> On 16 Apr 2021, at 10:03 PM, Barry Smith <[email protected]> wrote: > > > I am not sure what the point is here. Are you unable to configure? or make > all? or make check PETSc?
I’m unable to configure. $ git clone https://gitlab.com/petsc/petsc Cloning into 'petsc'... warning: redirecting to https://gitlab.com/petsc/petsc.git/ remote: Enumerating objects: 64141, done. remote: Counting objects: 100% (64141/64141), done. remote: Compressing objects: 100% (7098/7098), done. remote: Total 939408 (delta 62202), reused 57532 (delta 57038), pack-reused 875267 Receiving objects: 100% (939408/939408), 267.66 MiB | 1.07 MiB/s, done. Resolving deltas: 100% (720467/720467), done. Updating files: 100% (9849/9849), done. $ cd petsc $ export PETSC_DIR=`pwd` $ ./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 ******************************************************************************* configure.log is there: http://joliv.et/configure_broken_fortran_filter.log <http://joliv.et/configure_broken_fortran_filter.log> Workaround is: MACOSX_DEPLOYMENT_TARGET=11.2 ./configure FFLAGS="-mmacosx-version-min=11.2" I tried setting one and not the other additional flag but I respectively had failures re-compiling ParMETIS or Elemental. Thanks, Pierre > > 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 <[email protected] >> <mailto:[email protected]>> wrote: >> >> Barry, >> That issue + this commit: >> $ git bisect bad >> 36c166f2bbb44c2987d8fb7385fbe9e2d1cfb0c8 is the first bad commit >> commit 36c166f2bbb44c2987d8fb7385fbe9e2d1cfb0c8 >> Author: Barry Smith <[email protected] <mailto:[email protected]>> >> 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 <[email protected] >>> <mailto:[email protected]>> 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 <[email protected] >>>> <mailto:[email protected]>> 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 <[email protected] >>>>> <mailto:[email protected]>> 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 <[email protected] >>>>>> <mailto:[email protected]>> 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 <[email protected] >>>>>>>> <mailto:[email protected]>> 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 <[email protected] >>>>>>>>> <mailto:[email protected]> <mailto:[email protected] >>>>>>>>> <mailto:[email protected]>>> 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 <[email protected] >>>>>>>>>> <mailto:[email protected]> <mailto:[email protected] >>>>>>>>>> <mailto:[email protected]>>> 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 >>>>> >>>> >>> >> >
