Issues with mpich and latest xcode #4797

hauntsaninja · 2023-09-20T18:40:46Z

hauntsaninja
Sep 20, 2023

Output of `brew config`

[x86_64] ~ λ /usr/local/bin/brew config                             
HOMEBREW_VERSION: 4.1.12
ORIGIN: https://github.com/Homebrew/brew
HEAD: aa2a77b1f1ac1539e69e186bad1d569100448987
Last commit: 4 days ago
Core tap origin: https://github.com/Homebrew/homebrew-core
Core tap HEAD: bf900b81e5585f78143107f59a5d435cba286f4e
Core tap last commit: 9 days ago
Core tap branch: master
Core tap JSON: 20 Sep 18:31 UTC
HOMEBREW_PREFIX: /usr/local
HOMEBREW_BAT_THEME: GitHub
HOMEBREW_CASK_OPTS: []
HOMEBREW_EDITOR: vim
HOMEBREW_MAKE_JOBS: 10
Homebrew Ruby: 2.6.10 => /System/Library/Frameworks/Ruby.framework/Versions/2.6/usr/bin/ruby
CPU: 10-core 64-bit westmere
Clang: 15.0.0 build 1500
Git: 2.39.3 => /Library/Developer/CommandLineTools/usr/bin/git
Curl: 8.1.2 => /usr/bin/curl
macOS: 13.5.2-x86_64
CLT: 15.0.0.0.1.1694021235
Xcode: N/A
Rosetta 2: true

Output of `brew doctor`

[x86_64] ~ λ /usr/local/bin/brew doctor         
Please note that these warnings are just used to help the Homebrew maintainers
with debugging if you file an issue. If everything you use Homebrew for is
working fine: please don't worry or file an issue; just ignore this. Thanks!

Warning: You have unlinked kegs in your Cellar.
Leaving kegs unlinked can lead to build-trouble and cause formulae that depend on
those kegs to fail to run properly once built. Run `brew link` on these:
  openssl@3

Description of issue

I posted details here pmodels/mpich#6684 , mpich maintainer suggested that the bottle Homebrew provides might be out of date.

I'm using macOS 13.5.2 (22G91)

I installed mpich using brew:

λ /usr/local/bin/brew info mpich    
==> mpich: stable 4.1.2 (bottled), HEAD
Implementation of the MPI Message Passing Interface standard
https://www.mpich.org/
Conflicts with:
  libfabric (because both install `fabric.h`)
  open-mpi (because both install MPI compiler wrappers)
/usr/local/Cellar/mpich/4.1.2 (1,453 files, 135.3MB) *
  Poured from bottle using the formulae.brew.sh API on 2023-09-19 at 19:53:57
From: https://github.com/Homebrew/homebrew-core/blob/HEAD/Formula/m/mpich.rb
License: mpich2

I have the standard Xcode command line tools installed:

λ pkgutil --pkg-info=com.apple.pkg.CLTools_Executables                   
package-id: com.apple.pkg.CLTools_Executables
version: 15.0.0.0.1.1694021235
volume: /
location: /
install-time: 1695069030

This is the version of my linker:

λ ld -v
@(#)PROGRAM:ld  PROJECT:dyld-1015.7
BUILD 18:48:48 Aug 22 2023
configured to support archs: armv6 armv7 armv7s arm64 arm64e arm64_32 i386 x86_64 x86_64h armv6m armv7k armv7m armv7em
will use ld-classic for: armv6 armv7 armv7s arm64_32 i386 armv6m armv7k armv7m armv7em
LTO support using: LLVM version 15.0.0 (static support for 29, runtime is 29)
TAPI support using: Apple TAPI version 15.0.0 (tapi-1500.0.12.3)
Library search paths:
Framework search paths:

I'm trying to build mpi4py. It's failing with:

      ld: unknown options: -commons
      clang: error: linker command failed with exit code 1 (use -v to see invocation)

Full build log collapsed below:

