Fix openmp windows #41
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WalkthroughBumped app/version references from 0.9.2 → 0.9.4 in workflow and settings; enabled OpenMP and increased Ninja parallelism in the Windows CI; added a cmake token Changes
Estimated code review effort🎯 3 (Moderate) | ⏱️ ~20 minutes Possibly related PRs
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Actionable comments posted: 0
🧹 Nitpick comments (4)
settings.json (1)
4-4: Version bump to 0.9.4 looks correct and aligns with workflow APP_NAME.
Matches the workflow’s APP_NAME change to FLASHApp-0.9.4. No issues here.As a small safeguard: your build-executable job later overwrites settings.json.version with github.event.release.tag_name unconditionally. On non-release events this can become empty. Consider guarding that step to only run on releases, or falling back to this 0.9.4 value. Example approach (in the workflow, not here):
- name: Set Version in settings.json if: ${{ github.event_name == 'release' && github.event.release.tag_name != '' }} run: | $VERSION="${{ github.event.release.tag_name }}" $content = Get-Content -Raw settings.json | ConvertFrom-Json $content.version = $VERSION $content | ConvertTo-Json -Depth 100 | Set-Content settings.json.github/workflows/build-windows-executable-app.yaml (3)
17-17: APP_NAME updated to 0.9.4 — good consistency with settings.json.
This keeps installer names aligned with the app version. Consider deriving APP_NAME from a single source (e.g., settings.json or the release tag) to avoid future mismatches.Example pattern (optional): parse settings.json and set APP_NAME dynamically before packaging.
177-177: Use canonical CMake boolean casing for consistency (“ON” instead of “On”).
CMake handles booleans case-insensitively, but the file mixes “OFF/Off/On/ON”. Standardizing reduces confusion.Apply this minimal change:
- OPENMP: "On" + OPENMP: "ON"
180-180: Increased Ninja parallelism to -j4 — reasonable for GHA Windows runners.
This should speed up the build without oversubscribing cores too much. If build times fluctuate, you could make this configurable via an env var.
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.github/workflows/build-windows-executable-app.yaml(2 hunks)settings.json(1 hunks)
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.github/workflows/build-windows-executable-app.yaml (1)
177-177: Heads-up: enabling OpenMP on Windows may require runtime redistribution.
If OpenMS ends up linking against the MSVC OpenMP runtime, some target machines might need the corresponding VC++ Redistributable, or you may need to bundle the required OpenMP DLLs. Please test the MSI on a clean Windows VM to ensure no “missing DLL” errors at runtime.
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Dockerfile(1 hunks)
⏰ Context from checks skipped due to timeout of 90000ms. You can increase the timeout in your CodeRabbit configuration to a maximum of 15 minutes (900000ms). (2)
- GitHub Check: build-executable
- GitHub Check: build-full-app
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| # Configure. | ||
| RUN /bin/bash -c "cmake -DCMAKE_BUILD_TYPE='Release' -DCMAKE_PREFIX_PATH='/OpenMS/contrib-build/;/usr/;/usr/local' -DHAS_XSERVER=OFF -DBOOST_USE_STATIC=OFF -DPYOPENMS=ON ../OpenMS -DPY_MEMLEAK_DISABLE=On" | ||
| RUN /bin/bash -c "cmake -DCMAKE_BUILD_TYPE='Release' -DCMAKE_PREFIX_PATH='/OpenMS/contrib-build/;/usr/;/usr/local' -DHAS_XSERVER=OFF -DBOOST_USE_STATIC=OFF -DPYOPENMS=ON ../OpenMS -DPY_MEMLEAK_DISABLE=On DOPENMP=ON" |
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Fix missing -D prefix for OPENMP and place the source dir last in cmake invocation
The token DOPENMP=ON is missing the leading -, so CMake won’t treat it as a cache definition. Also, placing ../OpenMS before the final -D options is non-standard and brittle. Move all -D options before the source path and use -DOPENMP=ON. Consider consistent boolean casing as a minor cleanup.
[suggest_optional_refactor]
Apply this diff:
-RUN /bin/bash -c "cmake -DCMAKE_BUILD_TYPE='Release' -DCMAKE_PREFIX_PATH='/OpenMS/contrib-build/;/usr/;/usr/local' -DHAS_XSERVER=OFF -DBOOST_USE_STATIC=OFF -DPYOPENMS=ON ../OpenMS -DPY_MEMLEAK_DISABLE=On DOPENMP=ON"
+RUN /bin/bash -c "cmake -DCMAKE_BUILD_TYPE='Release' -DCMAKE_PREFIX_PATH='/OpenMS/contrib-build/;/usr/;/usr/local' -DHAS_XSERVER=OFF -DBOOST_USE_STATIC=OFF -DPYOPENMS=ON -DPY_MEMLEAK_DISABLE=ON -DOPENMP=ON ../OpenMS"If OpenMS expects a different CMake toggle for OpenMP (e.g., -DOPENMS_OPENMP=ON or -DUSE_OPENMP=ON), adjust accordingly. To confirm the correct flag in the upstream OpenMS CMake, please run this quick web query:
🌐 Web query:
What is the CMake option used by the OpenMS project to enable OpenMP?
