Please send configure.log (best to petsc-ma...@mcs.anl.gov).
> On Nov 13, 2023, at 11:41 AM, Abhinav Singh <abhinavrajen...@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.dylib
> /Library/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
>
>
>
>
>
>
>
>
>
