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

Tue Mar 28 15:41:21 CDT 2017

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
> > ============================================================
> > ====================
> 
> 
> 
> 
> 