{
  "capturedAt": "2026-09-06T23:49:07Z",
  "checks": [
    {
      "name": "anonymous_denied",
      "status": 401,
      "passed": true
    },
    {
      "name": "counts",
      "body": {
        "calculationVersion": "workflow-evidence-v1",
        "scope": "published tutorial/demo evidence plus your own runtime records",
        "workflowControlChecks": {
          "application": "relion",
          "applicationVersion": "5.1.0",
          "scope": "Native RELION Schemer operators, fork, cooperative abort-file polling, explicit resume node, incremental file arrival and reset. Operator-only loops required an explicit abort-file check. No movie processing or scientific dependency invalidation is established.",
          "capturedAt": "2026-09-06T23:35:42Z",
          "checks": [
            {
              "test": "abort_while_waiting_preserves_state",
              "passed": true
            },
            {
              "test": "resume_processes_arrival_once",
              "passed": true
            },
            {
              "test": "incremental_second_arrival",
              "passed": true
            },
            {
              "test": "reset_restores_variable_state",
              "passed": true
            }
          ],
          "note": "Control-flow verification only; excluded from scientific job counts."
        },
        "runtimeStoreReadStatus": "complete",
        "realApplicationsExecuted": 1,
        "realJobAttempts": 40,
        "successfulRealJobs": 39,
        "failedRealJobs": 1,
        "syntheticDemoRecords": 8,
        "applications": [
          {
            "application": "cellranger",
            "realJobAttempts": 0,
            "successfulRealJobs": 0,
            "syntheticDemoRecords": 2,
            "demoRunIds": [
              "demo-cellranger-001",
              "demo-cellranger-002"
            ]
          },
          {
            "application": "openfoam",
            "realJobAttempts": 0,
            "successfulRealJobs": 0,
            "syntheticDemoRecords": 2,
            "demoRunIds": [
              "demo-openfoam-001",
              "demo-openfoam-002"
            ]
          },
          {
            "application": "relion",
            "realJobAttempts": 40,
            "successfulRealJobs": 39,
            "syntheticDemoRecords": 2,
            "demoRunIds": [
              "demo-relion-001",
              "demo-relion-002"
            ]
          },
          {
            "application": "scanpy",
            "realJobAttempts": 0,
            "successfulRealJobs": 0,
            "syntheticDemoRecords": 2,
            "demoRunIds": [
              "demo-scanpy-001",
              "demo-scanpy-002"
            ]
          }
        ],
        "firstRealRunAt": "2026-09-06T00:47:34.582729+00:00",
        "lastRealRunAt": "2026-09-06T01:06:59.699920+00:00",
        "firstRealRunDisplay": {
          "utc": "2026-09-06 00:47:34 UTC",
          "eastern": "2026-09-05 20:47:34 EDT"
        },
        "lastRealRunDisplay": {
          "utc": "2026-09-06 01:06:59 UTC",
          "eastern": "2026-09-05 21:06:59 EDT"
        },
        "total": 48,
        "offset": 0,
        "nextOffset": 10,
        "runs": [
          {
            "runId": "holdout-4",
            "application": "relion",
            "status": "SUCCEEDED",
            "startedAt": "2026-09-06T01:06:59.699920+00:00",
            "finishedAt": "2026-09-06T01:07:12.989415+00:00",
            "wallSeconds": 12.77,
            "executionProvenance": "measured-real-execution",
            "campaign": "holdout-v1"
          },
          {
            "runId": "holdout-3",
            "application": "relion",
