LightGBM installation error_MacOSX10.14_Cmake

[AdityaJuvali]

gcc -v
Configured with: --prefix=/Library/Developer/CommandLineTools/usr --with-gxx-include-dir=/Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/c++/4.2.1
Apple LLVM version 10.0.0 (clang-1000.10.44.4)
Target: x86_64-apple-darwin18.2.0
Thread model: posix
InstalledDir: /Library/Developer/CommandLineTools/usr/bin

Issue:
I followed the installation guide and on 'cmake ..' step got following error:
############

-- The C compiler identification is Clang 4.0.1
-- The CXX compiler identification is Clang 4.0.1
-- Check for working C compiler: /anaconda3/bin/x86_64-apple-darwin13.4.0-clang
-- Check for working C compiler: /anaconda3/bin/x86_64-apple-darwin13.4.0-clang -- broken
CMake Error at /anaconda3/share/cmake-3.12/Modules/CMakeTestCCompiler.cmake:52 (message):
The C compiler

"/anaconda3/bin/x86_64-apple-darwin13.4.0-clang"

is not able to compile a simple test program.

It fails with the following output:

Change Dir: /Users/adityajuvali/LightGBM/build/CMakeFiles/CMakeTmp

Run Build Command:"/anaconda3/bin/make" "cmTC_4d700/fast"
/anaconda3/bin/make -f CMakeFiles/cmTC_4d700.dir/build.make CMakeFiles/cmTC_4d700.dir/build
make[1]: Entering directory '/Users/adityajuvali/LightGBM/build/CMakeFiles/CMakeTmp'
Building C object CMakeFiles/cmTC_4d700.dir/testCCompiler.c.o
/anaconda3/bin/x86_64-apple-darwin13.4.0-clang   -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe  -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk   -o CMakeFiles/cmTC_4d700.dir/testCCompiler.c.o   -c /Users/adityajuvali/LightGBM/build/CMakeFiles/CMakeTmp/testCCompiler.c
Linking C executable cmTC_4d700
/anaconda3/bin/cmake -E cmake_link_script CMakeFiles/cmTC_4d700.dir/link.txt --verbose=1
/anaconda3/bin/x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe  -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk -Wl,-search_paths_first -Wl,-headerpad_max_install_names -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs  CMakeFiles/cmTC_4d700.dir/testCCompiler.c.o  -o cmTC_4d700 
ld: warning: ignoring file /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/lib/libSystem.tbd, file was built for unsupported file format ( 0x2D 0x2D 0x2D 0x20 0x21 0x74 0x61 0x70 0x69 0x2D 0x74 0x62 0x64 0x2D 0x76 0x33 ) which is not the architecture being linked (x86_64): /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/lib/libSystem.tbd
ld: dynamic main executables must link with libSystem.dylib for architecture x86_64
clang-4.0: error: linker command failed with exit code 1 (use -v to see invocation)
make[1]: *** [CMakeFiles/cmTC_4d700.dir/build.make:87: cmTC_4d700] Error 1
make[1]: Leaving directory '/Users/adityajuvali/LightGBM/build/CMakeFiles/CMakeTmp'
make: *** [Makefile:121: cmTC_4d700/fast] Error 2

CMake will not be able to correctly generate this project.
Call Stack (most recent call first):
CMakeLists.txt:7 (PROJECT)

-- Configuring incomplete, errors occurred!

#######

Please help. I am not able install even other models due to this same error.

[StrikerRUS]

Hi @AdityaJuvali !

As it can be observed from your logs, CMake cannot find you system Clang compiler. Instead, it uses some compiler from Anaconda installation.

-- The C compiler identification is Clang 4.0.1
-- The CXX compiler identification is Clang 4.0.1
-- Check for working C compiler: /anaconda3/bin/x86_64-apple-darwin13.4.0-clang
-- Check for working C compiler: /anaconda3/bin/x86_64-apple-darwin13.4.0-clang -- broken

Try to specify right compilers by the following command:

export CXX=g++ CC=gcc

Or just remove /anaconda3/bin from your PATH variable.

[AdityaJuvali]

Hi @AdityaJuvali !

As it can be observed from your logs, CMake cannot find you system Clang compiler. Instead, it uses some compiler from Anaconda installation.

-- The C compiler identification is Clang 4.0.1
-- The CXX compiler identification is Clang 4.0.1
-- Check for working C compiler: /anaconda3/bin/x86_64-apple-darwin13.4.0-clang
-- Check for working C compiler: /anaconda3/bin/x86_64-apple-darwin13.4.0-clang -- broken

Try to specify right compilers by the following command:

export CXX=g++ CC=gcc

Or just remove /anaconda3/bin from your PATH variable.

Thank you for the supportive response. I tried this and got another error. It's anaconda again. Could you please help on changing the PATH variable that you mentioned. I am a beginner Data science student and haven't handled MacOSX before.

Error:
-- The C compiler identification is AppleClang 10.0.0.10001044
-- The CXX compiler identification is AppleClang 10.0.0.10001044
-- Check for working C compiler: /Library/Developer/CommandLineTools/usr/bin/gcc
-- Check for working C compiler: /Library/Developer/CommandLineTools/usr/bin/gcc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Check for working CXX compiler: /Library/Developer/CommandLineTools/usr/bin/g++
-- Check for working CXX compiler: /Library/Developer/CommandLineTools/usr/bin/g++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
CMake Error at /anaconda3/share/cmake-3.12/Modules/FindPackageHandleStandardArgs.cmake:137 (message):
Could NOT find OpenMP_C (missing: OpenMP_C_FLAGS OpenMP_C_LIB_NAMES)
Call Stack (most recent call first):
/anaconda3/share/cmake-3.12/Modules/FindPackageHandleStandardArgs.cmake:378 (_FPHSA_FAILURE_MESSAGE)
/anaconda3/share/cmake-3.12/Modules/FindOpenMP.cmake:466 (find_package_handle_standard_args)
CMakeLists.txt:78 (find_package)

-- Configuring incomplete, errors occurred!

