itkzlib-ng on windows name mangling

blowekamp · April 26, 2023, 12:05pm

I am building SimpleITK on vanilla Conda with the ITK third party zlib library. Other libraries are coming from conda and appear to use the Conda zlib library. I am seeing the following linking error on windows:

ITKTestKernel.vcxproj -> %SRC_DIR%\b\ITK-build\lib\MinSizeRel\ITKTestKernel-5.3.lib

[4136](https://github.com/SimpleITK/SimpleITKCondaRecipe/actions/runs/4797602534/jobs/8534800625#step:6:4137) 
Building Custom Rule C:/Miniconda/envs/bld/conda-bld/work/b/ITK/Modules/Core/TestKernel/src/CMakeLists.txt

[4137](https://github.com/SimpleITK/SimpleITKCondaRecipe/actions/runs/4797602534/jobs/8534800625#step:6:4138) 
itkTestDriver.cxx

[4138](https://github.com/SimpleITK/SimpleITKCondaRecipe/actions/runs/4797602534/jobs/8534800625#step:6:4139)
itkzlib-5.3.lib(deflate.obj) : error LNK2005: deflate already defined in z.lib(zlib.dll) [%SRC_DIR%\b\ITK-build\Modules\Core\TestKernel\src\itkTestDriver.vcxproj] [%SRC_DIR%\b\ITK.vcxproj]

[4139](https://github.com/SimpleITK/SimpleITKCondaRecipe/actions/runs/4797602534/jobs/8534800625#step:6:4140)
itkzlib-5.3.lib(deflate.obj) : error LNK2005: deflateEnd already defined in z.lib(zlib.dll) [%SRC_DIR%\b\ITK-build\Modules\Core\TestKernel\src\itkTestDriver.vcxproj] [%SRC_DIR%\b\ITK.vcxproj]

[4140](https://github.com/SimpleITK/SimpleITKCondaRecipe/actions/runs/4797602534/jobs/8534800625#step:6:4141)
itkzlib-5.3.lib(deflate.obj) : error LNK2005: deflateInit2_ already defined in z.lib(zlib.dll) [%SRC_DIR%\b\ITK-build\Modules\Core\TestKernel\src\itkTestDriver.vcxproj] [%SRC_DIR%\b\ITK.vcxproj]

These symbols seem to be name mangled with zlib.def.in. I don’t see where this file is configured, but I’m not familiar with these window def files.

Anyone have more insight into what is and is suppose to be occurring here?

Thanks,
Brad

dzenanz · April 28, 2023, 1:45pm

ZLIB_SYMBOL_PREFIX is defined by zlib-ng here:

github.com

InsightSoftwareConsortium/ITK/blob/v5.3.0/Modules/ThirdParty/ZLIB/src/itkzlib-ng/CMakeLists.txt#L94


      
          option(WITH_REDUCED_MEM "Reduced memory usage for special cases (reduces performance)" OFF)
          option(WITH_NEW_STRATEGIES "Use new strategies" ON)
          option(WITH_NATIVE_INSTRUCTIONS
              "Instruct the compiler to use the full instruction set on this host (gcc/clang -march=native)" OFF)
          option(WITH_MAINTAINER_WARNINGS "Build with project maintainer warnings" OFF)
          option(WITH_CODE_COVERAGE "Enable code coverage reporting" OFF)
          option(WITH_INFLATE_STRICT "Build with strict inflate distance checking" OFF)
          option(WITH_INFLATE_ALLOW_INVALID_DIST "Build with zero fill for inflate invalid distances" OFF)
          option(WITH_UNALIGNED "Support unaligned reads on platforms that support it" ON)
          
          
set(ZLIB_SYMBOL_PREFIX "" CACHE STRING "Give this prefix to all publicly exported symbols.
          Useful when embedding into a larger library.
          Default is no prefix (empty prefix).")
          
