7 Commits

Include renames

Author	SHA1	Message	Date
leonarski_fandClaude Opus 5.5	78c2a69267	Merge broker-rugnux-live into rc176: rugnux in jfjoch_broker as a live thread during a DECTRIS rotation collection (off by default), the rugnux library without file I/O (results in ProcessResult::outputs, the CLI writes them through JFJochRugnuxOutput), END carrying the merged table, map coefficients and placed model ... Branch reviewed at e16db07ff (review: owner's decisions accepted - _maps.mtz instead of .ccp4 in the viewer, -o "" computes everything incl. MR/validation, Ctrl+C/error paths may leave fewer files, the writer links gemmi/zlib) and merged at 55184eb09 with its review fixes (END size guard, frame drop as in Lite, outputs released before re-runs, pool priority, docs, frontend gating). Conflicts: rugnux/Rugnux.h (kept rc176's host_memory_budget_bytes, output_prefix removed as on the branch), rugnux/RugnuxPipeline.h (MtzTable future + rc176's GPUMerge pointer), MolecularReplacement.h/.cpp (rc176's GPU cost model, packed transform and split functions with the branch's RugnuxModel signature; search_model with rc176's other_budgets, result.model_name). tests/RugnuxLargeTest.cpp: rc176's host-budget test writes its files through WriteRugnuxOutputs now that the library writes none. Generated code (broker/gen, frontend client, Python client docs, Redoc) regenerated from the merged jfjoch_api.yaml with update_version.sh (version unchanged). Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01PXc1zD1yxHqaR1DGdCTHL4	2026-10-17 21:01:38 +02:00
leonarski_fandClaude Opus 5.5	4bf41983ed	rugnux: the model is parsed by the caller and handed in as RugnuxModel ... The analysis read the --model file itself, four to five times per run (the model kind, every validation, molecular replacement, the stills reference intensities) and located the PAE sidecar from the file name. The library is to do no file I/O, so the model now arrives in memory: - RugnuxModel (image_analysis/structure_refinement/RugnuxModel.h): the gemmi structure as read, whether it is ModelCIF, the PAE matrix where a prediction came with one, and the name the report gives it. - ParseRugnuxModel / ReadRugnuxModelFile (writer/RugnuxModelFile.h, in JFJochRugnuxFiles): bytes in, gzip by magic, PDB/mmCIF by content, _ma_qa_metric detection as before; the file reader takes the PAE JSON from the same place PaePathFor named. - ProcessConfig::model replaces model_path; PrepareSearchModel, RunMolecularReplacement, ValidateAgainstModel and ModelReferenceIntensities take the model; result fields name it by model_name. - rugnux reads the model before the run starts and stops with an error where the file holds no model (it used to run and report the model as not validated). The viewer reads it when the job is set up. - The broker parses an uploaded model at once and answers 400 where it is not one; it keeps the parsed model in memory, with no temporary directory or file. It takes no PAE. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>	2026-10-17 16:11:58 +02:00
leonarski_fandClaude Opus 5.5	80f634b641	MR GPU: engines spread over the cards; the transform packed where it is expected faster ... Engine placement: the rigid-body engines past this card's first go one card after the other in turn, from the next card and this one last, each within half of its budget. A small cell on four cards (24 engines of 0.09 GB) had put all of them on this card, which has room for them, where rc176 spread them; now 6/6/6/6. A large cell on four 15.6 GB cards keeps T+1/T+2/T+2/T+2. Layout: packing was refused wherever it cost any card an engine, which kept 4nwv plain on four T4s although the packed rotation function on ONE card (15.1 s) already beat plain over four (18.5 s). Now the two layouts' plans are compared on a small cost model, decided once before the search from sizes and counts alone: seconds = rotation interpolations (orientations x reflections x operators) x s/interpolation / cards with a copy + rigid-body fits at once x engine GB x s/(fit GB) / engines Constants measured on 4nwv on Tesla T4 (17255 x 244183 x 4 interpolations): 75.8 s plain and 15.1 s packed on one card; rescoring + null 28.5 s with one engine and 11.6 s with seven, 9 fits of 2.10 GB, so 19.7 s shared among the engines. Packing must still keep the search, the scores and (where plain has it) the rigid body on the GPU, and the budget must hold both grids while the packed one is made. Expected on four T4s: packed T+1/T+1/T+1/T+1, 8.7 s against 21.8 s plain. One card is unchanged (the engines are the same either way, so packed). The layout line now logs both expected times and the search's size. Layout and engine count change where the work runs, never a number. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01PXc1zD1yxHqaR1DGdCTHL4	2026-10-17 10:34:09 +02:00
