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Jungfraujoch/tests/ModelScaleGPUTest.cpp
T
leonarski_fandClaude Opus 5.5 274d42a2e7 ModelScaleGPU: FitSolvent 3x faster; a test on a model's own points 
- |Fcalc + solvent| is taken once per fit instead of at every step: the solvent pair is fixed for the
  whole of a fit.
- The per-step anisotropic factor and the derivatives are computed per point in float, and summed in
  double as before. Double arithmetic was most of the cost on a card with little double throughput. The
  final R of the grid stays in gemmi's double arithmetic.
- Each mode reduces only the slots it fills; 48 blocks per fit instead of 128.
- The first upload of a batch no longer adds a stream synchronisation.

FitSolvent per zone at 3.5 A (RTX 5080, real zone hkl sets, synthetic amplitudes): 3.2 ms at 3.3k
points, 9.2 ms at 72k and 21.6 ms at 213k, against 9.7 / 29.6 / 62.9 ms before. Fit() is 0.25-0.66 ms.
Against gemmi, k_overall and b* agree to 1e-9 - 1.4e-5 relative, and the grid winner is the same.

New test ModelScaleGPU_MatchesGemmiOnAModelsPoints: the rigid body's own points (the ClusterPdb
fixture with anisotropic atoms, its own amplitudes, a displaced placement, the rigid body's Fcalc and
mask), five groups at 6 and 3.5 A. The R tolerance of the synthetic cases is now 1e-5. That is the
resolution of gemmi's own fit: its Levenberg-Marquardt stops at a WSSR change of 1e-5, and perturbing
gemmi's own Fcalc by 1e-5 moves its answer by up to 1.2e-4 of <Fobs>.

Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01D1G8gJVAy6gp1K5Dz3NE5C
2026-09-28 19:28:56 +02:00

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// SPDX-FileCopyrightText: 2026 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
// SPDX-License-Identifier: GPL-3.0-only
#include <catch2/catch_all.hpp>
#include "../common/CUDAWrapper.h"
#ifdef JFJOCH_USE_CUDA
#include <algorithm>
#include <cmath>
#include <complex>
#include <cstring>
#include <random>
#include <vector>
#include <filesystem>
#include <fstream>
#include "gemmi/asumask.hpp"
#include "gemmi/mmread_gz.hpp"
#include "gemmi/scaling.hpp"
#include "gemmi/symmetry.hpp"
#include "gemmi/unitcell.hpp"
#include "../common/Logger.h"
#include "../rugnux/ModelFFT.h"
#include "../rugnux/ModelGrid.h"
#include "../rugnux/ModelScaling.h"
#include "../rugnux/ModelScaleGPU.h"
#include "../rugnux/ModelValidation.h"
#include "../rugnux/RigidBodyRefine.h"
namespace {
constexpr double PI_ = 3.14159265358979323846;
// Scaling points in the reciprocal asymmetric unit of `sg` to d_min, sorted as prepare_points() leaves
// them. Fcalc has random phases and a Wilson fall-off, the mask term is strong at low resolution and
// roughly opposite in phase, and |Fobs| comes from a known overall scale, anisotropic B and solvent pair
// with 5% noise - so the fit has a right answer and a realistic shape of residual.
