Every stage between the socket and the HDF5 write was bounded by a message count and never by
bytes: ZeroMQ receive watermark 100, cbor_fifo 200, outside_fifo 1000, repub_fifo 200 - up to
some 1500 images in flight per writer process, each a whole compressed image, so 6-12 GB for a
JUNGFRAU 4M and 30-60 GB for a 9M, and the writer's memory was a quantity nobody had chosen.
ReceiveRingBuffer is a fixed ring of bytes owned by the ImagePuller base class, so the ZeroMQ
and TCP pullers share it. A message is received straight into it (TCP reads the payload into
the ring; ZeroMQ copies the message in) and travels as a shared_ptr region in ImagePullerOutput;
the deserialised image points into that region, republish sends it as is, and the bytes come
back when the last holder lets go. Space is reclaimed in arrival order: a region released out
of turn - republish finishes with messages in its own order - is marked and waits for the ones
in front of it. Because of that, what republish may hold is capped at a quarter of the ring,
and an image over the cap is not republished, exactly as one that finds the republish queue
full; otherwise a stalled republish consumer would pin the ring and slow the writer to its
rate. A message larger than the whole ring (a START or END of a very long run) goes on the heap,
so it cannot wedge the receiver.
A full ring stalls the receive thread, and what that does depends on the stream. On TCP the
pusher waits behind the writer's BUSY heartbeats and gives up only after a minute in which no
image at all was written. On ZeroMQ the pusher's send blocks for one second, then drops the
image and sends without waiting for the rest of the run - so on ZeroMQ a ring that is smaller
than the writer's stalls costs images, where the old 1500-message queues absorbed them. That
is the trade: the budget is now a number, and it has to be chosen. jfjoch_writer sets it with
-m/--rcv_ring_mb, default 2048 MB per writer process; the ZeroMQ receive watermark default goes
from 100 to 10 messages, since it now only counts what sits beyond the ring. The ring's peak
use is in the end-of-run log line, and docs/JFJOCH_WRITER.md has a Memory section with the
sizing rule.
The puller's own default is no ring at all, which keeps every other user as it was: the
broker's DECTRIS stream2 puller (JFJochServices, JFJochReceiverService) stays zero-copy with
the ZeroMQ message as the buffer, and the broker's direct HDF5 writer (HDF5FilePusher ->
FileWriter) never goes through a puller. The puller threads now also catch std::exception, as
the writer does since the previous commit: deserialising the END message of a million-image
run allocates a vector per per-image array, and a bad_alloc leaving the thread ended the process.
Tests: ReceiveRingBufferTest (reuse, wrap-around, full ring, out-of-order release, heap
fallback, zero size, stop, a region outliving its ring); ZMQImageCommTest_SmallRingBuffer (64
one-megabyte images through a three-image ring, nothing lost, peak within the bound); one of
the two writers in TCPImageCommTest_2Writers_WithAck runs on a three-image ring.
Co-Authored-By: Claude Fable 5.1 <noreply@anthropic.com>
ProcessDataImage, ProcessEndMessage and NotifyReceiverOnFinalizedWrite caught only
JFJochException, while ProcessStartMessage and FinalizeDataCollection already caught
std::exception. Anything else - std::bad_alloc from a per-image array, filesystem_error from
a path check, the JSON library refusing a string that is not UTF-8 while publishing a
file-done notification - left CollectImages, and Run() logged "Exception not properly handled"
and returned with the state never reaching Finalized: no END acknowledgement, no writer
notification, the master's .tmp left behind until the next START. On the TCP image stream the
broker then waited for the END acknowledgement indefinitely, because the writer's heartbeat
thread keeps reporting it alive whatever state it is in.
Now the same catch as at the other sites: error state, fatal ACK, END processed, Finalized.
The new StreamWriter test provokes the JSON case through a sample name that is not UTF-8 with
the file-done socket enabled, and checks the run ends Finalized with no master written.
Co-Authored-By: Claude Fable 5.1 <noreply@anthropic.com>
So that rugnux can process a collection while it is written, the broker reports each data file once
a writer has closed it and renamed it into place:
- Writer: FileWriter takes a callback, called for every closed data file. StreamWriter uses it on TCP
to send an acknowledgement with ack_for = FILE_CLOSED (new TCPFrameType 10): file number and the
images the file holds. TCP protocol version 5. Files closed at END are reported before the END
acknowledgement.
- LiveCollection (image_pusher): the start message the writer of the master file received, the
closed files, the end. Fed by the TCP pusher (FILE_CLOSED acknowledgements; end once every writer
acknowledged END) and by the in-process HDF5 pusher (the FileWriter callback). The ZeroMQ pusher
has no back channel and offers none.
