync is a 560-line CLI with push, submit and push-submit implemented; the row understated it so far that the project looked unable to reach RAL at all. * ledger: README.md -> NOTES.md. ic50_workspace has no README.md; NOTES.md is its commentary ledger. Flagged in the note: NOTES.md is dated 2026-05-07 and predates the graphical-fit, HPC and profiling work, so it needs a refresh. * status: dormant -> active, partition: both -> ral. The blockers recorded on 2026-09-08 (dirty checkout, no results/ witness path) are cleared: the checkout is clean, results/ exists at the project root and matches the witness glob, and /mnt/ral/jnightin/ic50_workspace now exists and has run. tasks/ic50_workspace/ep_scale_up.md — planned -> ready -> submitted, runs 342408 (EP, sim, nlive 150, max_steps 12) and 342409 (graphical, sim, nlive 150), both on the ral partition. The task's "Ready when" line still told a reader to gate it on phase 2, which shipped on 2026-09-02; replaced with what actually happened, including that the RAL PyAutoFit mirror was checked for #1580 before submitting. Co-Authored-By: Claude Opus 5 (1M context) Claude-Session: https://claude.ai/code/session_01PMovQR9KqQUVBEg2b3EAsX --- projects.yaml | 10 +++++----- tasks/ic50_workspace/ep_scale_up.md | 16 +++++++++++++--- 2 files changed, 18 insertions(+), 8 deletions(-) diff --git a/projects.yaml b/projects.yaml index 332c74c..345a195 100644 --- a/projects.yaml +++ b/projects.yaml @@ -211,10 +211,10 @@ ic50_workspace: ral_root: /mnt/ral/jnightin/ic50_workspace mirror: none sync_cli: hpc/sync - sync_verbs: [pull] - ledger: README.md + sync_verbs: [push, pull, logs, sync, push-data-init, pull-full, status, submit, push-submit, jobs, sacct, cancel, wait-and-pull, tail, du, check, clear-logs] + ledger: NOTES.md assistant: none witness_file: results/**/*.json - partition: both - status: dormant - note: "personal remote, recorded as a fact — not a PyAutoLabs repo; ral_root planned, sync_verbs unverified" + partition: ral + status: active + note: "personal remote, recorded as a fact — not a PyAutoLabs repo; activated 2026-09-09 for graphical-ep phase 4, ral_root created and first runs submitted; NOTES.md predates the graphical/HPC work and needs a refresh" diff --git a/tasks/ic50_workspace/ep_scale_up.md b/tasks/ic50_workspace/ep_scale_up.md index 55f2ea3..7138bf4 100644 --- a/tasks/ic50_workspace/ep_scale_up.md +++ b/tasks/ic50_workspace/ep_scale_up.md @@ -2,11 +2,11 @@ Project: ic50_workspace Summary: Does EP match the graphical joint fit end to end -State: planned +State: submitted Gates: Witness: one committed EP-vs-graphical parity table (means ± errors) at small N, EP running at the largest N reached with per-rung timings committed, and any derived-variable or scaling blocker recorded as its own filed prompt Budget: 48:00 -Runs: +Runs: 342408, 342409 Ruling: Review-minutes: 25 Epic: graphical-ep @@ -15,7 +15,12 @@ Migrated-from: PyAutoMind/draft/research/graphical_ep/ic50_ep_scale_up.md ## Question -Ready when: graphical-ep phase 2 (Mind) is issued — add its ref to `Gates:` and move to `gated`. +Started 2026-09-09. Phases 1 and 2 of the campaign shipped on 2026-09-02 (the whole +D1–D6 PyAutoFit fix wave: #1558, #1560, #1562, #1572, #1573, #1574, #1576, #1578, +#1580), so the gate this task was waiting on is cleared and it went +`planned → ready → submitted` directly. The RAL PyAutoFit mirror was verified to +contain #1580 before submitting, so unlike phase 3's EP arm these runs carry the +stale-mask fixed-point fix. The IC50 cancer use case is the scale target: the end goal is graphical + EP fits at 10 000+ datasets, with a clear demonstration that EP matches the graphical joint fit at small N before @@ -55,9 +60,14 @@ Acceptance, verbatim from the Mind prompt: - Mind `draft/feature/autofit/ep_lbfgs_jax.md` — the development half (the speed lever) - Mind `research/graphical_ep/ep_campaign.md` phase 4 — the campaign row this feeds - Mind `research/autofit/autofit_profiling_bootstrap.md` — where the wrapper-overhead evidence goes +- `scripts/compare_graphical_ep.py` (in the project) — writes the parity table this + task's witness asks for, to `results/graphical_ep_comparison_.{txt,json}` ## Runs +- 342408: submitted — ral — submitted 2026-09-09 — wall 0:00 — EP sim, nlive 150, max_steps 12 +- 342409: submitted — ral — submitted 2026-09-09 — wall 0:00 — graphical sim joint Dynesty, nlive 150 + ## Ruling (none) From e994fe0444435f0010e9725548c0a9fbf0db2db3 Mon Sep 17 00:00:00 2001 From: Jammy2211 Date: Wed, 9 Sep 2026 17:25:55 -0400 Subject: [PATCH 2/2] cortex: regenerate dashboard for the ic50_workspace activation The two generated pages are ledger for the merge gate, and dashboard_refresh.yml errors rather than self-heals on a PR run, so the board has to be regenerated in the branch. Co-Authored-By: Claude Opus 5 (1M context) Claude-Session: https://claude.ai/code/session_01PMovQR9KqQUVBEg2b3EAsX --- dashboard.html | 17 ++++++++++++----- dashboard.md | 37 +++++++++++++++++++++++-------------- 2 files changed, 35 insertions(+), 19 deletions(-) diff --git a/dashboard.html b/dashboard.html index f9af242..c6d1334 100644 --- a/dashboard.html +++ b/dashboard.html @@ -236,7 +236,8 @@

