[petsc-users] link error and symbol error

[Satish Balay]

Do you have MacPorts installed? With Blas? Perhaps thats the source of conflict..

Satish

On Wed, 14 Sep 2016, Barry Smith wrote:

> 
>   Send configure.log to petsc-maint at mcs.anl.gov  Looks like a troubled BLAS/LAPACK install.
> 
>    Barry
> 
> > On Sep 14, 2016, at 12:52 PM, Gideon Simpson <gideon.simpson at gmail.com> wrote:
> > 
> > I was trying to compile a new version of 3.7.3, and I noticed the following.  First, when building the library, I see, at the end:
> > 
> > CLINKER /opt/petsc-3.7.3/arch-darwin-c-debug/lib/libpetsc.3.7.3.dylib
> > ld: warning: could not create compact unwind for _dhseqr_: stack subq instruction is too different from dwarf stack size
> >    DSYMUTIL /opt/petsc-3.7.3/arch-darwin-c-debug/lib/libpetsc.3.7.3.dylib
> > 
> > Next, when I try to run the tests, I see:
> > 
> > Running test examples to verify correct installation
> > Using PETSC_DIR=/opt/petsc-3.7.3 and PETSC_ARCH=arch-darwin-c-debug
> > *******************Error detected during compile or link!*******************
> > See http://www.mcs.anl.gov/petsc/documentation/faq.html
> > /opt/petsc-3.7.3/src/snes/examples/tutorials ex19
> > *********************************************************************************
> > /opt/petsc-3.7.3/arch-darwin-c-debug/bin/mpicc -o ex19.o -c -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -Qunused-arguments -fvisibility=hidden -g3   -I/opt/petsc-3.7.3/include -I/opt/petsc-3.7.3/arch-darwin-c-debug/include -I/opt/local/include -I/opt/X11/include    `pwd`/ex19.c
> > /opt/petsc-3.7.3/arch-darwin-c-debug/bin/mpicc -Wl,-multiply_defined,suppress -Wl,-multiply_defined -Wl,suppress -Wl,-commons,use_dylibs -Wl,-search_paths_first -Wl,-multiply_defined,suppress -Wl,-multiply_defined -Wl,suppress -Wl,-commons,use_dylibs -Wl,-search_paths_first    -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -Qunused-arguments -fvisibility=hidden -g3  -o ex19  ex19.o -Wl,-rpath,/opt/petsc-3.7.3/arch-darwin-c-debug/lib -L/opt/petsc-3.7.3/arch-darwin-c-debug/lib  -lpetsc -Wl,-rpath,/opt/petsc-3.7.3/arch-darwin-c-debug/lib -lsuperlu_dist -lcmumps -ldmumps -lsmumps -lzmumps -lmumps_common -lpord -lparmetis -lmetis -lsuperlu -lscalapack -lumfpack -lklu -lcholmod -lbtf -lccolamd -lcolamd -lcamd -lamd -lsuitesparseconfig -llapack -lblas -Wl,-rpath,/opt/local/lib -L/opt/local/lib -lhwloc -lptesmumps -lptscotch -lptscotcherr -lscotch -lscotcherr -Wl,-rpath,/opt/X11/lib -L/opt/X11/lib -lX11 -Wl,-rpath,/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/lib/clang/8.0.0/lib/darwin -L/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/lib/clang/8.0.0/lib/darwin -lmpifort -lgfortran -Wl,-rpath,/opt/local/lib/gcc5/gcc/x86_64-apple-darwin15/5.4.0 -L/opt/local/lib/gcc5/gcc/x86_64-apple-darwin15/5.4.0 -Wl,-rpath,/opt/local/lib/gcc5 -L/opt/local/lib/gcc5 -lgfortran -lgcc_ext.10.5 -lquadmath -lm -lclang_rt.osx -lmpicxx -lc++ -Wl,-rpath,/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/8.0.0/lib/darwin -L/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/8.0.0/lib/darwin -lclang_rt.osx -lm -lz -Wl,-rpath,/opt/petsc-3.7.3/arch-darwin-c-debug/lib -L/opt/petsc-3.7.3/arch-darwin-c-debug/lib -ldl -lmpi -lpmpi -lSystem -Wl,-rpath,/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/8.0.0/lib/darwin -L/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/8..0.0/lib/darwin -lclang_rt.osx -ldl 
> > Undefined symbols for architecture x86_64:
> >  "_ATL_cGetNB", referenced from:
> >      import-atom in libpetsc.dylib
> >  "_ATL_dGetNB", referenced from:
> >      import-atom in libpetsc.dylib
> >  "_ATL_dgemoveT", referenced from:
> >      import-atom in libpetsc.dylib
> >  "_ATL_dger", referenced from:
> >      import-atom in libpetsc.dylib
> >  "_ATL_dsqtrans", referenced from:
> >      import-atom in libpetsc.dylib
> >  "_ATL_sGetNB", referenced from:
> >      import-atom in libpetsc.dylib
> >  "_ATL_xerbla", referenced from:
> >      import-atom in libpetsc.dylib
> >  "_ATL_zGetNB", referenced from:
> >      import-atom in libpetsc.dylib
> > ld: symbol(s) not found for architecture x86_64
> > clang: error: linker command failed with exit code 1 (use -v to see invocation)
> > makefile:108: recipe for target 'ex19' failed
> > gmake[3]: [ex19] Error 1 (ignored)
> > /bin/rm -f ex19.o
> > 
> > 
> > -gideon
> > 
> 
>