CMake 3.16 build issues

[henryiii]

This may be an issue with CMake 3.16. Here's the methodology:

apt-get update && apt-get install -y wget python3-dev vim
wget -qO- "https://cmake.org/files/v3.15/cmake-3.15.7-Linux-x86_64.tar.gz" | tar --strip-components=1 -xz -C /usr/local
# Remove warning from this file:
vi /usr/local/cuda/targets/x86_64-linux/include/host_defines.h
cmake -S goofit -B build -DGOOFIT_TESTS=OFF -DGOOFIT_EXAMPLES=OFF -DGOOFIT_ARCH=3.5
cmake --build build -v | tee goofit/cmake315.log

(and likewise for 3.16.4)

And the differences:

> /usr/bin/make -f src/goofit/CMakeFiles/Application.dir/build.make src/goofit/CMakeFiles/Application.dir/depend
> make[2]: Entering directory '/build'
> cd /build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /goofit /goofit/src/goofit /build /build/src/goofit /build/src/goofit/CMakeFiles/Application.dir/DependInfo.cmake --color=
> Dependee "/build/src/goofit/CMakeFiles/Application.dir/DependInfo.cmake" is newer than depender "/build/src/goofit/CMakeFiles/Application.dir/depend.internal".
> Dependee "/build/src/goofit/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/src/goofit/CMakeFiles/Application.dir/depend.internal".
> Scanning dependencies of target Application
> make[2]: Leaving directory '/build'
> /usr/bin/make -f src/goofit/CMakeFiles/Application.dir/build.make src/goofit/CMakeFiles/Application.dir/build
> make[2]: Entering directory '/build'
> [ 27%] Building CXX object src/goofit/CMakeFiles/Application.dir/Application.cpp.o
> cd /build/src/goofit && /usr/bin/c++  -DMATHCORE_STANDALONE -DMCBOOSTER_BACKEND=CUDA -DROOT_Math_VecTypes -DTHRUST_DEVICE_SYSTEM=THRUST_DEVICE_SYSTEM_CUDA -DTHRUST_HOST_SYSTEM=THRUST_HOST_SYSTEM_CPP -I/goofit/include -I/build/include -I/goofit/extern/MCBooster -I/goofit/extern/generics -I/goofit/extern/Minuit2/inc -I/goofit/extern/CLI11/include -I/goofit/extern/FeatureDetector/src -I/goofit/extern/fmt/include -isystem /goofit/extern/thrust -isystem /goofit/extern/rang/include -isystem /goofit/extern/Eigen -isystem /usr/local/cuda/targets/x86_64-linux/include  -Wall -Wextra -Wno-unknown-pragmas -Wno-long-long -Wno-attributes -Wno-sign-compare -Wno-unused-parameter -O2 -g -DNDEBUG -fPIC -fvisibility=hidden   -march=native -isystem /usr/local/cuda/targets/x86_64-linux/include -std=c++11 -o CMakeFiles/Application.dir/Application.cpp.o -c /goofit/src/goofit/Application.cpp
> [ 27%] Linking CXX static library libApplication.a
> cd /build/src/goofit && /usr/local/bin/cmake -P CMakeFiles/Application.dir/cmake_clean_target.cmake
> cd /build/src/goofit && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/Application.dir/link.txt --verbose=1
> /usr/bin/ar qc libApplication.a  CMakeFiles/Application.dir/Application.cpp.o
> /usr/bin/ranlib libApplication.a
> make[2]: Leaving directory '/build'
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> /usr/bin/make -f src/goofit/CMakeFiles/DataSet.dir/build.make src/goofit/CMakeFiles/DataSet.dir/depend
> make[2]: Entering directory '/build'
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> Dependee "/build/src/goofit/CMakeFiles/DataSet.dir/DependInfo.cmake" is newer than depender "/build/src/goofit/CMakeFiles/DataSet.dir/depend.internal".
> Dependee "/build/src/goofit/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/src/goofit/CMakeFiles/DataSet.dir/depend.internal".
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> make[2]: Entering directory '/build'
> [ 27%] Building CXX object src/goofit/CMakeFiles/DataSet.dir/DataSet.cpp.o
> cd /build/src/goofit && /usr/bin/c++  -DMATHCORE_STANDALONE -DMCBOOSTER_BACKEND=CUDA -DROOT_Math_VecTypes -DTHRUST_DEVICE_SYSTEM=THRUST_DEVICE_SYSTEM_CUDA -DTHRUST_HOST_SYSTEM=THRUST_HOST_SYSTEM_CPP -I/goofit/include -I/build/include -I/goofit/extern/MCBooster -I/goofit/extern/generics -I/goofit/extern/Minuit2/inc -I/goofit/extern/CLI11/include -I/goofit/extern/FeatureDetector/src -I/goofit/extern/fmt/include -isystem /goofit/extern/thrust -isystem /goofit/extern/rang/include -isystem /goofit/extern/Eigen  -Wall -Wextra -Wno-unknown-pragmas -Wno-long-long -Wno-attributes -Wno-sign-compare -Wno-unused-parameter -O2 -g -DNDEBUG -fPIC -fvisibility=hidden   -march=native -isystem /usr/local/cuda/targets/x86_64-linux/include -std=c++11 -o CMakeFiles/DataSet.dir/DataSet.cpp.o -c /goofit/src/goofit/DataSet.cpp
