leonarski_f
749db470ca
Build Packages / build:rpm (rocky9) (push) Successful in 19m56s
Build Packages / Unit tests (push) Skipped
Build Packages / build:windows:nocuda (push) Successful in 16m57s
Build Packages / build:windows:cuda (push) Successful in 19m18s
Build Packages / build:viewer-tgz:cpu (push) Successful in 14m48s
Build Packages / build:viewer-tgz:cuda (push) Successful in 16m18s
Build Packages / build:rugnux-tgz (x86_64) (push) Successful in 14m19s
Build Packages / build:rugnux:windows (push) Successful in 10m34s
Build Packages / build:rugnux:aarch64 (cross) (push) Successful in 8m49s
Build Packages / build:rpm (rocky8_nocuda) (push) Successful in 20m55s
Build Packages / build:rpm (rocky9_nocuda) (push) Successful in 17m4s
Build Packages / build:rpm (ubuntu2204_nocuda) (push) Successful in 20m48s
Build Packages / build:rpm (ubuntu2404_nocuda) (push) Successful in 19m15s
Build Packages / build:rpm (rocky8_sls9) (push) Successful in 24m26s
Build Packages / build:rpm (rocky9_sls9) (push) Successful in 20m32s
Build Packages / build:rpm (rocky8) (push) Successful in 23m39s
Build Packages / Generate python client (push) Successful in 46s
Build Packages / Build documentation (push) Successful in 1m45s
Build Packages / Create release (push) Skipped
Build Packages / XDS test (durin plugin) (push) Successful in 11m3s
Build Packages / XDS test (JFJoch plugin) (push) Successful in 11m30s
Build Packages / build:rpm (ubuntu2404) (push) Successful in 20m10s
Build Packages / XDS test (neggia plugin) (push) Successful in 10m17s
Build Packages / build:rpm (ubuntu2204) (push) Successful in 23m12s
Build Packages / DIALS test (push) Successful in 20m12s
* 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>
3.4 KiB
3.4 KiB
Linux package repositories
For convenience, we are providing package repositories. With versions including and excluding CUDA linking.
We recommend to install Jungfraujoch viewer from nocuda repository and remaining packages from cuda12/cuda13 repository.
The repository name encodes two choices: the slsDetectorPackage version the packages
were built against (slsdet8 = 8.0.2, slsdet9 = 9.2.0 — it must match the detector firmware) and
whether CUDA is linked in. What ends up inside each package, and what it needs on the target
machine, is described in Release contents.
RHEL based systems
For RHEL systems we provide the following repositories:
| RHEL version | slsDetectorPackage | CUDA | Repository file |
|---|---|---|---|
| 8.x | 8.0.2 | 12.x | https://gitea.psi.ch/api/packages/mx/rpm/centos/el8/slsdet8-cuda12.repo |
| 8.x | 9.2.0 | 12.x | https://gitea.psi.ch/api/packages/mx/rpm/centos/el8/slsdet9-cuda12.repo |
| 8.x | 8.0.2 | - | https://gitea.psi.ch/api/packages/mx/rpm/centos/el8/slsdet8-nocuda.repo |
| 9.x | 8.0.2 | 13.x | https://gitea.psi.ch/api/packages/mx/rpm/centos/el9/slsdet8-cuda13.repo |
| 9.x | 9.2.0 | 13.x | https://gitea.psi.ch/api/packages/mx/rpm/centos/el9/slsdet9-cuda13.repo |
| 9.x | 8.0.2 | - | https://gitea.psi.ch/api/packages/mx/rpm/centos/el9/slsdet8-nocuda.repo |
To install the repository, run:
dnf config-manager --add-repo https://gitea.psi.ch/api/packages/mx/rpm/centos/el8/slsdet8-cuda12.repo
RPMs are signed by the Gitea package registry as they are uploaded. If your system cannot verify the
signature, set gpgcheck=0 in the repository file or install with --nogpgcheck.
We provide the following packages in the repository:
- jfjoch — broker, web frontend, FPGA and detector command-line tools
- jfjoch-driver-dkms — PCIe kernel-module source, built by DKMS
- jfjoch-writer — HDF5 writer service
- jfjoch-viewer — desktop viewer and the XDS plugin
- rugnux — offline analysis CLI, independent of the acquisition stack
Note that rugnux is named without the jfjoch- prefix, matching the program and the release
archive. Up to 1.0.0-rc.163 it was part of jfjoch-viewer; the package declares that move, so
installing it upgrades an older viewer rather than colliding with it.
Ubuntu based systems
For Ubuntu systems, we also provide the following repositories:
sudo curl https://gitea.psi.ch/api/packages/mx/debian/repository.key -o /etc/apt/keyrings/gitea-mx.asc
echo "deb [signed-by=/etc/apt/keyrings/gitea-mx.asc] https://gitea.psi.ch/api/packages/mx/debian $distribution $component" | sudo tee -a /etc/apt/sources.list.d/gitea.list
sudo apt update
$distribution uses Ubuntu names jammy (22.04) and noble (24.04). $component can be set to cuda13 and nocuda.
Only slsDetectorPackage 8.0.2 is built for Ubuntu.
The same five packages as above are provided: jfjoch, jfjoch-driver-dkms, jfjoch-writer,
jfjoch-viewer and rugnux. Up to 1.0.0-rc.160 the first of them was misnamed jfjoch-jfjoch; the current
package replaces it, so apt upgrade handles the rename.
Ubuntu packages are currently only going through a very limited testing.