Archive 4 checkpoints (1-4)

paper-releases/pbisc-diffusion/updates/20261012T130738Z-strictpairs-implementation/diffusion/dataset/server_1/model8/plans/paper_figures_strictpairs_20261012/archive/20261012T130738Z-strictpairs-implementation/LIVE_OBSERVATION.json

@@ -0,0 +1,136 @@
+{
+  "observed_at": "2026-10-12T13:07:42.485589+00:00",
+  "latest_archive": {
+    "control_archive": [
+      {
+        "archive_stat": {
+          "dev": 66306,
+          "ino": 2499425,
+          "mtime_ns": 1791808169874061406,
+          "size": 9187
+        },
+        "bundle_path": "updates/20261012T122929Z-introduction-transitions-lora/control/manifest.json",
+        "bytes": 9187,
+        "sha256": "856579482f2e25691849b3e15f880648dfc66a7f7496fb66b5b9158107f1aa0a"
+      },
+      {
+        "archive_stat": {
+          "dev": 66306,
+          "ino": 2499549,
+          "mtime_ns": 1791808213421880873,
+          "size": 39447
+        },
+        "bundle_path": "updates/20261012T122929Z-introduction-transitions-lora/control/receipts.jsonl",
+        "bytes": 39447,
+        "sha256": "00ff33c17f5b26eee8a93275939548118cd7d7d91e960d8f591a3f0de6277320"
+      },
+      {
+        "archive_stat": {
+          "dev": 66306,
+          "ino": 2499550,
+          "mtime_ns": 1791808213429697396,
+          "size": 195
+        },
+        "bundle_path": "updates/20261012T122929Z-introduction-transitions-lora/control/status.json",
+        "bytes": 195,
+        "sha256": "3fe07f4b4953951bbee1e30822b73e16b70c3d0303587d738d9b4c34e7d9ab59"
+      },
+      {
+        "archive_stat": {
+          "dev": 66306,
+          "ino": 2499551,
+          "mtime_ns": 1791808221997213140,
+          "size": 10947
+        },
+        "bundle_path": "updates/20261012T122929Z-introduction-transitions-lora/control/UPDATE_VERIFIED.json",
+        "bytes": 10947,
+        "sha256": "f69fb2127d950b4dc8f245a29582d5e20a9a3346fd1d78dc110be750a942f6a3"
+      }
+    ],
+    "id": "20261012T122929Z-introduction-transitions-lora",
+    "parent": {
+      "id": "20261012T121201Z-abstract-pretraining-lora",
+      "receipt_revision": "1b30942d4c9adfbe694e6dce3af33fe22eb5e9e7",
+      "verified_receipt_sha256": "44b10bc409f4744a12cc59b0fba3625fe67280068bae73ba2d7d311134028cd7"
+    },
+    "project_id": "pbisc-diffusion",
+    "receipt_revision": "4e925071758fbc25c176b44f3fbe9c74ea7e7904",
+    "schema": "pbisc.diffusion.latest.v1",
+    "verified_receipt_path": "paper-releases/pbisc-diffusion/updates/20261012T122929Z-introduction-transitions-lora/UPDATE_VERIFIED.json",
+    "verified_receipt_sha256": "f69fb2127d950b4dc8f245a29582d5e20a9a3346fd1d78dc110be750a942f6a3"
+  },
+  "server_1": [
+    {
+      "argv": [
+        "systemctl",
+        "--user",
+        "is-active",
+        "ml-memory-guard.service"
+      ],
+      "returncode": 0,
+      "stdout": "active",
+      "stderr": ""
+    },
+    {
+      "argv": [
+        "/home/sj_server_1/.local/libexec/ml-memory-guard",
+        "--check"
+      ],
+      "returncode": 0,
+      "stdout": "available_gib=74.02 threshold_gib=18.00 ml_populated=yes cgroup=/user.slice/user-1000.slice/user@1000.service/ml.slice",
