Add Google Benchmark and workflow

.github/workflows/benchmark.yml

@@ -0,0 +1,33 @@
+name: Benchmark
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+
+permissions:
+  contents: write
+
+jobs:
+  benchmark:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - name: Update submodules
+        run: git submodule update --init --recursive
+      - name: Install dependencies
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y g++ make clang-tidy clang-format libbenchmark-dev python3 python3-pip
+          pip3 install pandas pyarrow pytest
+      - name: Build benchmark
+        run: make bench
+      - name: Run benchmark
+        run: ./bench --benchmark_out=benchmark.json --benchmark_out_format=json
+      - name: Store benchmark result
+        uses: benchmark-action/github-action-benchmark@v1
+        with:
+          tool: 'googlecpp'
+          output-file-path: benchmark.json
+          github-token: ${{ secrets.GITHUB_TOKEN }}
+          auto-push: true

Makefile

@@ -1,23 +1,31 @@
 #!/usr/bin/env make
 
 TARGET = main
+BENCH = bench
+OBJ = main_bench.o
 
 $(TARGET): main.cpp
 	$(CXX) -O3 -std=c++20 -fopenmp -march=native -o $(TARGET) $<
 
+$(OBJ): main.cpp
+	$(CXX) -O3 -std=c++20 -fopenmp -march=native -DBENCH_LIB -c main.cpp -o $(OBJ)
+
+$(BENCH): $(OBJ) bench.cpp
+	$(CXX) -O3 -std=c++20 -fopenmp -march=native bench.cpp $(OBJ) -lbenchmark -lpthread -o $(BENCH)
+
 format:
 	clang-format -i main.cpp
 
 tidy:
 	clang-tidy main.cpp -- -std=c++20
 
 clean:
-	rm -f $(TARGET)
+	rm -f $(TARGET) $(BENCH) $(OBJ)
 
 test: $(TARGET)
 	pytest -q
 
 submodule:
 	git submodule update --init --recursive
 
-.PHONY: clean format tidy test submodule
+.PHONY: clean format tidy test submodule bench

README.md

@@ -43,6 +43,15 @@ pip install -r requirements.txt  # pandas and pyarrow are required
 pytest
 ```
 
+## Benchmark
+
+Build and run the Google Benchmark suite to measure performance:
+
+```bash
+make bench
+./bench --benchmark_out=benchmark.json --benchmark_out_format=json
+```
+
 ## License
 
 This project is provided for educational purposes and comes with no warranty.

bench.cpp

@@ -0,0 +1,20 @@
+#include <benchmark/benchmark.h>
+#include <string>
+#include <cstdio>
+
+size_t run_simulation(const std::string &csv,
+                      const std::string &act,
+                      const std::string &sil,
+                      size_t T);
+
+static void BM_Run(benchmark::State &state) {
+  for (auto _ : state) {
+    size_t spikes = run_simulation("test/test_connectome.csv",
+                                   "test/active.txt",
+                                   "test/silent.txt", 5);
+    benchmark::DoNotOptimize(spikes);
+    std::remove("spikes.bin");
+  }
+}
+BENCHMARK(BM_Run);
+BENCHMARK_MAIN();

docs/AGENT_PROMPTS.md

@@ -16,5 +16,6 @@ When preparing pull requests:
 
 1. Ensure `make` builds without warnings.
 2. Run `pytest` to verify all tests pass.
-3. Update this document and `README.md` if usage or behavior changes.
+3. Run `make bench` to build benchmarks when performance changes are expected.
+4. Update this document and `README.md` if usage or behavior changes.
 

main.cpp

@@ -169,24 +169,8 @@ struct Simulator {
   }
 };
 /* ---------- main ---------- */
-int main(int argc, char **argv) {
-  string csv, act, sil;
-  size_t T = 1000;
-  for (int i = 1; i < argc; ++i) {
-    string a = argv[i];
-    if (a == "--csv")
-      csv = argv[++i];
-    else if (a == "--active")
-      act = argv[++i];
-    else if (a == "--silent")
-      sil = argv[++i];
-    else if (a == "--t")
-      T = stoul(argv[++i]);
-  }
-  if (csv.empty()) {
-    cerr << "--csv required\n";
-    return 1;
-  }
+size_t run_simulation(const string &csv, const string &act, const string &sil,
+                      size_t T) {
   /* step 1: count neurons (max id+1) */
   size_t N = 0;
   {
@@ -199,15 +183,39 @@ int main(int argc, char **argv) {
       N = max(N, size_t(max(pre, post) + 1));
     }
   }
-  vector<uint8_t> silent(N, 0);
+  vector<uint8_t> silent_vec(N, 0);
   for (auto id : load_list(sil))
     if (id < N)
-      silent[id] = 1;
+      silent_vec[id] = 1;
 
-  CSR G = load_csv_to_csr(csv, N, silent);
+  CSR G = load_csv_to_csr(csv, N, silent_vec);
   Params P;
-  Simulator S(N, G, P, silent);
+  Simulator S(N, G, P, silent_vec);
   S.run(T, load_list(act));
   S.save_bin("spikes.bin");
-  cerr << "Spikes: " << S.spikes.size() << "\n";
+  return S.spikes.size();
 }
+
+#ifndef BENCH_LIB
+int main(int argc, char **argv) {
+  string csv, act, sil;
+  size_t T = 1000;
+  for (int i = 1; i < argc; ++i) {
+    string a = argv[i];
+    if (a == "--csv")
+      csv = argv[++i];
+    else if (a == "--active")
+      act = argv[++i];
+    else if (a == "--silent")
+      sil = argv[++i];
+    else if (a == "--t")
+      T = stoul(argv[++i]);
+  }
+  if (csv.empty()) {
+    cerr << "--csv required\n";
+    return 1;
+  }
+  size_t spikes = run_simulation(csv, act, sil, T);
+  cerr << "Spikes: " << spikes << "\n";
+}
+#endif