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The pipeline decompressed each image on the host and uploaded the result. On an 18 Mpx rotation dataset that made the host-to-device copy the bottleneck of the whole per-image loop: nsys puts the copies at 78% of the loop against 39% for every kernel combined - 3600 transfers of 72.4 MB - and they ran at only 12.5 GB/s of an available 27-28 because the host-side decompression was itself saturating host memory bandwidth. The GPU was mostly waiting. So the compressed chunk goes across instead, about 4 MB rather than 72 MB, and is decoded on the device. That removes the transfer and the host decompression that was throttling it, in one change. Measured on an idle machine, a run goes from 45.11 s to 24.97 s - 1.81x - with the merged output unchanged. THE APPROACH IS JON WRIGHT'S (ESRF): "Experiences with GPU decompression for bitshuffle + LZ4 data", HDF5 User Group 2021, and github.com/jonwright/ bslz4decoders. The kernels here are ours, but the idea and the demonstration that it is worth doing are his. Cited in docs/ACKNOWLEDGEMENT.md and in the new section 0 of docs/CPU_DATA_ANALYSIS.md. Two kernels mirror the CPU decoder. LZ4 runs one WARP per bitshuffle block: every lane parses the same sequence stream (a broadcast read, no divergence) and the literal and match copies are split across the 32 lanes so the stores coalesce; an overlapping match is treated as a pattern of period offset sourced from bytes that already precede the write position, which keeps it parallel rather than a serial byte loop. One thread per block instead measured 13x slower. The bitshuffle inverse then un-transposes each byte-plane through shared memory and interleaves the planes back into elements. Only BSHUF_LZ4 is decoded on the device. The zstd variants have no device decoder, and neither has an uncompressed or float image; Supports() returns false for those and the caller decompresses on the host exactly as before. The fallback is explicit, so a format we cannot decode on the device is a slower path and never a wrong answer. Tests hold the device decoder against the CPU one byte for byte, on data from the production compressor, for every element size the detectors emit - including the 8-bit DECTRIS modes, which take bitshuf_decode_block's separate elem_size == 1 branch - plus a many-block frame, the formats it must decline, and malformed containers, which must throw rather than run off a buffer. Battery: 37 crystals, no failures, identical to the host-decode run. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
160 lines
7.3 KiB
C++
160 lines
7.3 KiB
C++
// SPDX-FileCopyrightText: 2026 Filip Leonarski, Paul Scherrer Institute
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// SPDX-License-Identifier: GPL-3.0-only
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#include <catch2/catch_all.hpp>
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#include "../common/CUDAWrapper.h"
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#ifdef JFJOCH_USE_CUDA
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#include <random>
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#include <cstring>
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#include <limits>
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#include "../image_analysis/image_preprocessing/BSLZ4DecoderGPU.h"
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#include "../compression/JFJochCompressor.h"
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#include "../compression/JFJochDecompress.h"
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// The GPU decoder must agree with the CPU one BYTE FOR BYTE, on data produced by our own compressor,
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// for every element size the detectors emit - including the 8-bit DECTRIS modes, which take a
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// different branch in bitshuf_decode_block (bit un-transpose only, no byte interleave).
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//
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// Images are built to exercise what the LZ4 format actually does on detector data: long runs of a
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// repeated byte (offset == 1 matches, the overlapping-match path), isolated bright pixels
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// (literals), and a noisy region (short matches at assorted offsets). A uniformly random image
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// would be almost incompressible and would never reach the match code at all.
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namespace {
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template <class T>
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std::vector<T> MakeDetectorLikeImage(size_t npixels, uint32_t seed) {
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std::mt19937 rng(seed);
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std::vector<T> img(npixels, 0); // sparse background: long zero runs
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// A band of low-level noise, so matches are short and offsets vary.
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for (size_t i = npixels / 4; i < npixels / 2; i++)
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img[i] = static_cast<T>(rng() % 7);
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// Bright, isolated spots - these become literals.
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for (size_t s = 0; s < 64; s++) {
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const size_t c = rng() % npixels;
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for (size_t d = 0; d < 9 && c + d < npixels; d++)
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img[c + d] = static_cast<T>(std::numeric_limits<T>::max() / (2 + (d % 3)));
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}
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// A run of one repeated non-zero value, the classic offset==1 match.
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for (size_t i = npixels * 3 / 4; i < npixels * 3 / 4 + 5000 && i < npixels; i++)
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img[i] = static_cast<T>(42);
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return img;
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}
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template <class T>
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void RoundTrip(CompressedImageMode mode, size_t width, size_t height, uint32_t seed) {
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const size_t npixels = width * height;
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const auto original = MakeDetectorLikeImage<T>(npixels, seed);
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// Compress with the production compressor, so the container is exactly what the pipeline reads.
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JFJochBitShuffleCompressor compressor(CompressionAlgorithm::BSHUF_LZ4);
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const std::vector<uint8_t> compressed = compressor.Compress(original);
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REQUIRE(!compressed.empty());
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const CompressedImage image(compressed.data(), compressed.size(), width, height, mode,
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CompressionAlgorithm::BSHUF_LZ4);
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REQUIRE(BSLZ4DecoderGPU::Supports(image));
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REQUIRE(image.GetUncompressedSize() == npixels * sizeof(T));
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// CPU reference: the same call the host path makes.