> [ 28%] Building CXX object src/goofit/CMakeFiles/DataSet.dir/BinnedDataSet.cpp.o
> cd /build/src/goofit && /usr/bin/c++  -DMATHCORE_STANDALONE -DMCBOOSTER_BACKEND=CUDA -DROOT_Math_VecTypes -DTHRUST_DEVICE_SYSTEM=THRUST_DEVICE_SYSTEM_CUDA -DTHRUST_HOST_SYSTEM=THRUST_HOST_SYSTEM_CPP -I/goofit/include -I/build/include -I/goofit/extern/MCBooster -I/goofit/extern/generics -I/goofit/extern/Minuit2/inc -I/goofit/extern/CLI11/include -I/goofit/extern/FeatureDetector/src -I/goofit/extern/fmt/include -isystem /goofit/extern/thrust -isystem /goofit/extern/rang/include -isystem /goofit/extern/Eigen  -Wall -Wextra -Wno-unknown-pragmas -Wno-long-long -Wno-attributes -Wno-sign-compare -Wno-unused-parameter -O2 -g -DNDEBUG -fPIC -fvisibility=hidden   -march=native -isystem /usr/local/cuda/targets/x86_64-linux/include -std=c++11 -o CMakeFiles/DataSet.dir/BinnedDataSet.cpp.o -c /goofit/src/goofit/BinnedDataSet.cpp
> [ 28%] Building CXX object src/goofit/CMakeFiles/DataSet.dir/UnbinnedDataSet.cpp.o
> cd /build/src/goofit && /usr/bin/c++  -DMATHCORE_STANDALONE -DMCBOOSTER_BACKEND=CUDA -DROOT_Math_VecTypes -DTHRUST_DEVICE_SYSTEM=THRUST_DEVICE_SYSTEM_CUDA -DTHRUST_HOST_SYSTEM=THRUST_HOST_SYSTEM_CPP -I/goofit/include -I/build/include -I/goofit/extern/MCBooster -I/goofit/extern/generics -I/goofit/extern/Minuit2/inc -I/goofit/extern/CLI11/include -I/goofit/extern/FeatureDetector/src -I/goofit/extern/fmt/include -isystem /goofit/extern/thrust -isystem /goofit/extern/rang/include -isystem /goofit/extern/Eigen  -Wall -Wextra -Wno-unknown-pragmas -Wno-long-long -Wno-attributes -Wno-sign-compare -Wno-unused-parameter -O2 -g -DNDEBUG -fPIC -fvisibility=hidden   -march=native -isystem /usr/local/cuda/targets/x86_64-linux/include -std=c++11 -o CMakeFiles/DataSet.dir/UnbinnedDataSet.cpp.o -c /goofit/src/goofit/UnbinnedDataSet.cpp
> [ 28%] Linking CXX static library libDataSet.a
> cd /build/src/goofit && /usr/local/bin/cmake -P CMakeFiles/DataSet.dir/cmake_clean_target.cmake
> cd /build/src/goofit && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/DataSet.dir/link.txt --verbose=1
> /usr/bin/ar qc libDataSet.a  CMakeFiles/DataSet.dir/DataSet.cpp.o CMakeFiles/DataSet.dir/BinnedDataSet.cpp.o CMakeFiles/DataSet.dir/UnbinnedDataSet.cpp.o
> /usr/bin/ranlib libDataSet.a
> make[2]: Leaving directory '/build'
> [ 28%] Built target DataSet
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< make[2]: Entering directory '/build'
< cd /build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /goofit /goofit/src/goofit /build /build/src/goofit /build/src/goofit/CMakeFiles/DataSet.dir/DependInfo.cmake --color=
< Dependee "/build/src/goofit/CMakeFiles/DataSet.dir/DependInfo.cmake" is newer than depender "/build/src/goofit/CMakeFiles/DataSet.dir/depend.internal".
< Dependee "/build/src/goofit/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/src/goofit/CMakeFiles/DataSet.dir/depend.internal".
< Scanning dependencies of target DataSet
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< [ 30%] Building CXX object src/goofit/CMakeFiles/DataSet.dir/DataSet.cpp.o
< cd /build/src/goofit && /usr/bin/c++  -DMATHCORE_STANDALONE -DMCBOOSTER_BACKEND=CUDA -DROOT_Math_VecTypes -DTHRUST_DEVICE_SYSTEM=THRUST_DEVICE_SYSTEM_CUDA -DTHRUST_HOST_SYSTEM=THRUST_HOST_SYSTEM_CPP -I/goofit/include -I/build/include -I/goofit/extern/MCBooster -I/goofit/extern/generics -I/goofit/extern/Minuit2/inc -I/goofit/extern/CLI11/include -I/goofit/extern/FeatureDetector/src -I/goofit/extern/fmt/include -isystem /goofit/extern/thrust -isystem /goofit/extern/rang/include -isystem /goofit/extern/Eigen  -Wall -Wextra -Wno-unknown-pragmas -Wno-long-long -Wno-attributes -Wno-sign-compare -Wno-unused-parameter -O2 -g -DNDEBUG -fPIC -fvisibility=hidden   -march=native -isystem /usr/local/cuda/targets/x86_64-linux/include -std=c++11 -o CMakeFiles/DataSet.dir/DataSet.cpp.o -c /goofit/src/goofit/DataSet.cpp