leonarski_fandClaude Opus 5.5	0f461a65a2	Merge mr-transform-layout: the corner-packed molecular transform beside MR on every card ... Combines mr-multigpu (per-card engine budgets, a transform copy on each other card, the rotation/translation functions split over the cards) with mr-transform-layout (the GPU transform optionally held corner-packed, same bits, 2.2x faster rotation function). Conflict (MolecularReplacement.cpp): the two new functions side by side (PackMolecularTransformGPU next to SplitRotationFunction/SplitTranslationFunction). On top of the textual resolution: - One layout decision for all cards, not one per card: the functions are split into equal slices, so a mix of packed and plain cards would run at the speed of the plain ones; either layout gives the same bits. - PackMolecularTransformGPU now plans with the other cards' budgets too and packs only where every card keeps what the plain plan gives it: this card's transform, engines and score engine, and on every other card its copy and its engine count. A packed copy is made after the card's engines are reserved; copy and engines within half of that card's budget leave room for the plain grid it is made from. - The copies on the other cards are made in the chosen layout, and the per-card plan (copies, engines, room) is made with the bytes actually placed. - Test: four 15.6 GB cards stay plain (packed, each other card would fall from T+2 to T+1); with 24 GB cards beside, packed. So on a 4x T4 4nwv runs split and plain, on one card packed; whether giving up 3 of 7 engines for the packed rotation function would pay there is left to a server measurement. Workstation (1x RTX 5080, --gpulock), against rc176: battery timing --benchmark standard (9zlo, 9s02, 9gjx, 4nwv) and --benchmark inhouse (myob, cytc, 4nwv) on GPU, inhouse also --no-gpu: p.hkl, p_model.pdb and the MR_ report block byte-identical on every set. 4nwv GPU: rotation 5.53 -> 2.50 s, MR step 20.1 -> 16.5 s (packed, 2.28 GB in place of 0.84 GB). Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01PXc1zD1yxHqaR1DGdCTHL4	2026-10-16 18:46:58 +02:00
leonarski_fandClaude Opus 5.5	3aa67a6059	MR GPU: corner-packed molecular transform for the rotation function ... Each sample of the molecular transform interpolates over 8 grid corners that lie in four u-rows of the half-l grid, 4-5 32-byte sectors per sample. On the GPU the transform can now be held packed: every point (i, j, l) stores its four (v, w) corners, so the two neighbouring records hold all eight, read from two places. The packed grid is cut to |u| <= reach as the plain one already is in v, and has the conjugate plane l = -1 in front; below l = -1 the eight corners are read mirrored about -i0 - 1 and conjugated. Same floats, same accumulation order: rotation and translation functions give the same bits (checked in MolecularReplacement_GPUMatchesCPU). The layout is chosen up front from the budget (PackMolecularTransformGPU): packed where the answer merge's plan holds every part beside it that it holds beside the plain transform, and the budget holds both grids while the packed one is made from the plain one on the device; logged either way. The upload no longer stages a host copy of the grid. The CPU At() is unchanged: a microbenchmark gained 1.3x single-threaded and ~1.0-1.1x at 16-32 threads, not worth 2.7x the host memory. 4nwv (moved model, timing benchmark), RTX 5080: rotation 5.56 -> 2.48 s, MR step 20.9 -> 16.7 s; transform on the card 0.84 -> 2.28 GB. p.hkl, p_model.pdb and the MR_ report block byte-identical on the timing sets (GPU and --no-gpu) and on 4nwv, 8tyy, 6oel, 3inp. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01PXc1zD1yxHqaR1DGdCTHL4	2026-10-16 17:55:30 +02:00