λ python -m pip install --upgrade --force-reinstall --no-cache-dir mpi4py                                         130 
Collecting mpi4py
  Downloading mpi4py-3.1.4.tar.gz (2.5 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 2.5/2.5 MB 34.3 MB/s eta 0:00:00
  Installing build dependencies ... done
  Getting requirements to build wheel ... done
  Preparing metadata (pyproject.toml) ... done
Building wheels for collected packages: mpi4py
  Building wheel for mpi4py (pyproject.toml) ... error
  error: subprocess-exited-with-error
  
  × Building wheel for mpi4py (pyproject.toml) did not run successfully.
  │ exit code: 1
  ╰─> [200 lines of output]
      running bdist_wheel
      running build
      running build_src
      running build_py
      creating build
      creating build/lib.macosx-11.0-x86_64-cpython-311
      creating build/lib.macosx-11.0-x86_64-cpython-311/mpi4py
      copying src/mpi4py/run.py -> build/lib.macosx-11.0-x86_64-cpython-311/mpi4py
      copying src/mpi4py/__init__.py -> build/lib.macosx-11.0-x86_64-cpython-311/mpi4py
      copying src/mpi4py/bench.py -> build/lib.macosx-11.0-x86_64-cpython-311/mpi4py
      copying src/mpi4py/__main__.py -> build/lib.macosx-11.0-x86_64-cpython-311/mpi4py
      creating build/lib.macosx-11.0-x86_64-cpython-311/mpi4py/futures
      copying src/mpi4py/futures/_base.py -> build/lib.macosx-11.0-x86_64-cpython-311/mpi4py/futures
      copying src/mpi4py/futures/server.py -> build/lib.macosx-11.0-x86_64-cpython-311/mpi4py/futures
      copying src/mpi4py/futures/__init__.py -> build/lib.macosx-11.0-x86_64-cpython-311/mpi4py/futures
      copying src/mpi4py/futures/_core.py -> build/lib.macosx-11.0-x86_64-cpython-311/mpi4py/futures
      copying src/mpi4py/futures/pool.py -> build/lib.macosx-11.0-x86_64-cpython-311/mpi4py/futures
      copying src/mpi4py/futures/aplus.py -> build/lib.macosx-11.0-x86_64-cpython-311/mpi4py/futures
      copying src/mpi4py/futures/__main__.py -> build/lib.macosx-11.0-x86_64-cpython-311/mpi4py/futures
      copying src/mpi4py/futures/_lib.py -> build/lib.macosx-11.0-x86_64-cpython-311/mpi4py/futures
      creating build/lib.macosx-11.0-x86_64-cpython-311/mpi4py/util
      copying src/mpi4py/util/pkl5.py -> build/lib.macosx-11.0-x86_64-cpython-311/mpi4py/util
      copying src/mpi4py/util/dtlib.py -> build/lib.macosx-11.0-x86_64-cpython-311/mpi4py/util
      copying src/mpi4py/util/__init__.py -> build/lib.macosx-11.0-x86_64-cpython-311/mpi4py/util
      copying src/mpi4py/py.typed -> build/lib.macosx-11.0-x86_64-cpython-311/mpi4py
      copying src/mpi4py/__main__.pyi -> build/lib.macosx-11.0-x86_64-cpython-311/mpi4py
      copying src/mpi4py/__init__.pyi -> build/lib.macosx-11.0-x86_64-cpython-311/mpi4py
      copying src/mpi4py/run.pyi -> build/lib.macosx-11.0-x86_64-cpython-311/mpi4py
      copying src/mpi4py/bench.pyi -> build/lib.macosx-11.0-x86_64-cpython-311/mpi4py
      copying src/mpi4py/MPI.pyi -> build/lib.macosx-11.0-x86_64-cpython-311/mpi4py
      copying src/mpi4py/dl.pyi -> build/lib.macosx-11.0-x86_64-cpython-311/mpi4py
      copying src/mpi4py/__init__.pxd -> build/lib.macosx-11.0-x86_64-cpython-311/mpi4py
      copying src/mpi4py/libmpi.pxd -> build/lib.macosx-11.0-x86_64-cpython-311/mpi4py
      copying src/mpi4py/MPI.pxd -> build/lib.macosx-11.0-x86_64-cpython-311/mpi4py
      creating build/lib.macosx-11.0-x86_64-cpython-311/mpi4py/include
      creating build/lib.macosx-11.0-x86_64-cpython-311/mpi4py/include/mpi4py
      copying src/mpi4py/include/mpi4py/mpi4py.MPI.h -> build/lib.macosx-11.0-x86_64-cpython-311/mpi4py/include/mpi4py
      copying src/mpi4py/include/mpi4py/mpi4py.MPI_api.h -> build/lib.macosx-11.0-x86_64-cpython-311/mpi4py/include/mpi4py
