parsed small sim data; everything looks good

codegithubka · codegithubka · commit e82f43d3777e · 2026-01-25T19:09:34.000+01:00
diff --git a/.rsync-exclude b/.rsync-exclude
@@ -0,0 +1,15 @@
+# .rsync-exclude
+.venv/
+__pycache__/
+*.pyc
+.git/
+*.nbc
+*.nbi
+.pytest_cache/
+results/
+*.png
+*.pdf
+.DS_Store
+.ipynb_checkpoints/
+
+
diff --git a/docs/HPC_GUIDE.md b/docs/HPC_GUIDE.md
@@ -6,7 +6,8 @@ ssh kanagnostopoul@snellius.surf.nl
 # On a separate terminal run the following
 
 # Upload the entire project directory (including your models/ folder)
-scp -r ~/CSS_Project kanagnostopoul@snellius.surf.nl:~/
+rsync -avz --progress --exclude-from='.rsync-exclude' \
+    ~/CSS_Project/ kanagnostopoul@snellius.surf.nl:~/CSS_Project/
 
 # On the Snellius terminal
 
@@ -41,6 +42,7 @@ tail -f logs_<JOBID>.err
 
 # Watch task completetion
 
+watch -n 5 squeue -u $USER  
 watch -n 10 "ls -1 results_JOBID  | wc -l"
 
 # Fetching the results once the job is done
diff --git a/hpc/run_analysis.sh b/hpc/run_analysis.sh
@@ -1,37 +1,35 @@
 #!/bin/bash
-#SBATCH --job-name=pp_evo
-#SBATCH --partition=genoa
+#SBATCH --job-name=pp_phase1
+#SBATCH --partition=rome
 #SBATCH --nodes=1
 #SBATCH --ntasks=1
 #SBATCH --cpus-per-task=32
-#SBATCH --time=08:00:00
-#SBATCH --mem=32G
-#SBATCH --output=pp_analysis_%j.out
-#SBATCH --error=pp_analysis_%j.err
+#SBATCH --time=04:00:00
+#SBATCH --mem=16G
+#SBATCH --output=pp_phase1_%j.out
+#SBATCH --error=pp_phase1_%j.err
 
 # =============================================================================
-# PP Evolutionary Analysis - Snellius Job Script
+# PP Hydra Effect - Phase 1: Parameter Sweep
 # =============================================================================
 #
-# ESTIMATED RESOURCES:
-#   - Runtime: ~1.5-2 hours on 32 cores (15×15 grid, 25 reps)
+# PHASE 1: Find critical point via 2D sweep of prey_birth × prey_death
+#   - 15 × 15 × 15 reps × 2 (evo/non-evo) = 6,750 simulations
+#   - Estimated runtime: ~2 min on 32 cores
 #   - Memory: ~8 GB peak
-#   - CPU hours: ~50-60 core-hours
 #
-# SUBMIT:     sbatch run_analysis.sh
+# SUBMIT:     sbatch run_phase1.sh
 # MONITOR:    squeue -u $USER
 # CANCEL:     scancel <job_id>
-# OUTPUT:     results/ directory
 #
 # =============================================================================
 
 echo "========================================"
-echo "PP Evolutionary Analysis"
+echo "PP Hydra Effect - Phase 1"
 echo "========================================"
 echo "Job ID:     $SLURM_JOB_ID"
 echo "Node:       $(hostname)"
 echo "CPUs:       $SLURM_CPUS_PER_TASK"
-echo "Memory:     $SLURM_MEM_PER_NODE"
 echo "Start:      $(date)"
 echo "Working dir: $(pwd)"
 echo "========================================"
@@ -40,49 +38,60 @@ echo "========================================"
 # Environment Setup
 # -----------------------------------------------------------------------------
 
-# Load modules (adjust to your Snellius setup)
 source ~/snellius_venv/bin/activate
 
-# If you have a virtual environment with your models package:
-# source ~/venvs/ca_analysis/bin/activate
-
-# Prevent numpy/scipy from spawning extra threads (we use joblib instead)
+# 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 Analysis
+# Run Phase 1
 # -----------------------------------------------------------------------------
 
-OUTPUT_DIR="results_${SLURM_JOB_ID}"
+OUTPUT_DIR="results/phase1_${SLURM_JOB_ID}"
 mkdir -p $OUTPUT_DIR
 
 echo ""
 echo "Output directory: $OUTPUT_DIR"
 echo ""
 
-# Run the full analysis
-python3 -u scripts/pp_analysis.py \
-    --mode full \
+# Dry run first to verify setup
+echo "Dry run check:"
+python3 -u scripts/experiments.py \
+    --phase 1 \
     --output $OUTPUT_DIR \
-    --cores $SLURM_CPUS_PER_TASK
+    --cores $SLURM_CPUS_PER_TASK \
+    --dry-run
+
+echo ""
+echo "Starting Phase 1..."
+echo ""
 
-# For asynchronous execution (uncomment if needed)
-#python3 pp_analysis.py --mode full --output $OUTPUT_DIR --cores $SLURM_CPUS_PER_TASK --async
+# Run phase 1
+python3 -u scripts/experiments.py \
+    --phase 1 \
+    --output $OUTPUT_DIR \
+    --cores $SLURM_CPUS_PER_TASK
 
 # -----------------------------------------------------------------------------
 # Completion
 # -----------------------------------------------------------------------------
 
 echo ""
 echo "========================================"
-echo "Analysis Complete"
+echo "Phase 1 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 phase1_results.jsonl"
+echo "  2. Run analysis.py to find critical point"
+echo "  3. Update config.py with critical_prey_birth/death"
+echo "  4. Run phase 2-5"
 echo "========================================"
diff --git a/models/config.py b/models/config.py
@@ -196,7 +196,7 @@ def estimate_runtime(self, n_cores: int = 32) -> str:
     n_prey_death=15,
     prey_birth_range=(0.10, 0.35),
     prey_death_range=(0.001, 0.10),
-    n_replicates=15,
+    n_replicates=20,
     warmup_steps=300,
     measurement_steps=1000,
     collect_pcf=True,
diff --git a/notebooks/phase1.ipynb b/notebooks/phase1.ipynb
