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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>
123 lines
5.3 KiB
C++
123 lines
5.3 KiB
C++
// SPDX-FileCopyrightText: 2025 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
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// SPDX-License-Identifier: GPL-3.0-only
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#pragma once
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#include <thread>
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#include <mutex>
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#include <condition_variable>
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#include <queue>
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#include <functional>
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#include <future>
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#include <vector>
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#include <optional>
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#include <memory>
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#include <latch>
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#include "../common/JFJochMessages.h"
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#include "../common/DiffractionSpot.h"
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#include "../common/DiffractionExperiment.h"
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#include "Indexer.h"
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// When a worker builds its indexers.
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//
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// Preconstruct (the default, and what the online service needs): every indexer the requested
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// algorithm could resolve to is built while the pool is being constructed, so it is resident and
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// planned before the first frame arrives. Building one means a cuFFT plan plus ~0.6 GB of device
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// allocation, and the first cuFFT call in a process also pays the library's one-time init (0.3 s
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// measured); jfjoch_broker cannot have any of that land on the live data path, so holding an indexer
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// the resolved algorithm may never dispatch to is an accepted cost there.
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//
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// OnFirstUse (offline batch - rugnux, jfjoch_viewer): nothing is latency-critical, so the indexer is
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// built on the first frame that needs it. The algorithm is only resolved from the frame's
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// DiffractionExperiment (rotation -> FFT, stills with a known cell -> FFBIDX), so preconstructing
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// leaves each worker holding a fully allocated FFTIndexerGPU - 0.6 GB of cuFFT plan and histograms -
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// that can never be dispatched to.
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enum class IndexerConstruction { Preconstruct, OnFirstUse };
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// Force cuFFT's one-time library initialisation - 0.3 s measured, paid by whichever call happens to
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// be first - so it can be got out of the way on a background thread at startup rather than landing in
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// the middle of the first pass with nothing overlapping it. No-op without a GPU.
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void WarmUpCuFFT();
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// cuFFT plans are kept and reused for as long as one of these lives, and destroyed when the last one
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// ends (CudaFFTPlanScope): one per processing run, so no plan outlives the run that made it. Nothing
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// without CUDA.
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class CudaFFTPlanScope;
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class FFTPlanReuse {
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std::unique_ptr<CudaFFTPlanScope> scope;
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public:
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FFTPlanReuse();
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~FFTPlanReuse();
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FFTPlanReuse(const FFTPlanReuse &) = delete;
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FFTPlanReuse &operator=(const FFTPlanReuse &) = delete;
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};
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class IndexerThread {
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struct TaskInput {
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const DiffractionExperiment &experiment;
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const std::vector<Coord> &recip;
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const bool severity_only;
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};
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// Held by value: with IndexerConstruction::OnFirstUse the worker builds its indexer long after
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// the constructor returned, and pools are routinely built from a temporary - for instance
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// IndexerThreadPool(experiment.GetIndexingSettings()), which returns by value.
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const IndexingSettings settings_;
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const IndexerConstruction construction_;
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const bool beside_;
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bool stop = false;
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bool drop_indexers = false; // see Release()
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enum class TaskState {STARTING, IDLE, READY, RUNNING, COMPLETED, ERROR} state = TaskState::STARTING;
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std::mutex m;
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std::condition_variable c_running;
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std::condition_variable c_start;
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std::condition_variable c_done;
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std::unique_ptr<IndexerResult> result = nullptr;
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std::unique_ptr<TaskInput> task_input = nullptr;
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std::thread worker_thread;
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void Worker(int threadid);
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public:
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IndexerThread(const IndexingSettings& settings, int threadid, IndexerConstruction construction, bool beside);
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~IndexerThread();
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std::unique_ptr<IndexerResult> Run(const DiffractionExperiment &experiment, const std::vector<Coord> &recip,
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bool severity_only = false);
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// The thread drops the indexers it has built - once the frame it is on, if any, is done - and builds
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// them again on the next frame that needs one. Returns when they are gone.
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void Release();
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void Finalize();
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};
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class IndexerThreadPool {
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std::mutex m;
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std::condition_variable c;
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std::vector<uint8_t> worker_busy;
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size_t worker_free_count;
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std::vector<std::unique_ptr<IndexerThread>> tasks;
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const int64_t viable_cell_min_spots;
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const bool blocking;
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const IndexingSettings settings_;
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int GetFreeWorker();
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public:
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// beside: the pool serves a probe pass that holds GPUWorkBeside, so an FFT indexer that does not fit
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// the card waits for the main line's image pass to end, not for the probes - it is one of them (see
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// MakeFFTIndexerGPU).
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IndexerThreadPool(const IndexingSettings& settings,
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IndexerConstruction construction = IndexerConstruction::Preconstruct,
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bool beside = false);
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// The settings the pool's indexers were built with.
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[[nodiscard]] const IndexingSettings &Settings() const { return settings_; }
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// severity_only skips indexing and produces just the spindle severity - see Indexer::Run.
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IndexerResult Run(const DiffractionExperiment& experiment, const std::vector<Coord>& recip,
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bool severity_only = false);
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// Give back to the card the device memory of the indexers built so far - an FFT indexer holds
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// 0.6-1.2 GB of it - for a stretch with nothing to index. A frame that comes after all builds its
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// indexer again, as on first use, and the indexer it gets computes what the dropped one would.
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void ReleaseIndexers();
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};
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