Archive 4 checkpoints (1-4)

paper-releases/pbisc-diffusion/updates/20261014T112200Z-strict-priority-score-join/diffusion/dataset/server_1/model8/plans/paper_figures_strictpairs_20261012/recoveries/priority_server2_20261014/PLAN.md

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+# Server_2 strict comparator continuation with x4 priority
+
+User authorization: transfer 17 unstarted units and reuse Imperial draw3 partial completion; x4 downstream has priority.
+
+## Ownership and reuse
+- units.json contains exactly18 disjoint units. Original local worker and original two-host supervisor stopped while waiting for GPU, not during scientific computation. x4 training remains running.
+- Imperial draw3: PBISC adapter/lora/pairedcal complete; scSemi5/5 representatives trained and120/145 targets inferred. Probe verified all existing receipts and selected scinfer-120 as the first pending operation.
+- 913 staged files matched SHA256. Original remote deconvolution/finalizer helpers were preserved because they differ but are not executed by this compute-only worker. Raw source receipts preserved on server_2; only output stat metadata normalized for transport.
+- Remote worker runs compute only for18 units in list order. No other support/seed/hyperparameter changes. Collector transfers completed outputs, verifies SHA256, retains original completed receipts and CPU-scores on server_1.
+
+## Priority
+- No x4 controller/model/source files changed.
+- At checkpoint_epoch_016.pt appearance on shared NAS, lower-priority work stops launching new operations, GPU and CPU alike. An already-running operation finishes normally; it is not killed or repeated. scSemi inference operates in8-target chunks; handoff is at the next boundary, not instantaneous preemption.
+- Waiting occurs before acquiring ml-run/GPU lock. x4 may acquire both hosts normally.
+- After HF_CORE_VERIFIED.json confirms x4 core computation and backup, collector's independent watcher writes a shared release marker and lower-priority work resumes. If x4 fails, lower-priority work remains waiting for inspection rather than guessing that priority is released.
+- NAS absence fails closed. No automatic restart of failed jobs. The priority truth table was tested without launching experiments.
+
+## Durable services
+- server_2: pbisc-strict-priority-remote-20261014.service
+- server_1: pbisc-strict-priority-collect-v2-20261014.service
+- Original controller: pbisc-strict-two-host-controller-20261012.service (stopped)
+- Original local worker: pbisc-strict-resume-20261012-local.service (stopped)
+- Logs and priority/collection status in this directory on their corresponding host.
+
+## Preservation
+- No checkpoints or generated outputs deleted.
+- Completed18-unit results trigger the normal versioned paper archive/HF publisher: PBISC LoRA checkpoints, core score tables/metadata and hashed inference locations. Manuscript/deck are not overwritten.
+
+## Preserved CPU join
+The previous12 server_2 units had completed compute/import but not central scoring. After the transferred18 units, the collector verifies their import receipts and scores their existing outputs without training/generation. This preserves the retired controller's pending CPU join. These12 were previously described too broadly as completed comparisons; only their compute was complete.

paper-releases/pbisc-diffusion/updates/20261014T112200Z-strict-priority-score-join/diffusion/dataset/server_1/model8/plans/paper_figures_strictpairs_20261012/recoveries/priority_server2_20261014/collect.py

