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Jungfraujoch/docker/build_images.sh
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v1.0.0-rc.160 (#70)
This is an UNSTABLE release. It includes many experimental features, as well as many AI generated fixes. We recommend using rc.152 for production use.

* rugnux: Add `--model model.pdb` - score the merged data against an atomic model and compute initial maps. It reports R-work/R-free (scaling the model to the observed amplitudes with an overall scale, an anisotropic B and a flat bulk solvent - the standard few-parameter model, so a batch of maps stays directly comparable) and writes 2Fo-Fc / Fo-Fc electron-density maps (CCP4) plus a map-coefficient MTZ. The structure itself is not refined; the model is only re-fractionalised into the data cell.
* rugnux: The merged reflection output now carries French-Wilson amplitudes (|F| and its sigma) next to the intensities - MTZ `F`/`SIGF`, mmCIF `_refln.F_meas_au`, and the text HKL - computed with the correct centric/acentric Wilson prior and epsilon multiplicity, so a downstream program (e.g. phenix.refine) can refine against amplitudes. The intensity columns are unchanged.
* rugnux: R-free test-set flags are now assigned deterministically and consistently across symmetry - a Bijvoet pair I(+)/I(-) is never split between the work and free sets, and the assignment is a reproducible per-hkl hash that depends only on the reflection index, so every dataset of one crystal form gets the same ~5% free set (what a multi-dataset campaign such as PanDDA needs). On small data the fraction is floored so the test set stays large enough for a stable R-free (~500 reflections, capped at 10%); it stays flat at 5% on ordinary data. When a reference MTZ carries a `FreeR_flag` column its test set is imported instead, letting a whole campaign inherit one shared free set.
* rugnux: A reference MTZ (`--reference-mtz`) can now fix the space group and cell for rotation data too (previously rejected), without being used to scale - the rotation merge stays self-consistent. When the crystal has an indexing (merohedral) ambiguity - a lattice symmetry higher than its Laue symmetry, e.g. P3/P4/P6/C2 - the reference also resolves it: each candidate reindexing (identity plus the twin-law cosets of the metric symmetry) is scored by its intensity correlation against the reference and the data are re-merged in the best-correlating one. This is a metric-preserving relabelling of hkl (the cell is unchanged) and a no-op for a holohedral crystal such as lysozyme.
* rugnux: `--model` validation now aligns the data to the model before scoring - the observed reflections are reindexed into the model's enantiomorph when the two differ only by hand (indistinguishable from merged intensities). A merohedral indexing ambiguity is resolved against the reference MTZ when one is given (so a whole campaign shares one indexing convention); only with a model and no reference does validation fall back to fitting each candidate reindexing and keeping the lowest R-free.
* rugnux: De-novo symmetry - recover a genuine high-symmetry group whose data are imperfectly scaled. Such a merge's within-orbit chi² lands just past the self-consistency bound (each real symmetry step adds a little systematic scatter), right where a merohedral twin also lands, so the chi² ratio alone cannot separate them. The candidate is now rescued when the extra intensity-proportional systematic error it invokes stays small relative to the confirmed subgroup - a genuine symmetry step gains multiplicity without inflating the merge error model's b, whereas a twin forces non-equivalent reflections together and b balloons. Fixes cubic insulin (I23 instead of I222) with no change to any other crystal in the test battery, including the twins that must stay in their lower symmetry.
* Docs: Document the French-Wilson amplitude estimation, R-free flagging, reference-based space-group/ambiguity resolution, and model-based validation/maps in CPU_DATA_ANALYSIS.md.
* Frontend: The status-bar pill now shows a progress bar during detector calibration (previously only during measurement), and the calibration state and its button are labelled "Calibration"/"CALIBRATE" (the internal `Pedestal` state name is unchanged for back-compatibility).Reviewed-on: #70

Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>
2026-07-19 09:39:28 +02:00