gemmi::Scaling<float> MakeScaling(const gemmi::UnitCell &cell, const gemmi::SpaceGroup &sg, double d_min) {
gemmi::Scaling<float> scaling(cell, &sg);
scaling.use_solvent = true;
const gemmi::GroupOps gops = sg.operations();
const gemmi::ReciprocalAsu asu(&sg);
const gemmi::Miller lim = cell.get_hkl_limits(d_min);
std::vector<gemmi::Miller> hkl;
for (int h = -lim[0]; h <= lim[0]; h++)
for (int k = -lim[1]; k <= lim[1]; k++)
for (int l = -lim[2]; l <= lim[2]; l++) {
const gemmi::Miller m{{h, k, l}};
if ((h == 0 && k == 0 && l == 0) || cell.calculate_d(m) < d_min || !asu.is_in(m) ||
gops.is_systematically_absent(m))
continue;
hkl.push_back(m);
}
std::sort(hkl.begin(), hkl.end());
// B_cart of 25/35/30 A^2 with an off-diagonal term, as B*
gemmi::SMat33<double> b_cart{25, 35, 30, 4, -3, 2};
const gemmi::SMat33<double> b_star = b_cart.transformed_by(cell.frac.mat);
std::mt19937 rng(20260928);
std::uniform_real_distribution<double> uniform(0.0, 1.0);
std::normal_distribution<double> gauss(0.0, 1.0);
const double k_overall = 3.0, k_sol = 0.38, b_sol = 52.0;
for (const gemmi::Miller &m : hkl) {
const double stol2 = cell.calculate_stol_sq(m);
const double phase = 2 * PI_ * uniform(rng);
const double amp = 200.0 * std::exp(-10.0 * stol2) * std::sqrt(-std::log(1.0 - 0.999 * uniform(rng)));
const std::complex<double> fc = std::polar(amp, phase);
const std::complex<double> fm = std::polar(1500.0 * std::exp(-20.0 * stol2) * (0.5 + uniform(rng)),
phase + PI_ + 0.5 * gauss(rng));
const std::complex<float> fcf(fc), fmf(fm);
const std::complex<double> total = std::complex<double>(fcf) + k_sol * std::exp(-b_sol * stol2) * std::complex<double>(fmf);
const double fobs = k_overall * std::exp(-0.25 * b_star.r_u_r(m)) * std::abs(total) * (1.0 + 0.05 * gauss(rng));
gemmi::Scaling<float>::Point p{};
p.hkl = m;
p.stol2 = stol2;
p.fcmol = fcf;
p.fmask = fmf;
p.fobs = static_cast<float>(std::fabs(fobs));
p.sigma = static_cast<float>(0.05 * std::fabs(fobs) + 0.5);
scaling.points.push_back(p);
}
return scaling;
}
// A synthetic "protein" of 150 carbons, every third anisotropic, in `cryst` - ModelValidationTest.cpp's
// rigid-body fixture - and the Scaling points RigidBodyTarget::Residuals fits at a displaced
// placement q0: the model's own amplitudes as Fobs, and the Fcalc and bulk-solvent Fmask of the
// displaced model, gridded and composed as the rigid body does.
gemmi::Scaling<float> ModelPoints(const char *cryst, double zone) {
std::string pdb = cryst;
std::mt19937 rng(20260902);
std::uniform_real_distribution<double> x(2, 14), y(2, 16), z(2, 18);
char line[96];
for (int i = 1; i <= 150; i++) {
std::snprintf(line, sizeof line, "ATOM %5d C UNK A 1 %8.3f%8.3f%8.3f 1.00 20.00 C\n",
i, x(rng), y(rng), z(rng));
pdb += line;
}
pdb += "END\n";
const std::string path = "model_scale_gpu_test.pdb";
std::ofstream(path) << pdb;
Logger logger("ModelScaleGPUTest");
const auto reference = ModelReferenceIntensities(path, {}, {}, 3.0, logger);
gemmi::Structure st = gemmi::read_structure_gz(path, gemmi::CoorFormat::Detect);
std::filesystem::remove(path);
st.setup_cell_images();
int i = 0;
for (gemmi::Chain &ch : st.models[0].chains)
for (gemmi::Residue &r : ch.residues)
for (gemmi::Atom &a : r.atoms)
if (i++ % 3 == 0)
