Initial commit: Matrix alignment prototype for HPC performance demonstration

- Add C implementation demonstrating memory alignment effects (matrix_alignment_prototype.c)
- Include cache-blocked matrix multiplication with AVX SIMD optimizations
- Add automated benchmarking framework (run_all_tests.sh, run_benchmark_sizes.sh)
- Add Python visualization scripts (generate_plots.py)
- Include Makefile for building with AVX support
- Add benchmark results and generated plots
- Add README with build and usage instructions
- Configure .gitignore for C/Python project files

run_benchmark_sizes.sh

@@ -0,0 +1,61 @@
+#!/bin/bash
+# Benchmark script to test multiple matrix sizes
+# Based on OpenBLAS Issue #3879 performance variability analysis
+
+# Matrix sizes to test (from before the fix issue 3879.md)
+SIZES=(512 1024 1500 2048)
+
+# Output file for results
+RESULTS_FILE="benchmark_results.csv"
+
+echo "=========================================="
+echo "HPC Alignment Benchmark - Multiple Sizes"
+echo "=========================================="
+echo ""
+
+# Create results file with header
+echo "Matrix_Size,Aligned_Time,Misaligned_Time,Speedup" > "$RESULTS_FILE"
+
+# Build the prototype if needed
+if [ ! -f "matrix_alignment_prototype" ]; then
+    echo "Building prototype..."
+    make clean
+    make
+    if [ $? -ne 0 ]; then
+        echo "Error: Build failed"
+        exit 1
+    fi
+fi
+
+# Run benchmarks for each size
+for SIZE in "${SIZES[@]}"; do
+    echo "Testing matrix size: ${SIZE}x${SIZE}"
+    echo "----------------------------------------"
+    
+    # Run the benchmark with specific size in CSV mode
+    ./matrix_alignment_prototype -s "$SIZE" --csv >> "$RESULTS_FILE"
+    
+    if [ $? -ne 0 ]; then
+        echo "Error: Benchmark failed for size $SIZE"
+        exit 1
+    fi
+    
+    echo ""
+done
+
+echo "=========================================="
+echo "Benchmark complete!"
+echo "Results saved to: $RESULTS_FILE"
+echo "=========================================="
+
+# Generate plots
+if command -v python3 &> /dev/null; then
+    echo ""
+    echo "Generating plots..."
+    python3 generate_plots.py
+else
+    echo ""
+    echo "Python3 not found. Skipping plot generation."
+    echo "Install Python3 and matplotlib to generate plots."
+fi
+