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Merge pull request #19 from codegithubka/kimon
Kimon
2 parents 1369f14 + 1f6b450 commit ff0410b

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‎.gitignore‎

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@@ -10,4 +10,6 @@ results/
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.ipynb_checkpoints/
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# Data files
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data/
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.pytest_cache/
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.pytest_cache/
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.DS_Store

‎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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@@ -38,7 +39,7 @@ scancel <JOBID>
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# Monitoring live progress
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tail -f logs_<JOBID>.err
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tail -f logs_18702594.err
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# Watch task completetion
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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/phase1_ 18682575/ ./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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- 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/run_phase2.sh‎

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#SBATCH --ntasks=1
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#SBATCH --cpus-per-task=32
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#SBATCH --time=04:00:00
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#SBATCH --mem=16G
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#SBATCH --output=pp_phase2_%j.out
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#SBATCH --error=pp_phase2_%j.err
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#SBATCH --mem=64G
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#SBATCH --output=/home/kanagnostopoul/CSS_Project/pp_phase2_%j.out
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#SBATCH --error=/home/kanagnostopoul/CSS_Project/pp_phase2_%j.err
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# =============================================================================
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# PP Hydra Effect - Phase 2: Self-Organization (SOC Test)

‎hpc/run_phase3.sh‎

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#!/bin/bash
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#SBATCH --job-name=pp_phase3
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#SBATCH --partition=genoa
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#SBATCH --nodes=1
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#SBATCH --ntasks=1
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#SBATCH --cpus-per-task=64
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#SBATCH --time=02:00:00
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#SBATCH --mem=64G
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#SBATCH --output=/home/kanagnostopoul/CSS_Project/pp_phase3_%j.out
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#SBATCH --error=/home/kanagnostopoul/CSS_Project/pp_phase3_%j.err
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# =============================================================================
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# PP Hydra Effect - Phase 3: Finite-Size Scaling
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# =============================================================================
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#
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# PHASE 3: Test finite-size scaling at critical point
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# - Grid sizes: 50, 100, 250, 500, 1000
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# - 20 replicates per size = 100 simulations
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# - Cluster size distributions for power-law analysis
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#
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# SUBMIT: sbatch run_phase3.sh
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# MONITOR: squeue -u $USER
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# CANCEL: scancel <job_id>
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#
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# =============================================================================
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cd /home/kanagnostopoul/CSS_Project || exit 1
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echo "========================================"
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echo "PP Hydra Effect - Phase 3"
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echo "========================================"
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echo "Job ID: $SLURM_JOB_ID"
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echo "Node: $(hostname)"
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echo "CPUs: $SLURM_CPUS_PER_TASK"
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echo "Start: $(date)"
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echo "Working dir: $(pwd)"
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echo "========================================"
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# -----------------------------------------------------------------------------
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# Environment Setup
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# -----------------------------------------------------------------------------
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source ~/snellius_venv/bin/activate
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# Prevent numpy/scipy from spawning extra threads (joblib handles parallelism)
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export OMP_NUM_THREADS=1
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export OPENBLAS_NUM_THREADS=1
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export MKL_NUM_THREADS=1
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export NUMEXPR_NUM_THREADS=1
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# -----------------------------------------------------------------------------
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# Run Phase 3
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# -----------------------------------------------------------------------------
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OUTPUT_DIR="results/phase3_${SLURM_JOB_ID}"
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mkdir -p $OUTPUT_DIR
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echo ""
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echo "Output directory: $OUTPUT_DIR"
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echo ""
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# Dry run first to verify setup
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echo "Dry run check:"
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python3 -u scripts/experiments.py \
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--phase 3 \
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--output $OUTPUT_DIR \
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--cores $SLURM_CPUS_PER_TASK \
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--dry-run
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echo ""
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echo "Starting Phase 3..."
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echo ""
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# Run phase 3
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python3 -u scripts/experiments.py \
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--phase 3 \
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--output $OUTPUT_DIR \
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--cores $SLURM_CPUS_PER_TASK
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# -----------------------------------------------------------------------------
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# Completion
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# -----------------------------------------------------------------------------
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echo ""
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echo "========================================"
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echo "Phase 3 Complete"
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echo "========================================"
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echo "End time: $(date)"
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echo "Results in: $OUTPUT_DIR/"
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echo ""
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echo "Output files:"
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ls -lh $OUTPUT_DIR/
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echo ""
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echo "Next steps:"
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echo " 1. Download phase3_results.jsonl"
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echo " 2. Analyze cluster size distributions P(s) for each grid size"
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echo " 3. Fit power-law exponent tau from P(s) ~ s^(-tau)"
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echo " 4. Check finite-size cutoff s_max ~ L^D (fractal dimension)"
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echo "========================================"

