phase 2 shell script added

Author: codegithubka

hpc/run_phase4.sh

@@ -0,0 +1,98 @@
+#!/bin/bash
+#SBATCH --job-name=pp_phase4
+#SBATCH --partition=rome
+#SBATCH --nodes=1
+#SBATCH --ntasks=1
+#SBATCH --cpus-per-task=64
+#SBATCH --time=04:00:00
+#SBATCH --mem=64G
+#SBATCH --output=/home/kanagnostopoul/CSS_Project/pp_phase4_%j.out
+#SBATCH --error=/home/kanagnostopoul/CSS_Project/pp_phase4_%j.err
+
+# =============================================================================
+# PP Hydra Effect - Phase 4: Global Sensitivity Analysis
+# =============================================================================
+#
+# PHASE 4: Full 4D Parameter Sweep (Global Sensitivity)
+#   - Parameters: prey_birth, prey_death, pred_birth, pred_death
+#   - Sweep: 0.0 to 1.0 (11 values each) = 14,641 combinations
+#   - Replicates: 10 per combination
+#   - Total Simulations: ~146,410
+#   - Grid Size: 250x250
+#
+# SUBMIT:     sbatch run_phase4.sh
+# MONITOR:    squeue -u $USER
+# CANCEL:     scancel <job_id>
+#
+# =============================================================================
+
+cd /home/kanagnostopoul/CSS_Project || exit 1
+
+echo "========================================"
+echo "PP Hydra Effect - Phase 4"
+echo "========================================"
+echo "Job ID:     $SLURM_JOB_ID"
+echo "Node:       $(hostname)"
+echo "CPUs:       $SLURM_CPUS_PER_TASK"
+echo "Start:      $(date)"
+echo "Working dir: $(pwd)"
+echo "========================================"
+
+# -----------------------------------------------------------------------------
+# Environment Setup
+# -----------------------------------------------------------------------------
+source ~/snellius_venv/bin/activate
+
+# Prevent numpy/scipy from spawning extra threads (joblib handles parallelism)
+export OMP_NUM_THREADS=1
+export OPENBLAS_NUM_THREADS=1
+export MKL_NUM_THREADS=1
+export NUMEXPR_NUM_THREADS=1
+
+# -----------------------------------------------------------------------------
+# Run Phase 4
+# -----------------------------------------------------------------------------
+OUTPUT_DIR="results/phase4_${SLURM_JOB_ID}"
+mkdir -p $OUTPUT_DIR
+
+echo ""
+echo "Output directory: $OUTPUT_DIR"
+echo ""
+
+# Dry run first to verify setup and runtime estimate
+echo "Dry run check:"
+python3 -u scripts/experiments.py \
+    --phase 4 \
+    --output $OUTPUT_DIR \
+    --cores $SLURM_CPUS_PER_TASK \
+    --dry-run
+
+echo ""
+echo "Starting Phase 4 (4D Sweep)..."
+echo ""
+
+# Run phase 4
+python3 -u scripts/experiments.py \
+    --phase 4 \
+    --output $OUTPUT_DIR \
+    --cores $SLURM_CPUS_PER_TASK
+
+# -----------------------------------------------------------------------------
+# Completion
+# -----------------------------------------------------------------------------
+echo ""
+echo "========================================"
+echo "Phase 4 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 phase4_results.jsonl"
+echo "  2. Perform Global Sensitivity Analysis (Sobol Indices)"
+echo "  3. Identify parameter dominance for extinction events"
+echo "  4. Plot parameter heatmaps for predator/prey survival"
+echo "========================================"