+      "stderr": ""
+    },
+    {
+      "argv": [
+        "nvidia-smi",
+        "--query-compute-apps=pid,process_name,used_memory",
+        "--format=csv,noheader"
+      ],
+      "returncode": 0,
+      "stdout": "1795500, /home/sj_server_1/miniforge3/envs/b2sc-cu130/bin/python, 742 MiB",
+      "stderr": ""
+    },
+    {
+      "argv": [
+        "systemctl",
+        "--user",
+        "list-units",
+        "--all",
+        "--no-pager",
+        "pbisc-strict-*"
+      ],
+      "returncode": 0,
+      "stdout": "UNIT                                                                             LOAD   ACTIVE SUB     DESCRIPTION\n  pbisc-strict-archive-implementation-snapshot-1802422-1791810458189968550.service loaded active running /usr/bin/env CUDA_VISIBLE_DEVICES= PATH=/home/sj_server_1/.local/bin:/home/sj_server_1/miniforge3/bin:/usr/local/bin:/usr/bin:/bin PYTHONDONTWRITEBYTECODE=1 PYTHONUNBUFFERED=1 OMP_NUM_THREADS=2 OPENBLAS_NUM_THREADS=2 MKL_NUM_THREADS=2 NUMBA_NUM_THREADS=2 /home/sj_server_1/miniforge3/envs/cxg_corpus/bin/python tools/archive_completed.py --state in-progress --id 20261012T130738Z-strictpairs-implementation\n  pbisc-strict-full-campaign-20261012.service                                      loaded active running /usr/bin/env CUDA_VISIBLE_DEVICES= OMP_NUM_THREADS=2 OPENBLAS_NUM_THREADS=2 /home/sj_server_1/miniforge3/envs/cxg_corpus/bin/python -u tools/campaign.py run --stage all --wait-lock\n  pbisc-strict-global-controls-20261012.service                                    loaded active running /usr/bin/env CUDA_VISIBLE_DEVICES= OMP_NUM_THREADS=2 OPENBLAS_NUM_THREADS=2 /home/sj_server_1/miniforge3/envs/cxg_corpus/bin/python -u tools/campaign.py run --stage global\n\nLegend: LOAD   → Reflects whether the unit definition was properly loaded.\n        ACTIVE → The high-level unit activation state, i.e. generalization of SUB.\n        SUB    → The low-level unit activation state, values depend on unit type.\n\n3 loaded units listed.\nTo show all installed unit files use 'systemctl list-unit-files'.",
+      "stderr": ""
+    }
+  ],
+  "server_2": {
+    "argv": [
+      "ssh",
+      "-o",
+      "BatchMode=yes",
+      "-o",
+      "ConnectTimeout=10",
+      "spark-0110",
+      "nvidia-smi --query-compute-apps=pid,process_name,used_memory --format=csv,noheader"
+    ],
+    "returncode": 0,
+    "stdout": "",
+    "stderr": ""
+  },
+  "figure6": "waiting_user_data_no_execution",
+  "canonical_manuscript": {
+    "argv": [
+      "git",
+      "-C",
+      "/home/sj_server_1/PBISC/paper-release-20260928/manuscript",
+      "rev-parse",
+      "HEAD"
+    ],
+    "returncode": 0,
+    "stdout": "4f178dba8ed8bbab9eeb650dbe83503b0f0859a2",
+    "stderr": ""
+  },
+  "archive_state": "in-progress",
+  "preview_warning": "Restructuring PREVIEW; strict experiments/derived panels remain incomplete. This is not a final manuscript or final Figure 1--5 set."
+}

paper-releases/pbisc-diffusion/updates/20261012T130738Z-strictpairs-implementation/diffusion/dataset/server_1/model8/plans/paper_figures_strictpairs_20261012/archive/20261012T130738Z-strictpairs-implementation/snapshot/inference_metadata/global/imperial_eskd/raw.log

