Barry,
That issue + this commit:
$ git bisect bad
36c166f2bbb44c2987d8fb7385fbe9e2d1cfb0c8 is the first bad commit
commit 36c166f2bbb44c2987d8fb7385fbe9e2d1cfb0c8
Author: Barry Smith <[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]> 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
>>>
>>
>