- Two routes, protected by the dataset's bearer tokens like the other dataset routes:
- GET /live/start.cbor: that start message;
- GET /live/events: server-sent events (collection, file, end, superseded) with the history first
and a keepalive every 10 s. One follower at a time; a second gets 409.
Documented in jfjoch_api.yaml; they add no schema, so the generated C++ model is unchanged.
- The HTTP server's thread pool is set explicitly (16, up to 64): an event stream holds a thread for
the whole collection.
Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01SVmAWnzCmRKAXVUCdc4iNi
* `rugnux --model` adopts the model's space group as a label where the data were merged in its enantiomorph, instead of reindexing the reflections - which swapped I(+) with I(-).
* `rugnux --model` warns, naming the atom, when the anomalous density at the model's atoms comes out inverted, which means the data and the model are in opposite hands.
* `rugnux --model` writes an anomalous difference map (`<prefix>_anom.ccp4`) when the merge kept the Bijvoet split, and names the ten model atoms it peaks highest on as `ANOMALOUS_SITE_01`..`_10`.
* `MEAN_ATOM_DENSITY_SIGMA` is read from the map by cubic rather than linear interpolation and comes out around a tenth higher; it is no longer comparable with the figure earlier versions printed.
* `rugnux --model` reads an mmCIF coordinate file as well as a PDB one, gzipped or not, taking the format from the file's content rather than its name.
* A model `rugnux --model` cannot use is reported as a `WARNING:` line in the results report instead of only in the log.
* The rugnux results report has a `10. MODEL VALIDATION` section when `--model` was given; `REPORT_VERSION` is 4, `WARNINGS` moves to section 11 and no existing key changed.
* The rugnux results report records how the run was invoked, what it cost and what it ran on: `COMMAND_LINE=`, `WALL_TIME=` and `GPU_COUNT=` / `GPU=`.
* rugnux says which GPUs it can see before it starts processing.
* `rugnux --export-unmerged` also writes `<prefix>_unmerged.mtz` on a `--no-merge` run, and is ignored on a run with no output prefix instead of writing a file called `_unmerged.mtz`.
* `/start` asks the writer whether the run can be written before the detector is armed, so a run whose master file already exists, or whose output directory cannot be created, is refused up front with the writer's own message. This needs the TCP image stream or the built-in HDF5 writer; the ZeroMQ stream is unchanged.
* A calibration that fails goes to `Error` carrying the reason instead of `Inactive`, so `/wait_till_done` and `/wait_until_running` report it; a cancelled calibration still goes to `Inactive`.
* `/wait_till_done` answers 500 with the message when a collection ended in an error. A cancelled collection and a collection that only triggered a warning still answer 200.
* A pending start failure is discarded by `/cancel` and `/deactivate`, as it already was by `/start` and `/initialize`.
* `/scan_result` no longer reports the previous run's images after a collection that failed to start, or after `/deactivate`.
* The TCP image stream protocol version is 4. `jfjoch_writer` and `jfjoch_broker` have to be of the same release, as before.
Reviewed-on: #75
This is an UNSTABLE release. It includes many experimental features, as well as many AI generated fixes. We recommend using rc.152 for production use.
* rugnux: Rebrand the offline data-processing subsystem as `rugnux` and consolidate all offline analysis into the single `rugnux` binary - `jfjoch_process` is now `rugnux`, the former `jfjoch_azint` is now `rugnux --azint-only`, and `jfjoch_scale` is now `rugnux --scale` (see the new docs/NAMING.md and docs/RUGNUX.md). Scaling and merging are on by default for rotation and stills (`--no-merge` disables them), replacing the previous opt-in `-M, --scale-merge`.
* rugnux: CLI fixes - default `-N` to all hardware threads, parse numeric option arguments strictly (reject non-numeric or trailing input instead of silently yielding 0), require `--wavelength > 0`, and correct the reproduced command line and `--scale` reference-cell handling.
* rugnux: De-novo space-group improvements - recover genuine high symmetry and centred Bravais lattices from intensities, add an automatic CC1/2 high-resolution cutoff, and report L-test twinning statistics.
* rugnux: Index weakly-diffracting low-resolution rotation data that previously failed (e.g. F-cubic crystals that diffract only to ~4 A on a detector reaching ~1.5 A). The per-frame indexing gate now measures the indexed fraction only within the resolution range the lattice actually diffracts to, so the many sub-diffraction ice/noise spots no longer make the fraction floor unreachable; the two-pass first pass tries several image-sampling schemes (spread across the whole rotation vs a consecutive wedge whose native stride keeps a reflection's rocking curve continuous, letting the FFT resolve a long axis) and keeps the one that indexes the most frames; and the de-novo space-group search no longer discards all reflections (and crashes) when every resolution shell falls below <I/sigma> = 1.
