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Jungfraujoch/image_analysis/azint/AzIntEngineGPU.cu
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leonarski_fandFilip Leonarski 19b135186d
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v1.0.0-rc.175 (#85)
* Rugnux: Processes a collection live while jfjoch_broker writes it (`rugnux <master.h5> <broker URL>`).
* Rugnux: Processing starts on the first images and confirms its choices once all are in, so analysis can begin during collection.
* Rugnux: Faster processing, especially on servers with several GPUs and CPU sockets and on computers without a GPU (`--no-gpu`, macOS).
* Rugnux: Uses much less GPU memory, so large data sets stay on the GPU of smaller cards, and a data set too large for the card is processed on the CPU instead.
* Rugnux: On macOS, Bragg integration runs on the Apple GPU.
* Rugnux: Better handling of twinning and pseudo-symmetry, with the twin hypothesis written as `<prefix>_twin_<SG>.mtz`, and a wrong `--model` no longer confirms the data or decides the hand.
* Rugnux: `--model` accepts predicted (AlphaFold) models and falls back to molecular replacement when the model is not placed as a rigid body (experimental `--mr` forces it), settling space group, hand and twinning and writing a different answer as `<prefix>_mr.mtz`.
* Rugnux: Molecular replacement is faster and settles the space group in more cases with several copies in the asymmetric unit.
* Rugnux: Deposition-ready mmCIF, a richer report, and numbered steps on the terminal with the full log in `<prefix>_log.txt`; `_P1.mtz`, `--estimate-beam-center` and `--beam-center-search` are removed.
* Rugnux: The beam-stop shadow is found correctly on tilted detectors.
* Rugnux: Stills files that record a stationary goniometer axis get the default stills geometry refinement.
* jfjoch_viewer: "Analyze dataset" uses the same defaults as a bare `rugnux <file>`, and shows the results of processed CBF, marCCD and SMV sweeps.
* jfjoch_viewer: The Files panel refreshes on F5 and every few seconds, and the plot type and other selections stay put during live collection.
* jfjoch_writer: Memory stays bounded and old data files are closed efficiently on long runs, any failure ends the run in an error state the broker is told about, and the master file appears only after its data files; the ZeroMQ pusher logs when a stalled writer makes it drop images.
* Fixes: The TCP image pusher no longer blocks the broker's receiver, GPU out-of-memory failures stop with a clear message, and the XDS plugin masks module and chip edges.

---------

Co-authored-by: Filip Leonarski <jungfrau@filips-mac-mini.home>
Reviewed-on: #85
Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>
2026-10-16 15:34:43 +02:00

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// SPDX-FileCopyrightText: 2025 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
// SPDX-License-Identifier: GPL-3.0-only
#include "AzIntEngineGPU.h"
inline void cuda_err(cudaError_t val) {
if (val != cudaSuccess)
throw JFJochException(JFJochExceptionCategory::GPUCUDAError, cudaGetErrorString(val));
}
// The sums are fixed point, as the adaptive spot finder's corrected sums are (CORR_FIXED there): a
// float atomicAdd adds in whatever order the threads and blocks arrive, so the profile moved in its
// last bits between two runs on the same image. Quantised value by value, the sum is integer addition
// and no longer depends on the order. 2^12: a quantum of 2.4e-4 of a count, room for ~2e15 per ring.
constexpr float AZINT_FIXED = 4096.0f; // 2^12
// Signed, carried as two's complement for the unsigned 64-bit atomicAdd.
__device__ __forceinline__ unsigned long long azint_fixed(float v) {
return static_cast<unsigned long long>(static_cast<long long>(llrintf(v * AZINT_FIXED)));
}
// Pushes one ring run's totals to the shared accumulators; nothing for an empty run.