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std::vector<uint8_t> cpu_buffer;
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const uint8_t *cpu_out = image.GetUncompressedPtr(cpu_buffer);
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REQUIRE(std::memcmp(cpu_out, original.data(), npixels * sizeof(T)) == 0);
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auto stream = std::make_shared<CudaStream>();
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BSLZ4DecoderGPU decoder(npixels * sizeof(uint32_t), stream);
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CudaDevicePtr<uint8_t> gpu_out(npixels * sizeof(T));
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decoder.Decode(image, gpu_out.get());
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REQUIRE(cudaStreamSynchronize(*stream) == cudaSuccess);
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std::vector<T> gpu_result(npixels);
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REQUIRE(cudaMemcpy(gpu_result.data(), gpu_out.get(), npixels * sizeof(T),
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cudaMemcpyDeviceToHost) == cudaSuccess);
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REQUIRE(std::memcmp(gpu_result.data(), original.data(), npixels * sizeof(T)) == 0);
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}
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} // namespace
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TEST_CASE("BSLZ4DecoderGPU_MatchesCPU_AllElementSizes", "[BSLZ4DecoderGPU]") {
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if (get_gpu_count() == 0)
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SKIP("No CUDA GPU present");
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// Sizes chosen so the last block is partial and the leftover tail (the elements bitshuffle
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// leaves uncompressed because they do not fill a multiple of 8) is non-empty on some of them.
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RoundTrip<uint8_t>(CompressedImageMode::Uint8, 1030, 517, 1);
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RoundTrip<int8_t>(CompressedImageMode::Int8, 1030, 517, 2);
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RoundTrip<uint16_t>(CompressedImageMode::Uint16, 1030, 517, 3);
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RoundTrip<int16_t>(CompressedImageMode::Int16, 1030, 517, 4);
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RoundTrip<uint32_t>(CompressedImageMode::Uint32, 1030, 517, 5);
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RoundTrip<int32_t>(CompressedImageMode::Int32, 1030, 517, 6);
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}
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TEST_CASE("BSLZ4DecoderGPU_MatchesCPU_LargeFrame", "[BSLZ4DecoderGPU]") {
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if (get_gpu_count() == 0)
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SKIP("No CUDA GPU present");
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// Many blocks, so the per-block descriptor scan and the one-warp-per-block launch are exercised
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// at a realistic scale rather than on a handful of blocks.
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RoundTrip<uint32_t>(CompressedImageMode::Uint32, 2068, 2162, 7);
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}
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// A decoder that cannot handle an image must SAY so rather than produce something wrong: the caller
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// relies on Supports() to decide whether the host route is needed.
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TEST_CASE("BSLZ4DecoderGPU_DeclinesWhatItCannotDecode", "[BSLZ4DecoderGPU]") {
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std::vector<uint8_t> dummy(1024, 0);
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const size_t w = 16, h = 16;
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CHECK_FALSE(BSLZ4DecoderGPU::Supports(
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CompressedImage(dummy.data(), dummy.size(), w, h, CompressedImageMode::Uint32,
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CompressionAlgorithm::BSHUF_ZSTD)));
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CHECK_FALSE(BSLZ4DecoderGPU::Supports(
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CompressedImage(dummy.data(), dummy.size(), w, h, CompressedImageMode::Uint32,
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CompressionAlgorithm::BSHUF_ZSTD_RLE)));
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CHECK_FALSE(BSLZ4DecoderGPU::Supports(
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CompressedImage(dummy.data(), dummy.size(), w, h, CompressedImageMode::Uint32,
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CompressionAlgorithm::BSHUF_ZSTD_RLE_HUFF)));
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CHECK_FALSE(BSLZ4DecoderGPU::Supports(
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CompressedImage(dummy.data(), dummy.size(), w, h, CompressedImageMode::Uint32,
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CompressionAlgorithm::NO_COMPRESSION)));
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CHECK_FALSE(BSLZ4DecoderGPU::Supports(
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CompressedImage(dummy.data(), dummy.size(), w, h, CompressedImageMode::Float32,
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CompressionAlgorithm::BSHUF_LZ4)));
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CHECK(BSLZ4DecoderGPU::Supports(
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CompressedImage(dummy.data(), dummy.size(), w, h, CompressedImageMode::Uint32,
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CompressionAlgorithm::BSHUF_LZ4)));
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}
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// A malformed container comes off the network or off disk, so it must throw rather than run off
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// the end of a buffer on the device.
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TEST_CASE("BSLZ4DecoderGPU_RejectsMalformed", "[BSLZ4DecoderGPU]") {
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if (get_gpu_count() == 0)
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SKIP("No CUDA GPU present");
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const size_t width = 128, height = 128, npixels = width * height;
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const auto original = MakeDetectorLikeImage<uint32_t>(npixels, 11);
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JFJochBitShuffleCompressor compressor(CompressionAlgorithm::BSHUF_LZ4);
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const std::vector<uint8_t> compressed = compressor.Compress(original);
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auto stream = std::make_shared<CudaStream>();
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BSLZ4DecoderGPU decoder(npixels * sizeof(uint32_t), stream);
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CudaDevicePtr<uint8_t> gpu_out(npixels * sizeof(uint32_t));
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// Truncated mid-stream: the block header promises more than is there.
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const CompressedImage truncated(compressed.data(), compressed.size() / 2, width, height,
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CompressedImageMode::Uint32, CompressionAlgorithm::BSHUF_LZ4);
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CHECK_THROWS(decoder.Decode(truncated, gpu_out.get()));
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// Shorter than the 12-byte container header.
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const CompressedImage stub(compressed.data(), 8, width, height,
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CompressedImageMode::Uint32, CompressionAlgorithm::BSHUF_LZ4);
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CHECK_THROWS(decoder.Decode(stub, gpu_out.get()));
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}
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#endif
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