2 Commits

Include renames

Author	SHA1	Message	Date
leonarski_fandClaude Opus 5.5	b6392a3f58	RESULT-CHANGING (ulp level, CUDA builds): the CUDA model density is the CPU walk's, bit for bit ... ModelDensityGPU's gather had arithmetic of its own: per-thread offsets in Cartesian, the atom's nearest image to the brick, r2 = x x + y y + z z, the radius squared in float. It now does what UseDensityBoxesByPlane + AtomDensity (ModelGrid.cpp) and ModelDensityMetal.metal do, in their order: - each brick's atoms carry their box (c - d, wrapped start, 2 d); a point is in the box by a subtraction, and f = centre - (u, v, w) in the box's own unwrapped index; - x = m00 fx + (m01 fy + m02 fz), y = m11 fy + m12 fz, z = m22 fz with gemmi's orth_n (orth * (1/n), as Grid sets it) in float; r2 = (y y + z z) + x x against max_r2 = float(r^2) rounded from the double radius (new ModelDensityAtom field); - gemmi's expapprox, the five Gaussians in order, atoms in model order per point. Device code is already compiled with --fmad=false (top-level CMakeLists), so nothing is contracted. - The centres are no longer wrapped into the cell (ModelStructureFactorsGPU, RigidBodyGPU's place_kernel): float(fractional * n), as MakeDensityBox holds them; the mask keeps wrapped fractional coordinates. The 'narrow' nearest-image branch is gone: Supports() already leaves only boxes narrower than the cell. The target is PutModelDensityOnGrid() with no orbits to symmetrize (one copy of the content, which is what the gather grids; symmetry stays composed in reciprocal space). A rounding tie in the box centre c (float on the GPU, double on the CPU) changes no point: either box covers the sphere with half a spacing to spare. New ModelDensityGPU_BitIdenticalToCPU ([ModelValidation][gpu]) memcmps the grids: triclinic P1 and P 21 21 21 cells, 3000 atoms over -0.5..1.5 of the cell, a quarter anisotropic - 0 points differ. RTX 5080, alternating base (8d199cceb) / this, under the GPU lock: - gather kernel (nsys): 4nwv --model median 2.06 -> 2.55 ms, total 0.79 -> 0.97 s; 9s02 --mr median 0.30 -> 0.37 ms, total 0.94 -> 1.17 s (+~25%, the box test and per-point index arithmetic). - wall, two each: 4nwv --model 76.0/68.9 -> 74.4/71.0 s, --mr 71.3/71.1 -> 70.9/71.6 s; 9s02 --model 25.1/22.6 -> 23.3/23.5 s, --mr 23.3/23.6 -> 23.3/23.2 s; 5reo --model 6.2/5.5 -> 5.5/5.7 s. Model validation 4nwv 12.4/12.3 -> 12.3/11.7 s; MR 4nwv 15.4/15.2 -> 15.4/15.1 s, 9s02 2.3/2.4 -> 2.4/2.4 s: no change beyond noise. - outputs (each build run-to-run identical): p.hkl identical on all; R-work/R-free and every decision unchanged (4nwv validation 0.2982/0.2969, 9s02 MR AGREES P 21 21 2 0.2503/0.2517, 4nwv MR UNDECIDED I 2 2 2 / I 21 21 21). Moved: MODEL_FIT_SIGMA 9s02 99.21 -> 101.68, 5reo 103.96 -> 104.98; MR placement Z 9s02 142.1 -> 145.6, 4nwv 46.7 -> 46.2; 4nwv anomalous site 4.01 -> 4.02 sigma; 4nwv placed model 1322/125462 lines in the last digit (2fo-fc max |d| 0.04 rms, CC 0.99999994); 9s02/5reo models identical, maps to 2e-5 rms. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01PXc1zD1yxHqaR1DGdCTHL4	2026-10-18 18:10:23 +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