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  1. .gitattributes +5 -60
  2. LICENSE.txt +8 -0
  3. README.md +85 -1
  4. batch_summary.json +0 -0
  5. configs/torus_scalar/esn_h128_d1_torus_scalar/cross_task.json +181 -0
  6. configs/torus_scalar/esn_h128_d1_torus_scalar/dyn_variants.json +124 -0
  7. configs/torus_scalar/esn_h128_d1_torus_scalar/gs_convergence.json +16 -0
  8. configs/torus_scalar/esn_h128_d1_torus_scalar/history.json +146 -0
  9. configs/torus_scalar/esn_h128_d1_torus_scalar/post_analysis.json +63 -0
  10. configs/torus_scalar/esn_h128_d1_torus_scalar/results.json +531 -0
  11. configs/torus_scalar/esn_h128_d1_torus_scalar_s1/cross_task.json +181 -0
  12. configs/torus_scalar/esn_h128_d1_torus_scalar_s1/dyn_variants.json +124 -0
  13. configs/torus_scalar/esn_h128_d1_torus_scalar_s1/gs_convergence.json +16 -0
  14. configs/torus_scalar/esn_h128_d1_torus_scalar_s1/history.json +146 -0
  15. configs/torus_scalar/esn_h128_d1_torus_scalar_s1/post_analysis.json +63 -0
  16. configs/torus_scalar/esn_h128_d1_torus_scalar_s1/results.json +531 -0
  17. configs/torus_scalar/esn_h128_d1_torus_scalar_s10/cross_task.json +181 -0
  18. configs/torus_scalar/esn_h128_d1_torus_scalar_s10/dyn_variants.json +124 -0
  19. configs/torus_scalar/esn_h128_d1_torus_scalar_s10/gs_convergence.json +16 -0
  20. configs/torus_scalar/esn_h128_d1_torus_scalar_s10/history.json +146 -0
  21. configs/torus_scalar/esn_h128_d1_torus_scalar_s10/post_analysis.json +63 -0
  22. configs/torus_scalar/esn_h128_d1_torus_scalar_s10/results.json +531 -0
  23. configs/torus_scalar/esn_h128_d1_torus_scalar_s2/cross_task.json +181 -0
  24. configs/torus_scalar/esn_h128_d1_torus_scalar_s2/dyn_variants.json +102 -0
  25. configs/torus_scalar/esn_h128_d1_torus_scalar_s2/gs_convergence.json +16 -0
  26. configs/torus_scalar/esn_h128_d1_torus_scalar_s2/history.json +146 -0
  27. configs/torus_scalar/esn_h128_d1_torus_scalar_s2/post_analysis.json +63 -0
  28. configs/torus_scalar/esn_h128_d1_torus_scalar_s2/results.json +509 -0
  29. configs/torus_scalar/esn_h128_d1_torus_scalar_s3/cross_task.json +181 -0
  30. configs/torus_scalar/esn_h128_d1_torus_scalar_s3/dyn_variants.json +124 -0
  31. configs/torus_scalar/esn_h128_d1_torus_scalar_s3/gs_convergence.json +16 -0
  32. configs/torus_scalar/esn_h128_d1_torus_scalar_s3/history.json +77 -0
  33. configs/torus_scalar/esn_h128_d1_torus_scalar_s3/post_analysis.json +63 -0
  34. configs/torus_scalar/esn_h128_d1_torus_scalar_s3/results.json +531 -0
  35. configs/torus_scalar/esn_h128_d1_torus_scalar_s4/cross_task.json +181 -0
  36. configs/torus_scalar/esn_h128_d1_torus_scalar_s4/dyn_variants.json +124 -0
  37. configs/torus_scalar/esn_h128_d1_torus_scalar_s4/gs_convergence.json +16 -0
  38. configs/torus_scalar/esn_h128_d1_torus_scalar_s4/history.json +146 -0
  39. configs/torus_scalar/esn_h128_d1_torus_scalar_s4/post_analysis.json +63 -0
  40. configs/torus_scalar/esn_h128_d1_torus_scalar_s4/results.json +531 -0
  41. configs/torus_scalar/esn_h128_d1_torus_scalar_s5/cross_task.json +181 -0
  42. configs/torus_scalar/esn_h128_d1_torus_scalar_s5/dyn_variants.json +124 -0
  43. configs/torus_scalar/esn_h128_d1_torus_scalar_s5/gs_convergence.json +16 -0
  44. configs/torus_scalar/esn_h128_d1_torus_scalar_s5/history.json +146 -0
  45. configs/torus_scalar/esn_h128_d1_torus_scalar_s5/post_analysis.json +63 -0
  46. configs/torus_scalar/esn_h128_d1_torus_scalar_s6/cross_task.json +181 -0
  47. configs/torus_scalar/esn_h128_d1_torus_scalar_s6/dyn_variants.json +124 -0
  48. configs/torus_scalar/esn_h128_d1_torus_scalar_s6/gs_convergence.json +16 -0
  49. gpu_co2_report.json +496 -0
  50. gpu_co2_report.md +58 -0
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LICENSE.txt ADDED
@@ -0,0 +1,8 @@
 