            "status": "SUCCEEDED",
            "startedAt": "2026-09-06T01:06:46.315845+00:00",
            "finishedAt": "2026-09-06T01:06:59.609939+00:00",
            "wallSeconds": 12.33,
            "executionProvenance": "measured-real-execution",
            "campaign": "holdout-v1"
          },
          {
            "runId": "holdout-2",
            "application": "relion",
            "status": "SUCCEEDED",
            "startedAt": "2026-09-06T01:06:32.933715+00:00",
            "finishedAt": "2026-09-06T01:06:46.227860+00:00",
            "wallSeconds": 12.33,
            "executionProvenance": "measured-real-execution",
            "campaign": "holdout-v1"
          },
          {
            "runId": "holdout-1",
            "application": "relion",
            "status": "SUCCEEDED",
            "startedAt": "2026-09-06T01:06:19.551652+00:00",
            "finishedAt": "2026-09-06T01:06:32.844373+00:00",
            "wallSeconds": 12.51,
            "executionProvenance": "measured-real-execution",
            "campaign": "holdout-v1"
          },
          {
            "runId": "holdout-0",
            "application": "relion",
            "status": "SUCCEEDED",
            "startedAt": "2026-09-06T01:06:06.671601+00:00",
            "finishedAt": "2026-09-06T01:06:19.461297+00:00",
            "wallSeconds": 12.229999999999999,
            "executionProvenance": "measured-real-execution",
            "campaign": "holdout-v1"
          },
          {
            "runId": "local-vs-nfs-305-t4-local",
            "application": "relion",
            "status": "SUCCEEDED",
            "startedAt": "2026-09-06T01:05:52.013476+00:00",
            "finishedAt": "2026-09-06T01:06:04.796657+00:00",
            "wallSeconds": 12.03,
            "executionProvenance": "measured-real-execution",
            "campaign": "pilot-v1"
          },
          {
            "runId": "local-vs-nfs-305-t4-nfs",
            "application": "relion",
            "status": "SUCCEEDED",
            "startedAt": "2026-09-06T01:05:22.954527+00:00",
            "finishedAt": "2026-09-06T01:05:51.923018+00:00",
            "wallSeconds": 28.07,
            "executionProvenance": "measured-real-execution",
            "campaign": "pilot-v1"
          },
          {
            "runId": "local-vs-nfs-304-t4-nfs",
            "application": "relion",
            "status": "SUCCEEDED",
            "startedAt": "2026-09-06T01:04:53.332363+00:00",
            "finishedAt": "2026-09-06T01:05:22.804238+00:00",
            "wallSeconds": 28.98,
            "executionProvenance": "measured-real-execution",
            "campaign": "pilot-v1"
          },
          {
            "runId": "local-vs-nfs-304-t4-local",
            "application": "relion",
            "status": "SUCCEEDED",
            "startedAt": "2026-09-06T01:04:39.866152+00:00",
            "finishedAt": "2026-09-06T01:04:53.170659+00:00",
            "wallSeconds": 12.58,
            "executionProvenance": "measured-real-execution",
            "campaign": "pilot-v1"
          },
          {
            "runId": "local-vs-nfs-303-t4-local",
            "application": "relion",
            "status": "SUCCEEDED",
            "startedAt": "2026-09-06T01:04:25.967391+00:00",
            "finishedAt": "2026-09-06T01:04:39.775988+00:00",
            "wallSeconds": 13.18,
            "executionProvenance": "measured-real-execution",
            "campaign": "pilot-v1"
          }
        ],
        "excludedDuplicates": [],
        "note": "Synthetic records are not executed jobs. These counts are execution evidence, not catalog availability, installation verification, or enterprise certification."