a.aniso = {0.30f, 0.25f, 0.20f, 0.02f, -0.01f, 0.03f};
const gemmi::SpaceGroup &sg = *st.find_spacegroup();
gemmi::AsuData<gemmi::ValueSigma<float>> fobs;
fobs.unit_cell_ = st.cell;
fobs.spacegroup_ = &sg;
for (const auto &r : reference)
if (st.cell.calculate_d({{r.h, r.k, r.l}}) >= zone)
fobs.v.push_back({{{r.h, r.k, r.l}}, {std::sqrt(r.I), 1.0f}});
fobs.ensure_sorted();
gemmi::Model model = st.models[0];
RigidBodyTarget target(model, st.cell, sg, 4);
const double q0[6] = {0.12, -0.09, 0.07, 0.15, -0.10, 0.05};
target.Place(q0, model);
gemmi::Grid<float> grid;
grid.unit_cell = st.cell;
grid.spacegroup = &sg;
grid.set_size_from_spacing(zone / 3.0, gemmi::GridSizeRounding::Up);
std::vector<gemmi::Miller> hkl;
for (const auto &hv : fobs.v)
hkl.push_back(hv.hkl);
const SymmetryComposition composition(grid, zone, hkl);
gemmi::DensityCalculator<gemmi::IT92<float>, float> dc;
dc.d_min = zone;
dc.rate = 1.5;
dc.grid.unit_cell = st.cell;
dc.grid.spacegroup = &sg;
dc.set_refmac_compatible_blur(model);
PutModelDensityOnGrid(dc, model, {}, 4);
std::vector<std::complex<double>> fc;
composition.Compose(MapToFPhi(dc.grid), dc.blur, fc, nullptr, 4);
gemmi::Grid<float> mask = grid;
PutMaskOnGrid(mask, model, OrbitLeaders(mask, 4), 4);
const gemmi::FPhiGrid<float> fm = MapToFPhi(mask);
gemmi::AsuData<std::complex<float>> fcalc, fmask;
for (size_t m = 0; m < composition.Hkl().size(); m++) {
fcalc.v.push_back({composition.Hkl()[m], std::complex<float>(fc[m])});
fmask.v.push_back({composition.Hkl()[m], fm.get_value_by_hkl(composition.Hkl()[m])});
}
gemmi::Scaling<float> scaling(st.cell, &sg);
scaling.use_solvent = true;
scaling.prepare_points(fcalc, fobs, &fmask);
return scaling;
}
struct GpuPoints {
CudaStream stream;
ModelScaleGPU scale;
CudaDevicePtr<float2> fcmol, fmask;
explicit GpuPoints(const gemmi::Scaling<float> &s)
: scale(stream, s.points.size()), fcmol(s.points.size()), fmask(s.points.size()) {
std::vector<std::array<int, 3>> hkl;
std::vector<double> stol2;
std::vector<float> fobs, sigma;
std::vector<float2> fc, fm;
for (const auto &p : s.points) {
hkl.push_back(p.hkl);
stol2.push_back(p.stol2);
fobs.push_back(p.fobs);
sigma.push_back(p.sigma);
fc.push_back(make_float2(p.fcmol.real(), p.fcmol.imag()));
fm.push_back(make_float2(p.fmask.real(), p.fmask.imag()));
}
std::vector<std::array<double, 6>> constraints(s.constraint_matrix.begin(), s.constraint_matrix.end());
double frac[9];
for (int i = 0; i < 3; i++)
for (int j = 0; j < 3; j++)
frac[3 * i + j] = s.cell.frac.mat[i][j];
scale.SetPoints(hkl, stol2, fobs, sigma, constraints, frac);
cudaMemcpy(fcmol, fc.data(), fc.size() * sizeof(float2), cudaMemcpyHostToDevice);
cudaMemcpy(fmask, fm.data(), fm.size() * sizeof(float2), cudaMemcpyHostToDevice);
}
};
double MaxAbs(const double b[6]) {
double m = 0;
for (int i = 0; i < 6; i++)
m = std::max(m, std::fabs(b[i]));
return m;
}
// The tolerances are those of gemmi's fit rather than of the arithmetic. Its Levenberg-Marquardt stops
// when the WSSR has changed by less than 1e-5 twice, which leaves the scale short of the minimum by
// about sqrt(1e-5) of the residual, so where a step is accepted or the fit stops on a near-tie the last
// bit decides it: measured, gemmi moves by up to 1e-4 of <Fobs> when its own Fcalc changes by 1e-5.