 
 
 
 
 
 
 
 
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+ Creative Commons Attribution 4.0 International (CC BY 4.0)
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+
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+ This data release is licensed under the Creative Commons Attribution
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+ 4.0 International License. You may share and adapt the material for
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+ any purpose, including commercial, provided you give appropriate
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+ credit, link to the license, and indicate if changes were made.
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+
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+ Full text: https://creativecommons.org/licenses/by/4.0/legalcode
README.md CHANGED
@@ -1,3 +1,87 @@
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  ---
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- license: cc-by-nc-nd-4.0
 
 
 
 
 
 
 
 
 
 
 
 
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  ---
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
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  ---
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+ license: cc-by-4.0
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+ language: []
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+ pretty_name: "Exp 3B: Embedded topology in trained recurrent operators"
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+ size_categories:
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+ - 10K<n<100K
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+ tags:
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+ - dynamical-systems
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+ - delay-embedding
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+ - reservoir-computing
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+ - persistent-homology
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+ - recurrent-neural-networks
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+ - topology
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+ viewer: false
15
  ---
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+
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+ # Exp 3B: Embedded topology in trained recurrent operators
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+
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+ A 14,553-configuration computational sweep of recurrent network
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+ architectures trained on dynamical systems. Each configuration's
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+ hidden-state activations were measured for topological fidelity to
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+ the driving system using persistent homology and Gauss linking
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+ integrals. Six post-hoc analyses on saved checkpoints probe the
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+ operator properties the embedding theorems describe abstractly.
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+
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+ This dataset is the empirical companion to the manuscript
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+ "Topological reconstruction in trained recurrent operators: a
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+ 14,553-configuration empirical sweep" (O'Reilly-Shah, Selvitella,
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+ 2026; arXiv to follow).
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+
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+ ## Scope
32
+
33
+ - **7 architecture families**: VanillaRNN, GRU, LSTM, ESN, Mamba,
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+ RWKV, Transformer.
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+ - **9 hidden dimensions**: 3, 5, 8, 16, 32, 64, 128, 256, 512.
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+ - **3 depths**: 1, 2, 4.