      },
      "passed": true
    },
    {
      "name": "named_record",
      "body": {
        "record": {
          "runId": "threads1-vs4-301-t4-local",
          "pairId": "threads1-vs4-301",
          "seed": 301,
          "subset": "calibration-v2",
          "threads": 4,
          "storage": "local",
          "sourceRevision": "b916bf646366ea22adc1447d51f8bc3f2258ec6c",
          "scientificData": "real-public-tutorial",
          "executionProvenance": "measured-real-execution",
          "status": "SUCCEEDED",
          "startedAt": "2026-09-06T00:56:24.968432+00:00",
          "inputSha256": "de77f27125816085034b59432aa66a6bd2ace92965b95df23cb0b31dd8e1587a",
          "quantity": 1024,
          "stagingSeconds": 0.03150933699998859,
          "machine": "e2-standard-8",
          "nodeVcpus": 8,
          "allocatedThreads": 4,
          "nodes": 1,
          "workflow": "RELION rescale/normalize preprocessing -> 2D classification",
          "scientificParameters": {
            "iterations": 15,
            "classes": 10,
            "particleDiameterAngstrom": 200,
            "boxSize": 64,
            "backgroundRadius": 28,
            "psiStep": 30,
            "offsetRange": 2,
            "offsetStep": 2,
            "pixelAngstrom": 3.54
          },
          "workdir": "/var/tmp/numen-relion-testing/pilot-v1/threads1-vs4-301-t4-local",
          "stages": [
            {
              "command": [
                "/gcfs-software/numen-relion-testing/software/relion-5.1.0-linux-x86_64/bin/relion_preprocess",
                "--operate_on",
                "input.mrcs",
                "--operate_out",
                "normalized",
                "--scale",
                "64",
                "--norm",
                "--bg_radius",
                "28"
              ],
              "wallSeconds": 0.17,
              "userSeconds": 0.09,
              "systemSeconds": 0.06,
              "maxRssKiB": 8732,
              "exitCode": 0,
              "name": "preprocess",
              "logSha256": "193000f1e2c7044a001c2aa24ff182fec2222df123f923801c76b510f9c0fced",
              "logExcerpt": "....................................................~~(,_,\">[oo]\r   0/   0 sec .........................................................~~(,_,\">oo]\r   0/   0 sec .........................................................~~(,_,\">oo]\r   0/   0 sec ..........................................................~~(,_,\">o]\r   0/   0 sec ..........................................................~~(,_,\">o]\r   0/   0 sec ...........................................................~~(,_,\">]\r   0/   0 sec ...........................................................~~(,_,\">]\r   0/   0 sec ............................................................~~(,_,\"> yum!\n Done writing to normalized\n Done preprocessing!\n"
            },
            {
              "command": [
                "/gcfs-software/numen-relion-testing/software/relion-5.1.0-linux-x86_64/bin/relion_refine",
                "--i",
                "input.star",
                "--o",
                "./class2d",
                "--iter",
                "15",
                "--K",
                "10",
                "--tau2_fudge",
                "2",
                "--particle_diameter",
                "200",
                "--ctf",
                "--flatten_solvent",
                "--zero_mask",
                "--oversampling",
                "1",
                "--psi_step",
                "30",
                "--offset_range",
                "2",
                "--offset_step",
                "2",
                "--norm",
                "--scale",
                "--j",
                "4",
                "--random_seed",
                "301",
                "--pool",
                "3"
              ],
              "wallSeconds": 12.59,
              "userSeconds": 45.29,
              "systemSeconds": 0.23,
              "maxRssKiB": 19932,
              "exitCode": 0,
              "name": "class2d",
              "logSha256": "1c052a3eec634c421a4c0b5f6ee3c7c0c554d4efe4759ef264c034c7fb75a1c8",
