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* 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>
155 lines
5.5 KiB
C++
155 lines
5.5 KiB
C++
// SPDX-FileCopyrightText: 2024 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
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// SPDX-License-Identifier: GPL-3.0-only
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#include "HDF5FilePusher.h"
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#include "../frame_serialize/CBORStream2Deserializer.h"
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#include "../frame_serialize/CBORStream2Serializer.h"
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HDF5FilePusher::HDF5FilePusher(const std::string &repub_address,
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const std::optional<int32_t> &repub_watermark) {
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if (!repub_address.empty()) {
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repub_socket = std::make_unique<ZMQSocket>(ZMQSocketType::Push);
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repub_socket->SendWaterMark(repub_watermark.value_or(default_repub_watermark));
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repub_socket->SendTimeout(RepubTimeout);
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repub_socket->Bind(repub_address);
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}
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}
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void HDF5FilePusher::Preflight(StartMessage &message) {
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// In-process writer, so the check is the same call the FileWriter constructor will make.
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FileWriter::Preflight(message);
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}
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void HDF5FilePusher::StartDataCollection(StartMessage &message) {
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if (writer)
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throw JFJochException(JFJochExceptionCategory::WrongDAQState, "Image pusher is already writing images");
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writer = std::make_unique<FileWriter>(message);
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writer->FileClosedCallback([this](const HDF5DataFileStatistics &s) {
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live.FileClosed(s.file_number - 1, s.max_image_number + 1); // the statistics count files from 1
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});
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writer_future = std::async(std::launch::async, &HDF5FilePusher::WriterThread, this);
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images_written = 0;
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{
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serializer.SerializeSequenceStart(message);
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live.Begin(message, std::vector<uint8_t>(serialization_buffer.begin(),
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serialization_buffer.begin() + serializer.GetBufferSize()));
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}
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if (repub_socket) {
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try {
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StartMessage repub_message = message;
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repub_message.writer_notification_zmq_addr = "";
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serializer.SerializeSequenceStart(repub_message);
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repub_active = repub_socket->Send(serialization_buffer.data(), serializer.GetBufferSize(), true);
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if (repub_active)
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logger.Info("Republish active");
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} catch (const JFJochException &e) {
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logger.ErrorException(e);
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}
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}
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}
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bool HDF5FilePusher::EndDataCollection(const EndMessage &message) {
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if (!writer_future.valid())
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throw JFJochException(JFJochExceptionCategory::WrongDAQState, "Image pusher wasn't writing files");
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writer_queue.PutBlocking({.end = true});
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// Release the writer on every exit path. If finalization throws (e.g. a target
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// file already exists and overwrite is off) the writer must still be torn down,
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// otherwise the next collection fails with "already writing images".
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try {
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writer_future.get();
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if (!writer)
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throw JFJochException(JFJochExceptionCategory::WrongDAQState, "Image pusher not ready for writing images");
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writer->WriteHDF5(message);
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writer->Finalize();
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} catch (...) {
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writer.reset();
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live.End(message.max_image_number, "the writer failed to finish the collection");
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throw;
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}
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writer.reset();
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live.End(message.max_image_number);
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if (repub_socket) {
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try {
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serializer.SerializeSequenceEnd(message);
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if (repub_active)
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repub_socket->Send(serialization_buffer.data(), serializer.GetBufferSize(), true);
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} catch (const JFJochException &e) {
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logger.ErrorException(e);
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}
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if (repub_active)
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logger.Info("Republish finished");
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repub_active = false;
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}
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return true;
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}
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bool HDF5FilePusher::SendImage(const uint8_t *image_data, size_t image_size, int64_t image_number) {
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if (!writer)
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throw JFJochException(JFJochExceptionCategory::WrongDAQState, "Image pusher not ready for sending");
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auto deserialized = CBORStream2Deserialize(image_data, image_size);
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if (deserialized->data_message) {
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writer->Write(*deserialized->data_message);
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images_written++;
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if (repub_socket && repub_active) {
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try {
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repub_socket->Send(image_data, image_size, false);
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} catch (const JFJochException &e) {
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logger.ErrorException(e);
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}
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}
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} else
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throw JFJochException(JFJochExceptionCategory::InputParameterInvalid,
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"HDF5FilePusher::SendImage accepts only data image");
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return true;
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}
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bool HDF5FilePusher::SendImage(ZeroCopyReturnValue &z) {
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writer_queue.PutBlocking(ImagePusherQueueElement{
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.image_data = (uint8_t *) z.GetImage(),
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.z = &z,
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.end = false
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});
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return true;
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}
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bool HDF5FilePusher::SendCalibration(const CompressedImage &message) {
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if (!writer)
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throw JFJochException(JFJochExceptionCategory::WrongDAQState, "Image pusher not ready for sending");
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writer->WriteHDF5(message);
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return true;
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}
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void HDF5FilePusher::WriterThread() {
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ImagePusherQueueElement e = writer_queue.GetBlocking();
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while (!e.end) {
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SendImage(e.image_data, e.z->GetImageSize(), e.z->GetImageNumber());
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e.z->release();
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e = writer_queue.GetBlocking();
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}
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}
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std::string HDF5FilePusher::PrintSetup() const {
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std::filesystem::path currentPath = std::filesystem::current_path();
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return "HDF5FilePusher: Images are written directly to file in base directory " + currentPath.string();
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}
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std::optional<uint64_t> HDF5FilePusher::GetImagesWritten() const {
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return images_written;
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}
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size_t HDF5FilePusher::GetConnectedWriters() const {
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return 1;
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} |