One row per active project — the next thing, what it is holding, and when it last ruled.

- + +
ProjectNext taskAwaitingRunningLast ruling
euclid_dr1_prelimIs the ordered run's 8-nat gain ordering or library drift03-
euclid_dr1_prelimIs the ordered run's 8-nat gain ordering or library drift04-
ic50_workspaceDoes EP match the graphical joint fit end to end01-
slope_hierarchy_scaleDoes hierarchical slope recovery hold at N=25 to 5001-
subhalo_validationDoes rectangular_adapt false-detect a subhalo on the clumpy source052026-09-07
@@ -246,7 +247,6 @@

Nothing open

concrdormantnone cowls_dianadormantnone eucliddormantplanned 3 -ic50_workspacedormantplanned 1 pj011646dormantnone profilingdormantnone subhalo_simulationsdormantnone @@ -260,15 +260,22 @@

Nothing open

euclid_dr1_prelim

Local /mnt/c/Users/Jammy/Science/euclid_dr1_prelim

RAL /mnt/ral/jnightin/euclid_dr1_prelim

-

active · both partition · tasks: gated 1 · running 2 · submitted 1

+

active · both partition · tasks: running 2 · submitted 2

Is the ordered run's 8-nat gain ordering or library driftrunning — runs 342377_0 · wall 0:00 of 8:00 (0%)

Does ordering the MGE bases fix labelling on one tilerunning — runs 342375_[0-1] · wall 0:00 of 8:00 (0%)

Ten real DR1 lenses fitted from the pipeline repo alonesubmitted — runs 342301_[0-9], 342314_3 · wall 0:00 of 48:00 (0%)

-

Do ordered Nautilus reruns reproduce the euclid catalogue values?gated — euclid_strong_lens_modeling_pipeline#60

+

Do ordered Nautilus reruns reproduce the euclid catalogue values?submitted — runs 342398 · wall 0:00 of 36:00 (0%)

tasks/euclid_dr1_prelim/

+

ic50_workspace

+

Local /mnt/c/Users/Jammy/Science/ic50_workspace

+

RAL /mnt/ral/jnightin/ic50_workspace

+

active · ral partition · tasks: submitted 1

+

Does EP match the graphical joint fit end to endsubmitted — runs 342408, 342409 · wall 0:00 of 48:00 (0%)

