Install on mac os fails - The C++ compiler cannot find a working standard library and it is not li

geoffwoollard · January 7, 2023, 6:54am

GROMACS version: gromacs-2022.4
GROMACS modification: No

I am following the quick and dirty install guidelines at https://manual.gromacs.org/documentation/current/install-guide/index.html.

cmake is failing, see below. I also tried with different combinations of -DCMAKE_C_COMPILER and -DCMAKE_CXX_COMPILER set to clang/clang++.

I don’t really understand how to resolve the error The C++ compiler cannot find a working standard library and it is not libstdc++.

(base) gws-MacBook-Pro-6:build gw$ cmake ..  -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=OFF -DCMAKE_C_COMPILER=gcc -DGMX_GPLUSPLUS_PATH=g++ -DCMAKE_CXX_COMPILER=g++
-- The C compiler identification is AppleClang 10.0.0.10001145
-- The CXX compiler identification is AppleClang 10.0.0.10001145
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /usr/bin/gcc - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/g++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Performing Test CXX17_COMPILES
-- Performing Test CXX17_COMPILES - Failed
-- Performing Test USING_LIBSTDCXX
-- Performing Test USING_LIBSTDCXX - Failed
CMake Error at cmake/FindLibStdCpp.cmake:81 (message):
  The C++ compiler cannot find a working standard library and it is not
  libstdc++.  The GROMACS build cannot handle this case.  Please use a
  working C++17 compiler and standard library.
Call Stack (most recent call first):
  CMakeLists.txt:68 (find_package)


-- Configuring incomplete, errors occurred!
See also "/Users/gw/software/gromacs-2022.4/build/CMakeFiles/CMakeOutput.log".
See also "/Users/gw/software/gromacs-2022.4/build/CMakeFiles/CMakeError.log".

geoffwoollard · January 7, 2023, 6:57am

(base) gws-MacBook-Pro-6:build gw$ cat /Users/gw/software/gromacs-2022.4/build/CMakeFiles/CMakeOutput.log
The system is: Darwin - 17.7.0 - x86_64
Compiling the C compiler identification source file "CMakeCCompilerId.c" succeeded.
Compiler: /usr/bin/gcc
Build flags:
Id flags:

The output was:
0


Compilation of the C compiler identification source "CMakeCCompilerId.c" produced "a.out"

The C compiler identification is AppleClang, found in "/Users/gw/software/gromacs-2022.4/build/CMakeFiles/3.24.20220817-gb6cfa38/CompilerIdC/a.out"

Compiling the CXX compiler identification source file "CMakeCXXCompilerId.cpp" succeeded.
Compiler: /usr/bin/g++
Build flags:
Id flags:

The output was:
0


Compilation of the CXX compiler identification source "CMakeCXXCompilerId.cpp" produced "a.out"

The CXX compiler identification is AppleClang, found in "/Users/gw/software/gromacs-2022.4/build/CMakeFiles/3.24.20220817-gb6cfa38/CompilerIdCXX/a.out"

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(base) gws-MacBook-Pro-6:build gw$ cat /Users/gw/software/gromacs-2022.4/build/CMakeFiles/CMakeError.log
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Change Dir: /Users/gw/software/gromacs-2022.4/build/CMakeFiles/CMakeTmp

Run Build Command(s):/usr/bin/make -f Makefile cmTC_b3567/fast && /Applications/Xcode.app/Contents/Developer/usr/bin/make  -f CMakeFiles/cmTC_b3567.dir/build.make CMakeFiles/cmTC_b3567.dir/build
Building CXX object CMakeFiles/cmTC_b3567.dir/src.cxx.o
/usr/bin/g++ -DCXX17_COMPILES  -std=c++17 -MD -MT CMakeFiles/cmTC_b3567.dir/src.cxx.o -MF CMakeFiles/cmTC_b3567.dir/src.cxx.o.d -o CMakeFiles/cmTC_b3567.dir/src.cxx.o -c /Users/gw/software/gromacs-2022.4/build/CMakeFiles/CMakeTmp/src.cxx
/Users/gw/software/gromacs-2022.4/build/CMakeFiles/CMakeTmp/src.cxx:7:31: error: call to unavailable member function 'value': introduced in macOS 10.14
  std::string_view view(input.value());
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/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/optional:942:27: note: candidate function has been explicitly made unavailable
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/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/optional:933:33: note: candidate function has been explicitly made unavailable
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/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/optional:951:28: note: candidate function not viable: no known conversion from 'optional<...>' to 'optional<...>' for object argument
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/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/optional:960:34: note: candidate function not viable: no known conversion from 'optional<...>' to 'const optional<...>' for object argument
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Run Build Command(s):/usr/bin/make -f Makefile cmTC_b1afa/fast && /Applications/Xcode.app/Contents/Developer/usr/bin/make  -f CMakeFiles/cmTC_b1afa.dir/build.make CMakeFiles/cmTC_b1afa.dir/build
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/Users/gw/software/gromacs-2022.4/build/CMakeFiles/CMakeTmp/src.cxx:2:21: error: use of undeclared identifier '__GLIBCXX__'
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Source file was:
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geoffwoollard · January 7, 2023, 6:58am

