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Jungfraujoch/writer/StreamWriter.cpp
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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

433 lines
18 KiB
C++

// SPDX-FileCopyrightText: 2024 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
// SPDX-License-Identifier: GPL-3.0-only
#include "../common/JFJochException.h"
#include "StreamWriter.h"
#include <utility>
#include "FileWriter.h"
StreamWriter::StreamWriter(Logger &in_logger,
ImagePuller &in_image_puller,
std::string in_file_done_address,
bool in_verbose)
: verbose(in_verbose),
image_puller(in_image_puller),
logger(in_logger),
file_done_address(std::move(in_file_done_address)),
socket_number(0),
run_number(0),
max_image_number(0) {
}
void StreamWriter::NotifyTcpAck(TCPFrameType ack_for, bool ok, bool fatal, TCPAckCode code, const std::string &error_text) {
if (!image_puller.SupportsAck())
return;
PullerAckMessage ack;
ack.ack_for = ack_for;
ack.ok = ok;
ack.fatal = fatal;
ack.error_code = code;
ack.error_text = error_text;
ack.run_number = run_number;
ack.socket_number = static_cast<uint32_t>(socket_number);
ack.processed_images = processed_images.load();
if (image_puller_output.cbor && image_puller_output.cbor->data_message)
ack.image_number = image_puller_output.cbor->data_message->number;
if (!image_puller.SendAck(ack))
logger.Warning("Failed to send TCP ACK");
}
void StreamWriter::ProcessStartMessage() {
if (state == StreamWriterState::Finalized)
return; // Should not happen (?)
if (state != StreamWriterState::Idle)
FinalizeDataCollection();
err = "";
tcp_data_fatal_sent = false;
max_image_number = 0;
processed_images = 0;
processed_image_size = 0;
file_prefix = image_puller_output.cbor->start_message->file_prefix;
run_number = image_puller_output.cbor->start_message->run_number;
run_name = image_puller_output.cbor->start_message->run_name;
socket_number = 0;
if (image_puller_output.cbor->start_message->socket_number)
socket_number = image_puller_output.cbor->start_message->socket_number.value();
writer_notification_zmq_addr = image_puller_output.cbor->start_message->writer_notification_zmq_addr;
try {
// Fail fast on an overwrite conflict only when the transport can report it
// back to the broker (TCP ACK). The ZeroMQ path has no back-channel, so it
// keeps writing .tmp files and fails at the final rename instead.
file_writer = std::make_unique<FileWriter>(*image_puller_output.cbor->start_message,
image_puller.SupportsAck());
if (!file_done_address.empty())
file_writer->SetupFinalizedFileSocket(file_done_address);
if (image_puller.SupportsAck())
file_writer->FileClosedCallback([this](const HDF5DataFileStatistics &s) {
PullerAckMessage ack;
ack.ack_for = TCPFrameType::FILE_CLOSED;
ack.run_number = run_number;
ack.socket_number = static_cast<uint32_t>(socket_number);
ack.image_number = s.file_number - 1; // HDF5DataFileStatistics counts from 1
ack.processed_images = s.max_image_number + 1;
if (!image_puller.SendAck(ack))
logger.Warning("Failed to send TCP FILE_CLOSED");
});
logger.Info("Starting writing for dataset {} of {} images",
image_puller_output.cbor->start_message->file_prefix,
image_puller_output.cbor->start_message->number_of_images);
state = StreamWriterState::Started;
NotifyTcpAck(TCPFrameType::START, true, false, TCPAckCode::None);
} catch (const std::exception &e) {
// std::exception, not JFJochException: everything below this point - the error state, err,
// and above all the fatal ACK - is skipped if the exception escapes, and the broker is
// blocked on that ACK with the detector about to be armed. It would read the silence as a
// dead writer and report a timeout in place of the reason. Not every thrower here is ours:
// std::filesystem::exists throws filesystem_error when the output path cannot be walked,
// and SetupFinalizedFileSocket throws ZeroMQ's own type.
