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-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.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
> >
> >
> >
> >
> >
> >
> >
> >
> >
>