__device__ __forceinline__ void flush_azim_run(unsigned long long *s_sum, unsigned long long *s_sum2,
uint32_t *s_count, int b, unsigned long long r_sum,
unsigned long long r_sum2, uint32_t r_count) {
if (r_count == 0) return; // also covers the initial "no ring yet"
atomicAdd(&s_sum[b], r_sum);
atomicAdd(&s_sum2[b], r_sum2);
atomicAdd(&s_count[b], r_count);
}
__global__
void gpu_azim_shared(
const uint16_t *__restrict__ pixel_to_bin,
const float *__restrict__ corrections,
const int32_t *__restrict__ input_buffer,
unsigned long long *__restrict__ azint_sum,
unsigned long long *__restrict__ azint_sum2,
uint32_t *__restrict__ azint_count,
size_t num_pixels,
int azint_bins) {
extern __shared__ unsigned long long shared[];
unsigned long long *s_sum = shared;
unsigned long long *s_sum2 = &s_sum[azint_bins];
uint32_t *s_count = (uint32_t *) &s_sum2[azint_bins];
// Initialize shared memory
for (int i = threadIdx.x; i < azint_bins; i += blockDim.x) {
s_sum[i] = 0;
s_sum2[i] = 0;
s_count[i] = 0;
}
__syncthreads();
// Four pixels per thread, read as vector loads, and a running total per ring pushed to shared
// memory only when the ring changes: consecutive pixels along a row mostly share a ring, and an
// atomic per pixel on the same few addresses is what this kernel was limited by. The same scheme
// as the adaptive spot finder's ring pass (reduce_rings_shared). The buffers come straight from
// cudaMalloc, aligned for int4/float4; the npix % 4 leftovers are done one at a time below.
const size_t stride = static_cast<size_t>(blockDim.x) * gridDim.x;
const size_t nquad = num_pixels / 4;
for (size_t q = blockIdx.x * blockDim.x + threadIdx.x; q < nquad; q += stride) {
const int4 v4 = reinterpret_cast<const int4 *>(input_buffer)[q];
const ushort4 b4 = reinterpret_cast<const ushort4 *>(pixel_to_bin)[q];
const float4 c4 = reinterpret_cast<const float4 *>(corrections)[q];
const int32_t vq[4] = {v4.x, v4.y, v4.z, v4.w};
const uint16_t bq[4] = {b4.x, b4.y, b4.z, b4.w};
const float cq[4] = {c4.x, c4.y, c4.z, c4.w};
int r_b = -1;
unsigned long long r_sum = 0, r_sum2 = 0;
uint32_t r_count = 0;
#pragma unroll
for (int k = 0; k < 4; k++) {
const int32_t v = vq[k];
const int b = bq[k];
if (v == INT32_MIN || v == INT32_MAX || b >= azint_bins) continue;
if (b != r_b) {
flush_azim_run(s_sum, s_sum2, s_count, r_b, r_sum, r_sum2, r_count);
r_b = b;
r_sum = 0; r_sum2 = 0; r_count = 0;
}
const float val = static_cast<float>(v) * cq[k];
r_sum += azint_fixed(val);
r_sum2 += azint_fixed(val * val);
r_count += 1;
}
flush_azim_run(s_sum, s_sum2, s_count, r_b, r_sum, r_sum2, r_count);
}
for (size_t idx = 4 * nquad + blockIdx.x * blockDim.x + threadIdx.x; idx < num_pixels; idx += stride) {
const uint16_t bin = pixel_to_bin[idx];
const int32_t v = input_buffer[idx];
if (bin < azint_bins && v != INT32_MIN && v != INT32_MAX) {
const float val = static_cast<float>(v) * corrections[idx];
atomicAdd(&s_sum[bin], azint_fixed(val));
atomicAdd(&s_sum2[bin], azint_fixed(val * val));
atomicAdd(&s_count[bin], 1);
}
}
__syncthreads();
// Merge to global memory
for (unsigned int i = threadIdx.x; i < azint_bins; i += blockDim.x) {
atomicAdd(&azint_sum[i], s_sum[i]);
atomicAdd(&azint_sum2[i], s_sum2[i]);
atomicAdd(&azint_count[i], s_count[i]);
}
}
__global__
void gpu_azim(
const uint16_t *__restrict__ pixel_to_bin,
const float *__restrict__ corrections,
const int32_t *__restrict__ input_buffer,
unsigned long long *__restrict__ azint_sum,
