phase 3 config and removed phase 2 logic from main expriment run analysis function

Author: codegithubka

docs/HPC_GUIDE.md

@@ -47,7 +47,7 @@ watch -n 10 "ls -1 results_JOBID  | wc -l"
 
 # Fetching the results once the job is done
 
-scp -r kanagnostopoul@snellius.surf.nl:~/CSS_Project/results/phase1_ 18682575/ ./results/
+scp -r kanagnostopoul@snellius.surf.nl:~/CSS_Project/results/phase2_18693004/ ./results/
 ```
 
 The jobscript template can be found in ```run_analysis.sh``` (default rome paritition).

hpc/run_phase2.sh

@@ -4,10 +4,10 @@
 #SBATCH --nodes=1
 #SBATCH --ntasks=1
 #SBATCH --cpus-per-task=32
-#SBATCH --time=08:00:00
-#SBATCH --mem=16G
-#SBATCH --output=pp_phase2_%j.out
-#SBATCH --error=pp_phase2_%j.err
+#SBATCH --time=04:00:00
+#SBATCH --mem=64G
+#SBATCH --output=/home/kanagnostopoul/CSS_Project/pp_phase2_%j.out
+#SBATCH --error=/home/kanagnostopoul/CSS_Project/pp_phase2_%j.err
 
 # =============================================================================
 # PP Hydra Effect - Phase 2: Self-Organization (SOC Test)

hpc/run_phase3.sh

@@ -0,0 +1,97 @@
+#!/bin/bash
+#SBATCH --job-name=pp_phase3
+#SBATCH --partition=rome
+#SBATCH --nodes=1
+#SBATCH --ntasks=1
+#SBATCH --cpus-per-task=32
+#SBATCH --time=02:00:00
+#SBATCH --mem=64G
+#SBATCH --output=/home/kanagnostopoul/CSS_Project/pp_phase3_%j.out
+#SBATCH --error=/home/kanagnostopoul/CSS_Project/pp_phase3_%j.err
+
+# =============================================================================
+# PP Hydra Effect - Phase 3: Finite-Size Scaling
+# =============================================================================
+#
+# PHASE 3: Test finite-size scaling at critical point
+#   - Grid sizes: 50, 100, 250, 500, 1000
+#   - 20 replicates per size = 100 simulations
+#   - Cluster size distributions for power-law analysis
+#
+# SUBMIT:     sbatch run_phase3.sh
+# MONITOR:    squeue -u $USER
+# CANCEL:     scancel <job_id>
+#
+# =============================================================================
+
+cd /home/kanagnostopoul/CSS_Project || exit 1
+
+echo "========================================"
+echo "PP Hydra Effect - Phase 3"
+echo "========================================"
+echo "Job ID:     $SLURM_JOB_ID"
+echo "Node:       $(hostname)"
+echo "CPUs:       $SLURM_CPUS_PER_TASK"
+echo "Start:      $(date)"
+echo "Working dir: $(pwd)"
+echo "========================================"
+
+# -----------------------------------------------------------------------------
+# Environment Setup
+# -----------------------------------------------------------------------------
+source ~/snellius_venv/bin/activate
+
+# Prevent numpy/scipy from spawning extra threads (joblib handles parallelism)
+export OMP_NUM_THREADS=1
+export OPENBLAS_NUM_THREADS=1
+export MKL_NUM_THREADS=1
+export NUMEXPR_NUM_THREADS=1
+
+# -----------------------------------------------------------------------------
+# Run Phase 3
+# -----------------------------------------------------------------------------
+OUTPUT_DIR="results/phase3_${SLURM_JOB_ID}"
+mkdir -p $OUTPUT_DIR
+
+echo ""
+echo "Output directory: $OUTPUT_DIR"
+echo ""
+
+# Dry run first to verify setup
+echo "Dry run check:"
+python3 -u scripts/experiments.py \
+    --phase 3 \
+    --output $OUTPUT_DIR \
+    --cores $SLURM_CPUS_PER_TASK \
+    --dry-run
+
+echo ""
+echo "Starting Phase 3..."
+echo ""
+
+# Run phase 3
+python3 -u scripts/experiments.py \
+    --phase 3 \
+    --output $OUTPUT_DIR \
+    --cores $SLURM_CPUS_PER_TASK
+
+# -----------------------------------------------------------------------------
+# Completion
+# -----------------------------------------------------------------------------
+echo ""
+echo "========================================"
+echo "Phase 3 Complete"
+echo "========================================"
+echo "End time:   $(date)"
+echo "Results in: $OUTPUT_DIR/"
+echo ""
+echo "Output files:"
+ls -lh $OUTPUT_DIR/
+echo ""
+echo "Next steps:"
+echo "  1. Download phase3_results.jsonl"
+echo "  2. Analyze cluster size distributions P(s) for each grid size"
+echo "  3. Fit power-law exponent tau from P(s) ~ s^(-tau)"
+echo "  4. Check finite-size cutoff s_max ~ L^D (fractal dimension)"
+echo "========================================"
+EOF