              "logExcerpt": "                    [oo]\r   0/   0 sec ..................~~(,_,\">                                       [oo]\r   0/   0 sec .......................~~(,_,\">                                 [oo]\r   0/   0 sec ..............................~~(,_,\">                           [oo]\r   0/   0 sec ....................................~~(,_,\">                     [oo]\r   0/   0 sec ..........................................~~(,_,\">               [oo]\r   0/   0 sec ................................................~~(,_,\">         [oo]\r   0/   0 sec ......................................................~~(,_,\">   [oo]\r   0/   0 sec ............................................................~~(,_,\"> yum!\n"
            }
          ],
          "wallSeconds": 12.76,
          "quality": {
            "structurallyValid": true,
            "outputParticles": 1024,
            "classShape": [
              10,
              64,
              64
            ],
            "classStd": 1.0118881464004517,
            "scientificEquivalence": "requires paired evaluation"
          },
          "outputHashes": {
            "class2d_it015_classes.mrcs": "0fa555e4d90692a9f730a292917fdae10afd5d0533582bf9b20031a6ade81454",
            "class2d_it015_data.star": "f5c7331a28acc78e59e6f8d1d347e44ac1758d477c8b2ffc37938c31c340a76f"
          },
          "finishedAt": "2026-09-06T00:56:38.265444+00:00",
          "originalRunId": "threads1-vs4-301-t4-local",
          "kind": "job",
          "application": "relion",
          "applicationVersion": "5.1.0",
          "stage": "preprocess-and-class2d",
          "workload": "cryoem-particles",
          "campaign": "pilot-v1",
          "visibility": "published-demo",
          "evidenceOrigin": "historical-public-tutorial",
          "sourceRecordSha256": "0d07d6b843d51c3da64ac28feb3ae6bfb58c02877b01d993dc98f40aee8179b8",
          "instance": "numen-sn-workflowtesting-1cae",
          "synthetic": false,
          "vcpus": 4,
          "hours": 0.0035444444444444442,
          "allocationNote": "vcpus represents allocated RELION threads; physical node had 8 vCPUs. Not a billing quantity.",
          "artifactArchive": "gs://numen-gcp-sandbox-assets/experiments/relion-single-node/pilot-v1/remote-evidence.tar.gz",
          "artifactDirectory": "/gcfs-software/numen-relion-testing/runs/pilot-v1/threads1-vs4-301-t4-local",
          "startedAtDisplay": {
            "utc": "2026-09-06 00:56:24 UTC",
            "eastern": "2026-09-05 20:56:24 EDT"
          },
          "finishedAtDisplay": {
            "utc": "2026-09-06 00:56:38 UTC",
            "eastern": "2026-09-05 20:56:38 EDT"
          }
        },
        "found": true,
        "calculationVersion": "workflow-evidence-v1",
        "note": "Execution timestamps are historical; record presence does not imply a running VM. Artifact paths are references, not freshly read logs."
      },
      "passed": true
    }
  ],
  "boundedConcurrency": [
    {
      "status": 200,
      "seconds": 0.625,
      "passed": true
    },
    {
      "status": 200,
      "seconds": 0.5939999999973224,
      "passed": true
    },
    {
      "status": 200,
      "seconds": 0.625,
      "passed": true
    },
    {
      "status": 200,
      "seconds": 0.625,
      "passed": true
    },
    {
      "status": 200,
      "seconds": 0.5940000000009604,
      "passed": true
    },
    {
      "status": 200,
      "seconds": 0.5939999999973224,
      "passed": true
    },
    {
      "status": 200,
      "seconds": 0.5939999999973224,
      "passed": true
    },
    {
      "status": 200,
      "seconds": 0.5929999999971187,
      "passed": true
    },
    {
      "status": 200,
      "seconds": 0.7190000000009604,
      "passed": true
    },
    {
      "status": 200,
      "seconds": 0.75,
      "passed": true
    },
    {
      "status": 200,
      "seconds": 0.7350000000005821,
      "passed": true
    },
    {
      "status": 200,
      "seconds": 0.7190000000009604,
      "passed": true
    },
    {
      "status": 200,
      "seconds": 0.6409999999996217,
      "passed": true
    },
    {
      "status": 200,
      "seconds": 0.6559999999990396,
      "passed": true
    },
    {
      "status": 200,
      "seconds": 0.6090000000003783,
      "passed": true
    },
    {
      "status": 200,
      "seconds": 0.6399999999994179,
      "passed": true
    },
    {
      "status": 200,
      "seconds": 0.6880000000019209,
      "passed": true
    },
    {
      "status": 200,
      "seconds": 0.6559999999990396,
      "passed": true
    },
    {
      "status": 200,
      "seconds": 0.6880000000019209,
      "passed": true
    },
    {
      "status": 200,
      "seconds": 0.6570000000028813,
      "passed": true
    }
  ],
  "answers": [
    {
