Archive 4 checkpoints (1-4)

paper-releases/pbisc-diffusion/updates/20261013T144247Z-f01-trunk4x-campaign-launch/diffusion/dataset/server_1/model8/plans/f01_trunk4x_complete_20261013/ops/status.sh

@@ -0,0 +1,8 @@
+#!/usr/bin/env bash
+set -euo pipefail
+P=/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/f01_trunk4x_complete_20261013
+systemctl --user show pbisc-f01-trunk4x-campaign-v2-20261013 -p ActiveState -p SubState -p ExecMainStatus
+systemctl --user show pbisc-f01x4-nas-20261013 -p ActiveState -p SubState
+cat "$P/PRETRAIN_STATUS.json"
+if [[ -f "$P/payload/pretrain/f01_6k_trunk4x_seed20260627/RUN_STATUS.json" ]]; then cat "$P/payload/pretrain/f01_6k_trunk4x_seed20260627/RUN_STATUS.json"; fi
+if [[ -f "$P/DOWNSTREAM_STATUS.json" ]]; then cat "$P/DOWNSTREAM_STATUS.json"; fi

paper-releases/pbisc-diffusion/updates/20261013T144247Z-f01-trunk4x-campaign-launch/diffusion/dataset/server_1/model8/plans/f01_trunk4x_complete_20261013/payload/pretrain/profile128/ALLCELL_DATA_CONTRACT.json