logger.ErrorException(e);
logger.Error("Error writing start message - switching to error state");
state = StreamWriterState::Error;
err = e.what();
NotifyTcpAck(TCPFrameType::START, false, true, TCPAckCode::StartFailed, err);
}
}
// Dry run for a run that has not started: check that the output could be written and answer,
// without opening anything and without touching state - the writer stays Idle and ready for the
// START that follows.
void StreamWriter::ProcessPreflight() {
const StartMessage &msg = image_puller_output.cbor->start_message.value();
// The pusher's ACK reader discards frames whose run_number does not match the run it is about
// to start, so the ACK has to carry the run number of the message being checked - it is not yet
// the one ProcessStartMessage will store.
run_number = msg.run_number;
socket_number = msg.socket_number.value_or(0);
// std::exception, not JFJochException: the answer matters more than the diagnosis. The pusher is
// blocked on this ACK and reads its absence as a dead writer, so anything that escapes here costs
// the caller the real reason and hands it a five-second timeout instead. std::filesystem::exists
// is the concrete leak - it throws filesystem_error, not JFJochException, when the output path
// cannot be walked at all (a directory component with no search permission, a symlink loop),
// which is exactly the kind of misconfiguration the pre-flight exists to report before arming.
try {
FileWriter::Preflight(msg);
NotifyTcpAck(TCPFrameType::PREFLIGHT, true, false, TCPAckCode::None);
} catch (const std::exception &e) {
logger.Warning("Pre-flight check failed: {}", e.what());
// Not fatal: nothing was started, so the connection stays usable for the next attempt.
NotifyTcpAck(TCPFrameType::PREFLIGHT, false, false, TCPAckCode::StartFailed, e.what());
}
}
void StreamWriter::ProcessCalibrationImage() {
switch (state) {
case StreamWriterState::Started:
try {
file_writer->WriteHDF5(*image_puller_output.cbor->calibration);
} catch (const std::exception &e) {
logger.Warning(e.what());
logger.Warning("Error during writing calibration data - skipping");
NotifyTcpAck(TCPFrameType::CALIBRATION, false, false, TCPAckCode::DataWriteFailed, e.what());
}
break;
case StreamWriterState::Receiving:
logger.Warning("Unexpected calibration message");
break;
case StreamWriterState::Error:
case StreamWriterState::Idle:
case StreamWriterState::Finalized:
break;
}
}
void StreamWriter::ProcessDataImage() {
switch (state) {
case StreamWriterState::Idle:
logger.Warning("Missing meaningful image while waiting for START");
mute_data_msg_in_idle = true;
break;
case StreamWriterState::Started:
start_time = std::chrono::system_clock::now();
state = StreamWriterState::Receiving;
// Follow through to receiving - no brake!
case StreamWriterState::Receiving:
try {
if (verbose)
logger.Info("Received data message {}",
image_puller_output.cbor->data_message->number);
file_writer->Write(*image_puller_output.cbor->data_message);
if (max_image_number < image_puller_output.cbor->data_message->number + 1)
max_image_number = image_puller_output.cbor->data_message->number + 1;
processed_images++;
processed_image_size += image_puller_output.cbor->data_message->image.GetCompressedSize();
if (verbose)
logger.Info("Written");
NotifyTcpAck(TCPFrameType::DATA, true, false, TCPAckCode::None);
} catch (const std::exception &e) {
// std::exception, not JFJochException, for the reason given in ProcessStartMessage: an
// exception that leaves this function skips the error state and the fatal ACK, and the
// broker then waits for an END ACK that never comes. Not every thrower below is ours -
// std::bad_alloc from a per-image array, filesystem_error from a path check, the JSON
// library when a file-done notification carries a string that is not UTF-8.
logger.ErrorException(e);
logger.Warning("Error writing image - switching to error state");
state = StreamWriterState::Error;
err = e.what();
NotifyTcpAck(TCPFrameType::DATA, false, true, TCPAckCode::DataWriteFailed, err);
}
break;
case StreamWriterState::Error:
// Error state => Wait till end only
case StreamWriterState::Finalized:
break;
}
}
void StreamWriter::ProcessEndMessage() {
// Ignore end message when idle state!