< [ 31%] Building CXX object src/goofit/CMakeFiles/DataSet.dir/BinnedDataSet.cpp.o
< cd /build/src/goofit && /usr/bin/c++  -DMATHCORE_STANDALONE -DMCBOOSTER_BACKEND=CUDA -DROOT_Math_VecTypes -DTHRUST_DEVICE_SYSTEM=THRUST_DEVICE_SYSTEM_CUDA -DTHRUST_HOST_SYSTEM=THRUST_HOST_SYSTEM_CPP -I/goofit/include -I/build/include -I/goofit/extern/MCBooster -I/goofit/extern/generics -I/goofit/extern/Minuit2/inc -I/goofit/extern/CLI11/include -I/goofit/extern/FeatureDetector/src -I/goofit/extern/fmt/include -isystem /goofit/extern/thrust -isystem /goofit/extern/rang/include -isystem /goofit/extern/Eigen  -Wall -Wextra -Wno-unknown-pragmas -Wno-long-long -Wno-attributes -Wno-sign-compare -Wno-unused-parameter -O2 -g -DNDEBUG -fPIC -fvisibility=hidden   -march=native -isystem /usr/local/cuda/targets/x86_64-linux/include -std=c++11 -o CMakeFiles/DataSet.dir/BinnedDataSet.cpp.o -c /goofit/src/goofit/BinnedDataSet.cpp
< [ 31%] Building CXX object src/goofit/CMakeFiles/DataSet.dir/UnbinnedDataSet.cpp.o
< cd /build/src/goofit && /usr/bin/c++  -DMATHCORE_STANDALONE -DMCBOOSTER_BACKEND=CUDA -DROOT_Math_VecTypes -DTHRUST_DEVICE_SYSTEM=THRUST_DEVICE_SYSTEM_CUDA -DTHRUST_HOST_SYSTEM=THRUST_HOST_SYSTEM_CPP -I/goofit/include -I/build/include -I/goofit/extern/MCBooster -I/goofit/extern/generics -I/goofit/extern/Minuit2/inc -I/goofit/extern/CLI11/include -I/goofit/extern/FeatureDetector/src -I/goofit/extern/fmt/include -isystem /goofit/extern/thrust -isystem /goofit/extern/rang/include -isystem /goofit/extern/Eigen  -Wall -Wextra -Wno-unknown-pragmas -Wno-long-long -Wno-attributes -Wno-sign-compare -Wno-unused-parameter -O2 -g -DNDEBUG -fPIC -fvisibility=hidden   -march=native -isystem /usr/local/cuda/targets/x86_64-linux/include -std=c++11 -o CMakeFiles/DataSet.dir/UnbinnedDataSet.cpp.o -c /goofit/src/goofit/UnbinnedDataSet.cpp
< [ 31%] Linking CXX static library libDataSet.a
< cd /build/src/goofit && /usr/local/bin/cmake -P CMakeFiles/DataSet.dir/cmake_clean_target.cmake
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< /usr/bin/ar qc libDataSet.a  CMakeFiles/DataSet.dir/DataSet.cpp.o CMakeFiles/DataSet.dir/BinnedDataSet.cpp.o CMakeFiles/DataSet.dir/UnbinnedDataSet.cpp.o
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< Dependee "/build/src/goofit/CMakeFiles/Application.dir/DependInfo.cmake" is newer than depender "/build/src/goofit/CMakeFiles/Application.dir/depend.internal".
< Dependee "/build/src/goofit/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/src/goofit/CMakeFiles/Application.dir/depend.internal".
< Scanning dependencies of target Application
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< cd /build/src/goofit && /usr/bin/c++  -DMATHCORE_STANDALONE -DMCBOOSTER_BACKEND=CUDA -DROOT_Math_VecTypes -DTHRUST_DEVICE_SYSTEM=THRUST_DEVICE_SYSTEM_CUDA -DTHRUST_HOST_SYSTEM=THRUST_HOST_SYSTEM_CPP -I/goofit/include -I/build/include -I/goofit/extern/MCBooster -I/goofit/extern/generics -I/goofit/extern/Minuit2/inc -I/goofit/extern/CLI11/include -I/goofit/extern/FeatureDetector/src -I/goofit/extern/fmt/include -isystem /goofit/extern/thrust -isystem /goofit/extern/rang/include -isystem /goofit/extern/Eigen -isystem /usr/local/cuda/targets/x86_64-linux/include  -Wall -Wextra -Wno-unknown-pragmas -Wno-long-long -Wno-attributes -Wno-sign-compare -Wno-unused-parameter -O2 -g -DNDEBUG -fPIC -fvisibility=hidden   -march=native -isystem /usr/local/cuda/targets/x86_64-linux/include -std=c++11 -o CMakeFiles/Application.dir/Application.cpp.o -c /goofit/src/goofit/Application.cpp
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> cd /build/python && /usr/bin/c++  -Dlandau_EXPORTS -I/goofit/python/../include -I/goofit/extern/pybind11/include -I/usr/include/python3.6m  -Wall -Wextra -Wno-unknown-pragmas -Wno-long-long -Wno-attributes -Wno-sign-compare -Wno-unused-parameter -O2 -g -DNDEBUG -fPIC -fvisibility=hidden   -fvisibility=hidden -std=c++11 -o CMakeFiles/landau.dir/extras/landau.cpp.o -c /goofit/python/extras/landau.cpp
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cmake315.log
cmake316.log

