SlicerRT Slicer extension is not working on mac

[fedorov]

As discussed in this thread https://discourse.slicer.org/t/failure-to-load-rtstruct-dicom-file/33504/5, it has been failing at least since Slicer 5.6.1.

Qt]   Error(s):
[Qt]     Cannot load library /Applications/Slicer-5.7.0-20240306.app/Contents/Extensions-32750/SlicerRT/lib/Slicer-5.7/qt-loadable-modules/libqSlicerBeamsModule.dylib: (dlopen(/Applications/Slicer-5.7.0-20240306.app/Contents/Extensions-32750/SlicerRT/lib/Slicer-5.7/qt-loadable-modules/libqSlicerBeamsModule.dylib, 0x0085): Library not loaded: @rpath/libomp.dylib
[Qt]   Referenced from: <8CC410E5-7FE3-33F6-BC6E-A68391968FE8> /Applications/Slicer-5.7.0-20240306.app/Contents/Extensions-32750/SlicerRT/lib/Slicer-5.7/qt-loadable-modules/libvtkSlicerBeamsModuleMRML.dylib
[Qt]   Reason: tried: '/Applications/Slicer-5.7.0-20240306.app/Contents/bin/../Extensions-32750/QuantitativeReporting/lib/Slicer-5.7/libomp.dylib' (no such file), '/Applications/Slicer-5.7.0-20240306.app/Contents/bin/../Extensions-32750/SlicerDevelopmentToolbox/lib/Slicer-5.7/libomp.dylib' (no such file), '/Applications/Slicer-5.7.0-20240306.app/Contents/bin/../Extensions-32750/IDCBrowser/lib/Slicer-5.7/libomp.dylib' (no such file), '/Applications/Slicer-5.7.0-20240306.app/Contents/bin/../Extensions-32750/DCMQI/lib/Slicer-5.7/libomp.dylib' (no such file), '/Applications/Slicer-5.7.0-20240306.app/Contents/bin/../Extensions-32750/DCMQI/lib/Slicer-5.7/cli-modules/libomp.dylib' (no such file), '/Applications/Slicer-5.7.0-20240306.app/Contents/bin/../Extensions-32750/PETDICOMExtension/lib/Slicer-5.7/libomp.dylib' (no such file), '/Applications/Slicer-5.7.0-20240306.app/Contents/bin/../Extensions-32750/PETDICOMExtension/lib/Slicer-5.7/cli-modules/libomp.dylib' (no such file), '/Applications/Slicer-5.7.0-20240306.app/Contents/bin/../Extensions-32750/SlicerRT/lib/Slicer-5.7/libomp.dylib' (no such file), '/Applications/Slicer-5.7.0-20240306.app/Contents/bin/../Extensions-32750/SlicerRT/lib/Slicer-5.7/cli-modules/libomp.dylib' (no such file), '/Applications/Slicer-5.7.0-20240306.app/Contents/bin/../Extensions-32750/SlicerRT/lib/Slicer-5.7/qt-loadable-modules/libomp.dylib' (no such file), '/Applications/Slicer-5.7.0-20240306.app/Contents/bin/../bin/libomp.dylib' (no such file), '/Applications/Slicer-5.7.0-20240306.app/Contents/bin/../lib/Slicer-5.7/libomp.dylib' (no such file), '/Applications/Slicer-5.7.0-20240306.app/Contents/bin/../lib/Slicer-5.7/cli-modules/libomp.dylib' (no such file), '/Applications/Slicer-5.7.0-20240306.app/Contents/bin/../lib/Slicer-5.7/qt-loadable-modules/libomp.dylib' (no such file), '/Applications/Slicer-5.7.0-20240306.app/Contents/bin/../../lib/Slicer-5.7/qt-loadable-modules/libomp.dylib' (no such file), '/Applications/Slicer-5.7.0-20240306.app/Contents/bin/../lib/Python/lib/libomp.dylib' (no such file), '/Applications/Slicer-5.7.0-20240306.app/Contents/bin/../lib/Python/lib/python3.9/site-packages/numpy/core/libomp.dylib' (no such file), '/Applications/Slicer-5.7.0-20240306.app/Contents/bin/../lib/Python/lib/python3.9/site-packages/numpy/lib/libomp.dylib' (no such file), '/Applications/Slicer-5.7.0-20240306.app/Contents/../lib/Slicer-5.7/qt-loadable-modules/libomp.dylib' (no such file), '/Users/svc-dashboard/D/P/A/teem-build/bin/libomp.dylib' (no such file), '/System/Volumes/Preboot/Cryptexes/OS/Users/svc-dashboard/D/P/A/teem-build/bin/libomp.dylib' (no such file), '/Users/svc-dashboard/D/P/A/qRestAPI-build/libomp.dylib' (no such file), '/System/Volumes/Preboot/Cryptexes/OS/Users/svc-dashboard/D/P/A/qRestAPI-build/libomp.dylib' (no such file), '/Users/svc-dashboard/D/Support/clang+llvm-14.0.6-x86_64-apple-darwin/lib/libomp.dylib' (no such file), '/System/Volumes/Preboot/Cryptexes/OS/Users/svc-dashboard/D/Support/clang+llvm-14.0.6-x86_64-apple-darwin/lib/libomp.dylib' (no such file), '/Users/svc-dashboard/D/P/A/teem-build/bin/libomp.dylib' (no such file), '/System/Volumes/Preboot/Cryptexes/OS/Users/svc-dashboard/D/P/A/teem-build/bin/libomp.dylib' (no such file), '/Users/svc-dashboard/D/P/A/qRestAPI-build/libomp.dylib' (no such file), '/System/Volumes/Preboot/Cryptexes/OS/Users/svc-dashboard/D/P/A/qRestAPI-build/libomp.dylib' (no such file), '/Users/svc-dashboard/D/P/A/teem-build/bin/libomp.dylib' (no such file), '/System/Volumes/Preboot/Cryptexes/OS/Users/svc-dashboard/D/P/A/teem-build/bin/libomp.dylib' (no such file), '/Users/svc-dashboard/D/P/A/qRestAPI-build/libomp.dylib' (no such file), '/System/Volumes/Preboot/Cryptexes/OS/Users/svc-dashboard/D/P/A/qRestAPI-build/libomp.dylib' (no such file), '/Users/svc-dashboard/D/P/A/teem-build/bin/libomp.dylib' (no such file), '/System/Volumes/Preboot/Cryptexes/OS/Users/svc-dashboard/D/P/A/teem-build/bin/libomp.dylib' (no such file), '/Users/svc-dashboard/D/P/A/qRestAPI-build/libomp.dylib' (no such file), '/System/Volumes/Preboot/Cryptexes/OS/Users/svc-dashboard/D/P/A/qRestAPI-build/libomp.dylib' (no such file), '/Users/svc-dashboard/D/P/A/teem-build/bin/libomp.dylib' (no such file), '/System/Volumes/Preboot/Cryptexes/OS/Users/svc-dashboard/D/P/A/teem-build/bin/libomp.dylib' (no such file), '/Users/svc-dashboard/D/P/A/qRestAPI-build/libomp.dylib' (no such file), '/System/Volumes/Preboot/Cryptexes/OS/Users/svc-dashboard/D/P/A/qRestAPI-build/libomp.dylib' (no such file), '/Applications/Slicer-5.7.0-20240306.app/Contents/Frameworks/libomp.dylib' (no such file), '/Applications/Slicer-5.7.0-20240306.app/Contents/Frameworks/QtCore.framework/Versions/5/Frameworks/libomp.dylib' (no such file), '/Applications/Slicer-5.7.0-20240306.app/Contents/MacOS/../libomp.dylib' (no such file), '/Users/svc-dashboard/D/P/A/CTK-build/CMakeExternals/Install/lib/libomp.dylib' (no such file), '/System/Volumes/Preboot/Cryptexes/OS/Users/svc-dashboard/D/P/A/CTK-build/CMakeExternals/Install/lib/libomp.dylib' (no such file), '/Users/svc-dashboard/D/P/A/teem-build/bin/libomp.dylib' (no such file), '/System/Volumes/Preboot/Cryptexes/OS/Users/svc-dashboard/D/P/A/teem-build/bin/libomp.dylib' (no such file), '/usr/local/lib/libomp.dylib' (no such file), '/usr/lib/libomp.dylib' (no such file, not in dyld cache))

