Archive 4 checkpoints (1-4)

paper-releases/pbisc-diffusion/updates/20261015T065710Z-giroux-width-comparison/diffusion/dataset/server_1/model8/plans/paper_figures_strictpairs_20261012/recoveries/giroux_width_comparison_20261015/FIX_VERIFIED.json

@@ -0,0 +1,36 @@
+{
+  "original_failure_reproduced": true,
+  "all_five_imperial_arms_pass": true,
+  "wrong_hash_unknown_path_different_checkpoint_rejected": true,
+  "canonical_and_remote_checkpoint_bytes_identical": true,
+  "actual_checkpoint_model_config_x1": {
+    "n_genes": 6000,
+    "condition_dim": 18006,
+    "hidden_dims": [
+      1024,
+      1024,
+      512,
+      256
+    ],
+    "time_embedding_dim": 128,
+    "context_dim": 512,
+    "dropout": 0.0,
+    "max_time_period": 10000.0
+  },
+  "actual_checkpoint_model_config_x4": {
+    "n_genes": 6000,
+    "condition_dim": 18006,
+    "hidden_dims": [
+      4096,
+      4096,
+      2048,
+      1024
+    ],
+    "time_embedding_dim": 128,
+    "context_dim": 512,
+    "dropout": 0.0,
+    "max_time_period": 10000.0
+  },
+  "same_6000_gene_ids_order": true,
+  "cuda_initialized": false
+}

paper-releases/pbisc-diffusion/updates/20261015T065710Z-giroux-width-comparison/diffusion/dataset/server_1/model8/plans/paper_figures_strictpairs_20261012/recoveries/giroux_width_comparison_20261015/resume_collector.py

@@ -0,0 +1,17 @@
+"""Resume only CPU collection/scoring after explicit receipt-preserving repair."""
+from pathlib import Path
+import sys,json
+R=Path(__file__).resolve().parent;S=R.parents[1];old=S/'recoveries/priority_server2_20261014'
+sys.path[:0]=[str(old),str(S/'tools')]
+import collect
+from worker import LowPriorityRuntime
+class FixedRuntime(LowPriorityRuntime):
+ def wrapped_command(self,name,argv,resource,memory_gib,threads):
+  command=super().wrapped_command(name,argv,resource,memory_gib,threads)
+  if resource=='cpu' and str(S/'tools/score_strict.py') in argv:
+   command=[str(R/'score_cli.py') if x==str(S/'tools/score_strict.py') else x for x in command]
+  return command
+if __name__=='__main__':
+ collect.LowPriorityRuntime=FixedRuntime
+ try:collect.main()
+ except BaseException as e:collect.state('stopped_needs_inspection',error=str(e));raise

paper-releases/pbisc-diffusion/updates/20261015T065710Z-giroux-width-comparison/diffusion/dataset/server_1/model8/plans/paper_figures_strictpairs_20261012/recoveries/giroux_width_comparison_20261015/score_cli.py

@@ -0,0 +1,7 @@
+from pathlib import Path
+import sys
+R=Path(__file__).resolve().parent;S=R.parents[1];sys.path.insert(0,str(S/'tools'))
+import score_strict
+from validator_fix import install
+install(score_strict)
+if __name__=='__main__':raise SystemExit(score_strict.main())

paper-releases/pbisc-diffusion/updates/20261015T065710Z-giroux-width-comparison/diffusion/dataset/server_1/model8/plans/paper_figures_strictpairs_20261012/recoveries/giroux_width_comparison_20261015/verify_fix.py

@@ -0,0 +1,28 @@
+from pathlib import Path
+import sys,json,torch
+R=Path(__file__).resolve().parent;S=R.parents[1];M=S.parents[1];sys.path.insert(0,str(S/'tools'))
+import score_strict as ST
+from validator_fix import matches,install
+proof=json.loads((R/'CHECKPOINT_ALIAS_PROOF.json').read_text());sha=proof['sha256'];canonical=proof['canonical'];alias=proof['remote_resolved']
+a={'checkpoint':alias,'checkpoint_sha256':sha}
+assert matches(a,a,canonical,sha,proof)
+assert not matches(a,a,canonical,'0'*64,proof)
+assert not matches({**a,'checkpoint':'/unapproved/model.pt'},a,canonical,sha,proof)
+assert not matches(a,{**a,'checkpoint_sha256':'0'*64},canonical,sha,proof)
+assert not matches(a,a,'/another/canonical.pt',sha,proof)
+support=ST.read_support(S/'protocol/splits/imperial_eskd/disease/draw4/support.json');gen=S/'generated/imperial_eskd/disease/draw4'
+try:ST.validate_generation_arm('pairedcal',gen/'pairedcal.npz',support)
+except ValueError as e:assert str(e)=='generation checkpoint differs from strict source'
+else:raise AssertionError('Original failure not reproduced')
+install(ST)
+for arm in ['lora','pairedcal','scsemi','raw','refcal']:
+ p=gen/f'{arm}.npz' if arm not in ['raw','refcal'] else S/f'generated/global/imperial_eskd/{arm}.npz'
+ ST.validate_generation_arm(arm,p,support)
+ print('VALIDATED',arm,flush=True)
+X=M/'plans/f01_trunk4x_complete_20261013';a=torch.load(canonical,map_location='cpu',weights_only=False,mmap=True);b=torch.load(X/'base_cache/checkpoint_epoch_016.pt',map_location='cpu',weights_only=False,mmap=True)
+print('CONFIGS',a['model_config'],b['model_config'],flush=True)
+assert list(b['model_config']['hidden_dims'])==[4*x for x in a['model_config']['hidden_dims']]
+assert a['model_config']['context_dim']==b['model_config']['context_dim']==512
+assert a['model_config']['time_embedding_dim']==b['model_config']['time_embedding_dim']==128
+assert list(a['gene_ids'])==list(b['gene_ids']) and len(a['gene_ids'])==6000
+(R/'FIX_VERIFIED.json').write_text(json.dumps({'original_failure_reproduced':True,'all_five_imperial_arms_pass':True,'wrong_hash_unknown_path_different_checkpoint_rejected':True,'canonical_and_remote_checkpoint_bytes_identical':True,'actual_checkpoint_model_config_x1':a['model_config'],'actual_checkpoint_model_config_x4':b['model_config'],'same_6000_gene_ids_order':True,'cuda_initialized':torch.cuda.is_initialized()},indent=2)+'\n')