      copying src/mpi4py/include/mpi4py/mpi4py.h -> build/lib.macosx-11.0-x86_64-cpython-311/mpi4py/include/mpi4py
      copying src/mpi4py/include/mpi4py/mpi4py.i -> build/lib.macosx-11.0-x86_64-cpython-311/mpi4py/include/mpi4py
      copying src/mpi4py/include/mpi4py/mpi.pxi -> build/lib.macosx-11.0-x86_64-cpython-311/mpi4py/include/mpi4py
      copying src/mpi4py/futures/__main__.pyi -> build/lib.macosx-11.0-x86_64-cpython-311/mpi4py/futures
      copying src/mpi4py/futures/__init__.pyi -> build/lib.macosx-11.0-x86_64-cpython-311/mpi4py/futures
      copying src/mpi4py/futures/_core.pyi -> build/lib.macosx-11.0-x86_64-cpython-311/mpi4py/futures
      copying src/mpi4py/futures/aplus.pyi -> build/lib.macosx-11.0-x86_64-cpython-311/mpi4py/futures
      copying src/mpi4py/futures/server.pyi -> build/lib.macosx-11.0-x86_64-cpython-311/mpi4py/futures
      copying src/mpi4py/futures/pool.pyi -> build/lib.macosx-11.0-x86_64-cpython-311/mpi4py/futures
      copying src/mpi4py/futures/_lib.pyi -> build/lib.macosx-11.0-x86_64-cpython-311/mpi4py/futures
      copying src/mpi4py/util/__init__.pyi -> build/lib.macosx-11.0-x86_64-cpython-311/mpi4py/util
      copying src/mpi4py/util/dtlib.pyi -> build/lib.macosx-11.0-x86_64-cpython-311/mpi4py/util
      copying src/mpi4py/util/pkl5.pyi -> build/lib.macosx-11.0-x86_64-cpython-311/mpi4py/util
      running build_clib
      MPI configuration: [mpi] from 'mpi.cfg'
      MPI C compiler:    /usr/local/bin/mpicc
      MPI C++ compiler:  /usr/local/bin/mpicxx
      MPI F compiler:    /usr/local/bin/mpifort
      MPI F90 compiler:  /usr/local/bin/mpif90
      MPI F77 compiler:  /usr/local/bin/mpif77
      checking for library 'lmpe' ...
      /usr/local/bin/mpicc -DNDEBUG -g -fwrapv -O3 -Wall -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -march=native -mtune=native -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -c _configtest.c -o _configtest.o
      /usr/local/bin/mpicc -flat_namespace -undefined suppress _configtest.o -llmpe -o _configtest
      ld: warning: -undefined suppress is deprecated
      ld: warning: -undefined suppress is deprecated
      ld: unknown options: -commons
      clang: error: linker command failed with exit code 1 (use -v to see invocation)
      failure.
      removing: _configtest.c _configtest.o
      building 'mpe' dylib library
      creating build/temp.macosx-11.0-x86_64-cpython-311
      creating build/temp.macosx-11.0-x86_64-cpython-311/src
      creating build/temp.macosx-11.0-x86_64-cpython-311/src/lib-pmpi
      /usr/local/bin/mpicc -DNDEBUG -g -fwrapv -O3 -Wall -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -march=native -mtune=native -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -c src/lib-pmpi/mpe.c -o build/temp.macosx-11.0-x86_64-cpython-311/src/lib-pmpi/mpe.o
      creating build/lib.macosx-11.0-x86_64-cpython-311/mpi4py/lib-pmpi
      /usr/local/bin/mpicc -shared -undefined dynamic_lookup -L/usr/local/opt/readline/lib -L/usr/local/opt/readline/lib -L/Users/shantanu/.pyenv/versions/3.11.4/lib -L/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/lib -L/usr/local/opt/readline/lib -L/usr/local/opt/readline/lib -L/Users/shantanu/.pyenv/versions/3.11.4/lib -L/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/lib -install_name libmpe.dylib build/temp.macosx-11.0-x86_64-cpython-311/src/lib-pmpi/mpe.o -o build/lib.macosx-11.0-x86_64-cpython-311/mpi4py/lib-pmpi/libmpe.dylib
      ld: unknown options: -commons
      clang: error: linker command failed with exit code 1 (use -v to see invocation)
      warning: build_clib: command '/usr/local/bin/mpicc' failed with exit code 1
      