[cpinter]

Thanks @fedorov for creating the ticket! This has been an issue for a long time now, and it would be important to fix this. Unfortunately we don't use Mac at all, and I don't even have one (nor the experience to work on such issues on Mac). Can we add the high priority label for this? It can be a blocking issue for Mac users not to be able to install certain extensions.

[lassoan]

One solution could be to get rid of OpenMP.

Recently the same problem came up in Elastix extension, and after consulting with Jc and Matt McCormick, the decision was to disable use of OpenMP, because it usually does not provide perceivable performance improvement and often causes packaging problems like this.

[cpinter]

In terms of SlicerRT, this will need to be consulted with @gregsharp . If we can remove OpenMP from the package without having much effect on the current modules, then it sounds like an acceptable solution.

[kirbyju]

I just ran into this same problem. Any updates?

[lassoan]

In which Slicer version? Latest stable and preview should work fine.

[kirbyju]

v5.6.2. Here's the error message:

[lassoan]

Could you please copy the application log here? Not screenshots, as they are not searchable and show only a tiny piece of the full log. Please also test with the latest Slicer Preview Release. Thank you!

[cpinter]

Latest stable and preview should work fine

@lassoan Are you sure? There has been no activity in SlicerRT since we discussed the issue on Mac, see above. Did I miss something?

[kirbyju]

Here's the full log from 5.6.2.
slicer-5.6.2-slicerRT-error.txt

[lassoan]

Thank you. It is indeed the same OpenMP issue and I did not remember correctly (I made the same workaround for SlicerElastix and not for SlicerRT). I've pushed a commit now to disable OpenMP in Plastimatch. @kirbyju please test tomorrow and close this issue if SlicerRT works. Thank you!

[cpinter]

Excellent, thank you so much Andras!

[kirbyju]

Works in latest preview, thanks.

Edit: I'm not seeing any option to let me close the issue.

[fedorov]

Thank you Andras and Justin! I have not tested, but I take Justin's word for it, and will close the issue!