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Jungfraujoch/image_analysis/beam_stop/ShadowAccumulatorGPU.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: 2026 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
// SPDX-License-Identifier: GPL-3.0-only
#include "ShadowAccumulatorGPU.h"
#include <limits>
#include <type_traits>
#include "../../common/CUDAWrapper.h"
#include "../../common/JFJochException.h"
inline void cuda_err(cudaError_t val) {
if (val != cudaSuccess)
throw JFJochException(JFJochExceptionCategory::GPUCUDAError, cudaGetErrorString(val));
}
namespace {
// One frame folded into the projection. The sentinel test is predicated rather than branched: a
// warp straddling a module gap then costs the same as one that does not, against a per-frame memory
// bill of several hundred megabytes.
//
// The update is written exactly as the host writes it, including the "first value wins whatever it
// is" rule for the maximum - a pixel that has never been counted holds 0, which a genuinely negative
// maximum has to be allowed to replace. Each pixel is owned by one thread and the frames are
// separate launches on one stream, so there is no race and no atomic.
template <class T>
__global__ void accumulate_kernel(const T *__restrict__ frames, int nframes, size_t frame_stride,
int64_t *__restrict__ max_value, int64_t *__restrict__ sum_value,
uint32_t *__restrict__ valid_count, size_t npixels, T masked) {
for (size_t i = blockIdx.x * static_cast<size_t>(blockDim.x) + threadIdx.x; i < npixels;
i += static_cast<size_t>(blockDim.x) * gridDim.x) {
int64_t mx = max_value[i];
int64_t sm = sum_value[i];
uint32_t c = valid_count[i];
for (int k = 0; k < nframes; k++) {
const T v = frames[k * frame_stride + i];
if (v == masked)
continue;
const int64_t vi = static_cast<int64_t>(v);
if (c == 0 || vi > mx)
mx = vi;
sm += vi;
c++;
}
max_value[i] = mx;
sum_value[i] = sm;
valid_count[i] = c;
}
}
// Another card's projection folded into this one, with the update Add makes: the maximum is only taken
// from a projection that counted the pixel.
__global__ void fold_kernel(const int64_t *__restrict__ other_max, const int64_t *__restrict__ other_sum,
const uint32_t *__restrict__ other_count, int64_t *__restrict__ max_value,
int64_t *__restrict__ sum_value, uint32_t *__restrict__ valid_count, size_t npixels) {
for (size_t i = blockIdx.x * static_cast<size_t>(blockDim.x) + threadIdx.x; i < npixels;
i += static_cast<size_t>(blockDim.x) * gridDim.x) {
if (other_count[i] == 0)
continue;
if (valid_count[i] == 0 || other_max[i] > max_value[i])
max_value[i] = other_max[i];
sum_value[i] += other_sum[i];
valid_count[i] += other_count[i];
}
}
template <class T>
void launch(const uint8_t *raw, int nframes, size_t frame_bytes, int64_t *max_value,
int64_t *sum_value, uint32_t *valid_count, size_t npixels, int blocks,
cudaStream_t stream) {
T masked;
if constexpr (std::is_signed_v<T>)
masked = std::numeric_limits<T>::min();
else
masked = std::numeric_limits<T>::max();
accumulate_kernel<T><<<blocks, 256, 0, stream>>>(reinterpret_cast<const T *>(raw), nframes,
frame_bytes / sizeof(T), max_value, sum_value,
valid_count, npixels, masked);
cuda_err(cudaGetLastError());
}
} // namespace
ShadowAccumulatorGPU::ShadowAccumulatorGPU(size_t npixels)
: npixels(npixels),
stream(std::make_shared<CudaStream>()),
gpu_max(npixels),
gpu_sum(npixels),
gpu_count(npixels) {
cuda_err(cudaMemsetAsync(gpu_max, 0, sizeof(int64_t) * npixels, *stream));
cuda_err(cudaMemsetAsync(gpu_sum, 0, sizeof(int64_t) * npixels, *stream));
cuda_err(cudaMemsetAsync(gpu_count, 0, sizeof(uint32_t) * npixels, *stream));
cuda_err(cudaGetDevice(&device));
cudaDeviceProp prop{};
cuda_err(cudaGetDeviceProperties(&prop, device));
blocks = 8 * prop.multiProcessorCount;
// Size the batch for the widest pixel type there is, so nothing has to be allocated once frames
// start arriving - a cudaMalloc then would stall every worker behind it.
raw_capacity = npixels * sizeof(uint32_t) * BATCH;
raw = CudaDevicePtr<uint8_t>(raw_capacity);
cuda_err(cudaStreamSynchronize(*stream));
}
bool ShadowAccumulatorGPU::Supports(const CompressedImage &image) {
if (!BSLZ4DecoderGPU::Supports(image))
return false;
switch (image.GetMode()) {
case CompressedImageMode::Int8:
case CompressedImageMode::Uint8:
case CompressedImageMode::Int16:
case CompressedImageMode::Uint16:
case CompressedImageMode::Int32:
case CompressedImageMode::Uint32:
return true;
default:
return false;
}
}
void ShadowAccumulatorGPU::EnsureRawCapacity(size_t bytes_per_frame) {
if (bytes_per_frame * BATCH > raw_capacity) {
// The constructor already sized this for the widest pixel type, so in practice this only
// runs if that guess was too small. cudaMalloc and cudaFree both synchronise the whole
// device, which is why it is never done per frame.