      warning: build_clib: building optional library "mpe" failed
      
      checking for library 'vt-mpi' ...
      /usr/local/bin/mpicc -DNDEBUG -g -fwrapv -O3 -Wall -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -march=native -mtune=native -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -c _configtest.c -o _configtest.o
      /usr/local/bin/mpicc -flat_namespace -undefined suppress _configtest.o -lvt-mpi -o _configtest
      ld: warning: -undefined suppress is deprecated
      ld: warning: -undefined suppress is deprecated
      ld: unknown options: -commons
      clang: error: linker command failed with exit code 1 (use -v to see invocation)
      failure.
      removing: _configtest.c _configtest.o
      checking for library 'vt.mpi' ...
      /usr/local/bin/mpicc -DNDEBUG -g -fwrapv -O3 -Wall -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -march=native -mtune=native -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -c _configtest.c -o _configtest.o
      /usr/local/bin/mpicc -flat_namespace -undefined suppress _configtest.o -lvt.mpi -o _configtest
      ld: warning: -undefined suppress is deprecated
      ld: warning: -undefined suppress is deprecated
      ld: unknown options: -commons
      clang: error: linker command failed with exit code 1 (use -v to see invocation)
      failure.
      removing: _configtest.c _configtest.o
      building 'vt' dylib library
      /usr/local/bin/mpicc -DNDEBUG -g -fwrapv -O3 -Wall -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -march=native -mtune=native -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -c src/lib-pmpi/vt.c -o build/temp.macosx-11.0-x86_64-cpython-311/src/lib-pmpi/vt.o
      /usr/local/bin/mpicc -shared -undefined dynamic_lookup -L/usr/local/opt/readline/lib -L/usr/local/opt/readline/lib -L/Users/shantanu/.pyenv/versions/3.11.4/lib -L/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/lib -L/usr/local/opt/readline/lib -L/usr/local/opt/readline/lib -L/Users/shantanu/.pyenv/versions/3.11.4/lib -L/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/lib -install_name libvt.dylib build/temp.macosx-11.0-x86_64-cpython-311/src/lib-pmpi/vt.o -o build/lib.macosx-11.0-x86_64-cpython-311/mpi4py/lib-pmpi/libvt.dylib
      ld: unknown options: -commons
      clang: error: linker command failed with exit code 1 (use -v to see invocation)
      warning: build_clib: command '/usr/local/bin/mpicc' failed with exit code 1
      