@@ -0,0 +1,174 @@
+{
+  "expected_optimizer_steps_by_epoch": [
+    252
+  ],
+  "expected_target_cells_by_epoch": [
+    64000
+  ],
+  "original_recipe_coverage": {
+    "cell_coverage_fraction": 0.9397752899849071,
+    "mean_visits_all_cells": 5.8429673115603515,
+    "mean_visits_represented_cells": 6.217408963428045,
+    "never_visited_cells": 1995930,
+    "represented_cells": 31145450,
+    "target_exposures": 193644000,
+    "universe_cells": 33141380,
+    "visits_q00": 0.0,
+    "visits_q01": 0.0,
+    "visits_q05": 0.0,
+    "visits_q100": 228.0,
+    "visits_q25": 2.0,
+    "visits_q50": 4.0,
+    "visits_q75": 8.0,
+    "visits_q90": 12.0,
+    "visits_q95": 16.0,
+    "visits_q99": 29.0
+  },
+  "pairing": {
+    "batch_size": 256,
+    "cells_per_block": 4000,
+    "coverage_audit_sha256": "3904c5b4026f3a5358d6553948f0d4456c80494eab941ab2f7c2975f459d24c5",
+    "epochs": 1,
+    "fast_rows_note": "0 = Model 7 _csr_rows; >0 = pbisc_sdd.fast_rows (identical CSR, threaded chunk decode)",
+    "fast_rows_threads": 4,
+    "gradient_accumulation_steps": 1,
+    "num_workers": 4,
+    "pool_order_sha256": "b44aed91ab628de4fc7505c9ecc13296bc04d8cd78120d46aca3e50ae0267b3f",
+    "prefetch_factor": 32,
+    "prefetch_factor_note": "scheduling depth only; batch sequence independent of it",
+    "priming_policy": "all-train-first-then-validation-v1",
+    "recipe_schedule_sha256": "6de0abced43a612f1e263f9d042fdd1e4962d90e9a88665c634b99abf4169730",
+    "recipes_per_epoch": 8192,
+    "registered_recipes_per_epoch": 8192,
+    "seed": 20260627,
+    "source_corpus_fingerprint": "eeb609250457248225432b6df94573b26a8cad8ac743670b5ca43134fea7e007",
+    "source_pool_sha256": "5f272fba92c0b388a3d7cd27f1fcb5ccd3e7edb5490c95948a50bc2ba35da8d1",
+    "source_recipe_sha256": "018493f60745f026ea4979cfb8954ba6dc3e3f79f351d688382a84c6a360de4b",
+    "target_policy": "all-registered-K-plus-unseen-train-topup-v1",
+    "topup_manifest_sha256": "df300a6f7f758c865209c6640e51abcbec10bab9726ee48c3bc3434936316da1",
+    "total_recipe_counts_by_epoch": [
+      16
+    ]
+  },
+  "planned_coverage_after_topup": {
+    "annotation_fields_read": [],
+    "cell_identity": "topup_cell_ids.npy stores global source IDs; shard_offsets.csv maps to shard_id,row_index",
+    "coverage_dir": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/full_recipe_allcells_6k_broad_20260909/coverage_v1",
+    "coverage_pool_order_sha256": "b44aed91ab628de4fc7505c9ecc13296bc04d8cd78120d46aca3e50ae0267b3f",
+    "elapsed_seconds": 0.866,
+    "max_k": 4000,
+    "original_recipe_membership_sha256": "b28cef371a2ff5c42b77ec13a0a34cc239ff57ae8127f9e3a4ea81ee945e7fce",
+    "original_target_exposures": 193644000,
+    "original_train_recipes": 131072,
+    "policy": "unseen-train-explicit-sample-chunks-greedy-slots-v1",
+    "pool_policy": "Prime original registered train pools first. Topups use explicit IDs and must not be random-redrawn or require pool reprime.",
+    "raw_expression_files_read": [],
+    "schedule_slots": 16,
+    "schema_version": "pbisc_sdd.allcell_topup.v1",
+    "slot_assignment": "greedy lowest topup target-cell total; ties choose lowest slot index",
+    "slot_coverage": [
+      {
+        "schedule_slot": 0,
+        "topup_recipes": 242,
+        "topup_target_cells": 124512
+      },
+      {
+        "schedule_slot": 1,
+        "topup_recipes": 223,
+        "topup_target_cells": 124477
+      },
+      {
+        "schedule_slot": 2,
+        "topup_recipes": 225,
+        "topup_target_cells": 124259
+      },
+      {
+        "schedule_slot": 3,
+        "topup_recipes": 208,
+        "topup_target_cells": 124247
+      },
+      {
+        "schedule_slot": 4,
+        "topup_recipes": 241,
+        "topup_target_cells": 124571
+      },
+      {
+        "schedule_slot": 5,
+        "topup_recipes": 224,
+        "topup_target_cells": 124344
+      },
+      {
+        "schedule_slot": 6,
+        "topup_recipes": 233,
+        "topup_target_cells": 125938
+      },
+      {
+        "schedule_slot": 7,
+        "topup_recipes": 243,
+        "topup_target_cells": 124399
+      },
+      {
+        "schedule_slot": 8,
+        "topup_recipes": 202,
+        "topup_target_cells": 124310
+      },
+      {
+        "schedule_slot": 9,
+        "topup_recipes": 232,
+        "topup_target_cells": 127329
+      },
+      {
+        "schedule_slot": 10,
+        "topup_recipes": 237,
+        "topup_target_cells": 124626
+      },
+      {
+        "schedule_slot": 11,
+        "topup_recipes": 196,
+        "topup_target_cells": 124340
+      },
+      {
+        "schedule_slot": 12,
+        "topup_recipes": 255,
+        "topup_target_cells": 124158
+      },
+      {
+        "schedule_slot": 13,
+        "topup_recipes": 283,
+        "topup_target_cells": 124820
+      },
+      {
+        "schedule_slot": 14,
+        "topup_recipes": 197,
+        "topup_target_cells": 124263
+      },
+      {
+        "schedule_slot": 15,
+        "topup_recipes": 217,
+        "topup_target_cells": 125337
+      }
+    ],
+    "status": "PASS",
+    "tail_policy": "actual K without duplicate padding, including K below original 250 minimum",
+    "topup_recipes": 3658,
+    "topup_samples": 3599,
+    "topup_target_cells": 1995930,
+    "total_target_exposures_with_topup": 195639930,
+    "total_train_recipes_with_topup": 134730,
+    "train_cell_coverage_after_topup": 1.0,
+    "train_cells_covered_after_topup": 33141380,
+    "train_universe_cells": 33141380,
+    "validation": {
+      "duplicate_cells": 0,
+      "each_unseen_train_cell_exactly_once": true,
+      "nontrain_cells": 0,
+      "previously_seen_cells": 0,
+      "sample_boundary_violations": 0,
+      "status": "PASS",
+      "unique_topup_cells": 1995930,
+      "unseen_train_set_equality": true
+    }
+  },
+  "schema_version": "pbisc_sdd.allcell_data_contract.v1",
+  "status": "PROFILE_RUNNING"
+}

paper-releases/pbisc-diffusion/updates/20261013T144247Z-f01-trunk4x-campaign-launch/diffusion/dataset/server_1/model8/plans/f01_trunk4x_complete_20261013/payload/pretrain/profile128/ALLCELL_PROFILE.json