@@ -0,0 +1,29 @@
+{
+  "batch_size": 256,
+  "bulks": 157,
+  "cells": 235500,
+  "checkpoint": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/runs/f01_6k_1x_seed20260627/checkpoint_epoch_016.pt",
+  "checkpoint_schema_version": "pbisc_sdd.checkpoint.ladder.v1",
+  "checkpoint_sha256": "8c7cd0e83e2bc19fe03dfcbc084919a1e2f61be8cc8bc12f4caf543dfda91633",
+  "condition_npz": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/data/external_refcal/imperial_eskd/conditions_raw.npz",
+  "condition_sha256": "0ac35b61c09fb1d50ca64e314c62b1adb84f3759ae5b5b029a3496c7efade10f",
+  "conditioner_source": "embedded",
+  "corpus_fingerprint": "eeb609250457248225432b6df94573b26a8cad8ac743670b5ca43134fea7e007",
+  "corpus_fingerprint_validated": false,
+  "counts_numpy_expm1_max_gap": 0.000244140625,
+  "counts_torch_expm1_max_gap": 0.0001220703125,
+  "device": "cuda",
+  "eta": 0.0,
+  "generated_zero_fraction": 0.8917264366852616,
+  "genes": 6000,
+  "max_generated_log1p": 8.0,
+  "output": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/generated/global/imperial_eskd/raw.npz",
+  "output_sha256": "933d3797441cee599cc8da7a3df0a624edc71e71672f6f5bea877e88cbb53fb3",
+  "proportion_hint": null,
+  "seed": 20260928,
+  "source": "external_bulk_npz",
+  "steps": 50,
+  "torch_version": "2.14.0+cu130",
+  "unavailable_nonzero": 0,
+  "weights": "ema"
+}

paper-releases/pbisc-diffusion/updates/20261012T130738Z-strictpairs-implementation/diffusion/dataset/server_1/model8/plans/paper_figures_strictpairs_20261012/archive/20261012T130738Z-strictpairs-implementation/snapshot/inference_metadata/global/ye2026_sepsis/refcal.log

@@ -0,0 +1,29 @@
+{
+  "batch_size": 256,
+  "bulks": 82,
+  "cells": 123000,
+  "checkpoint": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/runs/f01_6k_1x_seed20260627/checkpoint_epoch_016.pt",
+  "checkpoint_schema_version": "pbisc_sdd.checkpoint.ladder.v1",
+  "checkpoint_sha256": "8c7cd0e83e2bc19fe03dfcbc084919a1e2f61be8cc8bc12f4caf543dfda91633",
+  "condition_npz": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/data/external_refcal/ye2026_sepsis/conditions_refcal.npz",
+  "condition_sha256": "3886924bfe4926914677850db7dac8a77a38bb0c0fc1a30ee663b2587eabc7dd",
+  "conditioner_source": "embedded",
+  "corpus_fingerprint": "eeb609250457248225432b6df94573b26a8cad8ac743670b5ca43134fea7e007",
+  "corpus_fingerprint_validated": false,
+  "counts_numpy_expm1_max_gap": 6.103515625e-05,
+  "counts_torch_expm1_max_gap": 0.0001220703125,
+  "device": "cuda",
+  "eta": 0.0,
+  "generated_zero_fraction": 0.9467414919889785,
+  "genes": 6000,
+  "max_generated_log1p": 7.283803939819336,
+  "output": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/generated/global/ye2026_sepsis/refcal.npz",
+  "output_sha256": "64784052e0289e347e2799523b4aa4ab07b16ddba6a54353a6011d9e77852891",
+  "proportion_hint": null,
+  "seed": 20260928,
+  "source": "external_bulk_npz",
+  "steps": 50,
+  "torch_version": "2.14.0+cu130",
+  "unavailable_nonzero": 0,
+  "weights": "ema"
+}