* rugnux: Lower the low-resolution R-meas for strongly-diffracting rotation data - drop edge-of-sweep truncated fulls whose rocking curve was captured below `--min-captured-fraction` (default 0.7 for rotation), and report R-meas only over the observations kept by outlier rejection (matching XDS). The 0.7 default also strips the partiality-extrapolated fulls that dominate the intensity second moment on weakly-diffracting crystals, so the de-novo space-group search is no longer starved by the error-model I/sigma floor and recovers the correct symmetry (e.g. the F-cubic Benas crystals: Benas_3 -> F432, Benas_7 -> P6122, instead of P4/P1); on the reference battery every other crystal keeps its space group.
* rugnux: Write the refined geometry (beam, tilt, axis) to _process.h5 and place non-standard mmCIF items under a reserved `jfjoch` prefix.
* jfjoch_broker: Ordinary acquisition failures (receiver/writer/analysis problems, missed packets, writer disconnect) now return to the Idle state with an Error-severity message, so a run can be retried without an expensive re-initialisation; only failures that leave the detector in an undefined state (new JFJochCriticalException, e.g. PCIe/FPGA faults) go to the Error state and force re-initialisation.
* jfjoch_broker: A synchronous /start now reports its failure to the HTTP caller instead of returning HTTP 200, and an incomplete or truncated dataset (missing packets, writer disconnect) is reported as an error rather than a "reduce frame rate" warning.
* jfjoch_broker: Drop uncollected placeholder rows (number = -1) from the scan_result REST endpoint.
* jfjoch_broker: Fix the inverted per-image compression ratio reported by the Lite receiver (was compressed/uncompressed instead of uncompressed/compressed).
* jfjoch_broker: Bragg integration adds a quantization-noise variance floor with a box-sum fallback, and treats the type-maximum marker as an invalid pixel for unsigned image types.
* jfjoch_writer: Detect file-overwrite conflicts at start for back-channel transports, and reset the writer when end-of-collection finalisation fails.
* jfjoch_viewer: Preview overlays follow the geometry (resolution/ROI arcs, true beam centre, predictions, coral secondary-lattice spots, legend), add save-as-JPEG, and fix an HTTP live-follow memory leak.
* Frontend: Improved aesthetics and usability, and added in-browser pixel-mask and JUNGFRAU-pedestal visualisation.
* CI: Name the Windows installer jfjoch-viewer-* instead of jfjoch-*.Reviewed-on: #67
Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>
This is an UNSTABLE release. The release has significant modifications for HDF5 writing logic - in case of troubles go back to 1.0.0-rc.144.
* **Default HDF5 writing mode is with VDS, not soft-links** - this improves DIALS compatibility and makes format more future-proof, NXmx legacy format might be phased-out in the future.
* XDS plugin: Improve performance of VDS reading.
* jfjoch_writer: Significant improvement on how file systems I/O are handled through a dedicated pass-through VFD.
* jfjoch_writer: Clean-up of HDF5 routines to better handle issues.
Reviewed-on: #55
This is an UNSTABLE release. The release has significant modifications and bug fixes, if things go wrong, it is better to revert to 1.0.0-rc.132.
* Multiple small bug fixes scattered across the whole code base. (detected with GPT-5.4)
* jfjoch_viewer: Improve image render performance
Reviewed-on: #44
Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>
Co-committed-by: Filip Leonarski <filip.leonarski@psi.ch>
This is an UNSTABLE release. The release has significant modifications and bug fixes, if things go wrong, it is better to revert to 1.0.0-rc.124.
* jfjoch_broker: Significant improvements in TCP image socket, as a viable alternative for ZeroMQ sockets (only a single port on broker side, dynamically change number of writers, acknowledgments for written files)
* jfjoch_broker: Delta phi is calculated also for still data in Bragg prediction
* jfjoch_broker: Image pusher statistics are accessible via the REST interface
* jfjoch_writer: Supports TCP image socket and for these auto-forking option
Reviewed-on: #36
Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>
Co-committed-by: Filip Leonarski <filip.leonarski@psi.ch>
* Writer can send a PUB message with information on closed file
* Writer uses getopt to format input parameters
* DiffractionExperiment: Add frame number limit
leonarski_fandClaude Fable 5.1