+

tasks/ic50_workspace/ · issues

+
+

slope_hierarchy_scale

Local /mnt/c/Users/Jammy/Science/slope_hierarchy_scale

RAL /mnt/ral/jnightin/slope_hierarchy_scale

diff --git a/dashboard.md b/dashboard.md index e764d3f..1936d10 100644 --- a/dashboard.md +++ b/dashboard.md @@ -29,7 +29,8 @@ One row per active project — the next thing, what it is holding, and when it l | Project | Next task | Awaiting | Running | Last ruling | |---|---|---:|---:|---| -| euclid_dr1_prelim | Is the ordered run's 8-nat gain ordering or library drift | 0 | 3 | - | +| euclid_dr1_prelim | Is the ordered run's 8-nat gain ordering or library drift | 0 | 4 | - | +| ic50_workspace | Does EP match the graphical joint fit end to end | 0 | 1 | - | | slope_hierarchy_scale | Does hierarchical slope recovery hold at N=25 to 50 | 0 | 1 | - | | subhalo_validation | Does rectangular_adapt false-detect a subhalo on the clumpy source | 0 | 5 | 2026-09-07 | @@ -40,7 +41,6 @@ One row per active project — the next thing, what it is holding, and when it l | concr | dormant | none | retire ↓ | | cowls_diana | dormant | none | retire ↓ | | euclid | dormant | planned 3 | retire ↓ | -| ic50_workspace | dormant | planned 1 | retire ↓ | | pj011646 | dormant | none | retire ↓ | | profiling | dormant | none | retire ↓ | | subhalo_simulations | dormant | none | retire ↓ | @@ -69,14 +69,6 @@ One row per active project — the next thing, what it is holding, and when it l -
📋 retire ic50_workspace - -``` -/cortex — retire the science project ic50_workspace: confirm it is holding nothing live, then in PyAutoCortex run `python3 scripts/cortex.py retire ic50_workspace --why ""`, `python3 scripts/cortex.py check`, `pyauto-brain cortex dashboard --apply`, and push the ledger. The row, its tasks and its rulings all stay — only the status and the note change. -``` - -
-
📋 retire pj011646 ``` @@ -118,7 +110,7 @@ One row per active project — the next thing, what it is holding, and when it l **RAL** `/mnt/ral/jnightin/euclid_dr1_prelim` -active · both partition · tasks: gated 1 · running 2 · submitted 1 +active · both partition · tasks: running 2 · submitted 2
📋 Is the ordered run's 8-nat gain ordering or library drift — running — runs 342377_0 · wall 0:00 of 8:00 (0%) @@ -144,17 +136,34 @@ Report where the runs of the PyAutoCortex task tasks/euclid_dr1_prelim/dr1_preli
-
📋 Do ordered Nautilus reruns reproduce the euclid catalogue values? — gated — euclid_strong_lens_modeling_pipeline#60 +
📋 Do ordered Nautilus reruns reproduce the euclid catalogue values? — submitted — runs 342398 · wall 0:00 of 36:00 (0%) ``` -python3 scripts/cortex.py gates # then, once they have closed: move tasks/euclid_dr1_prelim/ordered_rerun_catalogue_parity.md ready -# gates: euclid_strong_lens_modeling_pipeline#60 +Report where the runs of the PyAutoCortex task tasks/euclid_dr1_prelim/ordered_rerun_catalogue_parity.md (342398) stand. ```
[tasks/euclid_dr1_prelim/](https://github.com/PyAutoLabs/PyAutoCortex/tree/main/tasks/euclid_dr1_prelim/) +### ic50_workspace + +**Local** `/mnt/c/Users/Jammy/Science/ic50_workspace` + +**RAL** `/mnt/ral/jnightin/ic50_workspace` + +active · ral partition · tasks: submitted 1 + +
📋 Does EP match the graphical joint fit end to end — submitted — runs 342408, 342409 · wall 0:00 of 48:00 (0%) + +``` +cd /mnt/c/Users/Jammy/Science/ic50_workspace && hpc/sync jobs +``` + +
+ +[tasks/ic50_workspace/](https://github.com/PyAutoLabs/PyAutoCortex/tree/main/tasks/ic50_workspace/) · [issues](https://github.com/Jammy2211/ic50_workspace/issues) + ### slope_hierarchy_scale **Local** `/mnt/c/Users/Jammy/Science/slope_hierarchy_scale`