constexpr double R_TOLERANCE = 1e-5;
void CheckSameScale(const ModelScaleParams &gpu, const gemmi::Scaling<float> &cpu) {
const double b_cpu[6] = {cpu.b_star.u11, cpu.b_star.u22, cpu.b_star.u33,
cpu.b_star.u12, cpu.b_star.u13, cpu.b_star.u23};
CHECK(std::fabs(gpu.k_overall - cpu.k_overall) <= 1e-4 * std::fabs(cpu.k_overall));
for (int i = 0; i < 6; i++)
CHECK(std::fabs(gpu.b_star[i] - b_cpu[i]) <= 1e-4 * MaxAbs(b_cpu) + 1e-12);
}
struct Case {
const char *name;
double a, b, c, alpha, beta, gamma;
const char *hm;
};
const Case CASES[] = {
{"triclinic", 41, 47, 53, 82, 97, 104, "P 1"},
{"monoclinic", 72, 44, 51, 90, 112, 90, "C 1 2 1"},
{"tetragonal", 64, 64, 81, 90, 90, 90, "P 4"},
{"hexagonal", 58, 58, 96, 90, 90, 120, "P 6"},
{"cubic", 92, 92, 92, 90, 90, 90, "P 2 3"},
};
} // namespace
TEST_CASE("ModelScaleGPU_FitMatchesGemmi", "[ModelValidation][gpu]") {
if (get_gpu_count() == 0)
return;
for (const Case &c : CASES) {
INFO(c.name);
gemmi::UnitCell cell(c.a, c.b, c.c, c.alpha, c.beta, c.gamma);
const gemmi::SpaceGroup &sg = *gemmi::find_spacegroup_by_name(c.hm);
gemmi::Scaling<float> cpu = MakeScaling(cell, sg, 2.8);
REQUIRE(cpu.points.size() > 2000);
GpuPoints gpu(cpu);
for (const double k_sol : {0.25, 0.4})
for (const double b_sol : {30.0, 60.0}) {
gemmi::Scaling<float> ref = cpu;
ref.k_sol = k_sol;
ref.b_sol = b_sol;
ref.fix_k_sol = true;
ref.fix_b_sol = true;
ref.fit_isotropic_b_approximately();
ref.fit_parameters();
const ModelScaleParams p = gpu.scale.Fit(gpu.fcmol, gpu.fmask, k_sol, b_sol);
CheckSameScale(p, ref);
gemmi::Scaling<float> with_gpu = ref;
with_gpu.k_overall = p.k_overall;
with_gpu.b_star = {p.b_star[0], p.b_star[1], p.b_star[2], p.b_star[3], p.b_star[4], p.b_star[5]};
CHECK(std::fabs(with_gpu.calculate_r_factor() - ref.calculate_r_factor()) < R_TOLERANCE);
}
}
}
TEST_CASE("ModelScaleGPU_SolventGridMatchesFitModelScale", "[ModelValidation][gpu]") {
if (get_gpu_count() == 0)
return;
for (const Case &c : CASES) {
INFO(c.name);
gemmi::UnitCell cell(c.a, c.b, c.c, c.alpha, c.beta, c.gamma);
const gemmi::SpaceGroup &sg = *gemmi::find_spacegroup_by_name(c.hm);
gemmi::Scaling<float> cpu = MakeScaling(cell, sg, 2.8);
GpuPoints gpu(cpu);
const ModelScaleReport report = FitModelScale(cpu, {}, 8);
const ModelSolventFit fit = gpu.scale.FitSolvent(gpu.fcmol, gpu.fmask);
CHECK(fit.n_grid == report.n_grid);
CHECK(fit.k_sol == cpu.k_sol); // the same grid point, so the same double
CHECK(fit.b_sol == cpu.b_sol);
CHECK(std::fabs(fit.r - report.r_work_fit) < R_TOLERANCE);
CheckSameScale(fit.scale, cpu);
}
}
// The rigid body's own sequence on a model's points: FitModelScale once for the zone, then the
// per-evaluation fit at that solvent pair.
