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* Rugnux: Processes serial crystallography data from XFELs - SACLA (MPCCD), PAL-XFEL and European XFEL (CXI), LCLS (XTC) and SwissFEL Alvra (JUNGFRAU with a CrystFEL module geometry) - with several files or Jungfraujoch master files merged in one run (`rugnux *_master.h5`). * Rugnux: Stills processing takes a known unit cell and space group as a starting point, finds the beam centre (and, with a cell, the detector distance) from the images, detects the saturation level in other facilities' files and refines the placement of individual detector panels. * Rugnux: The stills report gives R_split and CC1/2 from frame half-sets, comparable with CrystFEL. * jfjoch_viewer: Opens the same XFEL file formats. * Validation: A stills battery checks Rugnux against deposited structures from SACLA, PAL-XFEL, LCLS, European XFEL and SwissFEL. * Rugnux: More reliable convergence of rotation scaling, and live molecular replacement starts as soon as the model is uploaded. * jfjoch_broker: Initialize clears the previous dataset's bearer tokens, image buffer and live Rugnux status, and a slow CUDA JIT cache is reported at start. Reviewed-on: #88 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>
177 lines
7.1 KiB
C++
177 lines
7.1 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 "ZMQImagePuller.h"
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#include "../frame_serialize/CBORStream2Serializer.h"
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#include <cstring>
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ZMQImagePuller::ZMQImagePuller(const std::string &in_addr,
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const std::string &repub_address,
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const std::optional<int32_t> &rcv_watermark,
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const std::optional<int32_t> &repub_watermark,
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const std::optional<size_t> &ring_size) :
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ImagePuller(DefaultQueueSize, ring_size.value_or(0)),
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socket (ZMQSocketType::Pull), addr(in_addr) {
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auto start_time = std::chrono::steady_clock::now();
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puller_thread = std::thread(&ZMQImagePuller::PullerThread, this);
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cbor_thread = std::thread(&ZMQImagePuller::CBORThread, this);
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socket.ReceiveWaterMark(rcv_watermark.value_or(default_receive_watermark));
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socket.ReceiveTimeout(ReceiveTimeout);
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socket.Connect(addr);
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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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repub_thread = std::thread(&ZMQImagePuller::RepubThread, this);
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}
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auto end_time = std::chrono::steady_clock::now();
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auto duration = std::chrono::duration<float>(end_time - start_time);
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logger.Info("ZMQImagePuller connected to {} in {:.3f} s", addr, duration.count());
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}
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ZMQImagePuller::~ZMQImagePuller() {
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ZMQImagePuller::Disconnect();
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}
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void ZMQImagePuller::Disconnect() {
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disconnect = 1;
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// The threads below hand messages on through bounded blocking queues, and by the time a puller
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// is disconnected nothing drains outside_fifo any more - the receiver that did is gone. A full
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// queue would then park CBORThread in PutBlocking for ever, back up cbor_fifo and park
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// PullerThread too, and the joins below would never return. Stop() releases them.
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cbor_fifo.Stop();
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repub_fifo.Stop();
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outside_fifo.Stop();
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// And PullerThread may be waiting for ring space that the stopped consumers will never free.
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ring.Stop();
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if (puller_thread.joinable())
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puller_thread.join();
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if (cbor_thread.joinable())
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cbor_thread.join();
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if (repub_thread.joinable())
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repub_thread.join();
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if (!addr.empty())
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socket.Disconnect(addr);
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addr = "";
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}
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void ZMQImagePuller::PullerThread() {
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while (true) {
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auto msg = std::make_shared<ZMQMessage>();
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bool received = false;
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while (!received) {
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if (disconnect) {
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cbor_fifo.PutBlocking(ImagePullerOutput{});
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return;
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}
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try {
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received = socket.Receive(*msg, false);
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if (!received)
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std::this_thread::sleep_for(std::chrono::milliseconds(1));
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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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ImagePullerOutput ret;
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ret.received = std::chrono::steady_clock::now();
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if (ring.GetCapacity() == 0) {
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// No ring: the ZeroMQ message itself is the buffer, kept alive by the region. No copy.
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ret.raw = std::shared_ptr<ReceiveBufferRegion>(new ReceiveBufferRegion{const_cast<uint8_t *>(msg->data()), msg->size()},
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[msg](ReceiveBufferRegion *r) { delete r; });
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} else {
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// Copied into the ring, and the ZeroMQ message is released with the next receive. When the
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// ring is full this waits and the socket is not read: its queue fills to the watermark and
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// the sender's send blocks - for as long as the sender is prepared to wait. The broker's
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// ZeroMQ pusher waits one second, then drops the image and sends without waiting for the
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// rest of the run, so a ring that is too small for the writer's stalls costs images.
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ret.raw = ring.Allocate(msg->size());
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if (!ret.raw) {
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// Stop() - the puller is being disconnected.
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cbor_fifo.PutBlocking(ImagePullerOutput{});
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return;
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}
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if (msg->size() > 0)
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memcpy(ret.raw->data, msg->data(), msg->size());
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}
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cbor_fifo.PutBlocking(ret);
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}
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}
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void ZMQImagePuller::CBORThread() {
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auto ret = cbor_fifo.GetBlocking();
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while (ret.raw) {
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try {
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ret.cbor = CBORStream2Deserialize(ret.raw->data, ret.raw->size);
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// Even if we suspend consuming of the messages by the receiver,
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// it is still reasonable to have them republished
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// so republish functionality is not affected by Suspend()
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if (!suspend)
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outside_fifo.PutBlocking(ret);
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if (repub_socket) {
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if ((ret.cbor->msg_type == CBORImageType::START)
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|| (ret.cbor->msg_type == CBORImageType::END))
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repub_fifo.PutBlocking(ret);
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else if (RepubCanHold(ret.raw->size) && repub_fifo.Put(ret))
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repub_bytes += ret.raw->size;
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}
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} catch (const std::exception &e) {
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// std::exception: the deserialiser allocates a vector per per-image array of an END message,
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// and a bad_alloc leaving this thread would end the process.
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logger.ErrorException(e);
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}
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ret = cbor_fifo.GetBlocking();
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}
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if (repub_socket)
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repub_fifo.PutBlocking(ret);
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outside_fifo.PutBlocking(ret);
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}
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void ZMQImagePuller::RepubThread() {
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auto ret = repub_fifo.GetBlocking();
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bool repub_active = false;
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while (ret.raw) {
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try {
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if (ret.cbor->msg_type == CBORImageType::START) {
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// Start message needs to be cleaned when running republish
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StartMessage msg = ret.cbor->start_message.value();
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msg.writer_notification_zmq_addr = "";
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std::vector<uint8_t> serialization_buffer(256*1024*1024);
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CBORStream2Serializer serializer(serialization_buffer.data(), serialization_buffer.size());
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serializer.SerializeSequenceStart(msg);
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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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} else {
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if (repub_active)
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repub_socket->Send(ret.raw->data, ret.raw->size, true);
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}
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} catch (const std::exception &e) {
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logger.ErrorException(e);
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}
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if (ret.cbor && (ret.cbor->msg_type != CBORImageType::START) && (ret.cbor->msg_type != CBORImageType::END))
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repub_bytes -= ret.raw->size;
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ret = repub_fifo.GetBlocking();
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}
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if (repub_active)
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logger.Info("Republish finished");
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}
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void ZMQImagePuller::Suspend() {
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suspend = true;
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}
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void ZMQImagePuller::ResumeAndClear() {
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outside_fifo.Clear();
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outside_fifo.ClearMaxUtilization();
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suspend = false;
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} |