‎hpc/run_phase4.sh‎

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#!/bin/bash
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#SBATCH --job-name=pp_phase4
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#SBATCH --partition=rome
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#SBATCH --nodes=1
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#SBATCH --ntasks=1
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#SBATCH --cpus-per-task=64
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#SBATCH --time=08:00:00
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#SBATCH --mem=16G
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#SBATCH --output=/home/kanagnostopoul/CSS_Project/pp_phase4_%j.out
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#SBATCH --error=/home/kanagnostopoul/CSS_Project/pp_phase4_%j.err
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# =============================================================================
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# PP Hydra Effect - Phase 4: Global Sensitivity Analysis
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# =============================================================================
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#
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# PHASE 4: Full 4D Parameter Sweep (Global Sensitivity)
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# - Parameters: prey_birth, prey_death, pred_birth, pred_death
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# - Sweep: 0.0 to 1.0 (11 values each) = 14,641 combinations
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# - Replicates: 10 per combination
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# - Total Simulations: ~146,410
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# - Grid Size: 250x250
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#
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# SUBMIT: sbatch run_phase4.sh
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# MONITOR: squeue -u $USER
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# CANCEL: scancel <job_id>
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#
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# =============================================================================
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cd /home/kanagnostopoul/CSS_Project || exit 1
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echo "========================================"
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echo "PP Hydra Effect - Phase 4"
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echo "========================================"
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echo "Job ID: $SLURM_JOB_ID"
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echo "Node: $(hostname)"
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echo "CPUs: $SLURM_CPUS_PER_TASK"
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echo "Start: $(date)"
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echo "Working dir: $(pwd)"
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echo "========================================"
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# -----------------------------------------------------------------------------
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# Environment Setup
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# -----------------------------------------------------------------------------
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source ~/snellius_venv/bin/activate
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# Prevent numpy/scipy from spawning extra threads (joblib handles parallelism)
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export OMP_NUM_THREADS=1
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export OPENBLAS_NUM_THREADS=1
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export MKL_NUM_THREADS=1
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export NUMEXPR_NUM_THREADS=1
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# -----------------------------------------------------------------------------
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# Run Phase 4
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# -----------------------------------------------------------------------------
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OUTPUT_DIR="results/phase4_${SLURM_JOB_ID}"
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mkdir -p $OUTPUT_DIR
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echo ""
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echo "Output directory: $OUTPUT_DIR"
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echo ""
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# Dry run first to verify setup and runtime estimate
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echo "Dry run check:"
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python3 -u scripts/experiments.py \
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--phase 4 \
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--output $OUTPUT_DIR \
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--cores $SLURM_CPUS_PER_TASK \
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--dry-run
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echo ""
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echo "Starting Phase 4 (4D Sweep)..."
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echo ""
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# Run phase 4
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python3 -u scripts/experiments.py \
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--phase 4 \
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--output $OUTPUT_DIR \
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--cores $SLURM_CPUS_PER_TASK
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# -----------------------------------------------------------------------------
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# Completion
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# -----------------------------------------------------------------------------
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echo ""
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echo "========================================"
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echo "Phase 4 Complete"
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echo "========================================"
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echo "End time: $(date)"
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echo "Results in: $OUTPUT_DIR/"
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echo ""
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echo "Output files:"
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ls -lh $OUTPUT_DIR/
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echo ""
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echo "Next steps:"
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echo " 1. Download phase4_results.jsonl"
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echo " 2. Perform Global Sensitivity Analysis (Sobol Indices)"
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echo " 3. Identify parameter dominance for extinction events"
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echo " 4. Plot parameter heatmaps for predator/prey survival"
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echo "========================================"

