October 2021 - petsc-dev - mailman3.cels.anl.gov

Re: [petsc-dev] libpetsc.so: undefined references
by Satish Balay 02 Oct '21

02 Oct '21

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(a)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(a)fedoraproject.org <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 > > > > -- > > --- > > Antonio Trande > > Fedora Project > > mailto: sagitter(a)fedoraproject.org <mailto:[email protected]> > > GPG key: 0x29FBC85D7A51CC2F > > GPG key server: https://keyserver1.pgp.com/ <https://keyserver1.pgp.com/> > >

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Re: [petsc-dev] libpetsc.so: undefined references
by Matthew Knepley 02 Oct '21

02 Oct '21

On Sat, Oct 2, 2021 at 12:14 PM Antonio T. sagitter < sagitter(a)fedoraproject.org> wrote: > Yes, i noted. Previous PETSc's versions worked with that flag, but the > 3.16.0 no longer. > Antonio, you are correct. I added support for C++ demangling in viewer output, but my configure check was inadequate. I did not manage to fix this by release time. I will have it fixed in the next point release. Thanks, Matt > On 10/2/21 17:48, Stefano Zampini wrote: > > 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 > > > > I'm removing '-std=[c/gnu]++17' > > On 10/2/21 17:38, Jacob Faibussowitsch wrote: > > 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. > > > > Thank you all. > -- > --- > Antonio Trande > Fedora Project > mailto: sagitter(a)fedoraproject.org > GPG key: 0x29FBC85D7A51CC2F > GPG key server: https://keyserver1.pgp.com/ > -- What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead. -- Norbert Wiener https://www.cse.buffalo.edu/~knepley/ <http://www.cse.buffalo.edu/~knepley/>

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Re: [petsc-dev] libpetsc.so: undefined references
by Satish Balay 02 Oct '21

02 Oct '21

BTW: LIBS is more appropriate as its a difference of: gcc -lstdc++ ex19.o -lpetsc vs gcc ex19.o -lpetsc -lstdc++ i.e $CLINKER $CC_LINKER_FLAGS $OBJ $PETSC_LIB $LIBS $FLINKER $FC_LINKER_FLAGS $OBJ $PETSC_LIB $LIBS Satish On Sat, 2 Oct 2021, Satish Balay via petsc-dev wrote: > --with-clib-autodetect=0 --with-fortranlib-autodetect=0 --with-cxxlib-autodetect=0 > --CC_LINKER_FLAGS="-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 " > --FC_LINKER_FLAGS="-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -lgfortran" > > > Since autodetect is disabled - its expected the required compiler libraries are passed in via LIBS or in this case CC_LINKER_FLAGS, FC_LINKER_FLAGS > > i.e add -lstdc++ to both. > > I'm surprised that you didn't need -lgfortran with CC_LINKER_FLAGS in there as well - but get [as libpetsc.so is built with CLINKER] > > > libgfortran.so.5 => /lib64/libgfortran.so.5 (0x00007f00d9dde000) > > > > Satish > > On Sat, 2 Oct 2021, Antonio T. sagitter wrote: > > > 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(a)fedoraproject.org > > GPG key: 0x29FBC85D7A51CC2F > > GPG key server: https://keyserver1.pgp.com/ > > > > >

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Re: [petsc-dev] libpetsc.so: undefined references
by Antonio T. sagitter 02 Oct '21

02 Oct '21

Yes, i noted. Previous PETSc's versions worked with that flag, but the 3.16.0 no longer. On 10/2/21 17:48, Stefano Zampini wrote: > 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 > I'm removing '-std=[c/gnu]++17' On 10/2/21 17:38, Jacob Faibussowitsch wrote: > 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. > Thank you all. -- --- Antonio Trande Fedora Project mailto: sagitter(a)fedoraproject.org GPG key: 0x29FBC85D7A51CC2F GPG key server: https://keyserver1.pgp.com/

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Re: [petsc-dev] libpetsc.so: undefined references
by Stefano Zampini 02 Oct '21

02 Oct '21

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(a)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(a)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(a)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(a)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(a)fedoraproject.org >> GPG key: 0x29FBC85D7A51CC2F >> GPG key server: https://keyserver1.pgp.com/ >> > > > -- Stefano

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Re: [petsc-dev] libpetsc.so: undefined references
by Satish Balay 02 Oct '21

02 Oct '21

--with-clib-autodetect=0 --with-fortranlib-autodetect=0 --with-cxxlib-autodetect=0 --CC_LINKER_FLAGS="-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 " --FC_LINKER_FLAGS="-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -lgfortran" Since autodetect is disabled - its expected the required compiler libraries are passed in via LIBS or in this case CC_LINKER_FLAGS, FC_LINKER_FLAGS i.e add -lstdc++ to both. I'm surprised that you didn't need -lgfortran with CC_LINKER_FLAGS in there as well - but get [as libpetsc.so is built with CLINKER] > libgfortran.so.5 => /lib64/libgfortran.so.5 (0x00007f00d9dde000) Satish On Sat, 2 Oct 2021, Antonio T. sagitter wrote: > 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(a)fedoraproject.org > GPG key: 0x29FBC85D7A51CC2F > GPG key server: https://keyserver1.pgp.com/ > >

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Re: [petsc-dev] libpetsc.so: undefined references
by Jacob Faibussowitsch 02 Oct '21

02 Oct '21

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(a)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(a)gmail.com <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 <sagitter(a)fedoraproject.org <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 >> >> -- >> --- >> Antonio Trande >> Fedora Project >> mailto: sagitter(a)fedoraproject.org <mailto:[email protected]> >> GPG key: 0x29FBC85D7A51CC2F >> GPG key server: https://keyserver1.pgp.com/ <https://keyserver1.pgp.com/> >

1 0

Re: [petsc-dev] libpetsc.so: undefined references
by Jacob Faibussowitsch 02 Oct '21

02 Oct '21

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(a)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(a)fedoraproject.org <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 > > -- > --- > Antonio Trande > Fedora Project > mailto: sagitter(a)fedoraproject.org <mailto:[email protected]> > GPG key: 0x29FBC85D7A51CC2F > GPG key server: https://keyserver1.pgp.com/ <https://keyserver1.pgp.com/>

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Re: [petsc-dev] libpetsc.so: undefined references
by Stefano Zampini 02 Oct '21

02 Oct '21

I knew this was coming.... https://gitlab.com/petsc/petsc/-/issues/997 Il Sab 2 Ott 2021, 15:48 Antonio T. sagitter <sagitter(a)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(a)fedoraproject.org > GPG key: 0x29FBC85D7A51CC2F > GPG key server: https://keyserver1.pgp.com/ >

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libpetsc.so: undefined references
by Antonio T. sagitter 02 Oct '21

02 Oct '21

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(a)fedoraproject.org GPG key: 0x29FBC85D7A51CC2F GPG key server: https://keyserver1.pgp.com/

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