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+"""Collect completed remote units only, keep original receipts, then CPU-score and archive."""
+from pathlib import Path
+import sys,json,subprocess,shlex,threading,time,fcntl,hashlib,copy,os
+R=Path(__file__).resolve().parent;S=R.parents[1];M=S.parents[1]
+sys.path[:0]=[str(R),str(S/'tools')]
+import campaign
+from worker import LowPriorityRuntime,X
+from runtime import atomic_json,sha256,stat_record,stamp
+from two_host_resume import unit_support,validate_snapshot,verify_import
+PY='/home/sj_server_2/miniforge3/envs/b2sc-infer/bin/python'
+def remote(argv,**kw):return subprocess.run(['ssh','-o','BatchMode=yes','spark-0110',shlex.join(argv)],check=True,**kw)
+def state(phase,**kw):atomic_json(R/'COLLECT_STATUS.json',{'phase':phase,'at':stamp(),**kw})
+def release_watch():
+ while True:
+  p=X/'HF_CORE_VERIFIED.json'
+  if p.exists() and json.loads(p.read_text()).get('state')=='verified':
+   atomic_json(X/'payload/priority/LOW_PRIORITY_RELEASE.json',{'reason':'x4 core computation and HF backup verified','receipt':str(p),'sha256':sha256(p),'at':stamp()});return
+  time.sleep(30)
+def collect(unit):
+ dest=R/'imported'/unit;dest.mkdir(parents=True,exist_ok=True)
+ done=dest/'IMPORTED.json'
+ if done.exists():return
+ snapshot=json.loads(remote([PY,str(S/'tools/two_host_resume.py'),'snapshot','--unit',unit],capture_output=True,text=True).stdout)
+ validate_snapshot(S,unit,snapshot)
+ atomic_json(dest/'snapshot.json',snapshot)
+ for row in snapshot['files']:
+  rel=Path(row['path']);target=dest/rel if rel.parts[0] in ['receipts','unit_status'] else S/rel
+  target.parent.mkdir(parents=True,exist_ok=True)
+  if target.exists() and sha256(target)!=row['sha256']:
+   # Only pre-existing mutable state/logs from the migrated partial unit may advance.
+   allowed=unit=='imperial_eskd-disease-draw3' and rel.parts[0] in ['scsemi','logs']
+   assert allowed,('unexpected conflicting artifact',target)
+   saved=dest/'before_import'/rel;saved.parent.mkdir(parents=True,exist_ok=True)
+   if not saved.exists():subprocess.run(['cp','-p',str(target),str(saved)],check=True)
+  subprocess.run(['rsync','-a','--protect-args','spark-0110:'+str(S/rel),str(target)],check=True)
+  assert target.stat().st_size==row['bytes'] and sha256(target)==row['sha256']
+ for raw in (dest/'receipts').glob('*.json'):
+  record=json.loads(raw.read_text());assert record['state']=='completed'
+  for out in record.get('outputs',[]):
+   f=Path(out['path']);assert sha256(f)==out['sha256'];out.update(stat_record(f))
+  original=S/'receipts'/raw.name
+  if original.exists():
+   old=json.loads(original.read_text());assert old['state']=='completed' and old['signature']==record['signature']
+   assert [o['sha256'] for o in old.get('outputs',[])]==[o['sha256'] for o in record.get('outputs',[])]
+   # Original source receipt remains unchanged; rsync preserved timestamps of immutable outputs.
+   for o in old.get('outputs',[]):assert stat_record(Path(o['path']))=={k:o[k] for k in ['path','bytes','mtime_ns']}
+  else:
+   record['remote_provenance']={'host':'server_2','raw_receipt':str(raw),'sha256':sha256(raw)};atomic_json(original,record)
+ atomic_json(done,{'state':'verified','unit':unit,'snapshot_sha256':sha256(dest/'snapshot.json'),'at':stamp()})
+def main():
+ threading.Thread(target=release_watch,daemon=True).start()
+ units=json.loads((R/'units.json').read_text());rt=LowPriorityRuntime(S)
+ with (S/'.campaign.lock').open('a') as lock:
+  fcntl.flock(lock,fcntl.LOCK_EX|fcntl.LOCK_NB)
+  for unit in units:
+   state('waiting_remote',unit=unit)
+   while True:
+    code='import pathlib,json,sys; p=pathlib.Path(sys.argv[1]); print(p.read_text() if p.exists() else "null")'
+    marker=json.loads(remote(['python3','-c',code,str(S/'unit_status'/f'{unit}.json')],capture_output=True,text=True).stdout)
+    if marker and marker.get('state')=='completed' and marker.get('stage')=='compute':break
+    props=remote(['/usr/bin/env','XDG_RUNTIME_DIR=/run/user/1000','DBUS_SESSION_BUS_ADDRESS=unix:path=/run/user/1000/bus','systemctl','--user','show','pbisc-strict-priority-remote-20261014.service','-p','ActiveState','-p','SubState'],capture_output=True,text=True).stdout
+    if 'ActiveState=failed' in props or 'ActiveState=inactive' in props:raise RuntimeError('Remote worker stopped before unit completion: '+props)
