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 <[email protected]> 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 <[email protected] <mailto:[email protected]>> 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 <[email protected] <mailto:[email protected]>> 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
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