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2511-eiger-mask

2511-eiger-mask-3

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2511-viewer-enh

2511-viewer-enh-2

2512-1.0.0-rc.121

2512-1.0.0-rc.122

2512-scaling-merging

2601-1.0.0-rc.123

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2601-completness

2602-residual

2602-scaling-d-limit

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2603-pipeline-upgrades

2603-rc.129

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2603-rc.131-2

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2604-async-start

2604-azint-mapping-parallel

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2604-hdf5-errors

2604-index-and-refine-fix

2604-more-fixes

2604-processing-options

2604-rc.135

2604-rc.136

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2605-b-factor

2605-hdf-fixes

2605-hdf5-enospc

2605-hdf5-vds

2605-scaling

2605-sigma-correction

2605-speed-up-preview-start

2606-azint

2606-eiger-calib

2606-eiger-module-fix

2606-force-cpu-azint

2606-pixel-refine

2606-q-spacing

2606-rc.156-fixes

2606-sgsearch

2606-tcp

2606-viewer-processing

2606-xds-plugin

2607-rc-160

2607-res-prediction

2607-state-machine

2607-win-viewer

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arm64-bitshuffle-bench

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Mono Color

• 1bd251cdd1 docs: GPU_DATA_ANALYSIS, every GPU engine of the crystallographic pipeline leonarski_fandClaude Opus 5.5 2026-10-13 09:03:31 +02:00
• 30cf5856d4 docs: bring the rugnux and analysis pages up to the code (MR fallback, GPU decode, live runs) leonarski_fandClaude Opus 5.5 2026-10-13 09:03:31 +02:00
• ec57236ae5 rugnux: offline, the first passes decide their near ties on all the frames from the start leonarski_fandClaude Opus 5.5 2026-10-13 08:36:35 +02:00
• cf082b2531 rugnux: the quality guard no longer runs beside the main engine on one card leonarski_fandClaude Opus 5.5 2026-10-13 08:27:36 +02:00
• b736c4cefb RotationScaleMerge::DeviceBytes: the resident ingest's peak as measured leonarski_fandClaude Opus 5.5 2026-10-13 08:27:36 +02:00
• 5e916fe120 docs: --model places by rigid body, then molecular replacement; --mr; <prefix>_mr files leonarski_fandClaude Opus 5.5 2026-10-13 08:07:44 +02:00
• e53c3f50cd CalcBraggPredictionTest: skip the GPU cases on a machine without a card leonarski_fandClaude Opus 5.5 2026-10-13 07:54:56 +02:00
• 463cd8eec3 CBF byte-offset decoder: plain stores instead of SSE streaming stores leonarski_fandClaude Opus 5.5 2026-10-13 07:54:56 +02:00
• 645d1cc1bb CHANGELOG: rc.175 says --model falls back to molecular replacement and takes predicted models; viewer refresh leonarski_fandClaude Opus 5.5 2026-10-13 07:41:37 +02:00
• 7ed9705038 build: no fused multiply-add contraction in device code either leonarski_fandClaude Opus 5.5 2026-10-12 00:56:42 +02:00
• 5636208278 battery: cytochrome c scored against the hand of its reference model; ZANUDA/POINTLESS evidence in the accepted-alternative texts leonarski_fandClaude Opus 5.5 2026-10-13 07:40:16 +02:00
• f8535968c6 Merge branch 'fix-9fhc' into rc175: marCCD frames copied into the engine's own pinned buffer (fixes a pre-scan race); ModelValidation test follows the null on every run leonarski_fandClaude Opus 5.5 2026-10-13 05:54:59 +02:00
• 2c6cd1ef38 ModelValidationTest: the null runs on every validation that judges its model leonarski_fandClaude Opus 5.5 2026-10-13 05:21:33 +02:00
• 34092a510f marCCD upload: stage the stored pixels instead of page-locking the frame in place leonarski_fandClaude Opus 5.5 2026-10-13 05:21:33 +02:00