if (state == StreamWriterState::Idle || state == StreamWriterState::Finalized)
return;
if (verbose)
logger.Info("Received end message");
if (state != StreamWriterState::Error) {
try {
if ((image_puller_output.cbor->end_message->max_image_number == 0) && (max_image_number > 0))
image_puller_output.cbor->end_message->max_image_number = max_image_number;
file_writer->WriteHDF5(*image_puller_output.cbor->end_message);
} catch (const std::exception &e) {
// std::exception for the same reason as in ProcessDataImage. Here the cost of a leak is the
// highest: the END ACK and the notification below are never sent, the state never reaches
// Finalized, and on TCP the broker waits for the ACK for as long as the writer keeps
// heartbeating - which it does, whatever state it is in.
logger.ErrorException(e);
logger.Error("Error writing end message - switching to error state");
state = StreamWriterState::Error;
err = e.what();
}
}
FinalizeDataCollection();
const bool error_state = (state == StreamWriterState::Error);
NotifyReceiverOnFinalizedWrite(writer_notification_zmq_addr);
NotifyTcpAck(TCPFrameType::END, !error_state, error_state,
error_state ? TCPAckCode::EndFailed : TCPAckCode::None,
error_state ? err : "");
// To exit main image loop in CollectImages(), state must be finalized
state = StreamWriterState::Finalized;
}
void StreamWriter::FinalizeDataCollection() {
end_time = std::chrono::system_clock::now();
bool finalize_error = false;
if (file_writer && (state != StreamWriterState::Error)) {
try {
hdf5_data_file_statistics = file_writer->Finalize();
} catch (const JFJochException &e) {
finalize_error = true;
state = StreamWriterState::Error;
err = e.what();
logger.ErrorException(e);
logger.Error("Error finalizing writing - switching to error state");
} catch (const std::exception &e) {
finalize_error = true;
state = StreamWriterState::Error;
err = e.what();
logger.Error("Error finalizing writing - switching to error state: {}", e.what());
}
} else {
hdf5_data_file_statistics.clear();
}
file_writer.reset();
logger.Info("Data writing finished");
if (!finalize_error && state != StreamWriterState::Error)
state = StreamWriterState::Finalized;
}
void StreamWriter::CollectImages() {
state = StreamWriterState::Idle;
mute_data_msg_in_idle = false;
bool run = true;
while (run && state != StreamWriterState::Finalized) {
run = WaitForImage();
// No new frame: WaitForImage leaves the previous one in image_puller_output, and the body
// below would go on to process it a second time - writing the last image twice, or
// repeating the last check - before the loop condition noticed.
if (!run)
break;
if (image_puller_output.tcp_msg &&
static_cast<TCPFrameType>(image_puller_output.tcp_msg->header.type) == TCPFrameType::CANCEL) {
logger.Warning("Received TCP CANCEL, finalizing data collection");
if (state != StreamWriterState::Idle)
FinalizeDataCollection();
const bool error_state = (state == StreamWriterState::Error);
NotifyTcpAck(TCPFrameType::CANCEL, !error_state, error_state,
error_state ? TCPAckCode::EndFailed : TCPAckCode::None,
error_state ? err : "");
state = StreamWriterState::Finalized;
continue;
}
if (!image_puller_output.cbor) {
logger.Warning("Missing CBOR payload for non-CANCEL TCP frame");
continue;
}
// A PREFLIGHT carries a StartMessage payload, so it has to be told apart by frame type
// before the payload-driven dispatch below would take it for a real START.
