leonarski_fandClaude Opus 5.5
234774ff09
battery.py timing --benchmark standard (now the default) runs 9zlo, 9s02 and
9gjx from their AlphaFold DB models (AF-P17090-F1, AF-P32322-F1, AF-Q65MG6-F1
v6, with their PAE, as the 2026-10-16 AlphaFold MR scan used them; all three
GREEN there) and 4nwv from its deposited model moved by the existing fixed
transform. --benchmark inhouse keeps the earlier myob_x10sa / cytc_x10sa /
4nwv list. Same checks; expected groups are the deposited ones, R-free <= 0.50
for the predictions (0.35 for 4nwv), placement CC >= 0.30.
So that a machine needs only the raw data:
- the deposited coordinates of 9zlo, 9s02, 9gjx, 4nwv and 4dc8 (the inhouse
myoglobin reference) are committed in tools/battery/models/pdb/ as the
compressed mmCIF RCSB serves (CC0; 50-660 kB each, 1.6 MB together), and
model_check.deposition reads an entry there before the pdb_cache, taking
its refinement record from the file itself - no cache JSON, no network;
- open/inhouse arms default their manifest and reference, so a site config
is just runs_root plus the data roots (site.timing.example.json);
- baseline_timing is now per benchmark ({"standard": RUN, "inhouse": RUN}).
Verified on the workstation through the GPU lock with a site config whose
pdb_cache is an empty directory (still empty afterwards): standard 4/4 pass
(9zlo 19 s, 9s02 30 s, 9gjx 21 s, 4nwv 89 s), inhouse 3/3 pass.
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01PXc1zD1yxHqaR1DGdCTHL4
12 KiB
Third-party software notices
Jungfraujoch is licensed under GPL-3.0 (see LICENSE); the FPGA design is
licensed under CERN-OHL-S-2.0 (see fpga/LICENSE). It builds on a number of
third-party components, acknowledged below as required by their licenses.
This file is the human-readable manifest. The verbatim license texts live in the
licenses/ directory (regenerate with bash licenses/COLLECT.sh). The frontend's
bundled JavaScript dependencies are listed separately in
frontend/dist/THIRD_PARTY_LICENSES.txt, generated at build time (npm run licenses).
All licenses below are GPL-3.0-compatible, with one exception: the NVIDIA CUDA Toolkit is used under its own EULA (see the notes at the end of this file).
Fetched at build time and statically linked into the C++ binaries
These are downloaded by CMake (FetchContent / ExternalProject) during the first configure and
linked into the Jungfraujoch executables.
| Component | Version | Copyright | License (SPDX) | License text |
|---|---|---|---|---|
| spdlog | 1.17.0 | Gabi Melman | MIT | spdlog.txt |
| Zstandard | 1.5.7 | Meta Platforms, Inc. | BSD-3-Clause | zstd.txt |
| HDF5 | 2.2.0 | The HDF Group; UIUC | BSD-3-Clause-style + Apache-2.0 | hdf5.txt |
| slsDetectorPackage | 8.0.2 / 9.2.0 | PSI | LGPL-3.0-or-later | LGPL, GPL |
| cpp-httplib | 0.56.0 | Yuji Hirose | MIT | cpp-httplib.txt |
| libzmq (ZeroMQ) | 4.3.5 | iMatix and contributors | MPL-2.0 | libzmq.txt |
| libtiff | 4.7.2 | Sam Leffler; SGI | libtiff (BSD-like) | libtiff.txt |
| FFTW | 3.3.10 | Matteo Frigo; MIT | GPL-2.0-or-later | fftw.txt |
| Ceres Solver | (pinned) | Google Inc. and contributors | BSD-3-Clause | ceres-solver.txt |
| Abseil | 20250127 (required by Ceres) | Google Inc. | Apache-2.0 | abseil.txt |
| fast-feedback-indexer | (pinned) | PSI | BSD-3-Clause | fast-feedback-indexer.txt |
| libjpeg-turbo | 3.2.0 | D. R. Commander and others; IJG | IJG + BSD-3-Clause + Zlib | libjpeg-turbo.txt |
| Mbed TLS (with TF-PSA-Crypto) | 4.2.0 | The Mbed TLS Contributors | Apache-2.0 OR GPL-2.0-or-later (used under Apache-2.0) | mbedtls.txt, tf-psa-crypto.txt |
| Catch2 | 3.16.0 | Catch2 Authors | BSL-1.0 | catch2.txt |
| zlib-ng | 2.3.3 | Jean-loup Gailly and Mark Adler; the zlib-ng contributors | Zlib | zlib.txt |
| Eigen | 3.4.1 | Benoit Jacob, Gael Guennebaud and contributors | MPL-2.0 (+ BSD parts) | eigen.txt, README |
Mbed TLS is fetched and statically linked only for viewer builds (JFJOCH_VIEWER_BUILD /
JFJOCH_VIEWER_ONLY), where it is the TLS backend of jfjoch_viewer's cpp-httplib client; the
broker and writer never link it.