unsigned long long *__restrict__ azint_sum2,
uint32_t *__restrict__ azint_count,
size_t num_pixels,
int azint_bins) {
for (size_t idx = blockIdx.x * blockDim.x + threadIdx.x;
idx < num_pixels;
idx += blockDim.x * gridDim.x) {
uint16_t bin = pixel_to_bin[idx];
int32_t v = input_buffer[idx];
bool valid = (v != INT32_MIN) & (v != INT32_MAX);
if (bin < azint_bins && valid) {
const float val = static_cast<float>(v) * corrections[idx];
atomicAdd(&azint_sum[bin], azint_fixed(val));
atomicAdd(&azint_sum2[bin], azint_fixed(val * val));
atomicAdd(&azint_count[bin], 1);
}
}
}
AzIntEngineGPU::AzIntEngineGPU(const AzimuthalIntegrationMapping &integration, std::shared_ptr<CudaStream> stream)
: AzIntEngine(integration),
stream(stream),
gpu_sum(azint_bins),
gpu_sum2(azint_bins),
gpu_count(azint_bins),
fixed_sum(azint_bins),
fixed_sum2(azint_bins),
cpu_sum_reg(fixed_sum),
cpu_sum2_reg(fixed_sum2),
cpu_count_reg(azint_count) {
int device = 0;
cuda_err(cudaGetDevice(&device)); // this worker's GPU, not necessarily 0
cudaDeviceProp prop{};
cuda_err(cudaGetDeviceProperties(&prop, device));
threads = 128;
blocks = 4 * prop.multiProcessorCount;
shared_size = prop.sharedMemPerBlock;
shared_needed = azint_bins * (2 * sizeof(unsigned long long) + sizeof(uint32_t));
// Geometry-only, so shared per GPU: the first engine on this device uploads them, the rest reuse
// them. Keyed by the mapping's own vectors, which outlive every engine built from it.
gpu_azint_correction = SharedDeviceTable(integration.Corrections().data(), npixel,
integration.Corrections().data(),
integration.GetCorrectionsChecksum(), *stream);
gpu_pixel_to_bin = SharedDeviceTable(integration.GetPixelToBin().data(), npixel,
integration.GetPixelToBin().data(),
integration.GetPixelToBinChecksum(), *stream);
}
void AzIntEngineGPU::Run(const ImagePreprocessorBuffer &image, AzimuthalIntegrationProfile &profile) {
if (image.size() != integration.GetPixelToBin().size())
throw std::runtime_error("ImageSpotFinder::AzimIntegration: Mismatch in size");
cuda_err(cudaMemsetAsync(gpu_sum, 0, sizeof(unsigned long long) * azint_bins, *stream));
cuda_err(cudaMemsetAsync(gpu_sum2, 0, sizeof(unsigned long long) * azint_bins, *stream));
cuda_err(cudaMemsetAsync(gpu_count, 0, sizeof(uint32_t) * azint_bins, *stream));
if (shared_needed < shared_size) {
gpu_azim_shared<<<blocks, threads, shared_needed, *stream>>>(
gpu_pixel_to_bin->get(),gpu_azint_correction->get(),image.getGPUBuffer(), gpu_sum, gpu_sum2,
gpu_count, npixel, azint_bins
);
cuda_err(cudaGetLastError());
} else {
gpu_azim<<<blocks, threads, 0, *stream>>>(
gpu_pixel_to_bin->get(),gpu_azint_correction->get(),image.getGPUBuffer(), gpu_sum, gpu_sum2,
gpu_count, npixel, azint_bins
);
cuda_err(cudaGetLastError());
}
cudaMemcpyAsync(fixed_sum.data(), gpu_sum, sizeof(unsigned long long) * azint_bins, cudaMemcpyDeviceToHost, *stream);
cudaMemcpyAsync(fixed_sum2.data(), gpu_sum2, sizeof(unsigned long long) * azint_bins, cudaMemcpyDeviceToHost, *stream);
cudaMemcpyAsync(azint_count.data(), gpu_count, sizeof(uint32_t) * azint_bins, cudaMemcpyDeviceToHost, *stream);
cuda_err(cudaStreamSynchronize(*stream));
for (int b = 0; b < azint_bins; b++) {
azint_sum[b] = static_cast<float>(static_cast<double>(static_cast<long long>(fixed_sum[b])) / AZINT_FIXED);
azint_sum2[b] = static_cast<float>(static_cast<double>(static_cast<long long>(fixed_sum2[b])) / AZINT_FIXED);
}
profile.Clear(integration);
profile.Add(azint_sum, azint_sum2, azint_count);
}