      warning: build_clib: building optional library "vt" failed
      
      checking for library 'vt-mpi' ...
      /usr/local/bin/mpicc -DNDEBUG -g -fwrapv -O3 -Wall -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -march=native -mtune=native -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -c _configtest.c -o _configtest.o
      /usr/local/bin/mpicc -flat_namespace -undefined suppress _configtest.o -lvt-mpi -o _configtest
      ld: warning: -undefined suppress is deprecated
      ld: warning: -undefined suppress is deprecated
      ld: unknown options: -commons
      clang: error: linker command failed with exit code 1 (use -v to see invocation)
      failure.
      removing: _configtest.c _configtest.o
      checking for library 'vt.mpi' ...
      /usr/local/bin/mpicc -DNDEBUG -g -fwrapv -O3 -Wall -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -march=native -mtune=native -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -c _configtest.c -o _configtest.o
      /usr/local/bin/mpicc -flat_namespace -undefined suppress _configtest.o -lvt.mpi -o _configtest
      ld: warning: -undefined suppress is deprecated
      ld: warning: -undefined suppress is deprecated
      ld: unknown options: -commons
      clang: error: linker command failed with exit code 1 (use -v to see invocation)
      failure.
      removing: _configtest.c _configtest.o
      building 'vt-mpi' dylib library
      /usr/local/bin/mpicc -DNDEBUG -g -fwrapv -O3 -Wall -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -march=native -mtune=native -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -c src/lib-pmpi/vt-mpi.c -o build/temp.macosx-11.0-x86_64-cpython-311/src/lib-pmpi/vt-mpi.o
      /usr/local/bin/mpicc -shared -undefined dynamic_lookup -L/usr/local/opt/readline/lib -L/usr/local/opt/readline/lib -L/Users/shantanu/.pyenv/versions/3.11.4/lib -L/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/lib -L/usr/local/opt/readline/lib -L/usr/local/opt/readline/lib -L/Users/shantanu/.pyenv/versions/3.11.4/lib -L/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/lib -install_name libvt-mpi.dylib build/temp.macosx-11.0-x86_64-cpython-311/src/lib-pmpi/vt-mpi.o -o build/lib.macosx-11.0-x86_64-cpython-311/mpi4py/lib-pmpi/libvt-mpi.dylib
      ld: unknown options: -commons
      clang: error: linker command failed with exit code 1 (use -v to see invocation)
      warning: build_clib: command '/usr/local/bin/mpicc' failed with exit code 1
      
      warning: build_clib: building optional library "vt-mpi" failed
      
      checking for library 'vt-hyb' ...
      /usr/local/bin/mpicc -DNDEBUG -g -fwrapv -O3 -Wall -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -march=native -mtune=native -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -c _configtest.c -o _configtest.o
      /usr/local/bin/mpicc -flat_namespace -undefined suppress _configtest.o -lvt-hyb -o _configtest
      ld: warning: -undefined suppress is deprecated
      ld: warning: -undefined suppress is deprecated
      ld: unknown options: -commons
      clang: error: linker command failed with exit code 1 (use -v to see invocation)
      failure.
      removing: _configtest.c _configtest.o
      checking for library 'vt.ompi' ...
      /usr/local/bin/mpicc -DNDEBUG -g -fwrapv -O3 -Wall -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -march=native -mtune=native -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -c _configtest.c -o _configtest.o
      /usr/local/bin/mpicc -flat_namespace -undefined suppress _configtest.o -lvt.ompi -o _configtest
      ld: warning: -undefined suppress is deprecated
      ld: warning: -undefined suppress is deprecated
      ld: unknown options: -commons
      clang: error: linker command failed with exit code 1 (use -v to see invocation)
      failure.
      removing: _configtest.c _configtest.o
      building 'vt-hyb' dylib library
      /usr/local/bin/mpicc -DNDEBUG -g -fwrapv -O3 -Wall -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -march=native -mtune=native -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -c src/lib-pmpi/vt-hyb.c -o build/temp.macosx-11.0-x86_64-cpython-311/src/lib-pmpi/vt-hyb.o
      /usr/local/bin/mpicc -shared -undefined dynamic_lookup -L/usr/local/opt/readline/lib -L/usr/local/opt/readline/lib -L/Users/shantanu/.pyenv/versions/3.11.4/lib -L/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/lib -L/usr/local/opt/readline/lib -L/usr/local/opt/readline/lib -L/Users/shantanu/.pyenv/versions/3.11.4/lib -L/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/lib -install_name libvt-hyb.dylib build/temp.macosx-11.0-x86_64-cpython-311/src/lib-pmpi/vt-hyb.o -o build/lib.macosx-11.0-x86_64-cpython-311/mpi4py/lib-pmpi/libvt-hyb.dylib
      ld: unknown options: -commons
      clang: error: linker command failed with exit code 1 (use -v to see invocation)
      warning: build_clib: command '/usr/local/bin/mpicc' failed with exit code 1
      
