[petsc-dev] libpetsc.so: undefined references

Stefano Zampini stefano.zampini at gmail.com
Sat Oct 2 10:48:48 CDT 2021 

The issue is that you have --with-cxxlib-autodetect=0 in your configure
log, so PETSc skip appending lstdc++ to the list of libraries used to link
the shared library.
If you don't care, just remove the configure flag

Il giorno sab 2 ott 2021 alle ore 18:38 Jacob Faibussowitsch <
jacob.fai at gmail.com> ha scritto:

> Can you try the following?
>
> In $PETSC_DIR/$PETSC_ARCH/lib/petsc/conf/petscvariables there are two
> variables, PETSC_EXTERNAL_LIB_BASIC and PETSC_WITH_EXTERNAL_LIB. Append
> -lstdc++ to both of them and re-run your make command with verbose output:
>
> $ make all V=1
> $ make check
>
> P.S. There is no longer a need to set -std=[c/gnu]++17 in your own flags;
> configure will detect up to c++17. For gnu-ish compilers (gcc/clang) it
> will try to use gnu extensions — in fact if you search for
> ‘checkCxxDialect' in you configure.log, you’ll see it appropriately selects
> gnu++17.
>
> Best regards,
>
> Jacob Faibussowitsch
> (Jacob Fai - booss - oh - vitch)
>
> On Oct 2, 2021, at 09:33, Jacob Faibussowitsch <jacob.fai at gmail.com>
> wrote:
>
> 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
>
> Il Sab 2 Ott 2021, 15:48 Antonio T. sagitter <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):
>>
>> /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
>> GPG key: 0x29FBC85D7A51CC2F
>> GPG key server: https://keyserver1.pgp.com/
>>
>
>
>

-- 
Stefano
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