add benchmark to test different chunk/shard/compression/storage confi…

…gurations (#22)

CMakeLists.txt

@@ -21,6 +21,7 @@ set(CMAKE_CXX_STANDARD_REQUIRED ON)
 set(CMAKE_CXX_EXTENSIONS OFF)
 
 option(BUILD_PYTHON "Build Python bindings" OFF)
+option(BUILD_BENCHMARK "Build benchmarks" OFF)
 
 if(CMAKE_PROJECT_NAME STREQUAL PROJECT_NAME)
     include(CTest)
@@ -33,7 +34,13 @@ else ()
     message(STATUS "Skipping test targets")
 endif ()
 
-if (${BUILD_PYTHON})
+if (BUILD_BENCHMARK)
+    add_subdirectory(benchmarks)
+else ()
+    message(STATUS "Skipping benchmarks")
+endif ()
+
+if (BUILD_PYTHON)
     add_subdirectory(python)
 else ()
     message(STATUS "Skipping Python bindings")

benchmarks/CMakeLists.txt

@@ -0,0 +1,18 @@
+set(project acquire-zarr)
+
+set(tgt acquire-zarr-benchmark)
+add_executable(${tgt} benchmark.cpp)
+target_compile_definitions(${tgt} PUBLIC "TEST=\"${tgt}\"")
+set_target_properties(${tgt} PROPERTIES
+        MSVC_RUNTIME_LIBRARY "MultiThreaded$<$<CONFIG:Debug>:Debug>"
+)
+target_include_directories(${tgt} PRIVATE
+        ${PROJECT_SOURCE_DIR}/include
+        ${PROJECT_SOURCE_DIR}/src/logger
+)
+target_link_libraries(${tgt} PRIVATE
+        acquire-logger
+        acquire-zarr
+        nlohmann_json::nlohmann_json
+        miniocpp::miniocpp
+)