      warning: build_clib: building optional library "vt-hyb" failed
      
      running build_ext
      MPI configuration: [mpi] from 'mpi.cfg'
      MPI C compiler:    /usr/local/bin/mpicc
      MPI C++ compiler:  /usr/local/bin/mpicxx
      MPI F compiler:    /usr/local/bin/mpifort
      MPI F90 compiler:  /usr/local/bin/mpif90
      MPI F77 compiler:  /usr/local/bin/mpif77
      checking for dlopen() availability ...
      checking for header 'dlfcn.h' ...
      clang -DNDEBUG -g -fwrapv -O3 -Wall -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -march=native -mtune=native -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -I/Users/shantanu/.virtualenvs/openai-jowu/include -I/Users/shantanu/.pyenv/versions/3.11.4/include/python3.11 -c _configtest.c -o _configtest.o
      success!
      removing: _configtest.c _configtest.o
      success!
      checking for library 'dl' ...
      clang -DNDEBUG -g -fwrapv -O3 -Wall -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -march=native -mtune=native -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -I/Users/shantanu/.virtualenvs/openai-jowu/include -I/Users/shantanu/.pyenv/versions/3.11.4/include/python3.11 -c _configtest.c -o _configtest.o
      clang -flat_namespace -undefined suppress _configtest.o -Lbuild/temp.macosx-11.0-x86_64-cpython-311 -ldl -o _configtest
      ld: warning: -undefined suppress is deprecated
      ld: warning: -undefined suppress is deprecated
      success!
      removing: _configtest.c _configtest.o _configtest
      checking for function 'dlopen' ...
      clang -DNDEBUG -g -fwrapv -O3 -Wall -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -march=native -mtune=native -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -I/Users/shantanu/.virtualenvs/openai-jowu/include -I/Users/shantanu/.pyenv/versions/3.11.4/include/python3.11 -c _configtest.c -o _configtest.o
      clang _configtest.o -Lbuild/temp.macosx-11.0-x86_64-cpython-311 -ldl -o _configtest
      success!
      removing: _configtest.c _configtest.o _configtest
      building 'mpi4py.dl' extension
      clang -DNDEBUG -g -fwrapv -O3 -Wall -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -march=native -mtune=native -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -DHAVE_DLFCN_H=1 -DHAVE_DLOPEN=1 -I/Users/shantanu/.virtualenvs/openai-jowu/include -I/Users/shantanu/.pyenv/versions/3.11.4/include/python3.11 -c src/dynload.c -o build/temp.macosx-11.0-x86_64-cpython-311/src/dynload.o
      clang -bundle -undefined dynamic_lookup -L/usr/local/opt/readline/lib -L/usr/local/opt/readline/lib -L/Users/shantanu/.pyenv/versions/3.11.4/lib -L/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/lib -L/usr/local/opt/readline/lib -L/usr/local/opt/readline/lib -L/Users/shantanu/.pyenv/versions/3.11.4/lib -L/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/lib build/temp.macosx-11.0-x86_64-cpython-311/src/dynload.o -Lbuild/temp.macosx-11.0-x86_64-cpython-311 -ldl -o build/lib.macosx-11.0-x86_64-cpython-311/mpi4py/dl.cpython-311-darwin.so
      checking for MPI compile and link ...
      /usr/local/bin/mpicc -DNDEBUG -g -fwrapv -O3 -Wall -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -march=native -mtune=native -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -I/Users/shantanu/.virtualenvs/openai-jowu/include -I/Users/shantanu/.pyenv/versions/3.11.4/include/python3.11 -c _configtest.c -o _configtest.o
      success!
      removing: _configtest.c _configtest.o
      /usr/local/bin/mpicc -DNDEBUG -g -fwrapv -O3 -Wall -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -march=native -mtune=native -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -I/Users/shantanu/.virtualenvs/openai-jowu/include -I/Users/shantanu/.pyenv/versions/3.11.4/include/python3.11 -c _configtest.c -o _configtest.o
      /usr/local/bin/mpicc _configtest.o -Lbuild/temp.macosx-11.0-x86_64-cpython-311 -o _configtest
      ld: unknown options: -commons
      clang: error: linker command failed with exit code 1 (use -v to see invocation)
      failure.
      removing: _configtest.c _configtest.o
      error: Cannot link MPI programs. Check your configuration!!!
      [end of output]
  