Catch2 is used only to build the test binary (jfjoch_test) and is not part of any shipped
artifact; it is listed here for completeness.
zlib is supplied by zlib-ng built in its zlib-compatible mode (same zlib.h, same API and symbol
names), so it is the zlib that HDF5, libtiff, cpp-httplib and GEMMI all link. It is
built during the configure rather than added as a subproject; the licence is the zlib licence
either way. Eigen is header-only: only its headers reach the binaries, and no Eigen CMake runs.
Vendored directly in the repository
These live in the source tree (see the path) rather than being fetched; traccc and the Ceres-derived minimiser are the exceptions - code adapted into first-party files rather than a vendored directory, see the notes at the end of this file.
| Component | Path | Copyright | License (SPDX) | License text |
|---|---|---|---|---|
| nlohmann/json | include/nlohmann/ |
Niels Lohmann | MIT | nlohmann-json.txt |
| Macaron Base64 | include/base64/ |
tomykaira | MIT | base64-macaron.txt |
| TinyCBOR | frame_serialize/tinycbor/ |
Intel Corporation | MIT | tinycbor.txt |
| Bitshuffle | compression/bitshuffle/ |
Kiyoshi Masui | MIT | bitshuffle.txt |
| Bitshuffle (h-perf) | compression/bitshuffle_hperf/ |
Kal Conley | Apache-2.0 | bitshuffle-hperf.txt |
| LZ4 | compression/lz4/ |
Yann Collet | BSD-2-Clause | lz4.txt |
| HLS arbitrary-precision types | fpga/include/ |
Xilinx, Inc. | Apache-2.0 | xilinx-hls-headers.txt |
| GEMMI | gemmi_gph/ |
Global Phasing Ltd. | MPL-2.0 | gemmi.txt |
| PEGTL | gemmi_gph/gemmi/third_party/tao/ |
Dr. Colin Hirsch and Daniel Frey | MIT | pegtl.txt |
| sajson | gemmi_gph/gemmi/third_party/sajson.h |
Chad Austin | MIT | sajson.txt |
| fast_float | gemmi_gph/gemmi/third_party/fast_float.h |
The fast_float authors (Daniel Lemire et al.) | Apache-2.0 OR MIT OR BSL-1.0 | fast-float.txt |
| half | gemmi_gph/gemmi/third_party/half.hpp |
Christian Rau | MIT | half.txt |
| pocketfft | gemmi_gph/gemmi/third_party/pocketfft_hdronly.h |
Max-Planck-Society; Peter Bell; MIT (FFTW-derived parts) | BSD-3-Clause | pocketfft.txt |
| tinydir | gemmi_gph/gemmi/third_party/tinydir.h |
Cong Xu, Lautis Sun, Baudouin Feildel, Andargor | BSD-2-Clause | tinydir.txt |
| traccc (ACTS) | image_analysis/spot_finding/StrongPixelSet.cpp, SpotExtractorGPU.cu |
CERN, for the benefit of the ACTS project | MPL-2.0 | traccc.txt |
| Ceres Solver (adapted) | image_analysis/geom_refinement/LMSolver.h, LMSolver.cpp |
Google Inc. | BSD-3-Clause | ceres-solver.txt |
| xbflash.qspi | tools/xbflash.qspi/ |
Xilinx / AMD | Apache-2.0 | xbflash-qspi.txt |
| wingetopt | tools/wingetopt/ |
Todd C. Miller; The NetBSD Foundation | ISC AND BSD-2-Clause | wingetopt.txt |
Data files in the repository
Not code and not linked into any binary: input files of the battery's timing benchmark
(tools/battery/timing.json), kept verbatim as downloaded.