[StrikerRUS]

@AdityaJuvali Now everything OK with your gcc (Apple Clang actually)! No need to do anything else, like PATH modification.

The current error says you don't have OpenMP on your machine.
Please follow the installation guide (step 2) to install it:
https://lightgbm.readthedocs.io/en/latest/Installation-Guide.html#apple-clang

[AdityaJuvali]

I have OpenMP on my pc. Please check below:

brew install libomp
Updating Homebrew...
==> Auto-updated Homebrew!
Updated 1 tap (homebrew/core).
==> New Formulae
postgresql@10
==> Updated Formulae
easyengine

Warning: libomp 7.0.0 is already installed and up-to-date
To reinstall 7.0.0, run brew reinstall libomp

[AdityaJuvali]

@AdityaJuvali Now everything OK with your gcc (Apple Clang actually)! No need to do anything else, like PATH modification.

The current error says you don't have OpenMP on your machine.
Please follow the installation guide (step 2) to install it:
https://lightgbm.readthedocs.io/en/latest/Installation-Guide.html#apple-clang

I have OpenMP on my pc. Please check below:

brew install libomp
Updating Homebrew...
==> Auto-updated Homebrew!
Updated 1 tap (homebrew/core).
==> New Formulae
postgresql@10
==> Updated Formulae
easyengine

Warning: libomp 7.0.0 is already installed and up-to-date
To reinstall 7.0.0, run brew reinstall libomp

[AdityaJuvali]

@AdityaJuvali Now everything OK with your gcc (Apple Clang actually)! No need to do anything else, like PATH modification.

The current error says you don't have OpenMP on your machine.
Please follow the installation guide (step 2) to install it:
https://lightgbm.readthedocs.io/en/latest/Installation-Guide.html#apple-clang

Is the OpenMP installation faulty? Please check below:

brew install libomp
==> Downloading https://homebrew.bintray.com/bottles/libomp-7.0.0.mojave.bottle.tar.gz
Already downloaded: /Users/MyName/Library/Caches/Homebrew/downloads/0aedeb35dcb855e8798934be27a1204ec12efb4b1833c6885416802fd0e9885f--libomp-7.0.0.mojave.bottle.tar.gz
==> Pouring libomp-7.0.0.mojave.bottle.tar.gz
==> Caveats
On Apple Clang, you need to add several options to use OpenMP's front end
instead of the standard driver option. This usually looks like
-Xpreprocessor -fopenmp -lomp

You might need to make sure the lib and include directories are discoverable
if /usr/local is not searched:

-L/usr/local/opt/libomp/lib -I/usr/local/opt/libomp/include

For CMake, the following flags will cause the OpenMP::OpenMP_CXX target to
be set up correctly:
-DOpenMP_CXX_FLAGS="-Xpreprocessor -fopenmp -I/usr/local/opt/libomp/include" -DOpenMP_CXX_LIB_NAMES="omp" -DOpenMP_omp_LIBRARY=/usr/local/opt/libomp/lib/libomp.dylib
==> Summary
🍺 /usr/local/Cellar/libomp/7.0.0: 12 files, 1.2MB

[StrikerRUS]

It seems that OpenMP is installed correctly.

Are you still getting the following error?

Could NOT find OpenMP_C (missing: OpenMP_C_FLAGS OpenMP_C_LIB_NAMES)

[AdityaJuvali]

It seems that OpenMP is installed correctly.

Are you still getting the following error?

Could NOT find OpenMP_C (missing: OpenMP_C_FLAGS OpenMP_C_LIB_NAMES)

Yes. I uninstalled everything and followed all your steps. I am getting the same error.

[StrikerRUS]

Then try to temporary remove all conda-associated items from your PATH variable and follow installation guide from the scratch.

[AdityaJuvali]

Then try to temporary remove all conda-associated items from your PATH variable and follow installation guide from the scratch.

you mean, should I uninstall anaconda3?
I don't know how to remove PATH temporarily, please give reference or steps.
Thank you so much for your help. Appreciated. 👍

[StrikerRUS]

you mean, should I uninstall anaconda3?

I suppose it's unneeded. Just try to remove all things connected to anaconda from PATH:
https://blog.just2us.com/2011/05/setting-path-variable-in-mac-permanently/

[AdityaJuvali]

I removed the variable 'anaconda3/bin' from the PATH. It moved ahead but again gave error as:

CMake Error at /usr/local/Cellar/cmake/3.13.1/share/cmake/Modules/FindPackageHandleStandardArgs.cmake:137 (message):
Could NOT find OpenMP_C (missing: OpenMP_C_FLAGS OpenMP_C_LIB_NAMES)
Call Stack (most recent call first):
/usr/local/Cellar/cmake/3.13.1/share/cmake/Modules/FindPackageHandleStandardArgs.cmake:378 (_FPHSA_FAILURE_MESSAGE)
/usr/local/Cellar/cmake/3.13.1/share/cmake/Modules/FindOpenMP.cmake:473 (find_package_handle_standard_args)
CMakeLists.txt:78 (find_package)

[StrikerRUS]

Try to brew reinstall libomp

[AdityaJuvali]

I tried that too. No progress. Please help!

[StrikerRUS]

Please provide the full sequence of actions you've performed and the error message.

Also try the following command: brew link openmp