• 59648587e3 Merge branch 'gpu-loops' into rc175: prediction ordered and selected on the GPU, CBF byte-offset decoded and marCCD widened on the GPU leonarski_fandClaude Opus 5.5 2026-10-13 03:28:19 +02:00
• 450266d6f7 Merge branch 'gpu-scaling' into rc175: merge ingest, delta-phi/partiality recompute and CSRs on the card; overload/ice in one parallel sweep; guard beside the main engine on one card leonarski_fandClaude Opus 5.5 2026-10-13 03:14:18 +02:00
• 11052bc376 CBFDecoderGPU: walk short parts from shared memory leonarski_fandClaude Opus 5.5 2026-10-13 02:53:52 +02:00
• 9cb19753c7 Merge branch 'gpu-modelval' into rc175: --model validation's scale fits on the GPU, change-of-basis scoring gridded once in parallel leonarski_fandClaude Opus 5.5 2026-10-13 02:47:06 +02:00
• eb7a65d051 rotation merge: the fulls' frame and group CSRs built on the card leonarski_fandClaude Opus 5.5 2026-10-13 02:01:30 +02:00
• 85e714f072 Merge branch 'unified-model' into rc175: --model runs molecular replacement when the rigid body cannot place the model leonarski_fandClaude Opus 5.5 2026-10-13 01:58:38 +02:00
• 2a32c28cca battery nullmodel: a section title is '# N. TITLE', not any comment line starting with a digit leonarski_fandClaude Opus 5.5 2026-10-13 00:29:06 +02:00
• 8f8d0c47f5 rugnux: one sweep over the reflections for the overload counts and the ice flags leonarski_fandClaude Opus 5.5 2026-10-12 23:42:21 +02:00
• 095814baed rugnux: place the quality guard from the pre-pass engine's size, before either ingest leonarski_fandClaude Opus 5.5 2026-10-12 23:31:49 +02:00
• 5f7b4d06bc rugnux: the post-refinement gather starts once the scaling engine has ingested leonarski_fandClaude Opus 5.5 2026-10-12 22:53:56 +02:00
• d5bf32763f rotation merge: the resident ingest smooths the geometry on the card (last-bit change) leonarski_fandClaude Opus 5.5 2026-10-12 22:46:06 +02:00
• 4158c48dfd rugnux: post-refinement gather beside the chain; quality guard beside the engine on one card leonarski_fandClaude Opus 5.5 2026-10-12 22:38:34 +02:00
• f88ff0440d rotation merge: the resident ingest sorts and cuts the reflections on the card leonarski_fandClaude Opus 5.5 2026-10-12 22:38:25 +02:00
• e24fb88b53 rugnux: count overloads and flag ice-ring reflections over the images on all threads leonarski_fandClaude Opus 5.5 2026-10-12 22:38:09 +02:00
• dfd69fcb91 marCCD frames are widened on the device leonarski_fandClaude Opus 5.5 2026-10-12 22:37:47 +02:00
• f4252ad39d miniCBF frames are decoded on the device leonarski_fandClaude Opus 5.5 2026-10-12 22:37:37 +02:00
• e8409ef608 BraggPredictionRotGPU: order and select the predictions on the device leonarski_fandClaude Opus 5.5 2026-10-12 22:36:31 +02:00
• d0d225cb99 rugnux --model: molecular replacement where the rigid body does not place the model leonarski_fandClaude Opus 5.5 2026-10-12 22:20:36 +02:00
• 1fe73bab41 Model validation: scale fits on the GPU, change-of-basis probe gridded once per frame on all threads leonarski_fandClaude Opus 5.5 2026-10-12 21:40:54 +02:00
• f567771d56 CHANGELOG: rc.175 names --mr, which takes predicted and experimental models leonarski_fandClaude Opus 5.5 2026-10-12 20:08:50 +02:00
• 07eecb3285 Merge branch 'mr-7qij' into rc175: --mr (predicted and experimental models), MR tNCS half-shift check, P1 single copy, carry rule, MR 2-4x faster leonarski_fandClaude Opus 5.5 2026-10-12 20:08:43 +02:00
• 3053455c1f Merge branch 'viewer-plot-combo' into rc175: jfjoch_viewer combo boxes no longer rebuilt on each live update leonarski_fandClaude Opus 5.5 2026-10-12 19:47:23 +02:00
• 9cf987cd4e jfjoch_viewer: live updates no longer rebuild open combo boxes leonarski_fandClaude Opus 5.5 2026-10-12 19:46:48 +02:00
