[petsc-dev] libpetsc.so: undefined references

Sat Oct 2 09:33:26 CDT 2021

Unrelated to the below (still reading the configure.log) but it looks like there’s a bug in the cuda compiler search:

TESTING: checkCUDACompiler from config.setCompilers(/builddir/build/BUILD/petsc-3.16.0/petsc-3.16.0/config/BuildSystem/config/setCompilers.py:862)
  Locate a functional CUDA compiler
Checking for program /usr/bin/nvcc...not found
Checking for program /bin/nvcc...not found
Checking for program /usr/sbin/nvcc...not found
Checking for program /sbin/nvcc...not found
Checking for program /usr/local/sbin/nvcc...not found
Checking for program /builddir/build/BUILD/petsc-3.16.0/petsc-3.16.0/lib/petsc/bin/win32fe/nvcc...not found
Checking for program /Developer/NVIDIA/CUDA-6.5/bin/nvcc...not found
Checking for program /builddir/build/BUILD/petsc-3.16.0/petsc-3.16.0/lib/petsc/bin/win32fe/nvcc...not found
  Unable to find programs ['nvcc'] providing listing of the specific search path
      Warning accessing /Developer/NVIDIA/CUDA-6.5/bin gives errors: can only concatenate str (not "builtin_function_or_method") to str
Checking for program /usr/local/cuda/bin/nvcc...not found
Checking for program /builddir/build/BUILD/petsc-3.16.0/petsc-3.16.0/lib/petsc/bin/win32fe/nvcc...not found
  Unable to find programs ['nvcc'] providing listing of the specific search path
      Warning accessing /usr/local/cuda/bin gives errors: can only concatenate str (not "builtin_function_or_method") to str

Best regards,

Jacob Faibussowitsch
(Jacob Fai - booss - oh - vitch)

