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Jungfraujoch/docker/build_images.sh
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leonarski_f 749db470ca
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v1.0.0-rc.164 (#74)
* rugnux now tells you whether a crystal diffracts anisotropically and how far it reaches in each direction, without a second program: a new `9. DIFFRACTION ANISOTROPY` section in `<prefix>_report.txt` and matching `_reflns.pdbx_aniso_B_tensor_*` / `_reflns.jfjoch_aniso_*` items in the merged mmCIF report the anisotropic deltaB, the diffraction limit along each principal direction, and a `NOT DETECTED` / `DETECTED` / `CANNOT DETERMINE` verdict measured against the data set's own systematic error. It is a description only - no intensity is corrected, no reflection is removed, and the merged data do not depend on direction.
* rugnux can hand its integrated observations to another scaling program: `--export-unmerged` writes `<prefix>_unmerged.mtz`, an unmerged MTZ readable by aimless, pointless, careless and `iotbx.merging_statistics`, in `--mode mx` and `--mode scale` alike. Each rotation reflection's partials are summed into one full; `--export-unmerged-partials` writes one row per image instead. Intensities carry the Lorentz-polarization factor and nothing else, since those programs scale the data themselves. Lattice-centring absences are not written; screw and glide absences are.
* rugnux integrates crystals with broad spots better - where it changes anything, per-shell mean I/sigma improves by up to 31% and R_meas by up to 24% - because on rotation data the integration signal radius is now taken from the crystal's own measured spot width instead of a fixed 4 px. `--adaptive-integration-radius=off` restores the fixed radius and an explicit `--integration-radius` still overrides both. The widened radius applies to the final integration pass only, and a pattern too dense for it is re-integrated at 4 px with a note in the log.
* rugnux discards fewer stills reflections for want of a background ring, improving per-shell R_meas over most of the signal-bearing range: the stills background ring now runs to 14 px instead of 12. The gain reverses in shells below a mean I/sigma of about 4.
* rugnux determines the space group with thresholds that mean the same thing on a weak crystal as on a strong one: symmetry operators are scored on resolution-normalised intensities (E squared) instead of raw merged intensities, and a reflection counts as genuinely present on its counting significance instead of on the merged I/sigma, which saturates at the merge's own ISa. The search resolution cut is no longer able to move the answer, and the twin-law H bound moves from 1.70 to 1.85, which stops one class of correct high-symmetry assignment being refused as twinning.
* rugnux says what the space-group search tested and what it could not: the twin-law disagreement H is printed for every operator together with the adopted point group's H ratio and its bound; alternatives that are not on the reported lattice are named with how their cell differs; and a lattice centring the data could not test - the crystal having been integrated on the primitive sub-cell, so the reflections it extinguishes were never measured - is marked `UNTESTED` and warned about where it is adopted, as coming from the lattice metric rather than from the intensities.
* rugnux `--mode scale` re-merges a `_process.h5` in the right symmetry without being told it: the file now records the space group on every run - a two-pass rotation run wrote none before, so re-merging defaulted to P1 - together with the change of basis under `/entry/MX/reindexMatrix` where the lattice was re-seated, and `--mode scale` also reports the Wilson B-factor estimate instead of `WILSON_B= nan`. A file written before this stops with a message naming the two cells and the override to use, instead of failing inside the merge. A third-party reader of a `_process.h5` must apply `reindexMatrix` where it is present.
* rugnux installs on its own, as a package called `rugnux` - `dnf install rugnux` or `apt install rugnux` - instead of arriving inside `jfjoch-viewer`. It pulls in none of the acquisition stack, so a machine that only processes data no longer has to carry the broker, the detector libraries or Qt to get it. Installing it over a `jfjoch-viewer` from rc.163 or earlier, which still owns `/usr/bin/rugnux`, upgrades cleanly rather than failing on the duplicate file.
* rugnux is also a standalone download, built for arm64 as well as x86_64: `rugnux-<version>-linux-{x86_64|aarch64}-cuda<major>.tgz` and `rugnux-<version>-win64-cuda<major>.zip` on the release page, for machines that are not managed by a package manager. The aarch64 build targets GH200 and DGX Spark, and is untested on hardware.
* Every portable Linux binary is now a single self-contained file: cuFFT is linked statically instead of being shipped beside the executable and found through an rpath, so `rugnux` and `jfjoch_viewer` need nothing but an NVIDIA driver, and only to use the GPU. The `.rpm`/`.deb` continue to take cuFFT from the distribution. The developer utilities `jfjoch_extract_hkl` and `jfjoch_recompress` are no longer packaged anywhere.