FoldPending();
cuda_err(cudaStreamSynchronize(*stream));
raw_capacity = bytes_per_frame * BATCH;
raw = CudaDevicePtr<uint8_t>(raw_capacity);
}
// Only once the pending batch has been folded: FoldPending strides the buffer by frame_bytes,
// so it has to keep describing the frames already in it until they are gone.
frame_bytes = bytes_per_frame;
}
// Fold the frames decoded so far into the projection. One pass over the accumulator for the whole
// batch rather than one per frame.
void ShadowAccumulatorGPU::FoldPending() {
if (pending == 0)
return;
switch (pending_mode) {
case CompressedImageMode::Int8:
launch<int8_t>(raw, pending, frame_bytes, gpu_max, gpu_sum, gpu_count, npixels, blocks, *stream); break;
case CompressedImageMode::Uint8:
launch<uint8_t>(raw, pending, frame_bytes, gpu_max, gpu_sum, gpu_count, npixels, blocks, *stream); break;
case CompressedImageMode::Int16:
launch<int16_t>(raw, pending, frame_bytes, gpu_max, gpu_sum, gpu_count, npixels, blocks, *stream); break;
case CompressedImageMode::Uint16:
launch<uint16_t>(raw, pending, frame_bytes, gpu_max, gpu_sum, gpu_count, npixels, blocks, *stream); break;
case CompressedImageMode::Int32:
launch<int32_t>(raw, pending, frame_bytes, gpu_max, gpu_sum, gpu_count, npixels, blocks, *stream); break;
case CompressedImageMode::Uint32:
launch<uint32_t>(raw, pending, frame_bytes, gpu_max, gpu_sum, gpu_count, npixels, blocks, *stream); break;
default:
throw JFJochException(JFJochExceptionCategory::InputParameterInvalid,
"ShadowAccumulatorGPU: unsupported image mode");
}
pending = 0;
}
void ShadowAccumulatorGPU::Add(const CompressedImage &image) {
if (!Supports(image))
throw JFJochException(JFJochExceptionCategory::InputParameterInvalid,
"ShadowAccumulatorGPU: image cannot be decoded on the device");
if (static_cast<size_t>(image.GetWidth()) * image.GetHeight() != npixels)
throw JFJochException(JFJochExceptionCategory::InputParameterInvalid,
"ShadowAccumulatorGPU: image size does not match the detector");
// A batch holds one pixel type and one frame size; a change of either closes the batch first,
// while frame_bytes and pending_mode still describe the frames already in it.
if (pending > 0 && (image.GetMode() != pending_mode
|| image.GetUncompressedSize() != frame_bytes))
FoldPending();
if (!decoder || image.GetUncompressedSize() != frame_bytes)
decoder = std::make_unique<BSLZ4DecoderGPU>(image.GetUncompressedSize(), stream);
EnsureRawCapacity(image.GetUncompressedSize());
pending_mode = image.GetMode();
decoder->Decode(image, raw.get() + static_cast<size_t>(pending) * frame_bytes);
// The decode has to be known good before its frame is counted, and the flag only arrives once
// the stream has drained.
cuda_err(cudaStreamSynchronize(*stream));
decoder->ThrowIfDecodeFailed();
pending++;
frames++;
if (pending == BATCH)
FoldPending();
}
void ShadowAccumulatorGPU::Fold(ShadowAccumulatorGPU &other) {
{
// The other card's last batch is folded on its own stream, with its card current.
ScopedGpuPin pin(other.device);
other.FoldPending();
cuda_err(cudaStreamSynchronize(*other.stream));
}
FoldPending();
CudaDevicePtr<int64_t> other_max(npixels), other_sum(npixels);
CudaDevicePtr<uint32_t> other_count(npixels);
cuda_err(cudaMemcpyPeerAsync(other_max, device, other.gpu_max, other.device, sizeof(int64_t) * npixels, *stream));
cuda_err(cudaMemcpyPeerAsync(other_sum, device, other.gpu_sum, other.device, sizeof(int64_t) * npixels, *stream));
cuda_err(cudaMemcpyPeerAsync(other_count, device, other.gpu_count, other.device, sizeof(uint32_t) * npixels,
*stream));
fold_kernel<<<blocks, 256, 0, *stream>>>(other_max, other_sum, other_count, gpu_max, gpu_sum, gpu_count, npixels);
cuda_err(cudaGetLastError());
// The temporaries are pooled: they go once the stream has used them (see CudaDevicePtr).
cuda_err(cudaStreamSynchronize(*stream));
frames += other.frames;
}
void ShadowAccumulatorGPU::Download(std::vector<int64_t> &max_value, std::vector<int64_t> &sum_value,
std::vector<uint32_t> &valid_count) {
FoldPending();
max_value.resize(npixels);
sum_value.resize(npixels);
valid_count.resize(npixels);
cuda_err(cudaMemcpyAsync(max_value.data(), gpu_max.get(), sizeof(int64_t) * npixels,
cudaMemcpyDeviceToHost, *stream));
cuda_err(cudaMemcpyAsync(sum_value.data(), gpu_sum.get(), sizeof(int64_t) * npixels,
cudaMemcpyDeviceToHost, *stream));
cuda_err(cudaMemcpyAsync(valid_count.data(), gpu_count.get(), sizeof(uint32_t) * npixels,
cudaMemcpyDeviceToHost, *stream));
cuda_err(cudaStreamSynchronize(*stream));
}
std::vector<uint32_t> ShadowAccumulatorGPU::Mask(const ShadowMaskSetup &setup, const std::vector<uint32_t> &pixel_mask) {
FoldPending();
return ShadowMaskOnDevice(setup, pixel_mask, gpu_max, gpu_sum, gpu_count, frames, *stream);
}
std::vector<float> ShadowAccumulatorGPU::MeanProjection(const std::vector<uint32_t> &pixel_mask) {
FoldPending();
return MeanProjectionOnDevice(pixel_mask, gpu_sum, gpu_count, npixels, *stream);
}