If I had understand from the beginning this was merely a bug report we could have processed it much quicker and easier.
Hopefully this will resolve the problem and can get into the release branch soon. https://gitlab.com/petsc/petsc/-/merge_requests/3884 <https://gitlab.com/petsc/petsc/-/merge_requests/3884> > On Apr 16, 2021, at 3:23 PM, Jacob Faibussowitsch <jacob....@gmail.com> wrote: > >> I am not sure what the point is here. Are you unable to configure? or make >> all? or make check PETSc? > > At least on my end, none of them are possible without setting > MAOSX_DEPLOYMENT_TARGET or --LDFLAGS=-mmacosx-version-min=11.2. Configure > fails when it tests fortran linkage capability. > > <configure.log> > > > Best regards, > > Jacob Faibussowitsch > (Jacob Fai - booss - oh - vitch) > >> On Apr 16, 2021, at 15:03, Barry Smith <bsm...@petsc.dev >> <mailto:bsm...@petsc.dev>> wrote: >> >> >> I am not sure what the point is here. Are you unable to configure? or >> make all? or make check PETSc? >> >> If so that should clearly be reported as a bug with all relevant >> information supplied. >> >> No, we have never and do not ever intend for PETSc users even developers >> to know or care about MACOSX_DEPLOYMENT_TARGET >> >> Anyways if you are reporting a bug and I am guess the bug correctly the >> fix is to add "was built for newer macOS version" to the list of filtered >> link warnings. There will be a bunch of such warnings that will need to be >> added to the filtering in the next few months but once they are in place the >> filtering should not be an issue. >> >> >> Barry >> >> >> >>> On Apr 16, 2021, at 6:20 AM, Pierre Jolivet <pie...@joliv.et >>> <mailto:pie...@joliv.et>> wrote: >>> >>> Barry, >>> That issue + this commit: >>> $ git bisect bad >>> 36c166f2bbb44c2987d8fb7385fbe9e2d1cfb0c8 is the first bad commit >>> commit 36c166f2bbb44c2987d8fb7385fbe9e2d1cfb0c8 >>> Author: Barry Smith <bsm...@mcs.anl.gov <mailto:bsm...@mcs.anl.gov>> >>> Date: Sat Apr 10 13:40:10 2021 -0500 >>> makes it actually impossible to ./configure on macOS. >>> Do we really expect all macOS users to know about the variable >>> MACOSX_DEPLOYMENT_TARGET? >>> >>> Thanks, >>> Pierre >>> >>> $ ./configure >>> =============================================================================== >>> Configuring PETSc to compile on your system >>> =============================================================================== >>> TESTING: checkFortranLibraries from >>> config.compilers(config/BuildSystem/config/compilers.py:921) >>> >>> >>> ******************************************************************************* >>> UNABLE to CONFIGURE with GIVEN OPTIONS (see configure.log for >>> details): >>> ------------------------------------------------------------------------------- >>> Fortran libraries cannot be used with C as linker >>> ******************************************************************************* >>> >>> Executing: mpicc -o >>> /var/folders/_9/0qn1m4z92wzbhz9434vx39fc0000gn/T/petsc-bhav6feq/config.setCompilers/conftest >>> -Wl,-bind_at_load -Wl,-multiply_defined,suppress -Wl,-multiply_defined >>> -Wl,suppress -Wl,-commons,use_dylibs -Wl,-search_paths_first >>> -Wl,-no_compact_unwind -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing >>> -Wno-unknown-pragmas -fstack-protector -fno-stack-check -Qunused-arguments >>> -fvisibility=hidden -g3 >>> /var/folders/_9/0qn1m4z92wzbhz9434vx39fc0000gn/T/petsc-bhav6feq/config.setCompilers/conftest.o >>> -lc++ -ldl -lc++ -ldl -Wl,-rpath,/usr/local/Cellar/mpich/3.4.1_1/lib >>> -L/usr/local/Cellar/mpich/3.4.1_1/lib -lmpifort -lmpi -lpmpi -lgfortran >>> -Wl,-rpath,/usr/local/Cellar/gcc/10.2.0_4/lib/gcc/10/gcc/x86_64-apple-darwin20/10.2.0 >>> >>> -L/usr/local/Cellar/gcc/10.2.0_4/lib/gcc/10/gcc/x86_64-apple-darwin20/10.2.0 >>> -Wl,-rpath,/usr/local/Cellar/gcc/10.2.0_4/lib/gcc/10 >>> -L/usr/local/Cellar/gcc/10.2.0_4/lib/gcc/10 -lgfortran -lquadmath -lm >>> Possible ERROR while running linker: >>> stderr: >>> ld: warning: dylib (/usr/local/Cellar/mpich/3.4.1_1/lib/libmpifort.dylib) >>> was built for newer macOS version (11.2) than being linked (11.0) >>> ld: warning: dylib >>> (/usr/local/Cellar/gcc/10.2.0_4/lib/gcc/10/libgfortran.dylib) was built for >>> newer macOS version (11.2) than being linked (11.0) >>> ld: warning: dylib >>> (/usr/local/Cellar/gcc/10.2.0_4/lib/gcc/10/libquadmath.dylib) was built for >>> newer macOS version (11.2) than being linked (11.0) >>> ld: warning: dylib >>> (/usr/local/Cellar/gcc/10.2.0_4/lib/gcc/10/libquadmath.0.dylib) was built >>> for newer macOS version (11.2) than being linked (11.0) >>> compilers: Cannot compile/link C with mpicc. >>> >>>> On 12 Mar 2021, at 6:16 PM, Barry Smith <bsm...@petsc.dev >>>> <mailto:bsm...@petsc.dev>> wrote: >>>> >>>> >>>> You should be able to edit lib/petsc/conf/rules and add it to the filter >>>> for .cu.PETSc .kokkos.cxx.PETSc .c.PETSc .cxx.PETSc: and .F.PETSc >>>> .F90.PETSc: >>>> >>>> I think it is fine to hide this warning; it is impossible for me to >>>> understand anyway :-(. >>>> >>>> Barry >>>> >>>> >>>> >>>> >>>>> On Mar 12, 2021, at 2:44 AM, Pierre Jolivet <pie...@joliv.et >>>>> <mailto:pie...@joliv.et>> wrote: >>>>> >>>>> Sorry to dig up this old thread, but this is triggering false positives >>>>> while make checking for people who don’t want to toy around with >>>>> MACOSX_DEPLOYMENT_TARGET. >>>>> Could/should we filter this somehow, or have BuildSystem tinker with the >>>>> environment variable itself? >>>>> >>>>> Thanks, >>>>> Pierre >>>>> >>>>> $ make check >>>>> Running check examples to verify correct installation >>>>> Using PETSC_DIR=/Users/jolivet/repo/petsc and >>>>> PETSC_ARCH=arch-darwin-c-debug-real >>>>> *******************Error detected during compile or >>>>> link!******************* >>>>> See http://www.mcs.anl.gov/petsc/documentation/faq.html >>>>> <http://www.mcs.anl.gov/petsc/documentation/faq.html> >>>>> /Users/jolivet/repo/petsc/src/snes/tutorials ex19 >>>>> ********************************************************************************* >>>>> mpicc -Wl,-bind_at_load -Wl,-multiply_defined,suppress >>>>> -Wl,-multiply_defined -Wl,suppress -Wl,-commons,use_dylibs >>>>> -Wl,-search_paths_first -Wl,-no_compact_unwind -Wall -g -Wall -g >>>>> -I/Users/jolivet/repo/petsc/include >>>>> -I/Users/jolivet/repo/petsc/arch-darwin-c-debug-real/include >>>>> -I/opt/intel/mkl/include ex19.c >>>>> -Wl,-rpath,/Users/jolivet/repo/petsc/arch-darwin-c-debug-real/lib >>>>> -L/Users/jolivet/repo/petsc/arch-darwin-c-debug-real/lib >>>>> -Wl,-rpath,/Users/jolivet/repo/petsc/arch-darwin-c-debug-real/lib >>>>> -L/Users/jolivet/repo/petsc/arch-darwin-c-debug-real/lib >>>>> -Wl,-rpath,/opt/intel/mkl/lib -L/opt/intel/mkl/lib >>>>> -Wl,-rpath,/opt/intel/lib -L/opt/intel/lib >>>>> -Wl,-rpath,/usr/local/Cellar/mpich/3.4.1_1/lib >>>>> -L/usr/local/Cellar/mpich/3.4.1_1/lib >>>>> -Wl,-rpath,/usr/local/Cellar/gcc/10.2.0_4/lib/gcc/10/gcc/x86_64-apple-darwin20/10.2.0 >>>>> >>>>> -L/usr/local/Cellar/gcc/10.2.0_4/lib/gcc/10/gcc/x86_64-apple-darwin20/10.2.0 >>>>> -Wl,-rpath,/usr/local/Cellar/gcc/10.2.0_4/lib/gcc/10 >>>>> -L/usr/local/Cellar/gcc/10.2.0_4/lib/gcc/10 -lpetsc -lHYPRE -lcmumps >>>>> -ldmumps -lsmumps -lzmumps -lmumps_common -lpord -lmkl_scalapack_lp64 >>>>> -lmkl_blacs_mpich_lp64 -lEl -lElSuiteSparse -lpmrrr -lp4est -lsc -liomp5 >>>>> -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -lparmmg -lmmg -lmmg3d >>>>> -lptesmumps -lptscotchparmetis -lptscotch -lptscotcherr -lesmumps >>>>> -lscotch -lscotcherr -lparmetis -lmetis -ltriangle -ltet -lz -lX11 -lc++ >>>>> -ldl -lmpifort -lmpi -lpmpi -lgfortran -lquadmath -lm -lc++ -ldl -o ex19 >>>>> ld: warning: dylib (/usr/local/Cellar/mpich/3.4.1_1/lib/libmpifort.dylib) >>>>> was built for newer macOS version (11.1) than being linked (11.0) >>>>> ld: warning: dylib >>>>> (/usr/local/Cellar/gcc/10.2.0_4/lib/gcc/10/libgfortran.dylib) was built >>>>> for newer macOS version (11.2) than being linked (11.0) >>>>> ld: warning: dylib >>>>> (/usr/local/Cellar/gcc/10.2.0_4/lib/gcc/10/libquadmath.dylib) was built >>>>> for newer macOS version (11.2) than being linked (11.0) >>>>> ld: warning: dylib >>>>> (/usr/local/Cellar/gcc/10.2.0_4/lib/gcc/10/libquadmath.0.dylib) was built >>>>> for newer macOS version (11.2) than being linked (11.0) >>>>> ld: warning: object file >>>>> (/Users/jolivet/repo/petsc/arch-darwin-c-debug-real/lib/libcmumps.a(cana_aux.o)) >>>>> was built for newer macOS version (11.2) than being linked (11.0) >>>>> ld: warning: object file >>>>> (/Users/jolivet/repo/petsc/arch-darwin-c-debug-real/lib/libdmumps.a(dana_aux.o)) >>>>> was built for newer macOS version (11.2) than being linked (11.0) >>>>> ld: warning: object file >>>>> (/Users/jolivet/repo/petsc/arch-darwin-c-debug-real/lib/libsmumps.a(sana_aux.o)) >>>>> was built for newer macOS version (11.2) than being linked (11.0) >>>>> ld: warning: object file >>>>> (/Users/jolivet/repo/petsc/arch-darwin-c-debug-real/lib/libzmumps.a(zana_aux.o)) >>>>> was built for newer macOS version (11.2) than being linked (11.0) >>>>> ld: warning: object file >>>>> (/Users/jolivet/repo/petsc/arch-darwin-c-debug-real/lib/libmumps_common.a(front_data_mgt_m.o)) >>>>> was built for newer macOS version (11.2) than being linked (11.0) >>>>> C/C++ example src/snes/tutorials/ex19 run successfully with 1 MPI process >>>>> >>>>> >>>>>> On 15 Feb 2021, at 6:08 PM, Jacob Faibussowitsch <jacob....@gmail.com >>>>>> <mailto:jacob....@gmail.com>> wrote: >>>>>> >>>>>> Yes, this also seems to work on my end. >>>>>> >>>>>> Best regards, >>>>>> >>>>>> Jacob Faibussowitsch >>>>>> (Jacob Fai - booss - oh - vitch) >>>>>> Cell: (312) 694-3391 >>>>>> >>>>>>> On Feb 15, 2021, at 12:05, Satish Balay <ba...