‎hpc_data/phase2_18693004/experiments.log‎

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2026-01-26 15:14:41,338 [INFO] ============================================================
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2026-01-26 15:14:41,338 [INFO] PREDATOR-PREY HYDRA EFFECT EXPERIMENTS
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2026-01-26 15:14:41,338 [INFO] ============================================================
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2026-01-26 15:14:41,338 [INFO] Phases: [2]
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2026-01-26 15:14:41,338 [INFO] Output: results/phase2_18693004
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2026-01-26 15:14:41,338 [INFO] Cores: 32
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2026-01-26 15:14:41,338 [INFO] Numba: ENABLED
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2026-01-26 15:14:41,338 [INFO]
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2026-01-26 15:14:41,338 [INFO] ============================================================
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2026-01-26 15:14:41,339 [INFO] PHASE 2
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2026-01-26 15:14:41,339 [INFO] ============================================================
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2026-01-26 15:14:41,339 [INFO] Estimated: 100 sims, ~0.4h on 32 cores (~14 core-hours)
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2026-01-26 15:14:41,339 [INFO] Dry run - skipping execution
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2026-01-26 15:14:41,339 [INFO]
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2026-01-26 15:14:41,339 [INFO] ============================================================
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2026-01-26 15:14:41,339 [INFO] EXPERIMENTS COMPLETE
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2026-01-26 15:14:41,339 [INFO] ============================================================
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2026-01-26 15:14:42,518 [INFO] ============================================================
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2026-01-26 15:14:42,518 [INFO] PREDATOR-PREY HYDRA EFFECT EXPERIMENTS
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2026-01-26 15:14:42,518 [INFO] ============================================================
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2026-01-26 15:14:42,518 [INFO] Phases: [2]
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2026-01-26 15:14:42,518 [INFO] Output: results/phase2_18693004
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2026-01-26 15:14:42,518 [INFO] Cores: 32
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2026-01-26 15:14:42,518 [INFO] Numba: ENABLED
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2026-01-26 15:14:42,518 [INFO]
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2026-01-26 15:14:42,518 [INFO] ============================================================
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2026-01-26 15:14:42,518 [INFO] PHASE 2
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2026-01-26 15:14:42,518 [INFO] ============================================================
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2026-01-26 15:14:42,518 [INFO] Estimated: 100 sims, ~0.4h on 32 cores (~14 core-hours)
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2026-01-26 15:14:48,474 [INFO] Phase 2: 200 simulations
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2026-01-26 15:14:48,475 [INFO] prey_birth value: 0.2
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2026-01-26 15:14:48,475 [INFO] initial prey_death values: 20
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2026-01-26 15:14:48,475 [INFO] Replicates: 10
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2026-01-26 15:49:17,385 [INFO] Phase 2 complete. Results: results/phase2_18693004/phase2_results.jsonl
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2026-01-26 15:49:17,403 [INFO] Phase 2 runtime: 34.6 minutes
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2026-01-26 15:49:17,403 [INFO]
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2026-01-26 15:49:17,403 [INFO] ============================================================
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2026-01-26 15:49:17,403 [INFO] EXPERIMENTS COMPLETE
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2026-01-26 15:49:17,403 [INFO] ============================================================

‎hpc_data/phase2_18693004/phase2_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": 1,
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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": 10,
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"warmup_steps": 1000,
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"measurement_steps": 5000,
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"with_evolution": true,
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"evolve_sd": 0.01,
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"evolve_min": 0.0,
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"evolve_max": 0.2,
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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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}

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