[henryiii]

The links for the PDF libraries are different in 3.16; this part disappears:

 -L/usr/local/cuda/targets/x86_64-linux/lib
  ../../../src/PDFs/basic/libPDFBasic.a ../../../src/PDFs/combine/libPDFCombine.a ../../../src/PDFs/physics/libPDFPhysics.a ../../../src/PDFs/libPDFCore.a ../../../src/goofit/libApplication.a  ../../../src/goofit/libFaddeeva.a ../../../src/goofit/libFunctorWriter.a ../../../src/goofit/libPdfBase.a ../../../src/goofit/libFitManager2.a ../../../src/goofit/libDataSet.a ../../../src/goofit/libVariable.a ../../../extern/Minuit2/src/libMinuit2.a ../../../extern/Minuit2/src/math/libMinuit2Math.a ../../../extern/FeatureDetector/src/x86/libFeatureDetector.a ../../../extern/fmt/libfmt.a
 -lcudadevrt -lcudart_static -lrt -lpthread -ldl

I think this is why 3.16 is producing the missing symbols seen on Conda-forge and in #234. Any quick thoughts as to why this may have started happening, @robertmaynard? It was fine in CMake 3.8-3.15.

ImportError: /__w/GooFit/GooFit/build/goofit/_goofit.cpython-36m-x86_64-linux-gnu.so: undefined symbol:
 __cudaRegisterLinkedBinary_41_tmpxft_00000ff9_00000000_6_FLATTE_cpp1_ii_06041a8e

(FWIW: every PDF's cudaRegisterLinkedBinary symbol is missing)

[robertmaynard]

Can you try 3.16.2 and see if that works? If it does it means that the following fix is at fault:
https://gitlab.kitware.com/cmake/cmake/merge_requests/4191/

[henryiii]

I've started a build with 3.16.2, though I think this fix was back ported into 3.15.7, and I tested that one when 3.15.7 came out and it worked (I was quite worried when I saw it in the changes for 3.15.7, but it passed).

[henryiii]

No, it did not build with 3.16.2. It builds correctly with 3.15.7, which has the same fix back ported.

[robertmaynard]

@henryiii Do you have time to make a small test case that can reproduce this issue? That would really help me track down the root issue, and propose a solution ( and fix CMake if necessary ).

[henryiii]

I'll try, but I'm traveling this week. Now that I know roughly what is different it will be easier to set up.