> On Oct 2, 2021, at 08:18, Stefano Zampini <stefano.zampini at gmail.com> wrote:
> 
> I knew this was coming....
> https://gitlab.com/petsc/petsc/-/issues/997 <https://gitlab.com/petsc/petsc/-/issues/997>
> 
> Il Sab 2 Ott 2021, 15:48 Antonio T. sagitter <sagitter at fedoraproject.org <mailto:sagitter at fedoraproject.org>> ha scritto:
> Hi all.
> 
> In PETSc-3.16.0, the linker is not working because of these undefined 
> references (see https://pastebin.com/izGTfmMp <https://pastebin.com/izGTfmMp>):
> 
> /usr/bin/ld: x86_64/lib/libpetsc.so: undefined reference to `operator 
> delete(void*, unsigned long)'
> 
> /usr/bin/ld: x86_64/lib/libpetsc.so: undefined reference to `__cxa_rethrow'
> 
> /usr/bin/ld: x86_64/lib/libpetsc.so: undefined reference to 
> `__gxx_personality_v0'
> 
> /usr/bin/ld: x86_64/lib/libpetsc.so: undefined reference to `operator 
> new(unsigned long)'
> 
> /usr/bin/ld: x86_64/lib/libpetsc.so: undefined reference to 
> `std::__throw_bad_alloc()'
> 
> /usr/bin/ld: x86_64/lib/libpetsc.so: undefined reference to 
> `std::terminate()'
> 
> /usr/bin/ld: x86_64/lib/libpetsc.so: undefined reference to 
> `std::__throw_bad_array_new_length()'
> 
> /usr/bin/ld: x86_64/lib/libpetsc.so: undefined reference to `typeinfo 
> for std::exception'
> 
> /usr/bin/ld: x86_64/lib/libpetsc.so: undefined reference to 
> `__cxa_begin_catch'
> 
> /usr/bin/ld: x86_64/lib/libpetsc.so: undefined reference to 
> `__cxa_end_catch'
> 
> /usr/bin/ld: x86_64/lib/libpetsc.so: undefined reference to 
> `std::__throw_length_error(char const*)'
> 
> collect2: error: ld returned 1 exit status
> 
> There are also
> 
> $ ldd -r build/BUILD/petsc-3.16.0/petsc-3.16.0/x86_64/lib/libpetsc.so'
> Start: shell
> 
>         linux-vdso.so.1 (0x00007fffbf347000)
> 
>         libsuperlu.so.5.2 => /lib64/libsuperlu.so.5.2 (0x00007f00dad0c000)
> 
>         libflexiblas.so.3 => /lib64/libflexiblas.so.3 (0x00007f00da95a000)
> 
>         libcgns.so.4.2 => /lib64/libcgns.so.4.2 (0x00007f00da873000)
> 
>         libhdf5.so.103 => /lib64/libhdf5.so.103 (0x00007f00da4d8000)
> 
>         libm.so.6 => /lib64/libm.so.6 (0x00007f00da3f8000)
> 
>         libX11.so.6 => /lib64/libX11.so.6 (0x00007f00da2ae000)
> 
>         libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x00007f00da294000)
> 
>         libc.so.6 => /lib64/libc.so.6 (0x00007f00da08b000)
> 
>         libgfortran.so.5 => /lib64/libgfortran.so.5 (0x00007f00d9dde000)
> 
>         libquadmath.so.0 => /lib64/libquadmath.so.0 (0x00007f00d9d94000)
> 
>         /lib64/ld-linux-x86-64.so.2 (0x00007f00dc18b000)
> 
>         libsz.so.2 => /lib64/libsz.so.2 (0x00007f00d9d8a000)
> 
>         libz.so.1 => /lib64/libz.so.1 (0x00007f00d9d6e000)
> 
>         libxcb.so.1 => /lib64/libxcb.so.1 (0x00007f00d9d43000)
> 
>         libXau.so.6 => /lib64/libXau.so.6 (0x00007f00d9d3d000)
> 
> undefined symbol: _ZTISt9exception 
> (build/BUILD/petsc-3.16.0/petsc-3.16.0/x86_64/lib/libpetsc.so)
> 
> undefined symbol: __gxx_personality_v0 
> (build/BUILD/petsc-3.16.0/petsc-3.16.0/x86_64/lib/libpetsc.so)
> 
> undefined symbol: _ZdlPvm 
> (build/BUILD/petsc-3.16.0/petsc-3.16.0/x86_64/lib/libpetsc.so)
> 
> undefined symbol: __cxa_rethrow 
> (build/BUILD/petsc-3.16.0/petsc-3.16.0/x86_64/lib/libpetsc.so)
> 
> undefined symbol: _Znwm 
> (build/BUILD/petsc-3.16.0/petsc-3.16.0/x86_64/lib/libpetsc.so)
> 
> undefined symbol: _ZSt17__throw_bad_allocv 
> (build/BUILD/petsc-3.16.0/petsc-3.16.0/x86_64/lib/libpetsc.so)
> 
> undefined symbol: _ZSt9terminatev 
> (build/BUILD/petsc-3.16.0/petsc-3.16.0/x86_64/lib/libpetsc.so)
> 
> undefined symbol: _ZSt28__throw_bad_array_new_lengthv 
> (build/BUILD/petsc-3.16.0/petsc-3.16.0/x86_64/lib/libpetsc.so)
> 
> undefined symbol: __cxa_begin_catch 
> (build/BUILD/petsc-3.16.0/petsc-3.16.0/x86_64/lib/libpetsc.so)
> 
> undefined symbol: __cxa_end_catch 
> (build/BUILD/petsc-3.16.0/petsc-3.16.0/x86_64/lib/libpetsc.so)
> 
> undefined symbol: _ZSt20__throw_length_errorPKc 
> (build/BUILD/petsc-3.16.0/petsc-3.16.0/x86_64/lib/libpetsc.so)
> 
> 
> 
> I'm attaching configure.log and make.log
> 
> --
> ---
> Antonio Trande
> Fedora Project
> mailto: sagitter at fedoraproject.org <mailto:sagitter at fedoraproject.org>
> GPG key: 0x29FBC85D7A51CC2F
> GPG key server: https://keyserver1.pgp.com/ <https://keyserver1.pgp.com/>

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