5 Commits

Include renames

Author	SHA1	Message	Date
leonarski_fandClaude Opus 5.5	868ad0c8f2	ModelGrid: the model density on the Apple GPU (Metal), bit-identical to the CPU ... On macOS, where a Metal device may be used (not under --no-gpu), PutModelDensityOnGrid puts the density on the grid with a Metal gather (ModelDensityMetal), as ModelDensityGPU.cu does under CUDA: the grid in bricks of 4^3 points, one threadgroup each; every point adds, in model order, each atom whose box holds it and whose radius reaches it. No float atomics. The arithmetic is the CPU walk's of the previous commit, spelled out in ModelDensityMetal.metal - the point's place in single precision in the same order, gemmi's float expapprox ported as is, fast math and contraction off - so the grid is the CPU's bit for bit (ModelDensityMetal_BitIdenticalToCPU, [portable][Metal]: a triclinic cell and a P 21 21 21 one, a quarter of the atoms anisotropic, boxes wrapping at every face). The symmetrize stays on the CPU. - Each brick's atoms: (brick, atom) pairs counted and filled on the CPU in parallel over slabs of w, each worker taking the atoms in order, so the lists keep model order; at most the atoms' boxes' bricks. - The kernel writes straight into the grid FFTW reads where its pages can be handed to the GPU (large vectors are page-aligned on macOS), into its own buffer and copied otherwise. - 4^3 bricks rather than CUDA's 8^3: every point tests each atom reaching its brick, and the smaller brick took a half to a third of the kernel time. The box test is a subtraction against a start the host wraps. - Every grid goes to the GPU: giving it only grids of 256k points or more, or models of 8000 atoms or more, left 9s02's MR 0.8 s slower. - A box wider than the cell (an atom reaching a point through two images) stays on the CPU, whose walk adds both. A Metal failure puts that grid and every later one on the CPU, with one warning. - Each call runs in an autorelease pool of its own (see the rotation function's). Apple M6 (16 GB), alternating with the rotation-function build (the previous commit but one), two each: - 4nwv: wall 295.8/292.6 -> 275.2/277.8 s; model validation 48.9/49.0 -> 41.0/40.9 s; MR 130.2/130.3 -> 121.4/122.5 s (rescoring 40.9/40.3 -> 35.6/36.5 s, null 31.7/32.1 -> 26.8/26.6 s); user CPU 1998/2011 -> 1692/1681 s; peak footprint 17.8/18.5 -> 17.2/18.6 GB. The density's CPU time, sampled over a whole run, 316 CPU-s (16% of the busy samples) -> none, the pairs' sort 31 CPU-s. - 9s02: wall 76.7/76.5 -> 72.9/73.1 s; MR 16.9/16.8 -> 13.5/13.4 s. - 9zlo: wall 70.4/70.7 -> 69.8/69.6 s; MR 3.1/3.1 -> 2.2/2.2 s. p.hkl, the placed model and the maps are byte-identical to the previous commit's (density on the CPU) on all three, and so are the MR and validation logs but for their timings. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_018My7tqt8a4LyKKjP3FhScT	2026-10-18 17:04:17 +02:00
leonarski_fandClaude Opus 5.5	fe58c5041c	RESULT-CHANGING (ulp level): the model density's walk places its points in single precision ... PutModelDensityOnGrid walked each atom's box as gemmi does, with every point's place relative to the atom and its test against the atom's radius in double. The Apple GPU has no double, so a Metal gather could only come to the same grid to rounding. The density now has its own walk, UseDensityBoxesByPlane: the same planes, atoms, box and order as before, with the point's place in single precision in one fixed order of operations (f = centre - (u, v, w); x = m00 fx + (m01 fy + m02 fz), y = m11 fy + m12 fz, z = m22 fz with gemmi's upper-triangular orth_n; r2 = (y y + z z) + x x, taken where not above the radius squared). A gather that spells the same arithmetic out then finds the same points with the same bits, and gemmi's float expapprox and the Gaussian sums are already single precision. The solvent mask keeps the double walk: its points are 0 or 1, and a point at the edge would flip. The density differs from gemmi's in the last bits, so everything computed from it moves at that level. 9s02 on an Apple M6 against the previous commit: p.hkl unchanged; the MR decision (AGREES, P 21 21 2) and every R-work/R-free within 0.001; validation R(all) 0.3719 -> 0.3718; the validation rigid body took 29 evaluations instead of 22 to the same place (rotation 0.003 deg); Z of rejected candidates in other groups by up to 0.7; the model and maps differ in their last digits. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_018My7tqt8a4LyKKjP3FhScT	2026-10-18 17:04:17 +02:00
leonarski_fandClaude Opus 5.5	6f361ccde5	HostWorkerPool: half the budget, MR placements reserve 16 B per grid point, output unchanged ... Without a GPU (macOS), rc176's worker pool - 1/3 of the 12.9 GB budget on a 16 GB Mac - let only two molecular-replacement placements run at once, as each reserved 32 B per grid point (2.1 GB on 4nwv) against a measured ~0.95 GB. MR rescoring went from 38.6 s to 69 s and 4nwv's wall time from 402 s (budget off) to 444 s. On the M6 Mac mini (16 GB), 4nwv, two runs each in alternating order on a quiet machine: - old build 234774ff0: 418.4 s, 20.0-21.3 GiB peak footprint, 576-682k swapouts - rc176 as shipped: 444.2 s, 14.5-15.2 GiB, 39-66k swapouts - this change: 402.4 s, 15.5-15.8 GiB, 66-93k swapouts - budget switched off: 401.7 s, 21.8-23.3 GiB, 268-433k swapouts 9zlo/9s02/9gjx: 71.9/79.0/82.8 s (old build 73.6/82.2/83.6), no swap. p.hkl byte-identical in every run: the pool decides only what runs at once. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_018My7tqt8a4LyKKjP3FhScT	2026-10-18 08:42:02 +02:00
leonarski_fandClaude Opus 5.5	43e836573d	MR and model validation on the CPU: workers bounded by their bytes, not the thread count ... - The CPU translation function runs as many rotations at once as the host worker pool holds (8 B per grid point each, 550 MiB on a 400 A cell; 33 at once at 32 threads was 18 GiB), at most nthreads. Counted, not reserved: the rotations run on ParallelFor's pool, whose workers must not wait on memory. - Null replicates (model validation's and MR's) whose structure factors are made on the CPU reserve 32 B per point of their grid (ModelGridPoints) against the pool before they start, so the nine replicates, and nulls run side by side, hold at most the pool between them. Every replicate and rotation computes what it did and is stored by index: no result depends on how many run at once. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01PXc1zD1yxHqaR1DGdCTHL4	2026-10-17 09:31:05 +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