  note: This error originates from a subprocess, and is likely not a problem with pip.
  ERROR: Failed building wheel for mpi4py
Failed to build mpi4py
ERROR: Could not build wheels for mpi4py, which is required to install pyproject.toml-based projects

This is where the linker flag appears to get set:

λ grep -C 3 commons /usr/local/bin/mpicc 

final_cflags="  -g"
final_cppflags=" "
final_ldflags="  -Wl,-commons,use_dylibs"
final_libs=""
if test "yes" = "no" -o "${interlib_deps}" = "no" ; then
    final_ldflags="${final_ldflags} "

Editing out -commons,use_dylibs in mpicc appears to make compilation succeed.

There's a long comment about the use of this option over here: https://github.com/pmodels/mpich/blob/d1a428ecdaaff6ad672708ecd3effc45bc200939/configure.ac#L4055

I couldn't find a changelog for the ld that Apple ships

marcalexanderschweitzer · 2023-09-22T01:16:21Z

marcalexanderschweitzer
Sep 22, 2023

Not an answer, just commenting that the same problem occurs with open-mpi on macOS using the Fortran wrappers (which use GCC).

ld: unknown options: -commons

The clang based mpicc/mpiCC work just fine.

0 replies

dalcinl · 2023-09-22T04:43:41Z

dalcinl
Sep 22, 2023

Hi, I'm the mpi4py author and maintainer here, experiencing the same issue. man ld still mentions the -commons option. After running with clang -v and playing around with the linker invocation, I believe this may be a regression from Apple in the last command line tools update.

0 replies

edoapra · 2023-09-30T00:17:15Z

edoapra
Sep 30, 2023

The following fixes this mpich link problem for me:

brew reinstall --build-from-source mpich

This command will result in the warning

Warning: building from source is not supported!
You're on your own. Failures are expected so don't create any issues, please!

However, once the mpich compilation is done, homebrew mpicc is not going to have
final_ldflags=" -Wl,-commons,use_dylibs"
as described in
pmodels/mpich#6684

4 replies

hauntsaninja Sep 30, 2023
Author

Yes, build from source works, but is very slow. Would be great if Homebrew could update their bottle!

I just opted to patch mpicc directly, e.g. something like sed -i '' 's/final_ldflags=" -Wl,-commons,use_dylibs"/final_ldflags=" -Wl"/' $(readlink -f /usr/local/bin/mpicc)

fxcoudert Oct 8, 2023

It took time to rebuild the bottles, for some reason it was not finding hwloc on its own anymore.

But now, another problem: on macOS Sonoma with Xcode 15, somehow the linker commons option issue is still present even after building from source. https://github.com/Homebrew/homebrew-core/actions/runs/6450035465/job/17509013771?pr=150225 Have not had time to understand why yet.

fxcoudert Oct 8, 2023

Any help with the pull request at Homebrew/homebrew-core#150225 would be appreciated

agiordan96 Nov 15, 2023

Hello, any updates on this? Will it be better with the next Xcode release? When will home-brew update its bottle?

edoapra · 2023-10-09T16:47:36Z

edoapra
Oct 9, 2023

Any help with the pull request at Homebrew/homebrew-core#150225 would be appreciated

I believe the current failure is not a linker problem, since autoconf correctly detects the linker options (see pmodels/mpich#6684 (comment)). I was able to build mpich from source myself using Xcode 15.