if (image_puller_output.tcp_msg &&
static_cast<TCPFrameType>(image_puller_output.tcp_msg->header.type) == TCPFrameType::PREFLIGHT) {
if (image_puller_output.cbor->start_message)
ProcessPreflight();
else
logger.Warning("PREFLIGHT frame without start message");
continue;
}
if (image_puller_output.cbor->start_message)
ProcessStartMessage();
else if (image_puller_output.cbor->calibration)
ProcessCalibrationImage();
else if (image_puller_output.cbor->data_message)
ProcessDataImage();
else if (image_puller_output.cbor->end_message)
ProcessEndMessage();
else
logger.Warning("Unknown message type");
}
}
void StreamWriter::Cancel() {
logger.Info("Cancel requested");
abort = true;
}
StreamWriterOutput StreamWriter::Run() {
hdf5_data_file_statistics.clear();
try {
CollectImages();
} catch (std::exception &e) {
// Error during collecting images will skip to end data collection
// End data collection will consume all images till the end
logger.ErrorException(e);
logger.Error("Exception not properly handled by CollectImages()");
}
StreamWriterOutput ret;
ret.data_file_stats = hdf5_data_file_statistics;
ret.stats = GetStatistics();
logger.Info("Write task done. Images = {} Throughput = {:.0f} MB/s Frame rate = {:.0f} Hz max occupation of FIFO {} ring buffer peak {} MB",
ret.stats.processed_images, ret.stats.performance_MBs, ret.stats.performance_Hz,
ret.stats.max_puller_fifo_utilization, image_puller.GetMaxRingBufferUtilization() >> 20);
return ret;
}
bool StreamWriter::WaitForImage() {
try {
std::optional<ImagePullerOutput> ret;
while (!ret && !abort)
ret = image_puller.PollImage();
if (ret.has_value())
image_puller_output = ret.value();
return ret.has_value();
} catch (const JFJochException &e) {
logger.ErrorException(e);
return false;
}
}
StreamWriterStatistics StreamWriter::GetStatistics() const {
float perf_MBs = 0.0f, perf_Hz = 0.0f;
if ((state != StreamWriterState::Started) && (processed_images > 0)) {
int64_t time_us;
if (state == StreamWriterState::Idle || state == StreamWriterState::Finalized)
time_us = std::chrono::duration_cast<std::chrono::microseconds>(end_time - start_time).count();
else
time_us = std::chrono::duration_cast<std::chrono::microseconds>(std::chrono::system_clock::now() - start_time).count();
// MByte/s ==> Byte/us
perf_MBs = static_cast<float>(processed_image_size) / static_cast<float>(time_us);
perf_Hz = static_cast<float>(processed_images) * 1e6f / static_cast<float>(time_us);
}
return {
.processed_images = processed_images,
.performance_MBs = perf_MBs,
.performance_Hz = perf_Hz,
.file_prefix = file_prefix,
.run_name = run_name,
.run_number = run_number,
.socket_number = socket_number,
.state = state,
.max_puller_fifo_utilization = image_puller.GetMaxFifoUtilization()
};
}
void StreamWriter::NotifyReceiverOnFinalizedWrite(const std::string &detector_update_zmq_addr) {
if (debug_skip_write_notification) {
logger.Info("StreamWriter: Skipping notification");
return;
}
if (detector_update_zmq_addr.empty())
return;
nlohmann::json j;
auto stats = GetStatistics();
j["socket_number"] = socket_number;
j["processed_images"] = processed_images.load();
j["socket_number"] = stats.socket_number;
j["run_number"] = stats.run_number;
j["run_name"] = stats.run_name;
j["performance_MBs"] = stats.performance_MBs;
if (state == StreamWriterState::Error) {
j["ok"] = false;
j["error"] = err;
} else
j["ok"] = true;
try {
logger.Info("Sending notification to {}", detector_update_zmq_addr);
ZMQSocket s(ZMQSocketType::Push);
s.SendTimeout(std::chrono::seconds(1));
s.Connect(detector_update_zmq_addr);
s.Send(j.dump());
} catch (const std::exception &e) {
// std::exception: json::dump throws its own type when run_name is not valid UTF-8.
logger.ErrorException(e);
logger.Error("Error sending notification to detector update socket");
}
}
void StreamWriter::DebugSkipWriteNotification(bool input) {
debug_skip_write_notification = input;
}