(base) gws-MacBook-Pro-6:build gw$ gcc --version
Configured with: --prefix=/Applications/Xcode.app/Contents/Developer/usr --with-gxx-include-dir=/usr/include/c++/4.2.1
Apple LLVM version 10.0.0 (clang-1000.11.45.5)
Target: x86_64-apple-darwin17.7.0
Thread model: posix
InstalledDir: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin


(base) gws-MacBook-Pro-6:build gw$ g++ --version
Configured with: --prefix=/Applications/Xcode.app/Contents/Developer/usr --with-gxx-include-dir=/usr/include/c++/4.2.1
Apple LLVM version 10.0.0 (clang-1000.11.45.5)
Target: x86_64-apple-darwin17.7.0
Thread model: posix
InstalledDir: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin


(base) gws-MacBook-Pro-6:build gw$ clang --version
Apple LLVM version 10.0.0 (clang-1000.11.45.5)
Target: x86_64-apple-darwin17.7.0
Thread model: posix
InstalledDir: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin


(base) gws-MacBook-Pro-6:build gw$ clang++ --version
Apple LLVM version 10.0.0 (clang-1000.11.45.5)
Target: x86_64-apple-darwin17.7.0
Thread model: posix
InstalledDir: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin

pbauer · January 7, 2023, 8:17am

Hello,

Can you please try compiling with the libc++ from clang instead? It looks like whatever MacOS is providing as g++ doesn’t work :)

As a note, I’ve been compiling this version of GROMACS on my Mac for months now without issue, so I hope this is just the default Mac clang being confused.

Cheers

Paul

geoffwoollard · January 7, 2023, 8:46am

How exactly do I do that? I googled “libc++ from apple clang” and read 5 links, but couldn’t figure it out.

How do I find the path for the libc++ from clang?
Once I have that path do I use it with the flag -DCMAKE_CXX_FLAGS ?

geoffwoollard · January 7, 2023, 8:53am

Using the flags -DCMAKE_C_COMPILER=clang -DCMAKE_CXX_COMPILER=clang++ \ -DCMAKE_CXX_FLAGS=-stdlib=libc++ isn’t working

(base) gws-MacBook-Pro-6:build gw$ cmake ..  -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=OFF -DCMAKE_C_COMPILER=clang -DCMAKE_CXX_COMPILER=clang++ -DCMAKE_CXX_FLAGS=-stdlib=libc++
-- The C compiler identification is AppleClang 10.0.0.10001145
-- The CXX compiler identification is AppleClang 10.0.0.10001145
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /usr/bin/clang - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/clang++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Performing Test CXX17_COMPILES
-- Performing Test CXX17_COMPILES - Failed
-- Performing Test USING_LIBSTDCXX
-- Performing Test USING_LIBSTDCXX - Failed
CMake Error at cmake/FindLibStdCpp.cmake:81 (message):
  The C++ compiler cannot find a working standard library and it is not
  libstdc++.  The GROMACS build cannot handle this case.  Please use a
  working C++17 compiler and standard library.
Call Stack (most recent call first):
  CMakeLists.txt:68 (find_package)


-- Configuring incomplete, errors occurred!
See also "/Users/gw/software/gromacs-2022.4/build/CMakeFiles/CMakeOutput.log".
See also "/Users/gw/software/gromacs-2022.4/build/CMakeFiles/CMakeError.log".

geoffwoollard · January 7, 2023, 9:00am

Also, if it helps

(base) gws-MacBook-Pro-6:developer gw$ clang++ test.cpp -o test.out -stdlib=libc++ # works fine
(base) gws-MacBook-Pro-6:developer gw$ clang++ test.cpp -o test.out -stdlib=libstdc++
clang: warning: libstdc++ is deprecated; move to libc++ [-Wdeprecated]

pbauer · January 7, 2023, 12:21pm

Hello,

you should just need to add -stdlib=libc++ to -DCMAKE_CXX_FLAGS, but
there must be a deeper issue with your compiler setup.

I just tried building release-2022.4 the same way as you did initially
and didn’t have any issues. But I’m using Homebrew on the Mac, so that
might affect things.

Cheers

Paul

geoffwoollard · January 8, 2023, 9:35pm

So any suggestions for trouble shooting the error message I’m getting with adding -stdlib=libc++ to -DCMAKE_CXX_FLAGS ?

Topic		Replies	Views
Problems with Mac installation User discussions	3	1438	August 26, 2020
Error During gromacs-2022 installation User discussions installation-error	1	862	April 22, 2022
Cmake problem 2023.2 User discussions installation-error	2	519	August 15, 2023
Build error : Gromacs 2021.3 with gcc 9.4 User discussions installation-error	0	1633	October 22, 2021
Installation issue User discussions cmake-error	1	1568	November 5, 2022

Install on mac os fails - The C++ compiler cannot find a working standard library and it is not li

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