~~Instead, I believe the github actions fails since it exceeds the 90 minutes limit.~~

1 reply

fxcoudert Oct 9, 2023

There is a failure on 14-arm64 even though it succeeds the build: test failure.

agiordan96 · 2023-11-15T17:02:56Z

agiordan96
Nov 15, 2023

@hauntsaninja what file and what line are to be edited in mpicc? Could you be more specific please?

1 reply

hauntsaninja Nov 15, 2023
Author

I put sed command in my comment https://github.com/orgs/Homebrew/discussions/4797#discussioncomment-7149266, that's about as specific as it can get :-)

tjahns · 2024-04-08T12:03:04Z

tjahns
Apr 8, 2024

Not sure why no one mentions it, but deactivating that flag also causes subtle bugs, i.e. certain parts of mpich stop working. Please see the attached source for an example that works (on versions of XCode that still support searching libmpifort.dylib for common symbols) but fails without the -Wl,-commons,use_dylibs option:

PROGRAM mpi_hello
!  INCLUDE "mpif.h"
  USE mpi
  USE iso_c_binding

  INTERFACE
    SUBROUTINE posix_exit(code) BIND(c, name="exit")
      IMPORT :: c_int
      INTEGER(c_int), VALUE, INTENT(in) :: code
    END SUBROUTINE posix_exit
  END INTERFACE

  INTEGER :: ierror, comm_size, comm_rank
  INTEGER :: procnum, acx_mpirun_num_tasks
  CALL mpi_init(ierror)
  CALL handle_mpi_error(ierror)
  CALL mpi_comm_rank(mpi_comm_world, comm_rank, ierror)
  CALL handle_mpi_error(ierror)
  CALL mpi_comm_size(mpi_comm_world, comm_size, ierror)
  CALL handle_mpi_error(ierror)
  acx_mpirun_num_tasks = 2
  procnum = 1
  CALL mpi_allreduce(mpi_in_place, procnum, 1, mpi_integer, &
       mpi_sum, mpi_comm_world, ierror)
  IF (procnum /= acx_mpirun_num_tasks) THEN
    CALL mpi_abort(mpi_comm_world, 1, ierror)
  END IF
  CALL mpi_finalize(ierror)
  CALL handle_mpi_error(ierror)
CONTAINS
  SUBROUTINE handle_mpi_error(ierror)
    INTEGER, INTENT(in) :: ierror

    INTEGER :: msg_len, msg_ierror
    CHARACTER(len=MPI_MAX_ERROR_STRING) :: msg

    IF (ierror /= MPI_SUCCESS) THEN
      CALL mpi_error_string(ierror, msg, msg_len, msg_ierror)
      WRITE (0, *) msg(1:msg_len)
      FLUSH(0)
      CALL posix_exit(1_c_int)
    END IF
  END SUBROUTINE handle_mpi_error

END PROGRAM mpi_hello

Test the build with

$ mpifort -o /tmp/hello yaxt/config/checksrc/mpi_fortran_startup.f90 && mpirun -n 2 /tmp/hello
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 1
$ mpifort -o /tmp/hello -Wl,-commons,use_dylibs yaxt/config/checksrc/mpi_fortran_startup.f90 && mpirun -n 2 /tmp/hello
$ echo $?
0
$

2 replies

dalcinl Apr 8, 2024

My guess is that very few people understand what's really going on. You are definitely right, without proper linker support for Fortran common blocks, the whole thing is irremediably broken, and Fortran+MPI cannot be used on macOS.

PS: The issue will occur when using any of the MPI buffer "constants" that cannot be used in initialization expressions, like MPI_IN_PLACE and MPI_BOTTOM (MPI 4.1 chap. 2 pp 20 for the full list). All other MPI things should still work.

tjahns Apr 9, 2024

For XCode 14 using -Wl,-commons,use_dylibs is sufficient, for XCode 15, perhaps also adding -Wl,-ld_classic might be needed for this to work.

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