Refinement: an exception in a trial slot or in RefineModel no longer ends the run
A slot builder thread that throws (gemmi's topology or hydrogen placement, bad_alloc) would call std::terminate - rugnux or the broker gone. The slot is now left out as one the card cannot take is, with a warning, and MakeOwnSlot's GPU engine catches std::exception, not only JFJochException. Both callers of RefineModel (after the merge, and --mode refine) catch std::exception: the refinement is reported NOT_PERFORMED with "refinement failed: <what>" and the run writes everything else (cell e.s.d.s, unmerged MTZ, report), as the refinement is processing-inert. Test: --mode refine on a cell too large for the bulk-solvent grid comes back with REFINE= NOT_PERFORMED and the reason, not an exception. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_015CeEGgpKdfkCTJb3YNMJcu (cherry picked from commit dc4e99fe4b3da2a9a3fa4290b5f70bfcc8c7bdb8)
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@@ -45,6 +45,62 @@ gemmi::Mtz MakeMtz(const std::vector<std::pair<std::string, char>> &columns,
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bool InTestSet(int h, int k, int l) { return (h * 7 + k * 13 + l * 17) % 10 == 0; }
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// Waters scattered over the test cell, and their own |F|^2 as the data: the model as given scores well.
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void SyntheticRefineInput(gemmi::Structure &st, RugnuxReflections &data) {
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const gemmi::SpaceGroup *sg = gemmi::find_spacegroup_by_name("P 21 21 21");
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st.cell = test_cell;
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st.spacegroup_hm = sg->xhm();
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st.setup_cell_images();
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gemmi::Model model(1);
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gemmi::Chain chain("A");
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std::mt19937 rng(7);
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std::uniform_real_distribution<double> frac(0.0, 1.0);
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for (int i = 0; i < 120; i++) {
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gemmi::Residue res;
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res.name = "HOH";
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res.seqid = gemmi::SeqId(i + 1, ' ');
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res.het_flag = 'H';
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gemmi::Atom a;
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a.name = "O";
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a.element = gemmi::El::O;
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a.pos = test_cell.orthogonalize(gemmi::Fractional(frac(rng), frac(rng), frac(rng)));
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a.b_iso = 15.0f;
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a.occ = 1.0f;
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res.atoms.push_back(a);
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chain.residues.push_back(res);
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}
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model.chains.push_back(chain);
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st.models.push_back(model);
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gemmi::DensityCalculator<gemmi::IT92<float>, float> dc;
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dc.d_min = 2.0;
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dc.grid.unit_cell = test_cell;
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dc.grid.spacegroup = sg;
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dc.set_refmac_compatible_blur(st.models[0]);
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dc.put_model_density_on_grid(st.models[0]);
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const gemmi::AsuData<std::complex<float>> f =
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gemmi::transform_map_to_f_phi(dc.grid, true).prepare_asu_data(2.0, dc.blur);
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data.name = "synthetic.mtz";
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data.source = "MTZ";
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data.cell = test_cell;
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data.space_group = sg->xhm();
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data.amplitudes = false;
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for (const auto &hv : f.v) {
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if (hv.hkl == gemmi::Miller{{0, 0, 0}})
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continue;
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const double fc = std::abs(hv.value);
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MergedReflection m;
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m.h = hv.hkl[0];
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m.k = hv.hkl[1];
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m.l = hv.hkl[2];
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m.d = static_cast<float>(test_cell.calculate_d(hv.hkl));
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m.I = static_cast<float>(fc * fc);
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m.sigma = static_cast<float>(0.02 * fc * fc + 1.0);
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data.reflections.push_back(m);
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}
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}
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} // namespace
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TEST_CASE("RugnuxReflectionsFromMtz takes observed amplitudes over map coefficients", "[refine_only]") {
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@@ -124,62 +180,9 @@ TEST_CASE("ParseRugnuxReflections reads an MTZ from its bytes", "[refine_only]")
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TEST_CASE("RunRefineOnly scores a model against intensities, with amplitudes and free flags made for it",
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"[refine_only]") {
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// Atoms scattered over the cell; the data are their own |F|^2, so the model as given scores well.