          
# Add multi-choice option
          set(WITH_SANITIZER AUTO CACHE STRING "Enable sanitizer support")
          set_property(CACHE WITH_SANITIZER PROPERTY STRINGS "Memory" "Address" "Undefined" "Thread")
          
          
if(BASEARCH_ARM_FOUND)
              option(WITH_ACLE "Build with ACLE" ON)
              option(WITH_NEON "Build with NEON intrinsics" ON)

It is initialized by ITK here:

github.com

InsightSoftwareConsortium/ITK/blob/v5.3.0/Modules/ThirdParty/ZLIB/src/CMakeLists.txt#L5


      
          set(INC_INSTALL_DIR "${ITKZLIB_INSTALL_INCLUDE_DIR}/itkzlib-ng")
          set(BIN_INSTALL_DIR "${ITKZLIB_INSTALL_RUNTIME_DIR}")
          set(LIB_INSTALL_DIR "${ITKZLIB_INSTALL_LIBRARY_DIR}")
          set(PKGCONFIG_INSTALL_DIR "${ITKZLIB_INSTALL_ARCHIVE_DIR}")
          set(ZLIB_SYMBOL_PREFIX "itkzlib_")
          set(ZLIB_COMPAT ON)
          set(ZLIB_DUAL_LINK OFF)
          set(ZLIB_ENABLE_TESTS OFF)
          add_subdirectory(itkzlib-ng)
          mark_as_advanced(FORCE
            BIN_INSTALL_DIR
            FORCE_TZCNT
            INC_INSTALL_DIR
            LIB_INSTALL_DIR
            PKGCONFIG_INSTALL_DIR

so all symbols in ITK’s bundled zlib should have itkzlib_ prefix.

zlib.def.in might only be used by the makefiles (not CMake), such as:

github.com

zlib-ng/zlib-ng/blob/1c2698f9be19a8d837a83d2a08e938f22c3f3202/win32/Makefile.msc#L41


      
          	-DX86_PCLMULQDQ_CRC \
          	-DX86_SSE2 \
          	-DX86_SSE42 \
          	-DX86_SSE42_CRC_INTRIN \
          	-DX86_SSSE3 \
          	-DX86_AVX2
          
          
LDFLAGS = -nologo -debug -incremental:no -opt:ref -manifest
          ARFLAGS = -nologo
          RCFLAGS = /dWIN32 /r
          DEFFILE = zlib.def
          RCFILE = zlib1.rc
          RESFILE = zlib1.res
          WITH_GZFILEOP = yes
          ZLIB_COMPAT =
          SUFFIX =
          
          
OBJS = \
          	adler32.obj \
          	adler32_avx2.obj \
          	adler32_avx512.obj \

But I am not sure of this, it might be implicitly be used by something in the build system. If it is not used, we could remove it from our bundle:

github.com

InsightSoftwareConsortium/ITK/blob/v5.3.0/Modules/ThirdParty/ZLIB/UpdateFromUpstream.sh#L29


      
          gzread.c.in
          zconf.h.in
          zlib.h.in
          zlib_name_mangling.h.in
          zlib_name_mangling.h.empty
          zlib.pc.cmakein
          
          
zlib.map
          win32/zlibcompat.def.in
          win32/zlib1.rc
          win32/zlib.def.in
          
          
.gitattributes
          README.md
          INDEX.md
          "
          
          

          
extract_source () {
              git_archive
              pushd "${extractdir}/${name}-reduced"

blowekamp · April 28, 2023, 1:57pm

Yes, they should. But the link error message appears to indicate that the symbols are not getting mangled on Windows.

dzenanz · April 28, 2023, 2:07pm

I last dealt with this in Improve symbol name mangling of zlib and HDF5 · Issue #3530 · InsightSoftwareConsortium/ITK · GitHub and Add missing symbol name mangling by dzenanz · Pull Request #1322 · zlib-ng/zlib-ng · GitHub. My issues were a lot more convoluted than deflate being already defined. I suggest starting diagnosis by looking into ITK’s CMakeCache.txt.