12 Commits

Include renames

Author	SHA1	Message	Date
leonarski_fandClaude Opus 5	8fa1ab7b05	CI: make the artifact checks capable of failing, and of passing ... The rugnux tarball built and packaged correctly; the step that verifies it did not. Two shell mistakes, both mine, both of the same family. `! find /tmp/rgx -name 'libcufft*'` can never pass: find exits 0 whether or not it matched anything, so the negation always fails. That is what broke the x86_64 job after a successful build. The aarch64 checks were worse, in the way that matters. Piping a large producer into `grep -q` kills the producer with SIGPIPE as soon as grep exits on its first match, and `set -o pipefail` promotes that to the pipeline's status: on `cuobjdump --list-elf | grep -q sm_90` over a 225 MB binary it fails a check that should pass, and on `! ... | grep -q "x86-64"` the leading `!` inverts it into a PASS -- so an x86 file leaking into an aarch64 tarball, the exact thing that check exists to catch, would have been reported as clean. Both now capture each producer's output to a file and grep the file, with explicit if/exit rather than exit-status negation. Verified by running the checks verbatim against the real artifacts rather than only reading them: both tarballs pass, and the checks were confirmed to FAIL when they should -- an x86_64 file planted in the extracted tree is caught, and an architecture absent from the fatbin is reported missing. The toolchain file now comes from the checkout rather than /opt/cross in the image. It describes how to build this source, so it belongs with the source: baked into the image, the Eigen fix in the previous commit could not reach CI without rebuilding and re-pushing the image, and appeared to have no effect. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01SQjneRUssfhi1k9rq8Ts3h	2026-08-25 21:21:11 +02:00
leonarski_fandClaude Opus 5	491312f263	Fix the packaging split where it was only exercised on one configuration ... Three failures, all from validating the rugnux path alone and assuming the rest followed. viewer/CMakeLists.txt had an unbalanced ENDIF: removing the cuFFT bundling block took its opening IF(JFJOCH_CUDA_AVAILABLE) with it and left the closer behind, so every configuration that adds viewer/ died on "flow control statements are not properly nested" -- both Windows jobs and the viewer tarball. The cross toolchain could not find Eigen. CMAKE_FIND_ROOT_PATH_MODE_PACKAGE ONLY confines find_package to the target roots, and the ubuntu2404 image installs Eigen from source in /opt/eigen-3.4 rather than as libeigen3-dev, so it sat outside them. It is header-only, so serving it from outside the target roots is safe; the root is now listed explicitly. Static cuFFT is not available everywhere. The Windows toolkit ships no cufft_static.lib, so CUDA::cufft_static does not exist there and linking it fails at generate time. Condition on the target rather than the platform, so a toolkit that gains or loses the static library needs no further change, and restore the Windows DLL bundling for both products -- now in the top-level CMakeLists, since rugnux needs it too and does not add viewer/. rugnux.exe therefore ships beside cufft64_*.dll rather than alone; the Linux and cross artifacts are still one file. That condition also has to keep the JFJOCH_PORTABLE_ONLY half. Testing only for the target quietly moved the SERVER build onto static cuFFT as well, where every executable -- broker, tests, tools -- would then need the CUDA device-link step and would fail on an undefined __cudaRegisterLinkedBinary_* at link. Configure still succeeds, so nothing catches that until the link; the server build keeps libcufft.so exactly as before. Checked by configuring all four flavours in the image CI actually uses -- rugnux, viewer and server on x86_64 plus the aarch64 cross -- and confirming each links the cuFFT it should. The rugnux archives now also carry their target architecture, since that build produces more than one: rugnux-<version>-linux-x86_64-cuda13.tar.gz beside the aarch64 one. CMAKE_SYSTEM_PROCESSOR is the target's, never the build host's. The viewer is x86_64-only and keeps its existing name. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01SQjneRUssfhi1k9rq8Ts3h	2026-08-25 20:53:49 +02:00