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const gemmi::SpaceGroup *sg = gemmi::find_spacegroup_by_name("P 21 21 21");
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gemmi::Structure st;
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st.cell = test_cell;
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st.spacegroup_hm = sg->xhm();
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st.setup_cell_images();
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gemmi::Model model(1);
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gemmi::Chain chain("A");
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std::mt19937 rng(7);
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std::uniform_real_distribution<double> frac(0.0, 1.0);
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for (int i = 0; i < 120; i++) {
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gemmi::Residue res;
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res.name = "HOH";
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res.seqid = gemmi::SeqId(i + 1, ' ');
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res.het_flag = 'H';
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gemmi::Atom a;
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a.name = "O";
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a.element = gemmi::El::O;
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a.pos = test_cell.orthogonalize(gemmi::Fractional(frac(rng), frac(rng), frac(rng)));
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a.b_iso = 15.0f;
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a.occ = 1.0f;
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res.atoms.push_back(a);
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chain.residues.push_back(res);
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}
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model.chains.push_back(chain);
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st.models.push_back(model);
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gemmi::DensityCalculator<gemmi::IT92<float>, float> dc;
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dc.d_min = 2.0;
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dc.grid.unit_cell = test_cell;
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dc.grid.spacegroup = sg;
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dc.set_refmac_compatible_blur(st.models[0]);
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dc.put_model_density_on_grid(st.models[0]);
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const gemmi::AsuData<std::complex<float>> f =
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gemmi::transform_map_to_f_phi(dc.grid, true).prepare_asu_data(2.0, dc.blur);
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RugnuxReflections data;
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data.name = "synthetic.mtz";
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data.source = "MTZ";
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data.cell = test_cell;
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data.space_group = sg->xhm();
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data.amplitudes = false;
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for (const auto &hv : f.v) {
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if (hv.hkl == gemmi::Miller{{0, 0, 0}})
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continue;
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const double fc = std::abs(hv.value);
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MergedReflection m;
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m.h = hv.hkl[0];
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m.k = hv.hkl[1];
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m.l = hv.hkl[2];
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m.d = static_cast<float>(test_cell.calculate_d(hv.hkl));
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m.I = static_cast<float>(fc * fc);
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m.sigma = static_cast<float>(0.02 * fc * fc + 1.0);
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data.reflections.push_back(m);
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}
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SyntheticRefineInput(st, data);
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RefinementSettings settings;
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settings.score_only = true;
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settings.gpu = false;
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@@ -205,3 +208,22 @@ TEST_CASE("RunRefineOnly scores a model against intensities, with amplitudes and
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CHECK(text.find("REFINE_FREE_FLAGS= GENERATED") != std::string::npos);
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CHECK(text.find("REFINE_FRENCH_WILSON= TRUE") != std::string::npos);
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}
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TEST_CASE("RunRefineOnly reports a refinement that throws as not performed, with the reason", "[refine_only]") {
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// The data's cell, a hundred metres on a side, makes the bulk-solvent mask's grid too large to allocate.
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gemmi::Structure st;
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RugnuxReflections data;
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SyntheticRefineInput(st, data);
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data.cell = gemmi::UnitCell(1e6, 1e6, 1e6, 90, 90, 90);
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RefinementSettings settings;
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settings.gpu = false;
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settings.nthreads = 2;
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Logger logger("RefineOnlyTest");
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RefineOnlyResult r;
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REQUIRE_NOTHROW(r = RunRefineOnly(data, st, 0.0, settings, logger));
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CHECK_FALSE(r.refinement.ok);
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CHECK(r.refinement.failure_reason.find("refinement failed") == 0);
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const std::string text = RenderReportText(BuildRefineReportDocument("out", "synthetic.mtz", "model.cif", r), true);
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CHECK(text.find("REFINE= NOT_PERFORMED") != std::string::npos);
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CHECK(text.find("REFINE_REASON= refinement failed") != std::string::npos);
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}
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