Re: [petsc-dev] Fortran macOS Linkage Warning
Better just to report the error then to make strange workarounds. https://gitlab.com/petsc/petsc/-/merge_requests/3884 <https://gitlab.com/petsc/petsc/-/merge_requests/3884> This complaint about MAOSX_DEPLOYMENT_TARGET has popped up forever. Previously when linking code PETSc ignored all "warning" messages so likely it just worked and you didn't feel the need to monkey with version min stuff. Anyways, hope this works and, if not, we may need some more filtering. Barry
On Apr 16, 2021, at 3:23 PM, Jacob Faibussowitsch <[email protected]> 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 <[email protected] <mailto:[email protected]>> 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 <[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
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Barry Smith