Where the validation in the model's setting, started beside the first on
the forecast (b5980c9ba), is going to be kept, it writes the maps, the map
coefficients and the placed model on the written axes, and the first
validation's p_2fofc/p_fofc/p_anom.ccp4 and p_maps.mtz were overwritten
unread. ModelValidationSchedule::maps_superseded is asked once the
verdict, the setting and the indexing are decided, before any map is
made; the first validation then makes none (the map coefficients and the
MTZ are not built, the three map transforms not run, nothing written).
The answer is the same rule that keeps the forecast validation
afterwards (forecast_kept, now one lambda for both). The kept validation
also brings back the reflections it relabelled, free set included, so
relabel_output does not reindex and redraw them a second time. Where the
forecast is discarded or was never started, everything runs as before,
and modelpar's delete-before-rewrite stays for those cases. If the kept
validation then fails, a warning says no maps were written.
Log lines that disappear (first validation only, kept-forecast runs):
"mean 2mFo-DFc density at atom centres = ...", "anomalous difference map
from ... Bijvoet pairs; strongest density ...", "wrote p_2fofc.ccp4, ...";
in their place: "no maps made here - the validation in the model's
setting writes them". (The "anomalous density ... inverted" warning would
also go; it cannot be raised where a forecast is kept.)
Verified on 8sa8, 8xtg, 9ea5 (forecast kept), 8tyy, 7qis, myob_x10sa (no
forecast): p.mtz, p.hkl, p.cif, the three maps, p_maps.mtz and
p_model.cif/pdb md5-identical to the merge commit, repeated and at -N 8;
the discard path (8sa8 with a rotated model) identical files and log.
Time saved is small with the maps already on the GPU: 8sa8 7.6 -> 7.4 s,
8xtg 5.1 -> 5.0 s, 9ea5 within noise.
Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01SVmAWnzCmRKAXVUCdc4iNi
Where a model that fits is written on other axes than the data, the files
take its setting and the validation is made a second time on the
relabelled data. That second validation depends on the first only through
the setting and the indexing the first settles, and both are known long
before the first has finished: the change of basis right after the frame
scoring, the indexing the probe prefers before the null. So ValidateAgainstModel
now reports them (ModelFrameForecast, through ModelValidationSchedule::
on_forecast), and the second validation is started there, on the
relabelling AdoptModelFrame and relabel_output would make, applied to a
copy of the merge - beside the first one's null, real fit and maps.
It is kept only where the first decides exactly what was forecast (the
model fits, same change of basis, same indexing; a model asserting the
other enantiomorph is not forecast, as the label is decided last, on the
anomalous map). Until then its log is held (Logger::Buffered, replayed
where the serial run logged it) and its files wait on a gate
(ModelValidationSchedule::write_gate) placed before the first map is
written; otherwise it is released with false and returns unwritten, and
the serial validation runs as before.
GPU memory: two validations at once take twice the rigid-body engines.
The parallel start is decided up front from sizes, never from what is
free: allowed where twice what the first pool asked for (bytes per engine
times the engines wanted) fits a quarter of the card's TOTAL memory, the
share one validation may take. Threads: both validations submit to the
one ParallelFor pool from threads outside it (the second runs on a
std::async thread, as the null's replicates do), so no pass runs inline
on a pool worker and the pool's size bounds the workers.
Measured on the loaded 16-core workstation, TIMING model validation:
8sa8 30.6 -> 19.7 s, 8xtg 19.9 -> 13.9 s, 9ea5 22.1 -> 16.4 s (this and
the previous commit together). p.mtz, p.hkl, p.cif, the three maps,
p_maps.mtz and p_model.cif/pdb md5-identical to the base on 8sa8, 8xtg,
9ea5, 7qis and myob_x10sa; the validation's log lines identical as a set
(the null's replicate lines were already in completion order).
Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01SVmAWnzCmRKAXVUCdc4iNi
Each candidate setting of the model was scored one after another on the
coarse shell (a density, an FFT and an isotropic scale fit, 0.2-0.5 s
each), and a run with a model in another setting scores them in both of
its validations. They share nothing but what they read, so they now run
on ParallelFor, each on its own copy of the model, and are read back in
their own order: the log lines, the ranking and the tie-break (first of
equal R wins) are those of the serial loop.
Measured (16-core workstation, loaded): 8sa8 3 candidates 0.64 s ->
0.22 s; 9ea5 3 candidates 1.47 s -> 0.50 s; 8xtg 1.45 s -> 0.40 s.
p.mtz, the maps, the map MTZ and the placed model md5-identical.
Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01SVmAWnzCmRKAXVUCdc4iNi
A pure move. ModelValidation, RigidBodyRefine, RigidBodyGPU, ModelFFT, ModelGrid,
ModelScaling, ModelMaskGPU, ModelScaleGPU and SigmaA - everything that works on an
atomic model - become the JFJochStructureRefinement library, linked by
JFJochImageAnalysis. WriteModel (the placed-model mmCIF/PDB writer) goes to writer/
as its own small JFJochModelWriter target, so JFJochWriter, which a writer-only build
compiles, does not gain a gemmi dependency. Only include paths and CMake lists change.
Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01SVmAWnzCmRKAXVUCdc4iNi
leonarski_fandClaude Opus 5.5