[petsc-dev] libpetsc.so: undefined references
Satish Balay
balay at mcs.anl.gov
Sat Oct 2 13:16:52 CDT 2021
Fix at https://gitlab.com/petsc/petsc/-/merge_requests/4402
thanks,
Satish
On Sat, 2 Oct 2021, Jacob Faibussowitsch 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 <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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