+    time.sleep(30)
+   state('collecting',unit=unit);collect(unit)
+   path,_,manifest=unit_support(S,unit)
+   state('scoring',unit=unit);campaign.run_score(rt,path)
+   atomic_json(S/'unit_status'/f'{unit}.json',{'state':'completed','stage':'all','support_sha256':manifest['sha256'],'at':stamp(),'source':'priority server2 migration'})
+   state('unit_completed',unit=unit)
+  state('all_18_completed',units=units)
+  # The retired controller also owned this CPU-only join. Preserve it without any new GPU work.
+  prior=json.loads((S/'recoveries/two_host/config.json').read_text())['remote_units']
+  for unit in prior:
+   verify_import(S,unit,S/'recoveries/two_host/imported'/unit)
+   path,_,manifest=unit_support(S,unit)
+   state('scoring_previously_generated',unit=unit);campaign.run_score(rt,path)
+   atomic_json(S/'unit_status'/f'{unit}.json',{'state':'completed','stage':'all','support_sha256':manifest['sha256'],'at':stamp(),'source':'CPU-only join of previously imported generation'})
+  units=units+prior
+  state('transferred_and_existing_scores_complete',units=units)
+  assets=[];locations=[]
+  for unit in units:
+   path,rel,_=unit_support(S,unit)
+   assets.extend([{'host':'server_1','source':str(path),'kind':'metadata','state':'completed'},
+                  {'host':'server_1','source':str(S/'runs'/rel/'lora/checkpoint_ft.pt'),'kind':'checkpoint','state':'completed'}])
+   for f in (S/'scores'/rel).rglob('*'):
+    if f.is_file() and f.suffix in ['.json','.csv'] and f.stat().st_size<4*2**20:
+     assets.append({'host':'server_1','source':str(f),'kind':'report' if f.suffix=='.json' else 'table','state':'completed'})
+   for f in (S/'generated'/rel).glob('*.npz'):
+    locations.append({'host':'server_1','path':str(f),'state':'completed','sha256':sha256(f),'reason':'Completed transferred strict-pair comparator output; source server_2 and imported receipts retained.'})
+  request={'project_id':'pbisc-diffusion','summary':'Completed18 transferred strict-pair units plus CPU-only evaluation of12 previously generated/imported units; Imperial draw3 first120 targets reused; x4 priority preserved.','assets':assets,'inference_locations':locations}
+  atomic_json(R/'FINAL_ARCHIVE_REQUEST.json',request)
+  from datetime import datetime,timezone
+  ident=datetime.now(timezone.utc).strftime('%Y%m%dT%H%M%SZ')+'-strict-priority-results'
+  release=M.parents[1]/'paper-release-20260928';cli=release/'maintenance/update.py'
+  with (R/'final_archive.log').open('x') as log:
+   for args in [['prepare','--request',str(R/'FINAL_ARCHIVE_REQUEST.json'),'--id',ident],['publish',ident,'--execute']]:
+    subprocess.run(['/home/sj_server_1/miniforge3/bin/python',str(cli),*args],check=True,stdout=log,stderr=subprocess.STDOUT)
+  receipt=release/'maintenance/updates'/ident/'UPDATE_VERIFIED.json';assert json.loads(receipt.read_text())['status']=='PASS'
+  state('complete_and_archived',units=units,archive_id=ident,receipt=str(receipt))
+if __name__=='__main__':
+ try:main()
+ except BaseException as e:state('stopped_needs_inspection',error=str(e));raise

paper-releases/pbisc-diffusion/updates/20261014T112200Z-strict-priority-score-join/diffusion/metadata/inference_locations.json

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+{
+  "locations": [],
+  "project_id": "pbisc-diffusion",
+  "update_id": "20261014T112200Z-strict-priority-score-join"
+}

paper-releases/pbisc-diffusion/updates/20261014T112200Z-strict-priority-score-join/diffusion/metadata/request.json

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+{
+  "assets": [
+    {
+      "host": "server_1",
+      "kind": "code",
+      "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/recoveries/priority_server2_20261014/collect.py",
+      "state": "completed"
+    },
+    {
+      "host": "server_1",
+      "kind": "report",
+      "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/recoveries/priority_server2_20261014/PLAN.md",
+      "state": "completed"
+    }
+  ],
+  "inference_locations": [],
+  "project_id": "pbisc-diffusion",
+  "summary": "Preserve retired strict controller CPU-only scoring join for12 previously generated units after18 transferred computations; no additional model training or generation; same x4 priority gate."
+}