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updates file and hpc data phase 3 available
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‎docs/HPC_GUIDE.md‎

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@@ -6,6 +6,7 @@ ssh kanagnostopoul@snellius.surf.nl
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# On a separate terminal run the following
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# Upload the entire project directory (including your models/ folder)
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rsync -avz --progress --exclude-from='.rsync-exclude' \
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~/CSS_Project/ kanagnostopoul@snellius.surf.nl:~/CSS_Project/
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@@ -47,7 +48,7 @@ watch -n 10 "ls -1 results_JOBID | wc -l"
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# Fetching the results once the job is done
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scp -r kanagnostopoul@snellius.surf.nl:~/CSS_Project/results/phase2_18693004/ ./results/
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scp -r kanagnostopoul@snellius.surf.nl:~/CSS_Project/results/phase3_18698382/ ./results/
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```
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The jobscript template can be found in ```run_analysis.sh``` (default rome paritition).

‎docs/kimon_updates.md‎

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@@ -284,4 +284,14 @@ Refactored ```experiments.py``` according to ```experiments.md```. Phase 4 and P
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- Phase 6: Will implement if all the other phases pass successfully.
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TODO: We need to start drafting a proper version of the analyis (```analysis.py```) for postprocessing of all the data we are currenlty collecting and plotting utilities to visualize them.
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TODO: We need to start drafting a proper version of the analyis (```analysis.py```) for postprocessing of all the data we are currenlty collecting and plotting utilities to visualize them.
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## Updates (26/1)
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Under ```hpc_data``` folder you can find:
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- ```../hpc_data/phase1_18677015```
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- ```../hpc_data/phase1.5_18682575``` (finer grid but ow same as phase 1)
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- ```../hpc_data/phase2_18693004```
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- ```../hpc_data/phase3_18698382```

‎hpc_data/phase3_18698382/experiments.log‎

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2026-01-26 16:53:51,318 [INFO] ============================================================
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2026-01-26 16:53:51,318 [INFO] PREDATOR-PREY HYDRA EFFECT EXPERIMENTS
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2026-01-26 16:53:51,318 [INFO] ============================================================
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2026-01-26 16:53:51,318 [INFO] Phases: [3]
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2026-01-26 16:53:51,318 [INFO] Output: results/phase3_18698382
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2026-01-26 16:53:51,318 [INFO] Cores: 32
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2026-01-26 16:53:51,319 [INFO] Numba: ENABLED
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2026-01-26 16:53:51,319 [INFO]
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2026-01-26 16:53:51,319 [INFO] ============================================================
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2026-01-26 16:53:51,319 [INFO] PHASE 3
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2026-01-26 16:53:51,319 [INFO] ============================================================
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2026-01-26 16:53:51,319 [INFO] Estimated: 1,500 sims, ~2.2h on 32 cores (~71 core-hours)
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2026-01-26 16:53:51,319 [INFO] Dry run - skipping execution
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2026-01-26 16:53:51,319 [INFO]
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2026-01-26 16:53:51,319 [INFO] ============================================================
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2026-01-26 16:53:51,319 [INFO] EXPERIMENTS COMPLETE
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2026-01-26 16:53:51,319 [INFO] ============================================================
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2026-01-26 16:53:52,501 [INFO] ============================================================
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2026-01-26 16:53:52,501 [INFO] PREDATOR-PREY HYDRA EFFECT EXPERIMENTS
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2026-01-26 16:53:52,501 [INFO] ============================================================
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2026-01-26 16:53:52,501 [INFO] Phases: [3]
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2026-01-26 16:53:52,501 [INFO] Output: results/phase3_18698382
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2026-01-26 16:53:52,501 [INFO] Cores: 32
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2026-01-26 16:53:52,501 [INFO] Numba: ENABLED
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2026-01-26 16:53:52,501 [INFO]
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2026-01-26 16:53:52,501 [INFO] ============================================================
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2026-01-26 16:53:52,501 [INFO] PHASE 3
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2026-01-26 16:53:52,501 [INFO] ============================================================
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2026-01-26 16:53:52,501 [INFO] Estimated: 1,500 sims, ~2.2h on 32 cores (~71 core-hours)
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2026-01-26 16:53:52,650 [INFO] Phase 3: FSS at critical point (pb=0.2, pd=0.0963)
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2026-01-26 16:54:07,348 [INFO] Grid sizes: (50, 100, 250, 500, 1000, 2500)
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2026-01-26 16:54:07,349 [INFO] Total simulations: 120
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2026-01-26 17:14:44,746 [INFO] Phase 3 complete. Results: results/phase3_18698382/phase3_results.jsonl
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2026-01-26 17:14:44,756 [INFO] Phase 3 runtime: 20.9 minutes
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2026-01-26 17:14:44,756 [INFO]
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2026-01-26 17:14:44,756 [INFO] ============================================================
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2026-01-26 17:14:44,756 [INFO] EXPERIMENTS COMPLETE
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2026-01-26 17:14:44,756 [INFO] ============================================================

‎hpc_data/phase3_18698382/phase3_config.json‎

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{
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"grid_size": 1000,
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"densities": [
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0.3,
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0.15
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],
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"grid_sizes": [
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50,
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100,
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250,
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500,
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1000,
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2500
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],
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"prey_birth": 0.2,
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"prey_death": 0.05,
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"predator_birth": 0.8,
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"predator_death": 0.05,
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"critical_prey_birth": 0.2,
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"critical_prey_death": 0.0963,
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"prey_death_range": [
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0.0,
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0.2
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],
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"n_prey_birth": 15,
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"n_prey_death": 5,
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"predator_birth_values": [
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0.15,
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0.2,
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0.25,
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0.3
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],
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"predator_death_values": [
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0.05,
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0.1,
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0.15,
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0.2
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],
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"prey_death_offsets": [
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-0.02,
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-0.01,
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0.0,
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0.01,
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0.02
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],
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"n_replicates": 20,
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"warmup_steps": 1000,
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"measurement_steps": 1000,
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"with_evolution": false,
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"evolve_sd": 0.1,
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"evolve_min": 0.0,
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"evolve_max": 0.1,
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"sensitivity_sd_values": [
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0.02,
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0.05,
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0.1,
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0.15,
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0.2
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],
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"synchronous": false,
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"directed_hunting": false,
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"directed_hunting_values": [
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false,
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true
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],
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"save_timeseries": false,
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"timeseries_subsample": 10,
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"collect_pcf": false,
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"pcf_sample_rate": 0.2,
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"pcf_max_distance": 20.0,
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"pcf_n_bins": 20,
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"min_density_for_analysis": 0.002,
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"perturbation_magnitude": 0.1,
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"n_jobs": 32
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}

‎hpc_data/phase3_18698382/phase3_metadata.json‎

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{
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"phase": 3,
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"description": "Finite-size scaling",
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"critical_point": {
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"prey_birth": 0.2,
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"prey_death": 0.0963
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},
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"grid_sizes": [
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50,
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100,
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250,
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500,
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1000,
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2500
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],
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"n_sims": 120,
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"timestamp": "2026-01-26 17:14:44"
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}

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