* `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
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Data streams
Jungfraujoch process (jfjoch_broker) operates three outputs.
All three can be operated/enabled independently.
These are:
- Image - all the images including metadata (ZeroMQ PUSH socket or custom TCP/IP socket)
- Preview - images with metadata at a reduced frame rate (PUB socket)
- Metadata - only metadata for all the images, bundled into packages (PUB socket)
Image stream
Images (with metadata) are serialized as CBOR image message. The stream will also include CBOR start message, calibration messages and end message with run metadata.
If file_prefix is not provided for a data collection, images won't be sent to image stream (or its HDF5/CBOR replacements).
Splitting image stream
Image stream can be split into multiple sockets to increase performance, in this case images will be split according to file number to which the image belongs. All sockets will forward start and end messages. Only first socket will forward calibration messages and will be marked to write master file.
ZeroMQ image stream
This is using PUSH ZeroMQ socket(s). It should be strictly avoided to have multiple receivers connected to one PUSH ZeroMQ socket. ZeroMQ will send the images in a round-robin basis to the receivers. In this case start and end messages will end up only with one receiver. Instead, Jungfraujoch feature of multiple sockets should be used. For ZeroMQ image stream, each writer connects to a different port.
Behavior is as following:
- Start message is sent with timeout of 1s per socket. If within the time the message cannot be put in the outgoing queue or there is no connected puller, an exception is thrown — data collection is stopped with an error due to absence of a writer.
- Calibration message is sent to the first socket only, with timeout of 1s.
- Images are sent via a per-socket writer thread. If a send times out, the pusher switches to non-blocking mode for the remainder of the collection (images may be dropped).
- End message is sent with timeout of 1s per socket. No exception is thrown on timeout, but a transmission error is recorded.
The format is generally interchangeable with DECTRIS Stream2 format.
ZeroMQ configuration
ZeroMQ image stream is configured in the broker JSON configuration file under the zeromq_settings section:
{
"image_socket": ["tcp://192.168.0.1:9000", "tcp://192.168.0.1:9001"],
"send_watermark": 100,
"send_buffer_size": 67108864,
"writer_notification_socket": "tcp://192.168.0.1:*"
}
image_socket: one or more PUSH socket addresses. Multiple entries split the image stream across sockets. Addresses follow ZeroMQ conventions (tcp://,ipc://).0.0.0.0binds on all network interfaces.send_watermark(optional): ZeroMQ send high-water mark (number of outstanding messages per socket).send_buffer_size(optional): OS-level send buffer size for the ZeroMQ socket.writer_notification_socket(optional): see Writer notification socket below.
TCP/IP image stream
This is using TCP/IP socket(s) with a fixed binary frame header followed by payload bytes. This format was introduced to Jungfraujoch as an alternative to ZeroMQ image stream. It allows two-way communication between the data collection and the writer, and is therefore more robust than ZeroMQ.
For TCP/IP image stream, Jungfraujoch listens on a single TCP port and all writers connect to it. Connections are persistent — writers connect once and stay connected across multiple data collections. Jungfraujoch sends periodic KEEPALIVE frames when no data collection is active to detect dead connections; writers are expected to respond with a KEEPALIVE pong.
Using * as port number (e.g. tcp://127.0.0.1:*) is supported — the OS assigns a free port and the actual bound address can be queried via GetAddress().
Payloads for PREFLIGHT, START, DATA, CALIBRATION and END frames are CBOR messages, equivalent in content to the ZeroMQ image stream messages.
ACK, CANCEL, KEEPALIVE and BUSY are control frames (no CBOR payload).
The data collection lifecycle on each connection follows:
PREFLIGHT → START → CALIBRATION (socket 0 only) → DATA (repeated) → END
If a START ACK fails on any connection, Jungfraujoch sends CANCEL to all already-started connections and rolls back.
For each frame:
- Read one
TcpFrameHeader(fixed size, 64-byte aligned). - Validate
magic(0x4A464A54/"JFJT") andversion(4). Both ends reject a frame of any other version, so writer and broker must be of the same release. - Read
payload_sizebytes (if non-zero).
Pre-flight
Before a data collection is started - before the detector is armed - Jungfraujoch sends a PREFLIGHT frame on every connection and waits for its ACK. It carries the same CBOR start message a START would, and asks the writer one question: could this run be written? The writer checks the output path, creates the output directory, and checks that no output file is in the way; it opens nothing, writes nothing, and does not change its state. A run that would fail on the first file it wrote is therefore refused while refusing it is free, with the writer's own message reported to the client by /start and /wait_until_running.
write_master_file is assigned exactly as it is for START (connection index 0), and the writer that owns the master file is the one that answers for the output files - the master and every data file the run will write, its siblings' included.
