[petsc-dev] Petsc compilation issues with Xcode 15 on macOS Sonoma

Satish Balay balay at mcs.anl.gov
Mon Nov 13 11:20:09 CST 2023 

Sounds like the issue is with using findPetsc - after petsc is installed [and petsc install went fine?]

I think the current recommendation is to use pkg-config file interface via cmake -instead of findPetsc

And the following works for me..

./configure  COPTFLAGS="-O3 -g" CXXOPTFLAGS="-O3 -g" FOPTFLAGS="-O3 -g" \
--download-openmpi --with-64-bit-indices --download-metis --download-parmetis \
--download-suitesparse --download-superlu_dist --download-hypre --download-scalapack --download-mumps \
--with-debugging=0 --with-clean

A couple of notes:

- we recommend not using 'sudo' when building PETSc [and build/use petsc from user account. one can also install in a system-wide location using a user account]
- not use --with-cxx-dialect - and let configure determine it.
- petsc does not use boost [its there for trilinos - but that part is broken]

Satish

On Mon, 13 Nov 2023, Barry Smith wrote:

> 
>   Please send configure.log (best to petsc-maint at mcs.anl.gov).
> 
> 
> > On Nov 13, 2023, at 11:41 AM, Abhinav Singh <abhinavrajendra at gmail.com> wrote:
> > 
> > Dear Petsc devs,
> > 
> > I have been having issues lately when compiling petsc on MacOS with various libraries. This is probably due to the updated linker in MacOS and unfortunately the newer operating systems do not allow using older toolchains.
> > 
> > on arm64, only 3.20 and up can be configured
> > 
> > 
> > My configure command usually looks like this:
> > 'sudo ./configure  COPTFLAGS=-O3 -g CXXOPTFLAGS=-O3 -g FOPTFLAGS=-O3 -g --with-cxx-dialect=C++11 --with-mpi-dir=/opt/openfpm/dep_clang/MPI --with-64-bit-indices  --with-parmetis-dir=/opt/openfpm/dep_clang/PARMETIS --with-metis-dir=/opt/openfpm/dep_clang/METIS --with-boost=yes --with-boost-dir=/opt/openfpm/dep_clang/BOOST --with-suitesparse-dir=/opt/openfpm/dep_clang/SUITESPARSE --download-superlu_dist --download-hypre --prefix=/opt/openfpm/dep_clang/PETSC --download-scalapack --download-mumps --with-debugging=0 --with-clean
> > '
> > 
> > There are two main issues:
> > 
> > 1) Duplicate 'LC_Paths' when compiling code with apple clang and gfortran. If I enable download_scalapack, the the cmake findPetsc fails with the following error on both x86 and arm64:
> > """
> >  kind: "try_run-v1"
> >     backtrace:
> >       - "/opt/homebrew/Cellar/cmake/3.27.7/share/cmake/Modules/Internal/CheckSourceRuns.cmake:93 (try_run)"
> >       - "/opt/homebrew/Cellar/cmake/3.27.7/share/cmake/Modules/CheckCSourceRuns.cmake:52 (cmake_check_source_runs)"
> >       - "cmake_modules/FindPackageMultipass.cmake:97 (check_c_source_runs)"
> >       - "cmake_modules/FindPETSc.cmake:284 (multipass_source_runs)"
> >       - "cmake_modules/FindPETSc.cmake:318 (petsc_test_runs)"
> >       - "CMakeLists.txt:69 (find_package)"
> >     checks:
