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john-bergelin

opened on Apr 9, 2024

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The ITKPythonBuilds release 5.3.0 doesn't include a build for manylinux2014_aarch64. How would I go about if I wanted to build a module for an aarch64 system running Ubuntu 18.04 with glibc 2.7?

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1. thewtex commented on Apr 9, 2024

   

   thewtex

   on Apr 9, 2024

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   Hi there @john-bergelin ,

   There are manylinux2014 and musl Linux aarch64 images here:

   https://quay.io/organization/pypa

   Python packages built with these toolchains should work on an Ubuntu 18.04 system with glibc 2.7.

   More specifics, directed towards the 5.4rc3 packages, on how the manylinux 2_28 aarch64 packages are built can be found here:

   https://github.com/InsightSoftwareConsortium/ITK/pull/4566/files
2. john-bergelin commented on Apr 18, 2024

   

   john-bergelin

   on Apr 18, 2024

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   Hi @thewtex,
   Thanks for pointing me in the right direction!

   I've tried building the python packages a couple of times now with these steps:

   git clone https://github.com/InsightSoftwareConsortium/ITKPythonPackage.git
   cd ITKPythonPackage
   git reset --hard HEAD
   git checkout release
   git pull origin release
   sudo git clean -fdx
   sudo rm -rf ITK-source
   git fetch origin manylinux2014
   git cherry-pick origin/manylinux2014
   docker run --privileged --rm tonistiigi/binfmt --install all
   docker run -it -v $(pwd):/work/ quay.io/pypa/manylinux2014_aarch64:2024-03-25-9206bd9 bash
   cd /work
   pipx upgrade cmake
   yum install sudo
   
   ./scripts/internal/manylinux-build-wheels.sh cp39
   

   But it always fails when trying to generate iktFixedArrayPython with this message:

   [2757/6010] Generating itkFixedArrayPython.cpp, ../../Generators/Python/itk/itkFixedArrayPython.py
   FAILED: Wrapping/Modules/ITKCommon/itkFixedArrayPython.cpp Wrapping/Generators/Python/itk/itkFixedArrayPython.py /work/ITK-cp39-cp39-manylinux2014_aarch64/Wrapping/Modules/ITKCommon/itkFixedArrayPython.cpp /work/ITK-cp39-cp39-manylinux2014_aarch64/Wrapping/Generators/Python/itk/itkFixedArrayPython.py
   cd /work/ITK-cp39-cp39-manylinux2014_aarch64/Wrapping/Typedefs/python && /work/ITK-cp39-cp39-manylinux2014_aarch64/Wrapping/Generators/SwigInterface/swiglinux-arm64-2024-03-26-master/bin/swig -c++ -python -fastdispatch -fvirtual -features autodoc=2 -doxygen -Werror -w302 -w303 -w312 -w314 -w361 -w362 -w350 -w383 -w384 -w389 -w394 -w395 -w467 -w508 -w509 -o /work/ITK-cp39-cp39-manylinux2014_aarch64/Wrapping/Modules/ITKCommon/itkFixedArrayPython.cpp -I/work/ITK-cp39-cp39-manylinux2014_aarch64/Wrapping/Generators/SwigInterface/swiglinux-arm64-2024-03-26-master/share/swig/4.3.0/python -I/work/ITK-cp39-cp39-manylinux2014_aarch64/Wrapping/Generators/SwigInterface/swiglinux-arm64-2024-03-26-master/share/swig/4.3.0 -I/work/ITK-source/ITK/Wrapping/Generators -I/work/ITK-cp39-cp39-manylinux2014_aarch64/Wrapping/Typedefs/python -I/work/ITK-cp39-cp39-manylinux2014_aarch64/Wrapping/Typedefs -outdir /work/ITK-cp39-cp39-manylinux2014_aarch64/Wrapping/Generators/Python/itk /work/ITK-cp39-cp39-manylinux2014_aarch64/Wrapping/Typedefs/itkFixedArray.i
   /work/ITK-cp39-cp39-manylinux2014_aarch64/Wrapping/Generators/SwigInterface/swiglinux-arm64-2024-03-26-master/bin/swig: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.20' not found (required by /work/ITK-cp39-cp39-manylinux2014_aarch64/Wrapping/Generators/SwigInterface/swiglinux-arm64-2024-03-26-master/bin/swig)
   /work/ITK-cp39-cp39-manylinux2014_aarch64/Wrapping/Generators/SwigInterface/swiglinux-arm64-2024-03-26-master/bin/swig: /usr/lib64/libstdc++.so.6: version `CXXABI_1.3.9' not found (required by /work/ITK-cp39-cp39-manylinux2014_aarch64/Wrapping/Generators/SwigInterface/swiglinux-arm64-2024-03-26-master/bin/swig)
   /work/ITK-cp39-cp39-manylinux2014_aarch64/Wrapping/Generators/SwigInterface/swiglinux-arm64-2024-03-26-master/bin/swig: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.21' not found (required by /work/ITK-cp39-cp39-manylinux2014_aarch64/Wrapping/Generators/SwigInterface/swiglinux-arm64-2024-03-26-master/bin/swig)
   [2770/6010] Run igenerator.py for ITKMesh
   ninja: build stopped: subcommand failed.
   + exit 1
   

   checking libstdc++.so.6 gives this:

   [root@31d4c24ebed6 lib64]# strings /usr/lib64/libstdc++.so.6 | grep GLIBCXX
   GLIBCXX_3.4
   GLIBCXX_3.4.1
   GLIBCXX_3.4.2
   GLIBCXX_3.4.3
   GLIBCXX_3.4.4
   GLIBCXX_3.4.5
   GLIBCXX_3.4.6
   GLIBCXX_3.4.7
   GLIBCXX_3.4.8
   GLIBCXX_3.4.9
   GLIBCXX_3.4.10
   GLIBCXX_3.4.11
   GLIBCXX_3.4.12
   GLIBCXX_3.4.13
   GLIBCXX_3.4.14
   GLIBCXX_3.4.15
   GLIBCXX_3.4.16
   GLIBCXX_3.4.17
   GLIBCXX_3.4.18
   GLIBCXX_3.4.19
   GLIBCXX_DEBUG_MESSAGE_LENGTH
   

   Any ideas on how I can add the other versions?

   I've also tried without the "cp39" argument but it fails at the same spot. Or do you know if another image of manylinux2014 is better suited? I used the one from the same date as in the Release.md.

   Cheers!
3. thewtex commented on Apr 18, 2024

   

   thewtex

   on Apr 18, 2024

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   Hi @john-bergelin,

   A few pointers:

   • Use the latest ITKPythonPackage release, which was recently updated.
   • The message means SWIG binary was built with a newer manylinux version, which is why it requires newer GLIBCXX. The solution is to build SWIG from source, then set the CMake variables ITK_USE_SYSTEM_SWIG to ON and SWIG_EXECUTABLE to the path to the swig binary. See:

   https://github.com/InsightSoftwareConsortium/ITK/blob/f383fe0a954620eccdaf69d649acf3fa5be8dc21/Wrapping/Generators/SwigInterface/CMakeLists.txt#L183-L231

   A recent bison is also required. I had to build from source, if I recall correctly. You can get it from here: https://ftp.gnu.org/gnu/bison/. It is an old-school autotools build.

   Please consider contributing the new swig binary if this is something you will want to update in the future.

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