leonarski_fandClaude Opus 5	8d32024dd1	Ship jfjoch_viewer and rugnux as two packages, and cross-build rugnux for arm64 ... The viewer tarball also carried rugnux, jfjoch_extract_hkl and jfjoch_recompress. A GUI download that contains a batch processor is confusing on its own, and it forced anyone who only wanted rugnux to take Qt with it. JFJOCH_RUGNUX_ONLY is the viewer-only subtree minus viewer/ and tools/, so it needs no Qt at all, and each of the two options now yields one artifact holding one program: JFJOCH_VIEWER_ONLY jfjoch_viewer .tar.gz / installer / .dmg JFJOCH_RUGNUX_ONLY rugnux .tar.gz / .zip The two CLI tools are still built and no longer installed anywhere. rugnux gets a CPack component of its own, so its notices land in share/doc/jfjoch_rugnux. What makes the split possible is linking cuFFT statically in both products. It was the only CUDA component still dynamic - cudart and the fast-feedback indexer were already static - and shipping it as a .so meant each self-contained archive had to carry the library beside its executables and find it again through an $ORIGIN rpath. That rpath was set on jfjoch_viewer alone, while the same tarball installed three more executables, so those shipped with no runpath at all (cmake strips the build-tree one, which points at the build host's CUDA directory) and could not load the libcufft lying next to them. Static, an artifact is one file that runs: the x86_64 rugnux tarball needs only libc, libstdc++, libgcc_s, libm, libpthread, librt and libdl. The bundling code and the rpath both go away. libcufft_static.a carries a relocatable-device-code object, so a consuming executable needs a CUDA device link; CUDA 13 no longer ships the libcufft_static_nocallback.a that used to avoid this. CUDA_RESOLVE_DEVICE_SYMBOLS emits that step while leaving the host link driver alone, so the -march and -flto flags CI passes still apply. The server build keeps the shared library: its .deb/.rpm take CUDA from the distro, and every executable there would otherwise need the same device link. The guards that exclude server-side targets keyed on NOT JFJOCH_VIEWER_ONLY, which a rugnux-only build does not satisfy - it failed on jfjoch_writer pulling in JFJochImagePuller. They now key on JFJOCH_PORTABLE_ONLY, true for either product, rather than on one product's option in five places. docker/ubuntu2404 additionally cross-compiles rugnux for arm64 SBSA, which is both DGX Spark (GB10, sm_121) and Grace Hopper (GH200, sm_90); one binary with both fatbins runs on either. It needed three things beyond a cross gcc. arm64 is published on ports.ubuntu.com and Noble's deb822 sources carry no Architectures: field, so adding the architecture without splitting the entries 404s on every index. The CUDA cross packages are in neither the x86_64 repo nor the sbsa one but in cross-linux-sbsa, whose fatbinary_section.h ships only in the x86_64 target tree even though it is architecture-neutral. And HDF5 has two try_run probes, so qemu-user-static is needed as CMAKE_CROSSCOMPILING_EMULATOR; every other fetched dependency either guards its run-checks or has none. The cross-built tarball is one ELF aarch64 binary carrying all 17 GPU modules for both sm_90 and sm_121, needing no cuFFT and no CUDA runtime at run time. It is untested on hardware: XDS is x86-64 only, so CI can show it links but only a Spark or a GH200 can show it works. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01SQjneRUssfhi1k9rq8Ts3h	2026-08-25 19:23:59 +02:00
leonarski_f	67dca388bd	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
leonarski_f	451310f43d	v1.0.0-rc.158 (#68) ... 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. * Analysis: The azimuthal-integration solid-angle correction now follows the incidence angle to the detector normal (`cos^3` of that angle) instead of `cos^3(2*theta)`, so it is correct for a tilted detector and matches PyFAI `solidAngleArray` and MAX IV azint (unchanged for an untilted detector). Crystal geometry refinement (`XtalOptimizer`) no longer silently ignores an imported PONI `rot3` (rotation about the beam): it is applied as a fixed rotation in the residual so refinement stays consistent with the rest of the pipeline. Polarization and azimuthal binning already honoured `rot3` through the full PONI rotation. * jfjoch_viewer: Open datasets on the WSL2/UNC filesystem (paths starting `\\`); write processing outputs next to the input file, with a Browse button and independent `_process.h5` / merged `.mtz`/`.cif` toggles; and show the determined space group in the merge-statistics window. * rugnux: Accept an absolute `-o` output prefix in offline processing. * Packaging: The self-contained Linux viewer `.tgz` now bundles cuFFT, so it runs without a system CUDA toolkit (`.deb`/`.rpm` are unchanged, distro-managed). * Docs: Bring the analysis references up to date with the code. `docs/CPU_DATA_ANALYSIS.md` now reflects the unified profile-fit Bragg integration engine, multi-lattice indexing, azimuthal phi binning, the radial parallax/bandwidth profile with sub-pixel centring, the rot3d capture-fraction handling and the automatic CC1/2 resolution cutoff, and drops the descriptions of features that were never implemented (French-Wilson amplitudes, the still excitation-error partiality model); `docs/RUGNUX.md` documents the new `--resolution-cutoff`/`--resolution-cc-target`/`--resolution-shells`, `--min-captured-fraction`, `--mosaicity`, `--reference-column`, the azimuthal correction toggles and the geometry-override options, and corrects the `-N` default. The outdated in-source design notes (ICE_RING_DETECTION, BRAGG_INTEGRATION_ENGINE, NEXTGEN_INTEGRATOR) are removed.Reviewed-on: #68 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>	2026-07-12 19:42:29 +02:00
leonarski_f	75e401f0e5	v1.0.0-rc.153 (#63) ... 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. * jfjoch_broker: Add EXPERIMENTAL pixelrefine mode for image processing * jfjoch_broker: Allow to load user mask from 8-bit and 16-bit TIFF files * jfjoch_broker: Add ROI calculation in non-FPGA workflow * jfjoch_broker: Fixes to TCP image pusher * jfjoch_broker: Remove NUMA bindings * jfjoch_broker: Improvements to indexing * jfjoch_broker: For PSI EIGER, trimming energies are taken from the detector configuration (now compulsory) instead of hardcoded values * jfjoch_writer: Save ROI definitions and the per-pixel ROI bitmap in the master file; azimuthal ROIs support phi (angular) sectors * jfjoch_viewer: Major redesign with dockable panels and saved layouts, plus on-canvas creation/move/resize of box, circle and azimuthal ROIs * jfjoch_viewer: Run jfjoch_process reprocessing jobs from inside the GUI and overlay per-run results Reviewed-on: #63	2026-06-23 20:29:49 +02:00
leonarski_f	4a852b4d6b	v1.0.0-rc.134 (#43) ... This is an UNSTABLE release. The release has significant modifications and bug fixes, if things go wrong, it is better to revert to 1.0.0-rc.132. * jfjoch_broker: Add better locking for detector object - should help, when detector initialization takes too long * jfjoch_writer: Enable writing single, integrated HDF5 file with both data and metadata * XDS plugin: Add generation of Jungfraujoch plugin for XDS * CI: Add tests with XDS and DIALS (`xia2.ssx`) Reviewed-on: #43	2026-04-09 13:30:47 +02:00
leonarski_f	81bd9a06a1	CI pipeline upgrade (#42) ... Updates to CI pipeline * New docker image for Ubuntu 22.04 with CMake 3.26 * New docker image for Rocky 9 with DIALS 3.27 * New automated test to check for DIALS processing with xia2.ssx Reviewed-on: #42	2026-03-28 20:06:23 +01:00
leonarski_f	8b356a7001	v1.0.0-rc.96 (#1) ... This is an UNSTABLE release. * Fixes in CI pipeline * jfjoch_broker: Remove PNG preview, no dependency on libpng * jfjoch_writer: Fix UTC timestamp being generated wrong (mix between milli- and microseconds) * jfjoch_viewer: Show data collection time in dataset tooltip * jfjoch_viewer: Allow to choose the calibrant (presets for LaB6 and silver behenate) * jfjoch_viewer: Auto foreground value * Use external libjpeg-turbo and libtiff: simpler build stack, these are built and linked statically in automated Docker builds * Remove OpenBLAS dependency Reviewed-on: #1 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch> Co-committed-by: Filip Leonarski <filip.leonarski@psi.ch>	2025-11-02 13:45:57 +01:00
leonarski_f	189f84be53	v1.0.0-rc.95	2025-10-28 16:44:04 +01:00
leonarski_f	b2abb0f92b	v1.0.0-rc.94	2025-10-25 22:05:47 +02:00
leonarski_f	5d9d2de4a4	v1.0.0-rc.81	2025-09-21 19:27:51 +02:00