diff --git a/.gitea/workflows/build_and_test.yml b/.gitea/workflows/build_and_test.yml
index 07d27f5e..6973cca9 100644
--- a/.gitea/workflows/build_and_test.yml
+++ b/.gitea/workflows/build_and_test.yml
@@ -1,7 +1,17 @@
name: Build Packages
env:
- MARCH_CMAKE_FLAGS: '-DCMAKE_CXX_FLAGS="-march=x86-64-v3" -DCMAKE_C_FLAGS="-march=x86-64-v3"'
+ # Architecture and link-time optimisation for every Linux configure. Both are deliberately absent
+ # from CMakeLists.txt so a site can pick its own (x86-64-v4 on an AVX-512 cluster, -march=native,
+ # or the plain baseline); CI pins what it ships.
+ #
+ # -flto=auto needs GCC >= 10 and both CI images put gcc-toolset-13 on PATH. Measured on rugnux
+ # against an otherwise identical build: 7-10% fewer retired instructions and a 9% smaller binary,
+ # but only ~1.5% off the wall clock, because the offline pipeline is GPU- and I/O-bound rather
+ # than CPU-instruction-bound. It costs about 3x on an INCREMENTAL rebuild (one file plus link,
+ # 9.8 s -> 30.1 s), which is why it belongs here and not in CMakeLists: CI always builds from
+ # scratch and ships the result, so it pays the link once and a developer never pays it at all.
+ LINUX_CMAKE_FLAGS: '-DCMAKE_CXX_FLAGS="-march=x86-64-v3 -flto=auto" -DCMAKE_C_FLAGS="-march=x86-64-v3 -flto=auto"'
# MSVC has no spelling for the x86-64-v2 level; /arch:AVX is the nearest and implies SSE4.1/4.2,
# which is what matters here - without it Eigen has no vectorised round and falls back to a libm
# call per element. AVX is Sandy Bridge (2011) and up, a safe floor for a desktop viewer.
@@ -50,7 +60,7 @@ jobs:
run: |
mkdir -p build
cd build
- cmake -G Ninja -DCMAKE_BUILD_TYPE=Release ${{ env.MARCH_CMAKE_FLAGS }} ..
+ cmake -G Ninja -DCMAKE_BUILD_TYPE=Release ${{ env.LINUX_CMAKE_FLAGS }} ..
ninja -j48 jfjoch_test jfjoch_hdf5_test jfjoch_hdf5_enospc_test enospc_shim
- name: Run unit tests
shell: bash
@@ -137,7 +147,7 @@ jobs:
run: |
mkdir -p build
cd build
- cmake -G Ninja -DJFJOCH_VIEWER_ONLY=ON -DJFJOCH_USE_CUDA=${{ matrix.use_cuda }} ${{ env.MARCH_CMAKE_FLAGS }} -DCMAKE_BUILD_TYPE=Release ..
+ cmake -G Ninja -DJFJOCH_VIEWER_ONLY=ON -DJFJOCH_USE_CUDA=${{ matrix.use_cuda }} ${{ env.LINUX_CMAKE_FLAGS }} -DCMAKE_BUILD_TYPE=Release ..
- name: Build viewer tgz
shell: bash
run: |
@@ -236,7 +246,7 @@ jobs:
run: |
mkdir -p build
cd build
- cmake -G Ninja -DJFJOCH_INSTALL_DRIVER_SOURCE=ON -DJFJOCH_VIEWER_BUILD=ON ${{ env.MARCH_CMAKE_FLAGS }} -DCMAKE_BUILD_TYPE=Release ${{ matrix.cmake_flags }} ..
+ cmake -G Ninja -DJFJOCH_INSTALL_DRIVER_SOURCE=ON -DJFJOCH_VIEWER_BUILD=ON ${{ env.LINUX_CMAKE_FLAGS }} -DCMAKE_BUILD_TYPE=Release ${{ matrix.cmake_flags }} ..
- name: Build packages
shell: bash
run: |
@@ -294,7 +304,7 @@ jobs:
run: |
mkdir -p build
cd build
- cmake -G Ninja -DCMAKE_BUILD_TYPE=Release ${{ env.MARCH_CMAKE_FLAGS }} ..
+ cmake -G Ninja -DCMAKE_BUILD_TYPE=Release ${{ env.LINUX_CMAKE_FLAGS }} ..
ninja -j16 jfjoch_hdf5_test
- name: Run DIALS processing on legacy format
shell: bash
@@ -330,7 +340,7 @@ jobs:
run: |
mkdir -p build
cd build
- cmake -G Ninja -DCMAKE_BUILD_TYPE=Release ${{ env.MARCH_CMAKE_FLAGS }} ..
+ cmake -G Ninja -DCMAKE_BUILD_TYPE=Release ${{ env.LINUX_CMAKE_FLAGS }} ..
ninja -j16 jfjoch_hdf5_test
- name: Run XDS with Durin and legacy HDF5 format
shell: bash
@@ -366,7 +376,7 @@ jobs:
run: |
mkdir -p build
cd build
- cmake -G Ninja -DCMAKE_BUILD_TYPE=Release ${{ env.MARCH_CMAKE_FLAGS }} ..