      "prompt": "How many applications have real execution tests? Give total real job attempts, successes, failures, synthetic record count, and first/last real execution timestamps in UTC.",
      "status": 200,
      "seconds": 5.311999999998079,
      "response": {
        "reply": "There is 1 application with real execution tests. There have been 40 total real job attempts, with 39 successes and 1 failure. There are 8 synthetic demo records. The first real execution was on 2026-09-06T00:47:34.582729+00:00 UTC, and the last real execution was on 2026-09-06T01:06:59.699920+00:00 UTC.",
        "toolsUsed": [
          "get_job_evidence"
        ],
        "backend": "vertex-gemini:us-central1",
        "model": "gemini-2.5-flash",
        "usage": {
          "input": 9847,
          "output": 819,
          "calls": 2,
          "estCostUsd": 0.004344
        },
        "provenance": [
          {
            "kind": "reference",
            "label": "authorized execution registry; historical real runs and explicitly synthetic demos are labeled per record",
            "tool": "get_job_evidence"
          }
        ],
        "cacheKey": "453ec687f179",
        "cacheHit": false,
        "truncated": false
      }
    },
    {
      "prompt": "Retrieve threads1-vs4-301-t4-local: exact runtime, input hash and stage durations.",
      "status": 200,
      "seconds": 2.985000000000582,
      "response": {
        "reply": "The run `threads1-vs4-301-t4-local` had a total wall clock runtime of 12.76 seconds.\n\nThe input hash for this run was `de77f27125816085034b59432aa66a6bd2ace92965b95df23cb0b31dd8e1587a`.\n\nThe stage durations were:\n*   `preprocess`: 0.17 seconds\n*   `class2d`: 12.59 seconds",
        "toolsUsed": [
          "get_job_evidence"
        ],
        "backend": "vertex-gemini:us-central1",
        "model": "gemini-2.5-flash",
        "usage": {
          "input": 9411,
          "output": 438,
          "calls": 2,
          "estCostUsd": 0.002945
        },
        "provenance": [
          {
            "kind": "reference",
            "label": "authorized execution registry; historical real runs and explicitly synthetic demos are labeled per record",
            "tool": "get_job_evidence"
          }
        ],
        "cacheKey": "db0e1482b8e3",
        "cacheHit": false,
        "truncated": false
      }
    },
    {
      "prompt": "Show demo-cellranger-001. Did it really run, when, and can it train a real performance model?",
      "status": 200,
      "seconds": 4.25,
      "response": {
        "reply": "No, the record for `demo-cellranger-001` is a synthetic demonstration and was not actually executed. Therefore, it did not run at any specific time, and it is not eligible for training a real performance model.",
        "toolsUsed": [
          "get_job_evidence"
        ],
        "backend": "vertex-gemini:us-central1",
        "model": "gemini-2.5-flash",
        "usage": {
          "input": 8229,
          "output": 602,
          "calls": 2,
          "estCostUsd": 0.003341
        },
        "provenance": [
          {
            "kind": "reference",
            "label": "authorized execution registry; historical real runs and explicitly synthetic demos are labeled per record",
            "tool": "get_job_evidence"
          }
        ],
        "cacheKey": "fa7d91acb73f",
        "cacheHit": false,
        "truncated": false
      }
    },
    {
      "prompt": "Show an OpenFOAM demo job and distinguish synthetic execution from real jobs.",
      "status": 200,
      "seconds": 4.422000000002299,
      "response": {
        "reply": "There are no real OpenFOAM jobs recorded for this project. All available OpenFOAM job records are synthetic demos, meaning they represent what a job *would* do but were not actually executed.\n\nHere is an example of a synthetic OpenFOAM demo job:\n\n*   **Run ID:** `demo-openfoam-001`\n*   **Application:** OpenFOAM\n*   **Campaign:** `synthetic-multiapp-v1`\n*   **Status:** SUCCEEDED\n*   **Wall Time:** 120 seconds\n*   **Execution Provenance:** `synthetic-demo-not-executed` (This confirms it is a synthetic demo and was not a real execution.)",
        "toolsUsed": [
          "get_job_evidence"
        ],
        "backend": "vertex-gemini:us-central1",
        "model": "gemini-2.5-flash",
        "usage": {
          "input": 8411,
          "output": 659,
          "calls": 2,
          "estCostUsd": 0.003568
        },
        "provenance": [
          {