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+ - **7 tasks**: circle ($S^1$), torus ($T^2$), torus3 ($T^3$),
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+ scalar circle, scalar torus, Lorenz, four-dimensional Qi system.
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+ - **11 random seeds** per cell.
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+ - **Total: 14,553 trained configurations.**
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+
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+ ## Layout
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+
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+ ```
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+ master_results.json aggregate of all per-config results
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+ master_results.jsonl streaming form of master_results.json
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+ gpu_co2_report.{md,json} compute footprint (GPU-hours, kWh, CO2)
48
+ batch_summary.json per-batch aggregated post-hoc metrics
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+ figures/ 20 PNG figures from the analysis pipeline
50
+ code/ analysis pipeline source
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+ configs/<task>/<run_id>/
52
+ results.json training output (loss, topology metrics)
53
+ post_analysis.json spectral radius + collision + novel-traj
54
+ dyn_variants.json altered-dynamics evaluation
55
+ lorenz_ic_sweep.json Lorenz only: 8-IC robustness
56
+ cross_task.json cross-task transfer evaluation
57
+ gs_convergence.json empirical ESP convergence test
58
+ history.json training curve + per-eval-epoch topology
59
+ epoch_*.pt final-epoch checkpoint
60
+ ```
61
+
62
+ Hostnames in source data have been mapped to opaque labels
63
+ (`host_A_a2000`, `host_B_rtx4000`, etc.) so the deposit does not
64
+ leak machine identity.
65
+
66
+ ## Reproducibility
67
+
68
+ Source code for the training and analysis pipeline is under `code/`.
69
+ Re-running requires PyTorch, NumPy, scipy, and ripser. See
70
+ `code/scripts/` for individual analyses and
71
+ `code/experiments/exp3b_taxonomy.py` for the master training script.
72
+
73
+ ## License
74
+
75
+ CC BY 4.0. Cite the accompanying manuscript when reusing.
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+
77
+ ## Citation
78
+
79
+ ```bibtex
80
+ @article{oreillyshah_exp3b_2026,
81
+ author = {O'Reilly-Shah, Vikas N. and Selvitella, Alessandro M.},
82
+ title = {Topological reconstruction in trained recurrent operators:
83
+ a 14,553-configuration empirical sweep},
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+ year = {2026},
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+ note = {arXiv preprint, DOI to be assigned}
86
+ }
87
+ ```
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+ "host": "hyak_g3081",
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+ {
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+ "host": "hyak_g3090",
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+ "host": "hyak_g3106",
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+ {
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+ "host": "host_C_gtx1080",
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+ "gpu": "GTX 1080",
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+ "kg_co2": 20.359307491798404,
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+ {
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+ "host": "host_B_rtx4000",
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+ "gpu": "Quadro RTX 4000",
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+ }
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+ ],
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+ "totals": {
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+ "wall_hours": 17338.03652264489,
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+ "a100_eq_hours": 13066.544941452685,
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+ "kwh": 4103.00356374613,
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+ "kg_co2": 410.3003563746128,
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+ "n_runs": 14553