• 30c7bee15f rugnux: --af-model becomes --mr, for predictions and experimental structures alike leonarski_fandClaude Opus 5.5 2026-10-12 17:44:48 +02:00
• e1f49dd729 rugnux --af-model: the further copies' translation function prepared once per group, the known copies' likelihood beside it leonarski_fandClaude Opus 5.5 2026-10-12 19:30:22 +02:00
• 83b1d85400 Merge branch 'viewer-refresh' into rc175: jfjoch_viewer Files panel reloads on F5 and polls every 3 s while visible leonarski_fandClaude Opus 5.5 2026-10-12 19:24:23 +02:00
• c27282e577 jfjoch_viewer: F5 and a 3 s poll refresh the Files panel leonarski_fandClaude Opus 5.5 2026-10-12 19:23:44 +02:00
• 4f5e419d79 Merge branch 'spot-width' into rc175: pre-scan spot measurement on per-spot tiles, engines built during the read, tiers looked ahead, repeated pre-scans memoised leonarski_fandClaude Opus 5.5 2026-10-12 18:18:19 +02:00
• aef1c84bf1 rugnux pre-scan: build the spot measurement's mapping on the cores the readers leave free leonarski_fandClaude Opus 5.5 2026-10-12 18:16:23 +02:00
• 9da57ba559 rugnux --af-model: beside tNCS, a poorly fitting placement cannot rule out a group by carrying its copies there leonarski_fandClaude Opus 5.5 2026-10-12 18:06:23 +02:00
• af796d0a6a rugnux --af-model: tNCS half-vector moves and P1's first copy decided on the evidence that can tell them leonarski_fandClaude Opus 5.5 2026-10-12 17:34:28 +02:00
• 6ee167df9a Merge rc175 (the null turns each copy about its own centroid) into mr-7qij leonarski_fandClaude Opus 5.5 2026-10-12 16:49:20 +02:00
• c6912e2a06 rugnux --af-model: tNCS half-vector moves checked, the merge's own group not ruled out beside tNCS, P1's first copy judged by its orientation (WIP, validation pending) leonarski_fandClaude Opus 5.5 2026-10-12 16:49:02 +02:00
• 1b21958828 Merge branch 'mr-tncs-null' into rc175: --af-model null turns each copy about its own centroid, so tNCS no longer lets wrong models pass leonarski_fandClaude Opus 5.5 2026-10-12 16:48:36 +02:00
• babff6d8bf rugnux --af-model: the null keeps the copies' arrangement leonarski_fandClaude Opus 5.5 2026-10-12 16:47:07 +02:00
• 6c8ead466a rugnux --af-model: molecular replacement faster - the score's scale fit on the GPU, the expected LLG gate, the serial parts side by side leonarski_fandClaude Opus 5.5 2026-10-12 16:39:03 +02:00
• 545cf3b13e rugnux pre-scan: spot width on per-spot squares, engines built during the read, tiers looked ahead, measurements memoised leonarski_fandClaude Opus 5.5 2026-10-12 16:11:14 +02:00
• 699bff1cb1 Merge branch 'sym-evidence' into rc175: POINTLESS/ZANUDA symmetry evidence for 18 open-arm sets, kept with the battery leonarski_fandClaude Opus 5.5 2026-10-12 16:02:51 +02:00
• 0bbe086b24 battery: symmetry evidence from POINTLESS and ZANUDA for 18 open-arm sets leonarski_fandClaude Opus 5.5 2026-10-12 16:02:01 +02:00
• 704f2b567a Merge branch 'ci-fix' into rc175: jfjoch_mr_replay leaves the repository; unit tests and the battery take turns on the CI GPU leonarski_fandClaude Opus 5.5 2026-10-12 14:28:45 +02:00
• 25e225a732 Merge branch 'changelog-rc175' into rc175: rc.175 release notes leonarski_fandClaude Opus 5.5 2026-10-12 14:10:51 +02:00
• aabee7423f CHANGELOG: rc.175 release notes leonarski_fandClaude Opus 5.5 2026-10-12 14:02:13 +02:00
• fa79d7587b Merge branch 'af-mr4' into rc175: --af-model likelihood rescoring, PAE domain search, twin comparison on the subgroup merge, refined tNCS rule leonarski_fandClaude Opus 5.5 2026-10-12 13:45:46 +02:00
• b28dff47e4 Merge branch 'merge-layout' into rc175: merge engine observations as a packed 16-byte record, the scale preparation folded into the per-frame fit leonarski_fandClaude Opus 5.5 2026-10-12 13:37:40 +02:00