| Component | Path | Copyright | License (SPDX) | License text |
|---|---|---|---|---|
| AlphaFold Protein Structure Database predictions AF-P68082-F1, AF-P62894-F1, AF-P17090-F1, AF-P32322-F1 and AF-Q65MG6-F1 (v6), with their predicted aligned error | tools/battery/models/AF-* |
DeepMind Technologies Limited; EMBL-EBI | CC-BY-4.0 | alphafold-db.txt |
| wwPDB entries 4DC8, 4NWV, 9GJX, 9S02 and 9ZLO, deposited coordinates (mmCIF as the RCSB PDB serves them) | tools/battery/models/pdb/ |
the depositors; the wwPDB | CC0-1.0 | wwPDB usage policy |
The deposited entries are the reference models the benchmark's placements are checked against, and 4NWV's is also moved by a fixed transform at run time to make one start model.
Runtime libraries and SDKs (shipped in binaries, not in the source tree)
| Component | Used by | License | Notice |
|---|---|---|---|
| Qt 6 | jfjoch_viewer |
LGPL-3.0 | notice, LGPL-3.0 |
| NVIDIA CUDA Toolkit (cudart, cuFFT) | CUDA builds | NVIDIA CUDA EULA | notice, EULA |
Frontend (npm) dependencies
The React/TypeScript frontend (frontend/) bundles a large transitive tree of npm packages,
overwhelmingly MIT/ISC/BSD/Apache-2.0 licensed. Their full notices are generated automatically:
cd frontend && npm run licenses # writes dist/THIRD_PARTY_LICENSES.txt
The generated file is produced as part of the frontend build target and installed alongside the
served frontend, so the shipped web UI carries its own attribution.
Notes on weak-copyleft and attribution-sensitive components
- MPL-2.0 (Eigen, GEMMI, libzmq, traccc): file-level copyleft. GEMMI is vendored in
gemmi_gph/in trimmed form; libzmq and Eigen are fetched at build time (Eigen is header-only). The corresponding source is available from each project upstream. - GEMMI's own bundled third-party headers — PEGTL, sajson, fast_float, half, pocketfft and
tinydir, all under
gemmi_gph/gemmi/third_party/— are listed separately above rather than being absorbed into GEMMI's row: they are other authors' code under other licences (MIT, BSD and Apache/MIT/BSL), and GEMMI's MPL-2.0 does not speak for them. Their terms are carried in the headers themselves rather than inLICENSEfiles, so thelicenses/*.txtcopies are kept by hand; only PEGTL ships aLICENSE, whichCOLLECT.shcopies. - traccc is the one entry that is not a vendored directory. Its sparse connected-component
labelling enters two otherwise first-party files:
StrongPixelSet.cppadapts the SparseCCL source, andSpotExtractorGPU.cufollows the design of its GPU counterpart. MPL-2.0 is file-level, so both files name the origin at the top and are covered bylicenses/traccc.txt. See ACKNOWLEDGEMENT.md for the citation. - Ceres Solver is also fetched and linked (table above); separately,
LMSolver.h/.cppre-implement its trust-region Levenberg-Marquardt minimiser, projected line search, polynomial step choice and sphere manifold for the crystal refinement, following its source. Both files name the origin at the top and are covered bylicenses/ceres-solver.txt. - FFTW is GPL-2.0-or-later — compatible with, and absorbed by, this project's GPL-3.0 license.
- Apache-2.0 components: where upstream ships a
NOTICEfile, it is reproduced in the correspondinglicenses/text. - Qt (LGPL-3.0) and NVIDIA CUDA (EULA) carry redistribution conditions beyond a copyright
notice; see their dedicated notice files. The verbatim LGPL-3.0 and CUDA EULA texts are bundled
(
licenses/Qt6-LGPL-3.0.txt,licenses/NVIDIA-CUDA-EULA.txt); the CUDA EULA is the one shipped with CUDA Toolkit 12.8 — replace it if you build against a different toolkit version.