[petsc-users] [3.7.5] strange config error on macOS with XCode 8.3 and Clang 8.1.0

Tue Mar 28 15:46:41 CDT 2017

   I'm updating Xcode now and will try to reproduce the issue.

> On Mar 28, 2017, at 3:41 PM, Satish Balay <balay at mcs.anl.gov> wrote:
> 
> It would be good to have the complete configure.log to see where this
> path is coming from.
> 
> Satish
> 
> On Tue, 28 Mar 2017, Matthew Knepley wrote:
> 
>> On Tue, Mar 28, 2017 at 3:12 PM, Denis Davydov <davydden at gmail.com> wrote:
>> 
>>> Dear all,
>>> 
>>> Yesterday I updated to the latest XCode and now have problems configuring
>>> PETSc (see below).
>>> I must say that a number of other packages which need MPI fortran wrappers
>>> compiled fine.
>>> 
>> 
>> This looks like bad parsing of the junk spit out by the C compiler:
>> 
>>  -Wl,-rpath,/Applications/Xcode.app/Contents/Developer/Tool
>> chains/XcodeDefault.xctoolchain/usr/lib -L/Applications/Xcode.app/Cont
>> ents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/lib -lLTO
>> 
>> you can just turn that off
>> 
>>  --with-clib-autodetect=0 --with-fortranlib-autodetect=0 --with-cxxlib-
>> autodetect=0
>> 
>> but then you are responsible for putting any compiler libraries in LIBS
>> that we needed to make Fortran and C work together.
>> 
>>  Thanks,
>> 
>>     Matt
>> 
>> 
>>> Regards,
>>> Denis.
>>> 
>>> ==========================
>>> 
>>> 
>>> Executing: /Users/davydden/spack/opt/spack/darwin-sierra-x86_64/clang-
>>> 8.1.0-apple/openmpi-2.1.0-rh7brts6lzesj46zopjj5rzmkcyiktx7/bin/mpif90 -c
>>> -o /var/folders/5k/sqpp24tx3ylds4fgm13pfht00000gn/T/petsc-
>>> eLXjKy/config.setCompilers/conftest.o -I/var/folders/5k/sqpp24tx3yld
>>> s4fgm13pfht00000gn/T/petsc-eLXjKy/config.setCompilers   -Wall
>>> -ffree-line-length-0 -Wno-unused-dummy-argument -g -O
>>> /var/folders/5k/sqpp24tx3ylds4fgm13pfht00000gn/T/petsc-
>>> eLXjKy/config.setCompilers/conftest.F
>>> Successful compile:
>>> Source:
>>>      program main
>>> 
>>>      end
>>> Executing: /Users/davydden/spack/opt/spack/darwin-sierra-x86_64/clang-
>>> 8.1.0-apple/openmpi-2.1.0-rh7brts6lzesj46zopjj5rzmkcyiktx7/bin/mpif90 -c
>>> -o /var/folders/5k/sqpp24tx3ylds4fgm13pfht00000gn/T/petsc-
>>> eLXjKy/config.setCompilers/conftest.o -I/var/folders/5k/sqpp24tx3yld
>>> s4fgm13pfht00000gn/T/petsc-eLXjKy/config.setCompilers   -Wall
>>> -ffree-line-length-0 -Wno-unused-dummy-argument -g -O
>>> /var/folders/5k/sqpp24tx3ylds4fgm13pfht00000gn/T/petsc-
>>> eLXjKy/config.setCompilers/conftest.F
>>> Successful compile:
>>> Source:
>>>      program main
>>> 
>>>      end
>>> Executing: /Users/davydden/spack/opt/spack/darwin-sierra-x86_64/clang-
>>> 8.1.0-apple/openmpi-2.1.0-rh7brts6lzesj46zopjj5rzmkcyiktx7/bin/mpif90  -o
>>> /var/folders/5k/sqpp24tx3ylds4fgm13pfht00000gn/T/petsc-
>>> eLXjKy/config.setCompilers/conftest  -Wl,-multiply_defined,suppress
