leonarski_fandClaude Opus 5.5
6f361ccde5
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
42 lines
2.4 KiB
C++
42 lines
2.4 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 <cstddef>
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#include <vector>
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#include "gemmi/dencalc.hpp" // DensityCalculator
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#include "gemmi/grid.hpp"
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#include "gemmi/it92.hpp" // IT92 x-ray form factors
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#include "gemmi/model.hpp"
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// gemmi's gridding of a model - the density of DensityCalculator::put_model_density_on_grid() and the
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// bulk-solvent mask of SolventMasker(AtomicRadiiSet::Refmac).put_mask_on_grid() - spread over
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// `nthreads` threads of ParallelFor's pool. Every grid point receives the same operations in the same
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// order as in gemmi's serial loops, so the grids are gemmi's, bit for bit, on any number of threads.
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// The points gemmi's Grid::symmetrize() reduces the orbits of this grid's size and space group into
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// (empty in P1). Both functions below take them, for a grid of the same size.
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std::vector<size_t> OrbitLeaders(const gemmi::Grid<float> &grid, size_t nthreads);
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// `dc` set up as for put_model_density_on_grid(): d_min, rate, blur, the grid's cell and group.
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void PutModelDensityOnGrid(gemmi::DensityCalculator<gemmi::IT92<float>, float> &dc, const gemmi::Model &model,
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const std::vector<size_t> &orbit_leaders, size_t nthreads);
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// `grid` sized, with its cell and group set.
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void PutMaskOnGrid(gemmi::Grid<float> &grid, const gemmi::Model &model, const std::vector<size_t> &orbit_leaders,
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size_t nthreads);
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// The number of points of the grid a model's structure factors to d_min are computed on at DensityCalculator's
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// `rate` (a spacing of d_min / (2 rate)) in this cell and space group: the grid's size, without making it.
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size_t ModelGridPoints(const gemmi::UnitCell &cell, const gemmi::SpaceGroup *sg, double d_min, double rate = 1.5);
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// What computing a model's structure factors on the CPU holds at its peak, per point of that grid: the density
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// and the bulk-solvent mask grids, and for each of them its transform's input copy, spectrum and coefficients,
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// with the two made at once (ModelValidation's compute_model_factors).
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constexpr size_t MODEL_FACTORS_BYTES_PER_GRID_POINT = 32;
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// What a molecular-replacement placement's structure factors and rigid body hold on the CPU at their peak, per
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// point of that grid: measured at under half of the above.
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constexpr size_t MODEL_PLACEMENT_BYTES_PER_GRID_POINT = 16;
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