💡 Result:
The OpenMS project uses the OPENMS_USE_OPENMP CMake option to enable or disable OpenMP support during the build process. You can set this option by passing -DOPENMS_USE_OPENMP=ON to your cmake command when configuring the build.
Example usage:
cmake -DOPENMS_USE_OPENMP=ON ..This option is specific to the OpenMS project and controls whether OpenMP parallelization is enabled in the compiled binaries. This approach is project-specific and complements the general CMake method for enabling OpenMP using the FindOpenMP module or manual flags for other projects[7][4].
If you are compiling OpenMS, be sure to use the exact name OPENMS_USE_OPENMP, as documented and used in the OpenMS source and CMake scripts.
Citations:
- 1: https://www.scivision.dev/cmake-openmp/
- 2: https://openmp.llvm.org/doxygen/index.html
- 3: How to enable OpenMP with CMake ?(Windows and VS2013) OpenMathLib/OpenBLAS#776
- 4: https://discourse.cmake.org/t/unique-way-to-enable-openmp-with-cmake/10350
- 5: Build error: OpenMP_libomp_LIBRARY on MacOs mapillary/OpenSfM#681
- 6: https://openmp.llvm.org
- 7: https://cmake.org/cmake/help/latest/module/FindOpenMP.html
- 8: https://community.sonarsource.com/t/microsoft-extension-activated-by-openmp-compiler-option-is-not-supported-de-upgrade/59435
- 9: https://forums.opensuse.org/t/how-to-enable-openmp-on-cmake-gcc-covid-sim/140653
- 10: https://learn.microsoft.com/en-us/cpp/build/reference/openmp-enable-openmp-2-0-support?view=msvc-170
Correct OpenMP CMake flag and reorder options in Dockerfile
The Dockerfile’s CMake invocation needs the proper OpenMS-specific flag (OPENMS_USE_OPENMP) and all -D options placed before the source directory. Also normalize boolean values to uppercase.
• File: Dockerfile
• Line: 106
Suggested diff:
-RUN /bin/bash -c "cmake -DCMAKE_BUILD_TYPE='Release' -DCMAKE_PREFIX_PATH='/OpenMS/contrib-build/;/usr/;/usr/local' -DHAS_XSERVER=OFF -DBOOST_USE_STATIC=OFF -DPYOPENMS=ON ../OpenMS -DPY_MEMLEAK_DISABLE=On DOPENMP=ON"
+RUN /bin/bash -c "cmake \
+ -DCMAKE_BUILD_TYPE=Release \
+ -DCMAKE_PREFIX_PATH='/OpenMS/contrib-build/;/usr/;/usr/local' \
+ -DHAS_XSERVER=OFF \
+ -DBOOST_USE_STATIC=OFF \
+ -DPYOPENMS=ON \
+ -DPY_MEMLEAK_DISABLE=ON \
+ -DOPENMS_USE_OPENMP=ON \
+ ../OpenMS"📝 Committable suggestion
‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.
| RUN /bin/bash -c "cmake -DCMAKE_BUILD_TYPE='Release' -DCMAKE_PREFIX_PATH='/OpenMS/contrib-build/;/usr/;/usr/local' -DHAS_XSERVER=OFF -DBOOST_USE_STATIC=OFF -DPYOPENMS=ON ../OpenMS -DPY_MEMLEAK_DISABLE=On DOPENMP=ON" | |
| RUN /bin/bash -c "cmake \ | |
| -DCMAKE_BUILD_TYPE=Release \ | |
| -DCMAKE_PREFIX_PATH='/OpenMS/contrib-build/;/usr/;/usr/local' \ | |
| -DHAS_XSERVER=OFF \ | |
| -DBOOST_USE_STATIC=OFF \ | |
| -DPYOPENMS=ON \ | |
| -DPY_MEMLEAK_DISABLE=ON \ | |
| -DOPENMS_USE_OPENMP=ON \ | |
| ../OpenMS" |
🤖 Prompt for AI Agents
In Dockerfile around line 106, the CMake command uses an incorrect OpenMP flag
and places -D options after the source dir; update the RUN line so all -D
options come before the source directory, replace the incorrect DOPENMP flag
with -DOPENMS_USE_OPENMP=ON, and normalize boolean values to uppercase (ON/OFF)
for flags like PYOPENMS and PY_MEMLEAK_DISABLE; ensure CMAKE_PREFIX_PATH and
other -D settings remain but appear before the final "../OpenMS" argument.
Summary by CodeRabbit
New Version
Performance
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