@@ -0,0 +1,43 @@
+{
+  "config_sha256": "28794ea42035de7225b8a812181b83932bf6604b5462e497e82af8dc5a017cd3",
+  "data_contract": "16 worst-K recipes available; step-limited profile, not a complete epoch",
+  "result": {
+    "best_validation_loss": 0.7309143933004533,
+    "completed_at": "2026-10-13T13:53:10.773337+00:00",
+    "condition_dim": 18006,
+    "corpus_fingerprint": "eeb609250457248225432b6df94573b26a8cad8ac743670b5ca43134fea7e007",
+    "device": "cuda",
+    "epochs_completed": 1,
+    "generated_zero_fraction_preview": 0.9482146501541138,
+    "global_step": 128,
+    "memory": {
+      "cuda_allocated_gib": 3.638111114501953,
+      "cuda_free_gib": 2.583820343017578,
+      "cuda_peak_allocated_gib": 5.497453689575195,
+      "cuda_reserved_gib": 5.75390625,
+      "cuda_total_gib": 121.68767166137695,
+      "system_available_gib": 92.58792114257812
+    },
+    "memory_policy": {
+      "cuda_allocator_fraction": 0.19722622408936663,
+      "cuda_allocator_limit_gib": 24.0,
+      "cuda_available_at_start_gib": 17.49688720703125,
+      "cuda_device_index": 0,
+      "cuda_memory_floor_gib": 0.0,
+      "cuda_temperature_at_start_c": 71.0,
+      "cuda_utilization_at_start_percent": 0.0,
+      "cuda_visible_total_gib": 121.68767166137695,
+      "system_available_at_start_gib": 109.79124069213867,
+      "system_memory_floor_gib": 32.0
+    },
+    "n_genes": 6000,
+    "parameters": 239955168,
+    "real_zero_fraction_preview": 0.8859309554100037,
+    "schema_version": "pbisc_sdd.status.v1",
+    "status": "COMPLETED",
+    "support_value_disagreement_fraction_preview": 0.0014409301802515984,
+    "training_contract": "pbisc_sdd.ladder_training.v1",
+    "wall_seconds": 309.6600242919958
+  },
+  "status": "COMPLETED"
+}

paper-releases/pbisc-diffusion/updates/20261013T144247Z-f01-trunk4x-campaign-launch/diffusion/dataset/server_1/model8/plans/f01_trunk4x_complete_20261013/payload/pretrain/profile128/PROCESS.json

@@ -0,0 +1,27 @@
+{
+  "argv": [
+    "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/scripts/train_allcell_sdd.py",
+    "--config",
+    "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/f01_trunk4x_complete_20261013/configs/profile.json",
+    "--expected-config-sha256",
+    "28794ea42035de7225b8a812181b83932bf6604b5462e497e82af8dc5a017cd3"
+  ],
+  "hostname": "spark-fa6b",
+  "memory_policy": {
+    "cuda_allocator_fraction": 0.19722622408936663,
+    "cuda_allocator_limit_gib": 24.0,
+    "cuda_available_at_start_gib": 17.49688720703125,
+    "cuda_device_index": 0,
+    "cuda_memory_floor_gib": 0.0,
+    "cuda_temperature_at_start_c": 71.0,
+    "cuda_utilization_at_start_percent": 0.0,
+    "cuda_visible_total_gib": 121.68767166137695,
+    "system_available_at_start_gib": 109.79124069213867,
+    "system_memory_floor_gib": 32.0
+  },
+  "output_dir": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/f01_trunk4x_complete_20261013/payload/pretrain/profile128",
+  "pid": 940604,
+  "schema_version": "pbisc_sdd.process.v1",
+  "started_at": "2026-10-13T13:48:01.113493+00:00",
+  "training_contract": "pbisc_sdd.ladder_training.v1"
+}