leonarski_fandClaude Opus 5.5	bfc6ca8487	MR and model validation: use every card's memory, split MR's functions over the cards ... On a multi-GPU host the structure stage ran essentially on one card: the rotation function's launches all went to the search's card, and the rigid-body engines of model validation and MR were admitted only within half of that one card's budget, although RigidBodyGPUPool already placed engines on other cards. On a 4x T4 server 4nwv's MR rotation function took 75.8 s on one card, validation queued its 10 fits on one engine and MR's rescoring and null got one engine. - PlanModelValidationGPU / PlanMolecularReplacementGPU: this card is planned exactly as on a machine with it alone (GPU-vs-CPU placement unchanged: 80% of the total, less what is resident). The rigid-body engines it has no room for go on the other cards in turn, each against its own budget (80% of its total, less the resident bytes, counted on every card) within half of it. MR also puts a copy of the molecular transform on each other card within half of its budget. - RigidBodyGPUPool::Reserve takes per-card engine counts. - Validation forwards the most it holds on any card as gpu_bytes to a validation beside, and may run one beside only where twice that fits every card's budget. - MR splits every rotation and translation function into contiguous slices of the orientation list over the cards holding a transform copy (and room for the call's buffers), one thread per card, gathered back in order. Each orientation is scored by itself (one block / one map), nothing is summed across orientations, so N cards give the bytes of one. - ScoreEngines keeps a room per card; score engines always go on the search's own card; function buffers are held on the card they run on. Byte-identical at N=1 (workstation, one RTX 5080): timing benchmark (myob, cytc, 4nwv) and 4nwv, 8tyy, 6oel, 3inp with --model give the same p.hkl, MTZ data, p_model.pdb, maps and report against rc176. New tests: per-card plans on four 15.6 GB cards (validation 1/3/3/3 engines, MR T+1/T+2/T+2/T+2), and the split driven over 1-4 virtual cards on one device, bitwise equal to one card. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01PXc1zD1yxHqaR1DGdCTHL4	2026-10-16 17:16:28 +02:00
leonarski_fandFilip Leonarski	19b135186d	v1.0.0-rc.175 (#85) ... * Rugnux: Processes a collection live while jfjoch_broker writes it (`rugnux <master.h5> <broker URL>`). * Rugnux: Processing starts on the first images and confirms its choices once all are in, so analysis can begin during collection. * Rugnux: Faster processing, especially on servers with several GPUs and CPU sockets and on computers without a GPU (`--no-gpu`, macOS). * Rugnux: Uses much less GPU memory, so large data sets stay on the GPU of smaller cards, and a data set too large for the card is processed on the CPU instead. * Rugnux: On macOS, Bragg integration runs on the Apple GPU. * Rugnux: Better handling of twinning and pseudo-symmetry, with the twin hypothesis written as `<prefix>_twin_<SG>.mtz`, and a wrong `--model` no longer confirms the data or decides the hand. * Rugnux: `--model` accepts predicted (AlphaFold) models and falls back to molecular replacement when the model is not placed as a rigid body (experimental `--mr` forces it), settling space group, hand and twinning and writing a different answer as `<prefix>_mr.mtz`. * Rugnux: Molecular replacement is faster and settles the space group in more cases with several copies in the asymmetric unit. * Rugnux: Deposition-ready mmCIF, a richer report, and numbered steps on the terminal with the full log in `<prefix>_log.txt`; `_P1.mtz`, `--estimate-beam-center` and `--beam-center-search` are removed. * Rugnux: The beam-stop shadow is found correctly on tilted detectors. * Rugnux: Stills files that record a stationary goniometer axis get the default stills geometry refinement. * jfjoch_viewer: "Analyze dataset" uses the same defaults as a bare `rugnux <file>`, and shows the results of processed CBF, marCCD and SMV sweeps. * jfjoch_viewer: The Files panel refreshes on F5 and every few seconds, and the plot type and other selections stay put during live collection. * jfjoch_writer: Memory stays bounded and old data files are closed efficiently on long runs, any failure ends the run in an error state the broker is told about, and the master file appears only after its data files; the ZeroMQ pusher logs when a stalled writer makes it drop images. * Fixes: The TCP image pusher no longer blocks the broker's receiver, GPU out-of-memory failures stop with a clear message, and the XDS plugin masks module and chip edges. --------- Co-authored-by: Filip Leonarski <jungfrau@filips-mac-mini.home> Reviewed-on: #85 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>	2026-10-16 15:34:43 +02:00