Add support for multiple manylinux versions

[jcfr]

Motivation for this change is to build wheels with C++ ABI compatible with Slicer built using newer g++ having _GLIBCXX_USE_CXX11_ABI defaulting to 0.

See https://gcc.gnu.org/onlinedocs/libstdc++/manual/using_dual_abi.html

Note that the latest Slicer release (5.0) is built using centos7 based ¹ environment having _GLIBCXX_USE_CXX11_ABI set to 0.

We should likely build wheels using both manylinux2014 and manylinux_2_28.

As of 2022.06.22, this pull-request uses 2_24, as commented ² by @henryiii, I will instead update dockcross ³ to add 2_28 based image (instead of 2_24).

References:

• https://gcc.gnu.org/onlinedocs/libstdc++/manual/using_dual_abi.html
• https://discuss.python.org/t/how-to-set-glibcxx-use-cxx11-abi-for-manylinux2014-and-manylinux2010-wheels/10551
• Status of pip wheels with _GLIBCXX_USE_CXX11_ABI=1 pytorch/pytorch#51039
• GCC version in manylinux_2_24 pypa/manylinux#1012
• Add manylinux 2 24 x64 dockcross/dockcross#705

Footnotes

1. https://github.com/Slicer/SlicerBuildEnvironment#supported-build-environments ↩

2. https://github.com/pypa/manylinux/issues/1332#issuecomment-1157666846 ↩

3. https://github.com/dockcross/dockcross/pull/705 ↩

[jcfr]

Attempting to build the wheels using the 2_24 image report the following error:

[633/5991] Building CXX object Modules/Core/Common/src/CMakeFiles/ITKCommon.dir/itkTotalProgressReporter.cxx.o
FAILED: Modules/Core/Common/src/CMakeFiles/ITKCommon.dir/itkTotalProgressReporter.cxx.o
/usr/bin/g++ -DTBB_DEPRECATED=0 -DTBB_USE_CAPTURED_EXCEPTION=0 -I/work/ITK-source/ITK/Modules/ThirdParty/DoubleConversion/src -I/work/ITK-cp39-cp39-manylinux_2_24_x64/Modules/ThirdParty/DoubleConversion/src/double-conversion -I/work/ITK-cp39-cp39-manylinux_2_24_x64/Modules/ThirdParty/Eigen3/src -I/work/ITK-cp39-cp39-manylinux_2_24_x64/Modules/ThirdParty/KWSys/src -I/work/ITK-source/ITK/Modules/ThirdParty/VNL/src/vxl/v3p/netlib -I/work/ITK-source/ITK/Modules/ThirdParty/VNL/src/vxl/vcl -I/work/ITK-source/ITK/Modules/ThirdParty/VNL/src/vxl/core -I/work/ITK-cp39-cp39-manylinux_2_24_x64/Modules/ThirdParty/VNL/src/vxl/v3p/netlib -I/work/ITK-cp39-cp39-manylinux_2_24_x64/Modules/ThirdParty/VNL/src/vxl/vcl -I/work/ITK-cp39-cp39-manylinux_2_24_x64/Modules/ThirdParty/VNL/src/vxl/core -I/work/ITK-cp39-cp39-manylinux_2_24_x64/Modules/Core/Common -I/work/ITK-source/ITK/Modules/Core/Common/include -I/work/ITK-source/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo -I/work/ITK-source/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl -I/work/ITK-cp39-cp39-manylinux_2_24_x64/Modules/ThirdParty/VNL/src/vxl/core/vnl -isystem /work/ITK-source/ITK/Modules/ThirdParty/Eigen3/src/itkeigen/.. -isystem /work/oneTBB-prefix/include -O3 -DNDEBUG  -mtune=generic -march=corei7 -Wall -Wcast-align -Wdisabled-optimization -Wextra -Wformat=2 -Winvalid-pch -Wno-format-nonliteral -Wpointer-arith -Wshadow -Wunused -Wwrite-strings -funit-at-a-time -Wno-strict-overflow -Wno-deprecated -Wno-invalid-offsetof -Woverloaded-virtual -Wstrict-null-sentinel  -O3 -DNDEBUG -fPIC -std=c++14 -MD -MT Modules/Core/Common/src/CMakeFiles/ITKCommon.dir/itkTotalProgressReporter.cxx.o -MF Modules/Core/Common/src/CMakeFiles/ITKCommon.dir/itkTotalProgressReporter.cxx.o.d -o Modules/Core/Common/src/CMakeFiles/ITKCommon.dir/itkTotalProgressReporter.cxx.o -c /work/ITK-source/ITK/Modules/Core/Common/src/itkTotalProgressReporter.cxx
In file included from /work/ITK-source/ITK/Modules/Core/Common/include/itkImageRegion.h:33:0,
                 from /work/ITK-source/ITK/Modules/Core/Common/include/itkMultiThreaderBase.h:35,
                 from /work/ITK-source/ITK/Modules/Core/Common/src/itkTotalProgressReporter.cxx:19:
/work/ITK-source/ITK/Modules/Core/Common/include/itkSize.h:242:27: error: ‘ptrdiff_t’ does not name a type
   using difference_type = ptrdiff_t;
                           ^~~~~~~~~
[654/5991] Building CXX object Modules/ThirdParty/VNL/src/vxl/core/vnl/CMakeFiles/itkvnl.dir/Templates/vnl_matrix_fixed+float.allsizes-.cxx.o
ninja: build stopped: subcommand failed.

[jcfr]

Likely a regression introduced by InsightSoftwareConsortium/ITK@c173dfd, I will follow up with a pull request adding #include <cstddef> // For ptrdiff_t where relevant.

[jcfr]

See InsightSoftwareConsortium/ITK#3472

[thewtex]

Thanks @jcfr !

We should go directly to 2_28. I believe I tried 2_24 or a similar version in the past and ran into the issues noted by others in other threads, namely regression in GCC version relative to manylinux2014. We do have remote modules that need C++17, so that is also a blocker for 2_24. And, recently, it has been agreed that 2_24 will be deprecated, as discussed in the PyPA issues.

[jcfr]

We should go directly to 2_28 [...] and recently, it has been agreed that 2_24 will be deprecated

Agreed.

I will then add new images for 2_28 in dockcross (and mark 2_24 as unsupported adding links to relevant discussions)

[jcfr]

Updates:

• With the 2_24 based itk wheels, I confirmed the gcc ABI issue is addressed ✅️

• After updating the hdf5 mangling specific to the ITK build used in Slicer, I was also able to avoid the segfault related to global symbol.

• Independentpy of HDF5 (with default loading of factory disabled), I am still having issues ... after I have a better idea I will provide a summary.

[h-vetinari]

We should go directly to 2_28 [...] and recently, it has been agreed that 2_24 will be deprecated

Agreed.

I will then add new images for 2_28 in dockcross (and mark 2_24 as unsupported adding links to relevant discussions)

Just a lurker, but it seems current work in dockcross/dockcross#705 is still focussing on 2_24?

[jcfr]

@h-vetinari Once the PR you referenced is integrated, I will follow up with a new dockcross one marking the 2_24 image as not longer maintained and adding 2_28 ...

Since there is already an 2_24 image pushed on dockerhub, it will allow to have a reference in the README and focus on the maintenance of the more recent one.

[thewtex]

Following up with 2_28 dockcross images / scripts.