>>> -Wl,-multiply_defined -Wl,suppress -Wl,-commons,use_dylibs
>>> -Wl,-search_paths_first -Wl,-no_compact_unwind   -Wall -ffree-line-length-0
>>> -Wno-unused-dummy-argument -g -O /var/folders/5k/sqpp24tx3ylds4
>>> fgm13pfht00000gn/T/petsc-eLXjKy/config.setCompilers/conftest.o
>>> -lto_library -Wl,-rpath,/Applications/Xcode.app/Contents/Developer/Toolch
>>> ains/XcodeDefault.xctoolchain/usr/lib -L/Applications/Xcode.app/Cont
>>> ents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/lib -lLTO
>>> -Wl,-rpath,/Users/davydden/spack/opt/spack/darwin-sierra-x86
>>> _64/clang-8.1.0-apple/hwloc-1.11.6-pkbyijayr66g3wq3hojj3l44qc7kjno3/lib
>>> -L/Users/davydden/spack/opt/spack/darwin-sierra-x86_64/clang
>>> -8.1.0-apple/hwloc-1.11.6-pkbyijayr66g3wq3hojj3l44qc7kjno3/lib
>>> -Wl,-rpath,/Users/davydden/spack/opt/spack/darwin-sierra-x86
>>> _64/clang-8.1.0-apple/openmpi-2.1.0-rh7brts6lzesj46zopjj5rzmkcyiktx7/lib
>>> -L/Users/davydden/spack/opt/spack/darwin-sierra-x86_64/clang
>>> -8.1.0-apple/openmpi-2.1.0-rh7brts6lzesj46zopjj5rzmkcyiktx7/lib -ldl
>>> -lmpi -lSystem -Wl,-rpath,/Applications/Xcode
>>> .app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/
>>> usr/bin/../lib/clang/8.1.0/lib/darwin -L/Applications/Xcode.app/Cont
>>> ents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/8.1.0/lib/darwin
>>> -lclang_rt.osx -ldl
>>> Possible ERROR while running linker: exit code 256
>>> stderr:
>>> ld: can't map file, errno=22 file '/Applications/Xcode.app/Conte
>>> nts/Developer/Toolchains/XcodeDefault.xctoolchain/usr/lib' for
>>> architecture x86_64
>>> collect2: error: ld returned 1 exit status
>>>                Popping language FC
>>>            compilers: Error message from compiling {Cannot compile/link
>>> FC with /Users/davydden/spack/opt/spack/darwin-sierra-x86_64/clang-
>>> 8.1.0-apple/openmpi-2.1.0-rh7brts6lzesj46zopjj5rzmkcyiktx7/bin/mpif90.}
>>> **** Configure header /var/folders/5k/sqpp24tx3ylds4
>>> fgm13pfht00000gn/T/petsc-eLXjKy/confdefs.h ****
>>> #if !defined(INCLUDED_UNKNOWN)
>>> #define INCLUDED_UNKNOWN
>>> 
>>> #ifndef PETSC_HAVE_DLFCN_H
>>> #define PETSC_HAVE_DLFCN_H 1
>>> #endif
>>> 
>>> #ifndef PETSC_HAVE_RTLD_NOW
>>> #define PETSC_HAVE_RTLD_NOW 1
>>> #endif
>>> 
>>> #ifndef PETSC_HAVE_RTLD_LOCAL
>>> #define PETSC_HAVE_RTLD_LOCAL 1
>>> #endif
>>> 
>>> #ifndef PETSC_HAVE_RTLD_LAZY
>>> #define PETSC_HAVE_RTLD_LAZY 1
>>> #endif
>>> 
>>> #ifndef PETSC_C_STATIC_INLINE
>>> #define PETSC_C_STATIC_INLINE static inline
>>> #endif
>>> 
>>> #ifndef PETSC_HAVE_RTLD_GLOBAL
>>> #define PETSC_HAVE_RTLD_GLOBAL 1
>>> #endif
>>> 
>>> #ifndef PETSC_C_RESTRICT
>>> #define PETSC_C_RESTRICT restrict
>>> #endif
>>> 
>>> #ifndef PETSC_HAVE_LIBDL
>>> #define PETSC_HAVE_LIBDL 1
>>> #endif
>>> 
>>> #ifndef PETSC_ARCH
>>> #define PETSC_ARCH "arch-darwin-c-opt"
>>> #endif
>>> 
>>> #ifndef PETSC_CLANGUAGE_C