benchmarks/benchmark.cpp

@@ -0,0 +1,233 @@
+#include "acquire.zarr.h"
+#include <chrono>
+#include <fstream>
+#include <vector>
+#include <filesystem>
+#include <iomanip>
+#include <iostream>
+#include <cmath>
+
+#define DIM(name_, type_, array_size, chunk_size, shard_size)                  \
+    { .name = (name_),                                                         \
+      .type = (type_),                                                         \
+      .array_size_px = (array_size),                                           \
+      .chunk_size_px = (chunk_size),                                           \
+      .shard_size_chunks = (shard_size) }
+
+namespace fs = std::filesystem;
+
+struct ChunkConfig
+{
+    unsigned int t, c, z, y, x;
+};
+
+const std::vector<ChunkConfig> CHUNK_CONFIGS = { { 1, 1, 64, 64, 64 },
+                                                 { 1, 1, 128, 128, 128 },
+                                                 { 1, 1, 256, 256, 256 } };
+
+const unsigned int ARRAY_WIDTH = 1920, ARRAY_HEIGHT = 1080, ARRAY_PLANES = 6,
+                   ARRAY_CHANNELS = 3, ARRAY_TIMEPOINTS = 10;
+
+const unsigned int NUM_RUNS = 5;
+
+struct BenchmarkConfig
+{
+    ChunkConfig chunk;
+    int zarr_version;
+    std::string compression;
+    std::string storage;
+    unsigned int chunks_per_shard_x;
+    unsigned int chunks_per_shard_y;
+    std::string s3_endpoint;
+    std::string s3_bucket;
+    std::string s3_access_key;
+    std::string s3_secret_key;
+};
+
+class Timer
+{
+    using Clock = std::chrono::high_resolution_clock;
+    Clock::time_point start;
+
+  public:
+    Timer()
+      : start(Clock::now())
+    {
+    }
+    double elapsed()
+    {
+        auto end = Clock::now();
+        return std::chrono::duration<double>(end - start).count();
+    }
+};
+
+ZarrStream*
+setup_stream(const BenchmarkConfig& config)
+{
+    ZarrStreamSettings settings = { .store_path = "benchmark.zarr",
+                                    .s3_settings = nullptr,
+                                    .compression_settings = nullptr,
+                                    .data_type = ZarrDataType_uint16,
+                                    .version = static_cast<ZarrVersion>(
+                                      config.zarr_version) };
+
+    ZarrCompressionSettings comp_settings = {};
+    if (config.compression != "none") {
+        comp_settings.compressor = ZarrCompressor_Blosc1;
+        comp_settings.codec = config.compression == "lz4"
+                                ? ZarrCompressionCodec_BloscLZ4
+                                : ZarrCompressionCodec_BloscZstd;
+        comp_settings.level = 1;
+        comp_settings.shuffle = 1;
+        settings.compression_settings = &comp_settings;
+    }
+
+    ZarrS3Settings s3_settings = {};
+    if (config.storage == "s3") {
+        s3_settings = {
+            .endpoint = config.s3_endpoint.c_str(),
+            .bucket_name = config.s3_bucket.c_str(),
+            .access_key_id = config.s3_access_key.c_str(),
+            .secret_access_key = config.s3_secret_key.c_str(),
+        };
+        settings.s3_settings = &s3_settings;
+    }
+
+    ZarrStreamSettings_create_dimension_array(&settings, 5);
+    auto* dims = settings.dimensions;
+
+    dims[0] =
+      DIM("t", ZarrDimensionType_Time, ARRAY_TIMEPOINTS, config.chunk.t, 1);
+    dims[1] =
+      DIM("c", ZarrDimensionType_Channel, ARRAY_CHANNELS, config.chunk.c, 1);
+    dims[2] =
+      DIM("z", ZarrDimensionType_Space, ARRAY_PLANES, config.chunk.z, 1);
+    dims[3] = DIM("y",
+                  ZarrDimensionType_Space,
+                  ARRAY_HEIGHT,
+                  config.chunk.y,
+                  config.chunks_per_shard_y);
+    dims[4] = DIM("x",
+                  ZarrDimensionType_Space,
+                  ARRAY_WIDTH,
+                  config.chunk.x,
+                  config.chunks_per_shard_x);
+
+    return ZarrStream_create(&settings);
+}
+
+double
+run_benchmark(const BenchmarkConfig& config)
+{
+    auto* stream = setup_stream(config);
+    if (!stream)
+        return -1.0;
+
+    const size_t frame_size = ARRAY_WIDTH * ARRAY_HEIGHT * sizeof(uint16_t);
+    std::vector<uint16_t> frame(ARRAY_WIDTH * ARRAY_HEIGHT, 0);
+    const auto num_frames = ARRAY_PLANES * ARRAY_CHANNELS * ARRAY_TIMEPOINTS;
+
+    Timer timer;
+    size_t bytes_out;
+    for (int i = 0; i < num_frames; ++i) {
+        if (ZarrStream_append(stream, frame.data(), frame_size, &bytes_out) !=
+            ZarrStatusCode_Success) {
+            ZarrStream_destroy(stream);
+            return -1.0;
+        }
+    }
+    double elapsed = timer.elapsed();
+
+    ZarrStream_destroy(stream);
+    if (config.storage == "filesystem") {
+        fs::remove_all("benchmark.zarr");
+    }
+    return elapsed;
+}
+
+int
+main()
+{
+    std::ofstream csv("zarr_benchmarks.csv");
+    csv << "chunk_size,zarr_version,compression,storage,chunks_per_shard_y,"
+           "chunks_per_shard_x,run,time_seconds\n";
+
+    std::vector<BenchmarkConfig> configs;
+    for (const auto& chunk : CHUNK_CONFIGS) {
+
+        // V2 configurations (no sharding)
+        for (const auto& compression : { "none", "lz4", "zstd" }) {
+            configs.push_back({ chunk, 2, compression, "filesystem", 1, 1 });
+
+            if (std::getenv("ZARR_S3_ENDPOINT")) {
+                configs.push_back({ chunk,
+                                    2,
+                                    compression,
+                                    "s3",
+                                    1,
+                                    1,
+                                    std::getenv("ZARR_S3_ENDPOINT"),
+                                    std::getenv("ZARR_S3_BUCKET_NAME"),
+                                    std::getenv("ZARR_S3_ACCESS_KEY_ID"),
+                                    std::getenv("ZARR_S3_SECRET_ACCESS_KEY") });
+            }
+        }
+
+        unsigned int max_cps_y = (ARRAY_HEIGHT + chunk.y - 1) / chunk.y;
+        unsigned int max_cps_x = (ARRAY_WIDTH + chunk.x - 1) / chunk.x;
+
+        // V3 configurations (with sharding)
+        for (unsigned int cps_y = 1; cps_y <= max_cps_y; cps_y *= 2) {
+            for (unsigned int cps_x = 1; cps_x <= max_cps_x; cps_x *= 2) {
+                for (const auto& compression : { "none", "lz4", "zstd" }) {
+                    configs.push_back(
+                      { chunk, 3, compression, "filesystem", cps_x, cps_y });
+
+                    if (std::getenv("ZARR_S3_ENDPOINT")) {
+                        configs.push_back(
+                          { chunk,
+                            3,
+                            compression,
+                            "s3",
+                            cps_x,
+                            cps_y,
+                            std::getenv("ZARR_S3_ENDPOINT"),
+                            std::getenv("ZARR_S3_BUCKET_NAME"),
+                            std::getenv("ZARR_S3_ACCESS_KEY_ID"),
+                            std::getenv("ZARR_S3_SECRET_ACCESS_KEY") });
+                    }
+                }
+            }
+        }
+    }
+
+    for (const auto& config : configs) {
+        std::string chunk_str = std::to_string(config.chunk.t) + "x" +
+                                std::to_string(config.chunk.c) + "x" +
+                                std::to_string(config.chunk.z) + "x" +
+                                std::to_string(config.chunk.y) + "x" +
+                                std::to_string(config.chunk.x);
+
+        for (unsigned int run = 1; run <= NUM_RUNS; ++run) {
+            std::cout << "Benchmarking " << chunk_str << " Zarr V"
+                      << config.zarr_version
+                      << ", compression: " << config.compression
+                      << ", storage: " << config.storage
+                      << ", CPS (y): " << config.chunks_per_shard_y
+                      << ", CPS (x): " << config.chunks_per_shard_x << ", (run "
+                      << run << " / " << NUM_RUNS << ")...";
+            double time = run_benchmark(config);
+            std::cout << " " << time << "s\n";
+            if (time >= 0) {
+                csv << chunk_str << "," << config.zarr_version << ","
+                    << config.compression << "," << config.storage << ","
+                    << config.chunks_per_shard_y << ","
+                    << config.chunks_per_shard_x << "," << run << ","
+                    << std::fixed << std::setprecision(3) << time << "\n";
+            }
+            csv.flush();
+        }
+    }
+
+    return 0;
+}