A sticky error (an illegal address, say) is reported by whichever worker synchronises next - usually
the bslz4 device decode - and MXAnalysisWithoutFPGA::Analyze and Rugnux::MaskDefectivePixels then
logged "falling back to host" and carried on, although the context is gone and the run fails anyway,
later and less clearly. cuda_throw_if_context_lost() now throws a GPUCUDAError ("CUDA device
unusable after an unrecoverable error: ...") there first, which the image loops already treat as
fatal (IsFatalResourceError), like a CUDA out-of-memory.
The last error cannot tell: once cudaGetLastError() has returned a sticky error, it and
cudaPeekAtLastError() both report success. cudaFree(nullptr) frees nothing and does not
synchronise, but returns the sticky error (checked: after an illegal-address kernel it returns
cudaErrorIllegalAddress; with only a pending out-of-memory it returns success), so a handled,
non-sticky decode failure still falls back - MXAnalysis_HandledDeviceDecodeFailureLeavesNoError
passes.
Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01D1G8gJVAy6gp1K5Dz3NE5C
- set_gpu_blocking_sync(): every device is put in
cudaDeviceScheduleBlockingSync before its context exists, so a host thread
waiting on the GPU sleeps instead of spinning on a core. On a 16M rotation
run a fifth of all CPU time was that spinning; wall time unchanged within
noise. Called first thing in rugnux.
- enable_gpu_numa_binding(): from then on pin_gpu() (and the new
pin_gpu(dev), used by the first-pass spot workers that take a card by
index) also keeps the thread on the CPUs of the NUMA node the card hangs
off. The node and its CPUs come from /sys (no libnuma), intersected with
the process's own mask; Linux only, and nothing happens on a machine with a
single node. rugnux turns it on; the broker does not.
- A thread inherits its creator's affinity, so the shared ParallelFor pool
would run every later pass on one socket if a pinned worker created it:
its threads now reset to the mask the process started with
(common/ThreadAffinity).
Byte-identical output. The NUMA part is a no-op on the single-node test box
and still has to be measured on a two-socket machine.
Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01D1G8gJVAy6gp1K5Dz3NE5C
* Fixed `jfjoch_broker` cancelling every data collection with a CUDA "out of memory" error after long operation: GPU memory no longer leaks with each collection.
* Rugnux scales a rotation sweep until the per-frame scales settle instead of for a fixed three rounds, and says so when they did not - merged intensities, and the space group, resolution cut and frame rejection read off them, change accordingly; `--scaling-iterations` is now the cap on that loop (default 100).
* Rugnux places every frame of a marCCD, SMV or miniCBF series at the spindle angle its own header states, so a series with missing frames, or with angles written modulo 360, is no longer read at the wrong geometry or refused.
* Every rotation run writes two diagnostic files beside its reflections: `<prefix>_detector.jpg`, the detector projection with the pixel mask and the detected beam-stop shadow drawn on it, and `<prefix>_plot.txt`, one row per image.
Reviewed-on: #82
Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>
* `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.
* jfjoch_broker: Add EXPERIMENTAL pixelrefine mode for image processing
* jfjoch_broker: Allow to load user mask from 8-bit and 16-bit TIFF files
* jfjoch_broker: Add ROI calculation in non-FPGA workflow
* jfjoch_broker: Fixes to TCP image pusher
* jfjoch_broker: Remove NUMA bindings
* jfjoch_broker: Improvements to indexing
* jfjoch_broker: For PSI EIGER, trimming energies are taken from the detector configuration (now compulsory) instead of hardcoded values
* jfjoch_writer: Save ROI definitions and the per-pixel ROI bitmap in the master file; azimuthal ROIs support phi (angular) sectors
* jfjoch_viewer: Major redesign with dockable panels and saved layouts, plus on-canvas creation/move/resize of box, circle and azimuthal ROIs
* jfjoch_viewer: Run jfjoch_process reprocessing jobs from inside the GUI and overlay per-run results
Reviewed-on: #63
leonarski_fandClaude Opus 5.5