• 0d33d7a40a rugnux --af-model: likelihood judging, PAE domains, twin comparison, tNCS carry test, faster multi-copy search leonarski_fandClaude Opus 5.5 2026-10-12 11:41:30 +02:00
• 140739a69f CI: unit tests and the validation battery take turns on the GPU leonarski_fandClaude Opus 5.5 2026-10-12 12:59:55 +02:00
• d172f22074 tools: remove jfjoch_mr_replay leonarski_fandClaude Opus 5.5 2026-10-12 12:59:43 +02:00
• d712eba00f Merge branch 'prescan-cards' into rc175: pre-scan projection and defective pixels one accumulator per card, sample read once, beam-stop detection memoised leonarski_fandClaude Opus 5.5 2026-10-12 11:54:51 +02:00
• 7d656c13de rugnux merge engine: the immutable fields the scaling gathers in one 16-byte record leonarski_fandClaude Opus 5.5 2026-10-12 09:10:22 +02:00
• be5e6feb15 rugnux pre-scan: a frame past the kept-frame budget is read into the worker's buffer leonarski_fandClaude Opus 5.5 2026-10-12 09:56:39 +02:00
• 230c5e3917 battery: 2ygz leaves the open arm; 6oww accepts P 41 21 2 as an open question leonarski_fandClaude Opus 5.5 2026-10-12 09:47:39 +02:00
• 70e11d9ab8 rugnux pre-scan: projection and defective pixels per card, the sample read once, beam stop memoised leonarski_fandClaude Opus 5.5 2026-10-12 08:07:10 +02:00
• fcbe92042b Merge branch 'af-mr3' into rc175: --af-model searches several copies per asymmetric unit (Matthews probability, sequential translation function, fixed-copy rigid body, tNCS) leonarski_fandClaude Opus 5.5 2026-10-12 01:36:26 +02:00
• d42d89b5f5 Merge slow-tail f3a405655 into rc175: near-tie re-checks with the same first-pass inputs are not run twice leonarski_fandClaude Opus 5.5 2026-10-12 01:06:16 +02:00
• 63e0a85467 rugnux --af-model: several copies in the asymmetric unit, tNCS, a search-matched null, faster leonarski_fandClaude Opus 5.5 2026-10-12 00:27:17 +02:00
• dcb01100e7 RefineRigidBody: a body refined beside fixed copies of it leonarski_fandClaude Opus 5.5 2026-10-12 00:26:49 +02:00
• f481f7f0df Merge branch 'wm-fix' into rc175: a wrong --model confirms no shell and fits no hand; wrong-model null as its own CI step; battery runs kept in the repository by machine role leonarski_fandClaude Opus 5.5 2026-10-12 00:08:46 +02:00
• f3a405655c rugnux: a near-tie re-check of a first pass already re-checked on the same inputs is not run again leonarski_fandClaude Opus 5.5 2026-10-11 23:09:15 +02:00
• d906868bb2 battery: kept runs by machine role (keep --as workstation|server); the server run complete leonarski_fandClaude Opus 5.5 2026-10-11 22:33:35 +02:00
• 695bc907b4 battery: keep runs in the repository (battery.py keep, tools/battery/results/<host>/<run>/) leonarski_fandClaude Opus 5.5 2026-10-11 22:22:29 +02:00
• eec8dcee9f battery: the wrong-model null as a CI step of its own (battery.py nullmodel) leonarski_fandClaude Opus 5.5 2026-10-11 21:30:34 +02:00
• ee350f1f74 rugnux --model: a wrong model confirms no shell, fits no hand, and fits the GPU reserve leonarski_fandClaude Opus 5.5 2026-10-11 21:30:34 +02:00
• f800669839 jfjoch_mr_replay: --af-model's molecular replacement re-run on a run's merged MTZ files leonarski_fandClaude Opus 5.5 2026-10-11 20:50:47 +02:00
• bd3c4efab6 Merge branch 'af-mr2' into rc175: --af-model hand decisions vetoed by the anomalous map, search on the GPU, hand check from the anomalous map alone leonarski_fandClaude Opus 5.5 2026-10-11 20:38:12 +02:00
• 323c5253de rugnux --af-model: each candidate space group once, not again on a shifted origin leonarski_fandClaude Opus 5.5 2026-10-11 19:09:27 +02:00