+ cmake -G Ninja -DCMAKE_BUILD_TYPE=Release ${{ env.LINUX_CMAKE_FLAGS }} ..
ninja -j16 jfjoch_hdf5_test
ninja -j16 jfjoch_xds_plugin
- name: Run XDS with legacy HDF5 format
@@ -402,7 +412,7 @@ jobs:
run: |
mkdir -p build
cd build
- cmake -G Ninja -DCMAKE_BUILD_TYPE=Release ${{ env.MARCH_CMAKE_FLAGS }} ..
+ cmake -G Ninja -DCMAKE_BUILD_TYPE=Release ${{ env.LINUX_CMAKE_FLAGS }} ..
ninja -j16 jfjoch_hdf5_test
- name: Run XDS with Neggia and legacy HDF5 format
shell: bash
diff --git a/CLAUDE.md b/CLAUDE.md
index c043d8ec..5720a3a5 100644
--- a/CLAUDE.md
+++ b/CLAUDE.md
@@ -43,13 +43,16 @@ Key CMake options:
- `SLS9` (default OFF) — build against slsDetectorPackage 9.2.0 instead of 8.0.2.
- `JFJOCH_INSTALL_DRIVER_SOURCE` (default OFF) — install the PCIe driver source for DKMS/RPM.
-### `-march` is deliberately NOT set in CMakeLists
+### `-march` and LTO are deliberately NOT set in CMakeLists
-The build system sets no architecture flags, so a site can pick its own — `x86-64-v4` on an
+The build system sets no architecture or LTO flags, so a site can pick its own — `x86-64-v4` on an
AVX-512 cluster, `-march=native`, or the plain baseline. **CI passes them explicitly**
-(`.gitea/workflows/build_and_test.yml`): every Linux configure gets
-`-march=x86-64-v3`, and the MSVC viewer job gets `/arch:AVX` (MSVC has no x86-64-v2 spelling;
-`/arch:AVX` is the nearest and implies SSE4.1/4.2).
+(`.gitea/workflows/build_and_test.yml`): every Linux configure gets `LINUX_CMAKE_FLAGS`
+(`-march=x86-64-v3 -flto=auto`), and the MSVC viewer job gets `/arch:AVX` (MSVC has no x86-64-v2
+spelling; `/arch:AVX` is the nearest and implies SSE4.1/4.2). LTO is CI-only on purpose: measured on
+rugnux it removes 7–10% of retired instructions and 9% of the binary but only ~1.5% of the wall
+clock (the pipeline is GPU- and I/O-bound), while costing ~3× on an incremental rebuild — a bad
+trade for a developer, a fine one for a build that happens once and is shipped.
**This matters when profiling.** A plain `cmake -DCMAKE_BUILD_TYPE=Release ..` produces a
*baseline* binary that is not what CI or production runs, and the difference is not uniform:
diff --git a/broker/redoc-static.html b/broker/redoc-static.html
index 973da47c..533c4e79 100644
--- a/broker/redoc-static.html
+++ b/broker/redoc-static.html
@@ -716,16 +716,25 @@ as far as the detector reaches, i.e. the detection is not clipped in resolution.
If enabled it will likely reduce performance of Jungfraujoch for datasets with a very high indexing rate.
(experimental feature)
ice_ring_width_q_recipA
required
number <float> [ 0 .. 1 ]
Default: 0.02
Width of ice ring in q-space in reciprocal space
-
high_res_gap_Q_recipA
number <float> [ 0.1 .. 5 ]
Default: 1.5
This parameter is used to remove spurious spots at a very high resolution, that sometimes appear due to very low background close to the edge of the detector.
+
high_res_gap_Q_recipA
number <float> [ 0.1 .. 5 ]
Default: 1.5
This parameter is used to remove spurious spots at a very high resolution, that sometimes appear due to very low background close to the edge of the detector.
If there is a gap in (1/d)-space between spots of at least this size, spots on the side of the gap with high resolution will be discarded. This is optional parameter.
This option should be turned OFF for small molecule datasets or for crystals with very low mosaicity, when it is expected to see only few spots in any case.
+
adaptive_threshold
boolean
Default: false
Self-calibrating spot detection: replace the fixed photon_count_threshold by a per-resolution-ring
+threshold derived from each image's own noise, so the same setting works across datasets without
+per-dataset tuning. photon_count_threshold is then ignored and false_pixels_per_frame sets the
+operating point instead.
+Only available on detectors whose images are analysed in software (the DECTRIS/SIMPLON workflow).
+The JUNGFRAU and EIGER workflows find spots on the FPGA, which applies its own fixed threshold,
+so enabling this there is rejected rather than silently ignored.
+
false_pixels_per_frame
number <float> [ 1 .. 100000 ]
Default: 100
Operating point of the adaptive threshold: the number of noise pixels tolerated per frame.
+About 100 suits a multi-megapixel detector. Ignored unless adaptive_threshold is set.
Apply polarization correction for azimuthal integration (polarization factor must be configured in dataset settings)
solid_angle_corr
required
boolean
Default: true
Apply solid angle correction for azimuthal integration
high_q_recipA
number <float> [ 0.00002 .. 10 ]
Upper q limit of the azimuthal integration [1/Angstrom]. Optional: if omitted, the integration
@@ -844,7 +853,7 @@ This can only be done when detector is Idle, Error or