@mcs.anl.gov >>>>>>> <mailto:ba...@mcs.anl.gov>> wrote: >>>>>>> >>>>>>> Does setting MACOSX_DEPLOYMENT_TARGET also work? >>>>>>> >>>>>>> Satish >>>>>>> >>>>>>> On Mon, 15 Feb 2021, Jacob Faibussowitsch wrote: >>>>>>> >>>>>>>> I think this problem ultimately stems from the fact that gcc/g++ and >>>>>>>> gfortran are not from the same people on macOS. It seems like clang is >>>>>>>> configured to build for 11.0 target, whilst gcc defaults to newest >>>>>>>> available target. And indeed if I change my compile command there is >>>>>>>> no warning: >>>>>>>> >>>>>>>> mkdir -p build && gfortran -c -o ./build/conftest.o conftest.F90 && >>>>>>>> gcc-10 -o ./build/libconftest.dylib ./build/conftest.o -dynamiclib >>>>>>>> -undefined dynamic_lookup && rm -rf ./build >>>>>>>> >>>>>>>> Note I now call gcc-10 as the linker which is the __actual__ gcc (not >>>>>>>> clang in a trench coat). >>>>>>>> >>>>>>>> Best regards, >>>>>>>> >>>>>>>> Jacob Faibussowitsch >>>>>>>> (Jacob Fai - booss - oh - vitch) >>>>>>>> Cell: (312) 694-3391 >>>>>>>> >>>>>>>>> On Feb 15, 2021, at 11:46, Jacob Faibussowitsch <jacob....@gmail.com >>>>>>>>> <mailto:jacob....@gmail.com>> wrote: >>>>>>>>> >>>>>>>>> Ok so if I pass -mmacosx-version-min=11.2 to the linker the warning >>>>>>>>> disappears... >>>>>>>>> >>>>>>>>> Best regards, >>>>>>>>> >>>>>>>>> Jacob Faibussowitsch >>>>>>>>> (Jacob Fai - booss - oh - vitch) >>>>>>>>> Cell: (312) 694-3391 >>>>>>>>> >>>>>>>>>> On Feb 15, 2021, at 11:41, Jacob Faibussowitsch <jacob....@gmail.com >>>>>>>>>> <mailto:jacob....@gmail.com> <mailto:jacob....@gmail.com >>>>>>>>>> <mailto:jacob....@gmail.com>>> wrote: >>>>>>>>>> >>>>>>>>>> I can reproduce the warning compiling just that simple code you >>>>>>>>>> listed. This is the compile command: >>>>>>>>>> >>>>>>>>>> mkdir -p build && gfortran -c -o ./build/conftest.o conftest.F90 && >>>>>>>>>> gcc -o ./build/libconftest.dylib ./build/conftest.o -dynamiclib >>>>>>>>>> -undefined dynamic_lookup && rm -rf ./build >>>>>>>>>> >>>>>>>>>> And error: >>>>>>>>>> ld: warning: object file (./build/conftest.o) was built for newer >>>>>>>>>> macOS version (11.2) than being linked (11.0) >>>>>>>>>> >>>>>>>>>> Note I recently uninstalled and reinstalled command line tools too, >>>>>>>>>> which does not seem to have fixed it. >>>>>>>>>> >>>>>>>>>> Best regards, >>>>>>>>>> >>>>>>>>>> Jacob Faibussowitsch >>>>>>>>>> (Jacob Fai - booss - oh - vitch) >>>>>>>>>> Cell: (312) 694-3391 >>>>>>>>>> >>>>>>>>>>> On Feb 15, 2021, at 11:30, Satish Balay <ba...@mcs.anl.gov >>>>>>>>>>> <mailto:ba...@mcs.anl.gov> <mailto:ba...@mcs.anl.gov >>>>>>>>>>> <mailto:ba...@mcs.anl.gov>>> wrote: >>>>>>>>>>> >>>>>>>>>>> Here is the compile command and the warning: >>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>> ===== Checking linker >>>>>>>>>>> Executing: gfortran -c -o >>>>>>>>>>> /var/folders/9w/7dlszmmn6q1gd5yf3r9n79bc0000gn/T/petsc-dk9aiv7x/config.setCompilers/conftest.o >>>>>>>>>>> >>>>>>>>>>> -I/var/folders/9w/7dlszmmn6q1gd5yf3r9n79bc0000gn/T/petsc-dk9aiv7x/config.setCompilers >>>>>>>>>>> >>>>>>>>>>> /var/folders/9w/7dlszmmn6q1gd5yf3r9n79bc0000gn/T/petsc-dk9aiv7x/config.setCompilers/conftest.F90 >>>>>>>>>>> >>>>>>>>>>> Successful compile: >>>>>>>>>>> Source: >>>>>>>>>>> function foo(a) >>>>>>>>>>> real:: a,x,bar >>>>>>>>>>> common /xx/ x >>>>>>>>>>> x=a >>>>>>>>>>> foo = bar(x) >>>>>>>>>>> end >>>>>>>>>>> Executing: gcc -o >>>>>>>>>>> /var/folders/9w/7dlszmmn6q1gd5yf3r9n79bc0000gn/T/petsc-dk9aiv7x/config.setCompilers/libconftest.dylib >>>>>>>>>>> -dynamiclib -single_module -undefined dynamic_lookup >>>>>>>>>>> -multiply_defined suppress >>>>>>>>>>> /var/folders/9w/7dlszmmn6q1gd5yf3r9n79bc0000gn/T/petsc-dk9aiv7x/config.setCompilers/conftest.o >>>>>>>>>>> >>>>>>>>>>> Possible ERROR while running linker: >>>>>>>>>>> stderr: >>>>>>>>>>> ld: warning: object file >>>>>>>>>>> (/var/folders/9w/7dlszmmn6q1gd5yf3r9n79bc0000gn/T/petsc-dk9aiv7x/config.setCompilers/conftest.o) >>>>>>>>>>> was built for newer macOS version (11.2) than being linked (11.0) >>>>>>>>>>> Accepted FC PIC code without compiler flag >>>>>>>>>>> >>>>>>>>>>> ============================================================================================= >>>>>>>>>>> <<<<<< >>>>>>>>>>> >>>>>>>>>>> Its likely due to the way brew built gfortran. You can try >>>>>>>>>>> compiling a simple test code and see if you can reproduce this >>>>>>>>>>> warning. >>>>>>>>>>> >>>>>>>>>>> There is a related issue at: >>>>>>>>>>> >>>>>>>>>>> https://github.com/spack/spack/issues/21644 >>>>>>>>>>> <https://github.com/spack/spack/issues/21644> >>>>>>>>>>> <https://github.com/spack/spack/issues/21644 >>>>>>>>>>> <https://github.com/spack/spack/issues/21644>> >>>>>>>>>>> >>>>>>>>>>> Satish >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> On Sat, 13 Feb 2021, Jacob Faibussowitsch wrote: >>>>>>>>>>> >>>>>>>>>>>> Hello All, >>>>>>>>>>>> >>>>>>>>>>>> I’ve been getting these warnings for weeks, at first I figured it >>>>>>>>>>>> was due to gfortran brew package not being updated for Big Sur, >>>>>>>>>>>> but since it has persisted through a few gfortran brew updates I’m >>>>>>>>>>>> thinking it may be petsc related. This is on clean build on master. >>>>>>>>>>>> >>>>>>>>>>>> ld: warning: object file >>>>>>>>>>>> (master-arch-darwin-c-debug/obj/sys/classes/bag/f2003-src/fsrc/bagenum.o) >>>>>>>>>>>> was built for newer macOS version (11.2) than being linked (11.0) >>>>>>>>>>>> ld: warning: object file >>>>>>>>>>>> (master-arch-darwin-c-debug/obj/sys/f90-src/fsrc/f90_fwrap.o) was >>>>>>>>>>>> built for newer macOS version (11.2) than being linked (11.0) >>>>>>>>>>>> ld: warning: object file >>>>>>>>>>>> (master-arch-darwin-c-debug/obj/sys/objects/f2003-src/fsrc/optionenum.o) >>>>>>>>>>>> was built for newer macOS version (11.2) than being linked (11.0) >>>>>>>>>>>> ld: warning: object file >>>>>>>>>>>> (master-arch-darwin-c-debug/obj/sys/fsrc/somefort.o) was built for >>>>>>>>>>>> newer macOS version (11.2) than being linked (11.0) >>>>>>>>>>>> ld: warning: object file >>>>>>>>>>>> (master-arch-darwin-c-debug/obj/sys/f90-mod/petscsysmod.o) was >>>>>>>>>>>> built for newer macOS version (11.2) than being linked (11.0) >>>>>>>>>>>> >>>>>>>>>>>> Best regards, >>>>>>>>>>>> >>>>>>>>>>>> Jacob Faibussowitsch >>>>>>>>>>>> (Jacob Fai - booss - oh - vitch) >>>>>>>>>>>> Cell: (312) 694-3391 >>>>>> >>>>> >>>> >>> >> >