            "kind": "reference",
            "label": "authorized execution registry; historical real runs and explicitly synthetic demos are labeled per record",
            "tool": "get_job_evidence"
          }
        ],
        "cacheKey": "2fe77bb7ea1d",
        "cacheHit": false,
        "truncated": false
      }
    },
    {
      "prompt": "Use calibration_run_id threads1-vs4-301-t4-local for plan_capacity: 1024 cryoem-particles, deadline_hours=10, parallelisable=false. Give seconds, accepted count and rejection reasons.",
      "status": 200,
      "seconds": 9.390999999999622,
      "response": {
        "reply": "For 1024 cryo-EM particles with a 10-hour deadline, running serially, using the calibration run `threads1-vs4-301-t4-local`, the estimated runtime is 12.82 seconds. This is a measured estimate.\n\nThe following runs were accepted for calibration:\ncalibration-v1:calibration-check, local-vs-nfs-301-t4-local, local-vs-nfs-302-t4-local, local-vs-nfs-303-t4-local, local-vs-nfs-304-t4-local, local-vs-nfs-305-t4-local, threads1-vs4-301-t4-local, threads1-vs4-302-t4-local, threads1-vs4-303-t4-local, threads1-vs4-304-t4-local, threads1-vs4-305-t4-local, threads4-vs8-301-t4-local, threads4-vs8-302-t4-local, threads4-vs8-303-t4-local, threads4-vs8-304-t4-local, threads4-vs8-305-t4-local.\n\nThe following runs were rejected for these reasons:\n*   `holdout-0`, `holdout-1`, `holdout-2`, `holdout-3`, `holdout-4`: reserved_holdout\n*   `local-vs-nfs-301-t4-nfs`, `local-vs-nfs-302-t4-nfs`, `local-vs-nfs-303-t4-nfs`, `local-vs-nfs-304-t4-nfs`, `local-vs-nfs-305-t4-nfs`: scientific_or_hardware_scope_mismatch\n*   `threads1-vs4-301-t1-local`, `threads1-vs4-302-t1-local`, `threads1-vs4-303-t1-local`, `threads1-vs4-304-t1-local`, `threads1-vs4-305-t1-local`: scientific_or_hardware_scope_mismatch\n*   `threads4-vs8-301-t8-local`, `threads4-vs8-302-t8-local`, `threads4-vs8-303-t8-local`, `threads4-vs8-304-t8-local`, `threads4-vs8-305-t8-local`: scientific_or_hardware_scope_mismatch\n*   `smoke-v1:smoke-0`: not_successful\n*   `smoke-v2:smoke-0`, `smoke-v2:smoke-1`, `smoke-v2:smoke-2`: scientific_or_hardware_scope_mismatch\n*   `demo-relion-001`, `demo-relion-002`: synthetic_execution",
        "toolsUsed": [
          "get_optimization_knowledge",
          "plan_capacity"
        ],
        "backend": "vertex-gemini:us-central1",
        "model": "gemini-2.5-flash",
        "usage": {
          "input": 13744,
          "output": 1394,
          "calls": 2,
          "estCostUsd": 0.006941
        },
        "provenance": [
          {
            "kind": "reference",
            "label": "Numen Encyclopedia methodology and scoped pilot evidence, not live telemetry",
            "tool": "get_optimization_knowledge"
          },
          {
            "kind": "measured",
            "label": "throughput measured from real runs here, or estimated and labelled as such where none exists",
            "tool": "plan_capacity"
          }
        ],
        "cacheKey": "342174105299",
        "cacheHit": false,
        "truncated": false
      }
    },
    {
      "prompt": "Which native RELION Scheme controls were actually tested? Distinguish them from scientific movie processing and independent biological validation.",
      "status": 200,
      "seconds": 4.109000000000378,
      "response": {
        "reply": "The native RELION Scheme control-flow tests covered explicit abort-file polling, resume, incremental file arrival, and reset. These tests are distinct from full movie-processing dependencies and independent biological validation, which remain unestablished. This information is from the Numen Encyclopedia's \"Workflow optimization in Numen\" reference, specifically the \"Job evidence integration update\" section, available at https://numen-gcp.clovertex.net/encyclopedia/workflow-optimization/.",
        "toolsUsed": [
          "get_optimization_knowledge"
        ],
        "backend": "vertex-gemini:us-central1",
        "model": "gemini-2.5-flash",
        "usage": {
          "input": 13916,
          "output": 341,
          "calls": 2,
          "estCostUsd": 0.003281
        },
        "provenance": [
          {
            "kind": "reference",
            "label": "Numen Encyclopedia methodology and scoped pilot evidence, not live telemetry",
            "tool": "get_optimization_knowledge"
          }
        ],
        "cacheKey": "44b4d628fe33",
        "cacheHit": false,
        "truncated": false
      }
    }
  ]
}