> >       - "Performing Test MULTIPASS_TEST_4_petsc_works_all"
> >     directories:
> >       source: "/Users/absingh/openfpm_pdata/build/CMakeFiles/CMakeScratch/TryCompile-LJcmJB"
> >       binary: "/Users/absingh/openfpm_pdata/build/CMakeFiles/CMakeScratch/TryCompile-LJcmJB"
> >     cmakeVariables:
> >       CMAKE_C_FLAGS: ""
> >       CMAKE_EXE_LINKER_FLAGS: ""
> >       CMAKE_MODULE_PATH: "/Users/absingh/openfpm_pdata/cmake_modules/"
> >       CMAKE_OSX_ARCHITECTURES: ""
> >       CMAKE_OSX_DEPLOYMENT_TARGET: ""
> >       CMAKE_OSX_SYSROOT: "/Library/Developer/CommandLineTools/SDKs/MacOSX14.0.sdk"
> >     buildResult:
> >       variable: "MULTIPASS_TEST_4_petsc_works_all_COMPILED"
> >       cached: true
> >       stdout: |
> >         Change Dir: '/Users/absingh/openfpm_pdata/build/CMakeFiles/CMakeScratch/TryCompile-LJcmJB'
> >         
> >         Run Build Command(s): /opt/homebrew/Cellar/cmake/3.27.7/bin/cmake -E env VERBOSE=1 /usr/bin/make -f Makefile cmTC_e0165/fast
> >         /Library/Developer/CommandLineTools/usr/bin/make  -f CMakeFiles/cmTC_e0165.dir/build.make CMakeFiles/cmTC_e0165.dir/build
> >         Building C object CMakeFiles/cmTC_e0165.dir/src.c.o
> >         /Library/Developer/CommandLineTools/usr/bin/cc -DMULTIPASS_TEST_4_petsc_works_all -I/opt/openfpm/dep_clang/PETSC/include -I/opt/openfpm/dep_clang/SUITESPARSE/include -I/opt/openfpm/dep_clang/PARMETIS/include -I/opt/openfpm/dep_clang/METIS/include -I/opt/openfpm/dep_clang/BOOST/include -I/opt/openfpm/dep_clang/MPI/include -arch arm64 -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX14.0.sdk -MD -MT CMakeFiles/cmTC_e0165.dir/src.c.o -MF CMakeFiles/cmTC_e0165.dir/src.c.o.d -o CMakeFiles/cmTC_e0165.dir/src.c.o -c /Users/absingh/openfpm_pdata/build/CMakeFiles/CMakeScratch/TryCompile-LJcmJB/src.c
> >         Linking C executable cmTC_e0165
> >         /opt/homebrew/Cellar/cmake/3.27.7/bin/cmake -E cmake_link_script CMakeFiles/cmTC_e0165.dir/link.txt --verbose=1
> >         /Library/Developer/CommandLineTools/usr/bin/cc  -arch arm64 -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX14.0.sdk -Wl,-search_paths_first -Wl,-headerpad_max_install_names CMakeFiles/cmTC_e0165.dir/src.c.o -o cmTC_e0165  -Wl,-rpath,/opt/openfpm/dep_clang/PETSC/lib -Wl,-rpath,/opt/openfpm/dep_clang/SUITESPARSE/lib /opt/openfpm/dep_clang/PETSC/lib/libpetsc.dylib /opt/openfpm/dep_clang/PETSC/lib/libHYPRE.dylib /opt/openfpm/dep_clang/SUITESPARSE/lib/libspqr.dylib /opt/openfpm/dep_clang/SUITESPARSE/lib/libumfpack.dylib /opt/openfpm/dep_clang/SUITESPARSE/lib/libklu.dylib /opt/openfpm/dep_clang/SUITESPARSE/lib/libcholmod.dylib /opt/openfpm/dep_clang/SUITESPARSE/lib/libbtf.dylib /opt/openfpm/dep_clang/SUITESPARSE/lib/libccolamd.dylib /opt/openfpm/dep_clang/SUITESPARSE/lib/libcolamd.dylib /opt/openfpm/dep_clang/SUITESPARSE/lib/libcamd.dylib /opt/openfpm/dep_clang/SUITESPARSE/lib/libamd.dylib /opt/openfpm/dep_clang/SUITESPARSE/lib/libsuitesparseconfig.dylib /opt/
