[petsc-users] link error and symbol error

[Gideon Simpson]

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