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#!/usr/bin/env bash
# Build (and optionally push) the jungfraujoch build-environment images, in parallel.
#
# Each docker/<variant>/Dockerfile is a *self-contained build environment* (toolchain, static Qt,
# static libdbus, static OpenSSL, Eigen, DIALS, XDS, Node, ...). It does NOT copy the project in --
# the source is mounted and built at run time (see build_in_rocky9.sh). So the build context is just
# the per-variant directory; the huge repo is never sent to the Docker daemon.
#
# Images are tagged gitea.psi.ch/leonarski_f/jfjoch_<variant>:<TAG> (matches the CI runner images).
#
# Concurrency (JOBS):
# JOBS controls how many image builds run at once (default 2). Each build internally runs
# `make -j$(nproc)` for Qt/dbus, so J parallel builds ~= J*nproc compile threads and several GB of
# RAM each at link time. JOBS=2 is a safe default that overlaps the (network-bound) base-image
# pull / package-install / source-download phases across builds without thrashing the CPU. Bump to
# 4 for full parallelism on a big machine (enough RAM + disk for 4 CUDA bases), or JOBS=1 for serial.
#
# Usage:
# docker/build_images.sh # all four, JOBS=2
# docker/build_images.sh rocky9 rocky8 # subset
# JOBS=4 docker/build_images.sh # all four at once
# JOBS=1 docker/build_images.sh # serial
# TAG=2607b docker/build_images.sh # override the tag (default 2607b)
# PUSH=1 docker/build_images.sh # build (parallel) then push (serial; needs docker login)
#
# Parallel stdout would be an unreadable interleave, so each build streams to its own log file:
# docker/build-logs/<variant>-<TAG>.log (follow live with: tail -f docker/build-logs/*.log)
set -euo pipefail
REGISTRY="${REGISTRY:-gitea.psi.ch/leonarski_f}"
TAG="${TAG:-2607b}"
PUSH="${PUSH:-0}"
JOBS="${JOBS:-2}"
here="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
logdir="$here/build-logs"
mkdir -p "$logdir"
all=(rocky8 rocky9 ubuntu2204 ubuntu2404)
variants=("$@"); [ "${#variants[@]}" -eq 0 ] && variants=("${all[@]}")
for v in "${variants[@]}"; do
[ -f "$here/$v/Dockerfile" ] || { echo "!! no Dockerfile for variant '$v' ($here/$v/Dockerfile)"; exit 1; }
done
# One image build. Records OK/FAIL to a status file so the parent can summarise after wait; never
# returns non-zero itself, so the job-pool's `wait -n` under `set -e` stays happy.
build_one() {
local v="$1"
local img="$REGISTRY/jfjoch_$v:$TAG"
local log="$logdir/${v}-${TAG}.log"
if docker build --pull -t "$img" "$here/$v" >"$log" 2>&1; then
echo OK > "$logdir/${v}-${TAG}.status"
else
echo FAIL > "$logdir/${v}-${TAG}.status"
fi
}
echo "==> building ${#variants[@]} image(s): ${variants[*]}"
echo "==> JOBS=$JOBS TAG=$TAG REGISTRY=$REGISTRY"
echo "==> logs in $logdir/ (follow: tail -f $logdir/*.log)"
echo
# Launch with a concurrency cap of JOBS. `wait -n` reaps exactly one finished build before the next
# is started once we are at the cap; the trailing `wait` drains the rest.
running=0
for v in "${variants[@]}"; do
if [ "$running" -ge "$JOBS" ]; then wait -n || true; running=$((running - 1)); fi
: > "$logdir/${v}-${TAG}.status" # clear any stale status from a previous run
echo "==> [$v] started -> $REGISTRY/jfjoch_$v:$TAG"
build_one "$v" &
running=$((running + 1))
done
wait
echo
echo "===================== build summary ====================="
rc=0; ok_variants=()
for v in "${variants[@]}"; do
s="$(cat "$logdir/${v}-${TAG}.status" 2>/dev/null || echo '??')"
printf " %-12s %s\n" "$v" "$s"
if [ "$s" = OK ]; then ok_variants+=("$v"); else rc=1; fi
done
[ "$rc" -eq 0 ] || echo "!! one or more builds FAILED -- see the per-variant logs above"
echo
if [ "$PUSH" = "1" ]; then
for v in "${ok_variants[@]}"; do
img="$REGISTRY/jfjoch_$v:$TAG"
echo "==> push $img"
docker push "$img"
done
else
echo "Built locally. To push the successful ones (after 'docker login gitea.psi.ch'):"
for v in "${ok_variants[@]}"; do echo " docker push $REGISTRY/jfjoch_$v:$TAG"; done
fi
exit "$rc"