* Jungfraujoch needs six fewer shared libraries on the machine - libopenblas and libmetis, and libgfortran, libquadmath, libgomp and libz behind them - because the Ceres LAPACK, METIS and SuiteSparse back-ends are no longer built. Nothing in the code ever selected them, and results are unchanged.
* The PCIe driver DKMS package builds for the kernel it is being installed for instead of the running one, so a module built while a kernel update is being applied loads after the reboot.
* The PCIe driver builds on RHEL 9.5 and later, and on their CentOS Stream, Rocky and AlmaLinux equivalents, where the `vm_flags` kernel interface was backported into the 5.14 kernel.
* A data collection started with `async_start` that fails to start - a writer refusing to overwrite an existing file, for instance - is reported as an error by `/wait_until_running` and `/wait_till_done` instead of as a timeout and a successful collection respectively. The error message is the one the writer gave.
* A calibration that is cancelled or that fails to collect its pedestals is no longer reported as a successful one. The broker goes to `Inactive` with an error message and has to be initialized again, instead of sitting in `Idle` looking ready to measure while holding partial pedestals - data collected in that state was silently mis-converted.
* A failed `/initialize` is reported to `/wait_until_running` and `/wait_till_done` as soon as it happens, instead of when their timeout expires.
* `space_group_number` accepts space groups up to 230 in the API schema, so cubic space groups can be recorded. The broker always accepted them; the generated clients rejected them before the request was sent.
* The results report's `REPORT_VERSION` is 3, two sections having been added. Existing key names and table columns are unchanged.
* The merged statistics table has **9** resolution shells instead of 10, which is what XDS reports. The bins were already XDS's - equal steps in 1/d^2 between the lowest- and the highest-resolution reflection the merge kept - so at the same resolution limits the two tables now have the same shell boundaries and can be read row for row. `--resolution-shells` sets a different count.
* `rugnux --model` now settles the frame the merged reflections are written in, not only the frame the R-factors and the maps are computed in: the `.mtz`/`.cif`/`.hkl` come out in the model's indexing, and where the data were merged in the model's enantiomorph they take the model's hand and space group - which on anomalous data puts I(+) and I(-) the right way round. The indexing choice is logged with the winning R-free and the runner-up, so a decision made within noise is visible.
* `rugnux --model` can resolve the indexing ambiguity of a **serial stills** run, which a model could not do before: structure factors computed from the model become the per-image reference, the same role a reference MTZ plays. It needs the cell and space group up front (`-C` / `-S`). Without one or the other, a merohedral serial run still merges both hands together and says so.
* The rugnux documentation opens with a quick start - the default run, and runs with a reference MTZ, with a model, or with the space group and cell pinned - and explains the indexing ambiguity: what it costs on rotation and on serial data, and which of `-z` / `--model` resolves it in each case. The long reference pages now carry a table of contents.

Reviewed-on: #74
Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>
2026-08-26 22:47:00 +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$(nproc)` for Qt/dbus, so J parallel builds ~= J*nproc compile threads and several GB of
# RAM each at link time. JOBS=2 is a safe default that overlaps the (network-bound) base-image
# pull / package-install / source-download phases across builds without thrashing the CPU. Bump to
# 4 for full parallelism on a big machine (enough RAM + disk for 4 CUDA bases), or JOBS=1 for serial.
#
# Usage:
# docker/build_images.sh # all four, JOBS=2
# docker/build_images.sh rocky9 rocky8 # subset
# JOBS=4 docker/build_images.sh # all four at once
# JOBS=1 docker/build_images.sh # serial
# TAG=2607b docker/build_images.sh # override the tag (default 2607b)
#
# The tag has to match what .gitea/workflows/build_and_test.yml asks the runner for, or CI pulls a
# different image than the one just built. Currently jfjoch_rocky8:2511 and jfjoch_ubuntu2404:2508 --
# ubuntu2404 being the image that also carries the aarch64 cross toolchain, so:
# TAG=2508 docker/build_images.sh ubuntu2404
# PUSH=1 docker/build_images.sh # build (parallel) then push (serial; needs docker login)
#
# Parallel stdout would be an unreadable interleave, so each build streams to its own log file:
# docker/build-logs/<variant>-<TAG>.log (follow live with: tail -f docker/build-logs/*.log)
set -euo pipefail
REGISTRY="${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"