The PREFLIGHT payload describes the run but carries none of the per-pixel arrays a START does - no pixel mask, no azimuthal-integration map, no ROI map - so it stays small: about 1.4 kB on a JUNGFRAU 9M, against about 540 kB for the START that follows.
A rejected PREFLIGHT is not fatal: nothing was started, so the connection stays usable and the next attempt (a different file prefix, or overwrite set) proceeds on it. The check cannot be exhaustive - a file created in the moment between the pre-flight and the start still fails at the start, and free space and quota are not inspected - so it lowers how often a run fails on its output, it does not remove the case.
When image stream is split into multiple connections:
STARTandENDare sent on all connections,CALIBRATIONis sent only on connection 0,DATAframes are distributed by file grouping: connection index =(image_number / images_per_file) % num_connections.
TCP/IP configuration
TCP/IP image stream is configured in the broker JSON configuration file under the tcp_settings section:
{
"image_socket": "tcp://192.168.0.1:9100",
"nwriters": 2,
"send_buffer_size": 67108864
}
addr: listen address intcp://<IP>:<port>format.0.0.0.0binds on all interfaces.*as port selects a random free port.nwriters(optional): maximum number of simultaneous writer connections accepted.send_buffer_size(optional): OS-levelSO_SNDBUFsize for accepted connections.
ACK handling
ACK handling is mandatory for correct operation:
PREFLIGHTmust be acknowledged (ack_for=PREFLIGHT) on each connection within 5 seconds, otherwise the collection is not started. A rejected pre-flight (OKclear) carries the reason as error text and does not break the connection.STARTmust be acknowledged (ACKwithack_for=START) on each connection within 5 seconds, otherwise collection start fails and a rollback is triggered.ENDmust be acknowledged (ack_for=END) on each connection within 10 seconds for successful completion.CANCELshould be acknowledged during rollback paths (500ms timeout).DATAshould be acknowledged for every frame. ADATAACK withFATALflag set reports a downstream error (e.g. disk full) which is propagated tojfjoch_brokerviaFinalize(). A failedDATAACK does not break the TCP connection on its own — data continues to flow.CALIBRATIONis not acknowledged at this time.KEEPALIVEframes are not acknowledged via ACK; the writer responds with aKEEPALIVEpong frame instead.
Keepalive
When no data collection is active, Jungfraujoch sends KEEPALIVE frames approximately every 5 seconds on each persistent connection. Writers should respond with a KEEPALIVE frame (pong). OS-level TCP keepalive is also enabled (TCP_KEEPIDLE=30s, TCP_KEEPINTVL=10s, TCP_KEEPCNT=3) as a secondary safety net. Dead connections are automatically removed from the pool.
Zero-copy transmission
On Linux, large payload transmission (DATA and CALIBRATION frames) can use kernel TCP zero-copy (SO_ZEROCOPY/MSG_ZEROCOPY) when available. If the kernel does not support it or the socket option fails, transmission transparently falls back to normal send() behavior. Zero-copy completion notifications are processed by a dedicated per-connection thread.
Frame types
| Value | Name | Purpose |
|---|---|---|
| 1 | START |
Start-of-run metadata |
| 2 | DATA |
One image payload |
| 3 | CALIBRATION |
Calibration payload |
| 4 | END |
End-of-run metadata |
| 5 | ACK |
Acknowledgement / error reporting |
| 6 | CANCEL |
Cancel run initialization/stream |
| 7 | KEEPALIVE |
Connection liveness probe/pong |
| 8 | BUSY |
Writer alive but stalled; carries its FIFO occupancy |
| 9 | PREFLIGHT |
Dry run before a collection starts: can this run be written? |
TCP frame header (TcpFrameHeader)
| Field | Type | Description |
|---|---|---|
magic |
uint32_t |
Protocol magic (0x4A464A54, "JFJT") |
version |
uint16_t |
Protocol version (4) |
type |
uint16_t |
Frame type (see table above) |
image_number |
uint64_t |
Image index for DATA frames |
payload_size |
uint64_t |
Number of payload bytes after header |
socket_number |
uint32_t |
Connection index in split-stream mode |
flags |
uint32_t |
ACK flags (OK, FATAL, HAS_ERROR_TEXT) |
run_number |
uint64_t |
Run identifier |
ack_processed_images |
uint32_t |
In ACK: number of images processed by receiver |
ack_code |
uint16_t |
In ACK: error/status code |
ack_for |
uint16_t |
In ACK: frame type being acknowledged |
ack_fifo_occupancy |
uint16_t |
In ACK: occupancy of input FIFO in the jfjoch_writer |
ack_fifo_max_occupancy |
uint64_t |
In ACK: max occupancy of input FIFO |
The header is 64-byte aligned (alignas(64)).