TEST_CASE("ModelScaleGPU_MatchesGemmiOnAModelsPoints", "[ModelValidation][gpu]") {
if (get_gpu_count() == 0)
return;
const char *crysts[] = {
"CRYST1 40.000 50.000 60.000 90.00 90.00 90.00 P 1 1\n",
"CRYST1 40.000 50.000 60.000 90.00 100.00 90.00 C 1 2 1 4\n",
"CRYST1 40.000 50.000 60.000 90.00 90.00 90.00 P 21 21 21 4\n",
"CRYST1 60.000 60.000 60.000 90.00 90.00 90.00 I 2 3 24\n",
"CRYST1 80.000 80.000 80.000 90.00 90.00 90.00 F 41 3 2 96\n",
};
for (const char *cryst : crysts)
for (const double zone : {6.0, 3.5}) {
INFO(cryst << " at " << zone << " A");
gemmi::Scaling<float> cpu = ModelPoints(cryst, zone);
REQUIRE(cpu.points.size() > 50);
GpuPoints gpu(cpu);
const ModelScaleReport report = FitModelScale(cpu, {}, 4);
const ModelSolventFit solvent = gpu.scale.FitSolvent(gpu.fcmol, gpu.fmask);
CHECK(solvent.k_sol == cpu.k_sol);
CHECK(solvent.b_sol == cpu.b_sol);
CHECK(std::fabs(solvent.r - report.r_work_fit) < R_TOLERANCE);
CheckSameScale(solvent.scale, cpu);
gemmi::Scaling<float> ref = cpu;
ref.fix_k_sol = true;
ref.fix_b_sol = true;
ref.k_overall = 1;
ref.b_star = {0, 0, 0, 0, 0, 0};
ref.fit_isotropic_b_approximately();
ref.fit_parameters();
const ModelScaleParams p = gpu.scale.Fit(gpu.fcmol, gpu.fmask, cpu.k_sol, cpu.b_sol);
CheckSameScale(p, ref);
}
}
TEST_CASE("ModelScaleGPU_Deterministic", "[ModelValidation][gpu]") {
if (get_gpu_count() == 0)
return;
gemmi::UnitCell cell(72, 44, 51, 90, 112, 90);
gemmi::Scaling<float> cpu = MakeScaling(cell, *gemmi::find_spacegroup_by_name("C 1 2 1"), 2.5);
GpuPoints gpu(cpu);
const ModelSolventFit first = gpu.scale.FitSolvent(gpu.fcmol, gpu.fmask);
const ModelScaleParams first_fit = gpu.scale.Fit(gpu.fcmol, gpu.fmask, first.k_sol, first.b_sol);
for (int repeat = 0; repeat < 3; repeat++) {
const ModelSolventFit again = gpu.scale.FitSolvent(gpu.fcmol, gpu.fmask);
CHECK(again.k_sol == first.k_sol);
CHECK(again.b_sol == first.b_sol);
CHECK(std::memcmp(&again.r, &first.r, sizeof(double)) == 0);
CHECK(std::memcmp(&again.scale, &first.scale, sizeof(ModelScaleParams)) == 0);
const ModelScaleParams fit = gpu.scale.Fit(gpu.fcmol, gpu.fmask, first.k_sol, first.b_sol);
CHECK(std::memcmp(&fit, &first_fit, sizeof(ModelScaleParams)) == 0);
}
}
#endif
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