>>> #define PETSC_CLANGUAGE_C 1
>>> #endif
>>> 
>>> #ifndef PETSC_HAVE_DYNAMIC_LIBRARIES
>>> #define PETSC_HAVE_DYNAMIC_LIBRARIES 1
>>> #endif
>>> 
>>> #ifndef PETSC_HAVE_SHARED_LIBRARIES
>>> #define PETSC_HAVE_SHARED_LIBRARIES 1
>>> #endif
>>> 
>>> #ifndef PETSC_USE_SHARED_LIBRARIES
>>> #define PETSC_USE_SHARED_LIBRARIES 1
>>> #endif
>>> 
>>> #ifndef PETSC_USE_ERRORCHECKING
>>> #define PETSC_USE_ERRORCHECKING 1
>>> #endif
>>> 
>>> #endif
>>> **** C specific Configure header /var/folders/5k/sqpp24tx3ylds4
>>> fgm13pfht00000gn/T/petsc-eLXjKy/conffix.h ****
>>> #if !defined(INCLUDED_UNKNOWN)
>>> #define INCLUDED_UNKNOWN
>>> 
>>> #if defined(__cplusplus)
>>> extern "C" {
>>> }
>>> #else
>>> #endif
>>> #endif
>>> ************************************************************
>>> *******************
>>>         UNABLE to CONFIGURE with GIVEN OPTIONS    (see configure.log for
>>> details):
>>> ------------------------------------------------------------
>>> -------------------
>>> C libraries cannot directly be used from Fortran
>>> ************************************************************
>>> *******************
>>>  File "./config/configure.py", line 405, in petsc_configure
>>>    framework.configure(out = sys.stdout)
>>>  File "/Users/davydden/spack/var/spack/stage/petsc-3.7.5-tpsz2lfsp
>>> kqa7tq2keqowsk4xrebsfwi/petsc-3.7.5/config/BuildSystem/config/framework.py",
>>> line 1090, in configure
>>>    self.processChildren()
>>>  File "/Users/davydden/spack/var/spack/stage/petsc-3.7.5-tpsz2lfsp
>>> kqa7tq2keqowsk4xrebsfwi/petsc-3.7.5/config/BuildSystem/config/framework.py",
>>> line 1079, in processChildren
>>>    self.serialEvaluation(self.childGraph)
>>>  File "/Users/davydden/spack/var/spack/stage/petsc-3.7.5-tpsz2lfsp
>>> kqa7tq2keqowsk4xrebsfwi/petsc-3.7.5/config/BuildSystem/config/framework.py",
>>> line 1060, in serialEvaluation
>>>    child.configure()
>>>  File "/Users/davydden/spack/var/spack/stage/petsc-3.7.5-tpsz2lfsp
>>> kqa7tq2keqowsk4xrebsfwi/petsc-3.7.5/config/BuildSystem/config/compilers.py",
>>> line 1438, in configure
>>>    self.executeTest(self.checkCLibraries)
>>>  File "/Users/davydden/spack/var/spack/stage/petsc-3.7.5-tpsz2lfsp
>>> kqa7tq2keqowsk4xrebsfwi/petsc-3.7.5/config/BuildSystem/config/base.py",
>>> line 126, in executeTest
>>>    ret = test(*args,**kargs)
>>>  File "/Users/davydden/spack/var/spack/stage/petsc-3.7.5-tpsz2lfsp
>>> kqa7tq2keqowsk4xrebsfwi/petsc-3.7.5/config/BuildSystem/config/compilers.py",
>>> line 313, in checkCLibraries
>>>    raise RuntimeError('C libraries cannot directly be used from Fortran')
>>> ============================================================
>>> ====================
>>> Finishing Configure Run at Tue Mar 28 21:56:48 2017
>>> ============================================================
>>> ====================
>> 
>> 
>> 
>> 
>> 
> 