ACK semantics
ACKframes useack_forto indicate which frame type is acknowledged.flags:OK(bit 0): operation accepted/successful,FATAL(bit 1): receiver reports unrecoverable error (primarily forDATA),HAS_ERROR_TEXT(bit 2): ACK payload contains UTF-8 error text.
ack_codecan be used to categorize errors:
| Code | Name | Meaning |
|---|---|---|
| 0 | None |
No error |
| 1 | StartFailed |
START processing failed |
| 2 | DataWriteFailed |
Image write failed |
| 3 | EndFailed |
END processing failed |
| 4 | DiskQuotaExceeded |
Disk quota exceeded |
| 5 | NoSpaceLeft |
No space left on device |
| 6 | PermissionDenied |
Permission denied |
| 7 | IoError |
General I/O error |
| 8 | ProtocolError |
Protocol-level error |
Image stream replacement
Image stream can be replaced with direct HDF5 writer and CBOR dump image pushers, or it can be disabled by selecting "None" image pusher for all the measurements.
Writer notification socket
The writer notification socket is used only with ZeroMQ image stream. Since ZeroMQ is asynchronous, jfjoch_broker does not know whether messages were properly handled downstream (e.g. written to disk). The writer notification socket allows downstream code to report back.
For TCP/IP image stream, this mechanism is not needed — ACK frames provide synchronous feedback for each control and data frame.
To use writer notification socket, it has to be first enabled in the JSON configuration file of broker with writer_notification_socket entry:
{
"writer_notification_socket":"tcp://192.168.0.1:*"
}
Such entry will create PULL socket on 192.168.0.1 network interface listening on one, random TCP port. When data processing is started, the
image stream will send CBOR start message. This message will include information on writer_notification_zmq_addr,
which needs to be used by downstream code. Since the start message must reference the address of jfjoch_broker host, notification
socket should always listen on a particular network interface, and should not be configured with placeholder address 0.0.0.0. It is, however, OK
to use placeholder :* for network port, as it will be substituted for the one chosen by ZeroMQ.
For every image stream socket, downstream code must send the following message to the PULL socket:
{
"run_number":135,
"run_name": "sample_1",
"socket_number": 1,
"processed_images":250,
"ok": true
}
Here run_number, run_name and socket_number must match information from the start message.
ok is boolean confirming if the writing process was OK.
processed_images is number of images that were written/processed, this is to track how many images were ignored by non-blocking ZeroMQ procedures.
If not, it is possible to include error message:
{
"run_number":135,
"run_name": "sample_1",
"socket_number": 1,
"processed_images": 0,
"ok": false,
"error": "Permission error"
}
This way errors from the downstream code are propagated to jfjoch_broker.
If writer notification socket is configured, but downstream code doesn't send proper notification, jfjoch_broker will time out after 60 seconds producing an error message.
Preview stream
Jungfraujoch can also send images (with metadata) at a reduced frame rate for preview purpose. Images are serialized as CBOR image message. The stream will also include CBOR start message and end message with run metadata. Only start and image messages are sent.
This is using PUB socket with conflate option. I.e., only the last message is kept by ZeroMQ, so if receiver cannot cope with the messages, it will always receive the last generated message (no backlog). For this reason it is also recommended to use the same option on receiver side.
Given PUB socket properties, it is possible to connect multiple viewers to a single socket --- all the viewers should receive all the images sent.
Metadata stream
Jungfraujoch can also send pure metadata for the purpose of archiving such information. Metadata are serialized as CBOR metadata message. This is very similar as image message, but excludes the actual image array and spot positions. As metadata are relatively small, to avoid large number of messages, Jungfraujoch bundles metadata of many images in one message. Order of images within bundle, as well a size of the bundle, are not guaranteed. The stream will also include CBOR start message and end message with run metadata.
This is using PUB socket with watermark, so there is some queuing of messages with ZeroMQ. Multiple receivers can be connected.