 openfpm/
 dep_clang/PETSC/lib/libdmumps.a /opt/openfpm/dep_clang/PETSC/lib/libmumps_common.a /opt/openfpm/dep_clang/PETSC/lib/libpord.a /Library/Developer/CommandLineTools/SDKs/MacOSX14.0.sdk/usr/lib/libpthread.tbd /opt/openfpm/dep_clang/PETSC/lib/libscalapack.dylib /opt/openfpm/dep_clang/PETSC/lib/libsuperlu_dist.dylib /Library/Developer/CommandLineTools/SDKs/MacOSX14.0.sdk/usr/lib/liblapack.tbd /Library/Developer/CommandLineTools/SDKs/MacOSX14.0.sdk/usr/lib/libblas.tbd /opt/openfpm/dep_clang/PARMETIS/lib/libparmetis.a /opt/openfpm/dep_clang/METIS/lib/libmetis.dylib /opt/openfpm/dep_clang/MPI/lib/libmpi_usempif08.dylib /opt/openfpm/dep_clang/MPI/lib/libmpi_usempi_ignore_tkr.a /opt/openfpm/dep_clang/MPI/lib/libmpi_mpifh.dylib /opt/openfpm/dep_clang/MPI/lib/libmpi.dylib /opt/homebrew/Cellar/gcc/13.2.0/lib/gcc/current/libgfortran.dylib /opt/homebrew/Cellar/gcc/13.2.0/lib/gcc/current/gcc/aarch64-apple-darwin23/13/libemutls_w.a /opt/homebrew/Cellar/gcc/13.2.0/lib/gcc/current/libquadmath.d
 ylib /Li
 brary/Developer/CommandLineTools/SDKs/MacOSX14.0.sdk/usr/lib/libc++.tbd /Library/Developer/CommandLineTools/SDKs/MacOSX14.0.sdk/usr/lib/libgcc_s.1.tbd 
> >         ld: warning: duplicate LC_RPATH are deprecated ('/opt/homebrew/Cellar/gcc/13.2.0/lib/gcc/current/gcc/aarch64-apple-darwin23/13')
> >         ld: warning: duplicate LC_RPATH are deprecated ('/opt/homebrew/Cellar/gcc/13.2.0/lib/gcc/current/gcc')
> >         ld: warning: duplicate LC_RPATH are deprecated ('/opt/homebrew/Cellar/gcc/13.2.0/lib/gcc/current')
> >         ld: warning: duplicate LC_RPATH are deprecated ('/opt/homebrew/Cellar/gcc/13.2.0/lib/gcc/current/gcc/aarch64-apple-darwin23/13')
> >         ld: warning: duplicate LC_RPATH are deprecated ('/opt/homebrew/Cellar/gcc/13.2.0/lib/gcc/current/gcc')
> >         ld: warning: duplicate LC_RPATH are deprecated ('/opt/homebrew/Cellar/gcc/13.2.0/lib/gcc/current')
> >         ld: duplicate LC_RPATH '/opt/homebrew/Cellar/gcc/13.2.0/lib/gcc/current/gcc/aarch64-apple-darwin23/13' in '/opt/openfpm/dep_clang/PETSC/lib/libscalapack.2.2.1.dylib'
> >         clang: error: linker command failed with exit code 1 (use -v to see invocation)
> >         make[1]: *** [cmTC_e0165] Error 1
> >         make: *** [cmTC_e0165/fast] Error 2
> >         
> >       exitCode: 2
> >     runResult:
> >       variable: "MULTIPASS_TEST_4_petsc_works_all_EXITCODE"
> >       cached: true
> > """
> > 
> > Second, on arm64, I am unable to use the option "with-metis-dir=/path/to/metis". The installation works fine but when I run make check, I get the error that 'libmetis.dylib' is not found. This behavior continues even when I export 'DYLD_LIBRARY_PATH' to have the libmetis. CMake findPetsc also fails with the same error.
> > 
> > Any advice would be great. 
> > 
> > Thank you!
> > Abhinav
> > 
> > 
> > 
> > 
> > 
> > 
> > 
> > 
> > 
>

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