• 50e3b59fb7 rugnux --af-model: hand check reads only the anomalous map, on MR's placement and solvent leonarski_fandClaude Opus 5.5 2026-10-11 18:11:01 +02:00
• 2a3d60fb82 rugnux --af-model: anomalous veto on the enantiomorph, search on the GPU, cheaper rescoring leonarski_fandClaude Opus 5.5 2026-10-11 17:10:48 +02:00
• 0fd3d1742b Merge branch 'fft-admit-test' into rc175: the FFT indexer wait test fills every card, as indexer workers pick theirs round-robin leonarski_fandClaude Opus 5.5 2026-10-11 16:40:00 +02:00
• 52f94d2953 tests: FFT-indexer admission test fills every card, right before each Run leonarski_fandClaude Opus 5.5 2026-10-11 16:39:43 +02:00
• 54993911f1 Merge branch 'wrongmodel' into rc175: wrong-model null step with every ci-tier battery run (fails until the false CC significance, the fragile fit gate and the rigid-body reserve are fixed) leonarski_fandClaude Opus 5.5 2026-10-11 14:42:27 +02:00
• 57fef1cf44 Merge branch 'af-mr' into rc175: experimental --af-model, single-copy molecular replacement deciding open symmetry hypotheses into p_mr.mtz leonarski_fandClaude Opus 5.5 2026-10-11 14:38:08 +02:00
• 4d17aae4e3 battery: wrong-model null takes about 6 minutes of rugnux (measured) leonarski_fandClaude Opus 5.5 2026-10-11 14:36:12 +02:00
• 62b7d8b2b9 Merge branch 'u5-ingest' into rc175: merge ingest reads the reflections 4 times instead of 7; the all-observation arm copies the staged observations on the card leonarski_fandClaude Opus 5.5 2026-10-11 14:26:01 +02:00
• ee8c95de1c CUDAMemHelpers test: the FFT indexer wait case trims the allocation pool after its pools leonarski_fandClaude Opus 5.5 2026-10-11 14:25:56 +02:00
• 8dbaa9f8d7 Merge branch 'fft-admit' into rc175: FFT indexer construction waits for GPU work beside it before failing leonarski_fandClaude Opus 5.5 2026-10-11 14:06:12 +02:00
• 8fa3e0a6c9 Merge branch 'u12-numa' into rc175: with automatic -N, threads confined to the GPUs' sockets on a multi-socket machine leonarski_fandClaude Opus 5.5 2026-10-11 13:59:04 +02:00
• 136b1f24e9 Merge branch 'decode-bounds' into rc175: decode kernel launch bounds allow five resident blocks on sm_120 leonarski_fandClaude Opus 5.5 2026-10-11 13:45:14 +02:00
• d14e32b19a decode kernel: __launch_bounds__(256, 5), so sm_120 keeps the five blocks its shared memory allows leonarski_fandClaude Opus 5.5 2026-10-11 13:44:30 +02:00
• 60a8bf3981 rugnux --af-model (experimental): single-copy molecular replacement of a predicted model leonarski_fandClaude Opus 5.5 2026-10-11 13:35:05 +02:00
• 35f0cffaa4 Merge branch 'b2-radius-early' into rc175: the canonical pass picks its integration radius before it runs leonarski_fandClaude Opus 5.5 2026-10-11 13:02:07 +02:00
• a609f6ba1c rugnux two-pass: the integration radius decided on the pre-pass frames, before the canonical pass leonarski_fandClaude Opus 5.5 2026-10-11 09:54:47 +02:00
• e55750e1e0 rugnux merge ingest: keep d beside zeta only under an energy bandwidth leonarski_fandClaude Opus 5.5 2026-10-11 12:38:04 +02:00
• c6574a887d Merge branch 'u11-pin' into rc175: process-wide pinned host buffer free list; compressed chunks staged through it leonarski_fandClaude Opus 5.5 2026-10-11 12:22:40 +02:00
• 0a3fadb9ef battery: wrong-model null step, run with every ci-tier run leonarski_fandClaude Opus 5.5 2026-10-11 11:50:21 +02:00
• 3befddd649 rugnux: an FFT indexer that does not fit waits for the GPU work beside it, then is built again leonarski_fandClaude Opus 5.5 2026-10-11 11:11:42 +02:00
• b46b4a4657 rugnux all-observation arm: observations copied on the card, not staged from the reflections again leonarski_fandClaude Opus 5.5 2026-10-11 10:52:57 +02:00