Two ways the scale fit's normal matrix went singular and gemmi's jordan_solve threw "Trying to
reverse singular matrix. Column 0 is zeroed.", ending the run:
1. The isotropic start (fit_isotropic_b_approximately) takes log(Fobs/|Fcalc|) over the strong
reflections. At a phase-restricted reflection whose Fcalc and Fmask share a phase, some solvent
pair of the k_sol/b_sol grid can cancel the model exactly in float, |Fcalc + k_sol
exp(-b_sol s^2) Fmask| = 0. log(Fobs/0) = inf made that grid point's k_overall and B NaN, every
sum of the Levenberg-Marquardt NaN, and the solve failed. This is what stopped three open-arm
sets in the output pass after MR on the GPU (the scale fit after model validation's rigid body):
one strong reflection, one grid point. The CPU path has the same exposure; which grid point
hits an exact zero depends on the last bits of Fcalc, so the --no-gpu run of the same set went
through. Such a reflection has no log ratio and is now left out of the start - in the GPU kernel,
in FixedSolventFit::Start and, as a marked local change, in gemmi's own
fit_isotropic_b_approximately, so the three stay equal and the held-solvent fits are covered too.
2. In FitModelScale's CPU Levenberg-Marquardt (ModelValidation_CCModelUnrelatedModelConfirmsNothing
in a CUDA=OFF build): on 66 reflections of an unrelated model the fit walked to k_overall -424
and a B where k exp(-B s^2) |F| underflows at every reflection; the squares in J^T J were all 0
while J^T r kept a residue near 1e-210, which jordan_solve rejects. The fit now ends there, at
its best so far, as it would at the lambda limit; that grid point then loses on R. The GPU fit
takes the derivatives in float and their squares in double, so it cannot reach this state.
Both changes only touch fits that threw before. Byte identity checked against an rc176 build on
the standard and inhouse timing benchmarks and on 4nwv, 8tyy, 6oel (p.hkl, p_model.pdb, MTZ data,
MR_* report keys).
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01PXc1zD1yxHqaR1DGdCTHL4
leonarski_fandClaude Opus 5.5
210664f454