leonarski_fandClaude Opus 5.5
51706641fa
The molecular transform's FFT went to the GPU only where its buffers took at most a quarter of the card (MapToFPhiGPUFits), the last quarter rule left in molecular replacement. On a large cell that is never: 4nwv's 768^3 box needs 5.45 GB, so on a 16 GB card it ran on the CPU in FFTW, single-threaded - 12.5 s of the search's 31 s. Now it is judged, as every other part of the search, against the search's budget (80% of the card less what is resident; the search holds nothing else yet when it runs), and the device writes only the cropped transform the search keeps (CropHalfL, moved to ModelFFT), so it needs 4.46 GB instead of 5.45. cuFFT and FFTW agree to float rounding, not bit for bit, so wherever the transform moves to the GPU the search's functions can differ in their last bits: on 4nwv on 16 GB and 8.55 GB cards it moves (it now does on any card above about 5.6 GB, before above 21.8 GB); the small boxes were on the GPU before and give the same values (the same kernel, cropped). Measured on the RTX 5080, timing benchmark: 4nwv's transform 14.1 -> 2.2 s, MR 31.6 -> 20.1 s, run 93.0 -> 89.2 s; MR's peak device memory unchanged at 8.7 GB (the FFT's own 5.2 GB comes before anything else is held). On this card the reflection files, maps, placed models, reports and the MR candidate lines of myob, cytc and 4nwv still came out byte-identical to rc175-metal-merge. [MolecularReplacement] passes. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
30 lines
1.8 KiB
C
30 lines
1.8 KiB
C
// SPDX-FileCopyrightText: 2026 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
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// SPDX-License-Identifier: GPL-3.0-only
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#pragma once
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#include "gemmi/grid.hpp"
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#include "gemmi/recgrid.hpp"
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// The structure factors of a real-space map on the model path (Fcalc from the model density, Fmask
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// from the bulk-solvent mask): what gemmi::transform_map_to_f_phi(map, true) returns - the
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// conjugated forward transform (F = sum rho exp(+2 pi i h.x)) scaled by V/N, kept for l >= 0 on an (nu, nv, nw/2+1) grid in the map's own XYZ order,
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// ready for prepare_asu_data() - computed with FFTW rather than gemmi's single-threaded pocketfft.
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// The same transform, not the same bits: the two libraries order their arithmetic differently.
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//
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// Plans are FFTW_ESTIMATE only - MEASURE would time candidate algorithms and could pick a different
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// one from run to run - and made once per grid size and kept, so the rigid body's hundred-odd
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// evaluations on one grid plan once. Safe to call from several threads at once.
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gemmi::FPhiGrid<float> MapToFPhi(const gemmi::Grid<float> &map);
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// The inverse: the real-space map of an (nu, nv, nw/2+1) half-l coefficient grid in XYZ order, as
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// get_f_phi_on_grid() fills it - what gemmi::transform_f_phi_grid_to_map() returns (rho = 1/V sum F
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// exp(-2 pi i h.x) on an (nu, nv, 2*(nw-1)) grid, NaN coefficients read as zero), computed with FFTW
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// under the same planning rules.
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gemmi::Grid<float> MapFromFPhi(const gemmi::FPhiGrid<float> &hkl);
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// The half-l grid `full` with only the indices |k|, l <= reach kept, on a grid of full.nu x (2 reach + 1) x
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// (reach + 1) that an index wraps into as it wraps into the whole one (the molecular transform's, which is
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// read no further out).
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gemmi::FPhiGrid<float> CropHalfL(const gemmi::FPhiGrid<float> &full, int reach);
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