490
+ },
491
+ "scan": {
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+ "n_total_results": 14553,
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+ "n_with_host_and_elapsed": 14553,
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+ "n_missing_elapsed": 0
495
+ }
496
+ }
gpu_co2_report.md ADDED
@@ -0,0 +1,58 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ # GPU-hours and CO2 emissions: Exp 3B
2
+
3
+ Scanned **14553** results.json; **14553** had host + elapsed_sec; **0** missing elapsed_sec.
4
+
5
+
6
+ ## Per-host
7
+
8
+ | Host | GPU | Runs | Wall hr | A100-eq hr | kWh | Region | kg CO2 |
9
+ |---|---|---:|---:|---:|---:|---|---:|
10
+ | P3Vikas | RTX A2000 | 406 | 1502.4 | 615.6 | 105.2 | PNW | 10.52 |
11
+ | deptmed-apmdl01 | Titan RTX | 1843 | 2399.6 | 2007.0 | 671.9 | PNW | 67.19 |
12
+ | g3003 | Quadro RTX 6000 | 252 | 209.8 | 175.5 | 54.6 | PNW | 5.46 |
13
+ | g3013 | Quadro RTX 6000 | 77 | 73.3 | 61.3 | 19.1 | PNW | 1.91 |
14
+ | g3025 | Quadro RTX 6000 | 487 | 492.5 | 412.0 | 128.1 | PNW | 12.81 |
15
+ | g3026 | Quadro RTX 6000 | 1022 | 985.9 | 824.6 | 256.3 | PNW | 25.63 |
16
+ | g3030 | Quadro RTX 6000 | 388 | 491.9 | 411.4 | 127.9 | PNW | 12.79 |
17
+ | g3031 | Quadro RTX 6000 | 398 | 792.9 | 663.2 | 206.1 | PNW | 20.61 |
18
+ | g3032 | Quadro RTX 6000 | 243 | 281.4 | 235.3 | 73.2 | PNW | 7.32 |
19
+ | g3033 | Quadro RTX 6000 | 717 | 570.6 | 477.2 | 148.4 | PNW | 14.84 |
20
+ | g3034 | Quadro RTX 6000 | 122 | 255.3 | 213.5 | 66.4 | PNW | 6.64 |
21
+ | g3035 | Quadro RTX 6000 | 1054 | 1419.9 | 1187.6 | 369.2 | PNW | 36.92 |
22
+ | g3036 | Quadro RTX 6000 | 44 | 93.1 | 77.8 | 24.2 | PNW | 2.42 |
23
+ | g3050 | Quadro RTX 6000 | 84 | 176.5 | 147.6 | 45.9 | PNW | 4.59 |
24
+ | g3056 | Quadro RTX 6000 | 162 | 167.9 | 140.4 | 43.7 | PNW | 4.37 |
25
+ | g3057 | Quadro RTX 6000 | 34 | 24.3 | 20.3 | 6.3 | PNW | 0.63 |
26
+ | g3064 | Quadro RTX 6000 | 96 | 169.1 | 141.4 | 44.0 | PNW | 4.40 |
27
+ | g3073 | Quadro RTX 6000 | 93 | 209.7 | 175.4 | 54.5 | PNW | 5.45 |
28
+ | g3081 | Quadro RTX 6000 | 135 | 204.8 | 171.3 | 53.2 | PNW | 5.32 |
29
+ | g3090 | Quadro RTX 6000 | 385 | 271.3 | 226.9 | 70.5 | PNW | 7.05 |
30
+ | g3092 | Quadro RTX 6000 | 6 | 2.0 | 1.7 | 0.5 | PNW | 0.05 |
31
+ | g3093 | Quadro RTX 6000 | 121 | 77.9 | 65.2 | 20.3 | PNW | 2.03 |
32
+ | g3094 | Quadro RTX 6000 | 13 | 10.5 | 8.8 | 2.7 | PNW | 0.27 |
33
+ | g3095 | Quadro RTX 6000 | 675 | 796.0 | 665.8 | 207.0 | PNW | 20.70 |
34
+ | g3096 | Quadro RTX 6000 | 82 | 206.2 | 172.5 | 53.6 | PNW | 5.36 |
35
+ | g3097 | Quadro RTX 6000 | 558 | 509.3 | 426.0 | 132.4 | PNW | 13.24 |
36
+ | g3099 | Quadro RTX 6000 | 557 | 535.3 | 447.8 | 139.2 | PNW | 13.92 |
37
+ | g3101 | Quadro RTX 6000 | 519 | 517.8 | 433.1 | 134.6 | PNW | 13.46 |
38
+ | g3102 | Quadro RTX 6000 | 5 | 0.8 | 0.7 | 0.2 | PNW | 0.02 |
39
+ | g3105 | Quadro RTX 6000 | 3 | 0.7 | 0.6 | 0.2 | PNW | 0.02 |
40
+ | g3106 | Quadro RTX 6000 | 459 | 260.8 | 218.1 | 67.8 | PNW | 6.78 |
41
+ | g3107 | Quadro RTX 6000 | 100 | 107.9 | 90.2 | 28.0 | PNW | 2.80 |
42
+ | g3111 | Quadro RTX 6000 | 197 | 143.9 | 120.4 | 37.4 | PNW | 3.74 |
43
+ | g3116 | Quadro RTX 6000 | 66 | 40.4 | 33.8 | 10.5 | PNW | 1.05 |
44
+ | g3117 | Quadro RTX 6000 | 243 | 251.0 | 209.9 | 65.2 | PNW | 6.52 |
45
+ | g3122 | Quadro RTX 6000 | 116 | 106.7 | 89.2 | 27.7 | PNW | 2.77 |
46
+ | g3128 | Quadro RTX 6000 | 393 | 517.7 | 433.0 | 134.6 | PNW | 13.46 |
47
+ | g3130 | Quadro RTX 6000 | 355 | 560.7 | 469.0 | 145.8 | PNW | 14.58 |
48
+ | vikas-dell-gtx1080 | GTX 1080 | 1051 | 1131.1 | 514.5 | 203.6 | PNW | 20.36 |
49
+ | vikas-p53 | Quadro RTX 4000 | 992 | 769.4 | 280.9 | 123.1 | PNW | 12.31 |
50
+
51
+ ## Totals
52
+
53
+ - Wall-clock GPU-hours: **17338.0**
54
+ - A100-equivalent GPU-hours: **13066.5**
55
+ - Energy: **4103.0 kWh**
56
+ - Estimated CO2: **410.3 kg**
57
+
58
+ *Method: per-host elapsed_sec summed from results.json; TDP-based energy (TDP_W * hours / 1000); CO2 from regional grid intensity (PNW = 0.100 kg/kWh, US avg = 0.390). TDP overestimates real draw under partial GPU load. A100-equivalent uses fp32 TFLOPS ratio, not real workload scaling.*