leonarski_fandClaude Opus 5.5 6e9b891eb4 MR score-engine cache and merge buffers: no hang, no doubled wait; near-tie doc follows offline decide-late ...

- MolecularReplacement: an engine whose making throws anything (std::bad_alloc, a gemmi error), not
  only a JFJochException, is refused and its reservation given back, so a thread waiting for the
  same engine is woken instead of waiting forever.
- RotationScaleMergeGPU::Alloc waits for the GPU work beside itself (GPU_BUSY_TIMEOUT), so its
  buffers are allocated plainly Synchronous; SynchronousAfterWorkBeside added a second 10-minute wait
  in front of it.
- CPU_DATA_ANALYSIS_INDEXING: an offline run decides its near ties on the whole sweep from the start;
  only a live run (broker URL or --simulate-live) decides early and re-checks.

Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>

2026-10-13 21:25:15 +02:00

..

azint

GPU engines wait for their stream before their buffers go; a lost context fails where it is seen

2026-10-10 10:59:24 +02:00

beam_stop

rugnux pre-scan: projection and defective pixels per card, the sample read once, beam stop memoised

2026-10-12 08:11:05 +02:00

bragg_integration

rugnux pre-scan: spot width on per-spot squares, engines built during the read, tiers looked ahead, measurements memoised

2026-10-12 16:11:14 +02:00

bragg_prediction

Bragg prediction: rotation partiality in the tail from erfc, the same on CPU and GPU

2026-10-13 16:10:38 +02:00

dark_mask_analysis

v1.0.0-rc.148 (#58)

2026-06-08 08:30:35 +02:00

geom_refinement

rugnux hypothesis arms read their residual on the pre-pass frames

2026-10-11 07:12:05 +02:00

hot_pixels

rugnux pre-scan: projection and defective pixels per card, the sample read once, beam stop memoised

2026-10-12 08:11:05 +02:00

image_preprocessing

marCCD upload: stage the stored pixels instead of page-locking the frame in place

2026-10-13 05:21:33 +02:00

indexing

rotation merge: helper buffers wait for the probe pass beside them, as the engine's own do

2026-10-13 16:07:33 +02:00

lattice_search

v1.0.0-rc.173 (#83)

2026-09-29 15:57:32 +02:00

roi

GPU engines wait for their stream before their buffers go; a lost context fails where it is seen

2026-10-10 10:59:24 +02:00

rotation_indexer

Indexer failures are thrown, not read as "no lattice"; GPU memory errors say what to do

2026-10-10 18:56:00 +02:00

scale_merge

MR score-engine cache and merge buffers: no hang, no doubled wait; near-tie doc follows offline decide-late

2026-10-13 21:25:15 +02:00

spot_finding

Pinned host memory from a process-wide pool; the compressed chunk uploaded from pinned staging

2026-10-11 10:37:23 +02:00

structure_refinement

MR score-engine cache and merge buffers: no hang, no doubled wait; near-tie doc follows offline decide-late

2026-10-13 21:25:15 +02:00

CMakeLists.txt

Move the atomic-model code to image_analysis/structure_refinement/ and WriteModel to writer/

2026-10-07 14:05:37 +02:00

IndexAndRefine.cpp

Indexer failures are thrown, not read as "no lattice"; GPU memory errors say what to do

2026-10-10 18:56:00 +02:00

IndexAndRefine.h

Indexer failures are thrown, not read as "no lattice"; GPU memory errors say what to do

2026-10-10 18:56:00 +02:00

IntegrationOutcome.h

v1.0.0-rc.172 (#82)

2026-09-22 06:48:37 +02:00

LoadFCalcFromMtz.cpp

v1.0.0-rc.173 (#83)

2026-09-29 15:57:32 +02:00

LoadFCalcFromMtz.h

v1.0.0-rc.173 (#83)

2026-09-29 15:57:32 +02:00

MXAnalysisAfterFPGA.cpp

1.0.0-rc.174 (#84)

2026-10-06 14:03:18 +02:00

MXAnalysisAfterFPGA.h

v1.0.0-rc.156 (#66)

2026-07-03 19:18:56 +02:00

MXAnalysisWithoutFPGA.cpp

marCCD frames are widened on the device

2026-10-12 22:37:47 +02:00

MXAnalysisWithoutFPGA.h

rugnux two-pass: the integration radius decided on the pre-pass frames, before the canonical pass

2026-10-11 13:01:23 +02:00

ReflectionArena.h

v1.0.0-rc.172 (#82)

2026-09-22 06:48:37 +02:00

SensorAbsorption.h

v1.0.0-rc.173 (#83)

2026-09-29 15:57:32 +02:00

UpdateReflectionResolution.cpp

v1.0.0-rc.167 (#77)

2026-09-09 07:25:13 +02:00

UpdateReflectionResolution.h

v1.0.0-rc.172 (#82)

2026-09-22 06:48:37 +02:00

WriteReflections.cpp

Anisotropy verdict: the directional limits are a second hypothesis beside the tensor

2026-10-11 02:21:32 +02:00

WriteReflections.h

Merged mmCIF: drop the scaled unmerged block

2026-10-09 18:51:56 +02:00