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micwoj92/gist:5dd3d97b929e0867a04d05cf2126e761

Created July 30, 2024 22:47
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gistfile1.txt
================================================================================
Starting Configure Run at Wed Jul 31 00:44:39 2024
Configure Options: --prefix=/build/slepc/pkg/slepc/opt/slepc/linux-c-opt --with-clean=1 --with-slepc4py=1
Working directory: /build/slepc/src/slepc-3.21.1
Python version:
3.12.4 (main, Jun 7 2024, 06:33:07) [GCC 14.1.1 20240522]
make: /usr/bin/make
PETSc source directory: /opt/petsc/linux-c-opt
PETSc install directory: /opt/petsc/linux-c-opt
PETSc version: 3.21.3
SLEPc source directory: /build/slepc/src/slepc-3.21.1
SLEPc install directory: /build/slepc/pkg/slepc/opt/slepc/linux-c-opt
SLEPc version: 3.21.1
Checking configure hashfile
No previous hashfile found
================================================================================
Checking PETSc installation...
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Checking link with code:
#include "petscsnes.h"
int main() {
PetscErrorCode ierr; Vec v; Mat m; KSP k;
ierr = PetscInitializeNoArguments();
ierr = VecCreate(PETSC_COMM_WORLD,&v);
ierr = MatCreate(PETSC_COMM_WORLD,&m);
ierr = KSPCreate(PETSC_COMM_WORLD,&k);
(void)ierr;
return 0;
}
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Running command:
cd /tmp/slepc-ulbnu8f4;/usr/bin/make checklink LINKFLAGS=""
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Output:
/usr/bin/mpicc -o checklink.o -c -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -g -ffile-prefix-map=/build/petsc/src=/usr/src/debug/petsc -flto=auto -fPIC -I/opt/petsc/linux-c-opt/include -I/usr/include/suitesparse -I/usr/include -I/usr/include/superlu checklink.c
/usr/bin/mpicc -Wl,-O1 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,-z,pack-relative-relocs -flto=auto -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -g -ffile-prefix-map=/build/petsc/src=/usr/src/debug/petsc -flto=auto -fPIC -o checklink checklink.o -Wl,-rpath,/opt/petsc/linux-c-opt/lib -L/opt/petsc/linux-c-opt/lib -Wl,-rpath,/usr/lib/gcc/x86_64-pc-linux-gnu/14.1.1 -L/usr/lib/gcc/x86_64-pc-linux-gnu/14.1.1 -lpetsc -lspqr -lumfpack -lklu -lcholmod -lamd -lsuperlu -lfftw3_mpi -lfftw3 -llapack -lblas -lzfp -lnetcdf -lhdf5hl_fortran -lhdf5_fortran -lhdf5_hl -lhdf5 -lm -lz -lgsl -lgslcblas -ljpeg -lyaml -lmpi_usempif08 -lmpi_usempi_ignore_tkr -lmpi_mpifh -lmpi -lgfortran -lm -lgfortran -lm -lgcc_s -lquadmath
/usr/bin/ld: /opt/petsc/linux-c-opt/lib/libpetsc.so: undefined reference to `VTT for std::__cxx11::basic_ostringstream<char, std::char_traits<char>, std::allocator<char> >'
/usr/bin/ld: /opt/petsc/linux-c-opt/lib/libpetsc.so: undefined reference to `std::locale::locale()'
/usr/bin/ld: /opt/petsc/linux-c-opt/lib/libpetsc.so: undefined reference to `std::basic_ios<char, std::char_traits<char> >::init(std::basic_streambuf<char, std::char_traits<char> >*)'
/usr/bin/ld: /opt/petsc/linux-c-opt/lib/libpetsc.so: undefined reference to `std::ios_base::ios_base()'
/usr/bin/ld: /opt/petsc/linux-c-opt/lib/libpetsc.so: undefined reference to `std::locale::~locale()'
/usr/bin/ld: /opt/petsc/linux-c-opt/lib/libpetsc.so: undefined reference to `std::ostream& std::ostream::_M_insert<long>(long)'
/usr/bin/ld: /opt/petsc/linux-c-opt/lib/libpetsc.so: undefined reference to `typeinfo for std::exception'
/usr/bin/ld: /opt/petsc/linux-c-opt/lib/libpetsc.so: undefined reference to `std::nothrow'
/usr/bin/ld: /opt/petsc/linux-c-opt/lib/libpetsc.so: undefined reference to `__cxa_begin_catch'
/usr/bin/ld: /opt/petsc/linux-c-opt/lib/libpetsc.so: undefined reference to `std::ios_base::~ios_base()'
/usr/bin/ld: /opt/petsc/linux-c-opt/lib/libpetsc.so: undefined reference to `vtable for __cxxabiv1::__si_class_type_info'
/usr/bin/ld: /opt/petsc/linux-c-opt/lib/libpetsc.so: undefined reference to `vtable for std::__cxx11::basic_stringbuf<char, std::char_traits<char>, std::allocator<char> >'
/usr/bin/ld: /opt/petsc/linux-c-opt/lib/libpetsc.so: undefined reference to `vtable for std::__cxx11::basic_ostringstream<char, std::char_traits<char>, std::allocator<char> >'
/usr/bin/ld: /opt/petsc/linux-c-opt/lib/libpetsc.so: undefined reference to `std::basic_ostream<char, std::char_traits<char> >& std::__ostream_insert<char, std::char_traits<char> >(std::basic_ostream<char, std::char_traits<char> >&, char const*, long)'
/usr/bin/ld: /opt/petsc/linux-c-opt/lib/libpetsc.so: undefined reference to `operator delete(void*, unsigned long)'
/usr/bin/ld: /opt/petsc/linux-c-opt/lib/libpetsc.so: undefined reference to `__cxa_call_terminate'
/usr/bin/ld: /opt/petsc/linux-c-opt/lib/libpetsc.so: undefined reference to `vtable for __cxxabiv1::__class_type_info'
/usr/bin/ld: /opt/petsc/linux-c-opt/lib/libpetsc.so: undefined reference to `vtable for std::basic_streambuf<char, std::char_traits<char> >'
/usr/bin/ld: /opt/petsc/linux-c-opt/lib/libpetsc.so: undefined reference to `__cxa_rethrow'
/usr/bin/ld: /opt/petsc/linux-c-opt/lib/libpetsc.so: undefined reference to `std::__throw_logic_error(char const*)'
/usr/bin/ld: /opt/petsc/linux-c-opt/lib/libpetsc.so: undefined reference to `operator new(unsigned long)'
/usr/bin/ld: /opt/petsc/linux-c-opt/lib/libpetsc.so: undefined reference to `std::__cxx11::basic_ostringstream<char, std::char_traits<char>, std::allocator<char> >::~basic_ostringstream()'
/usr/bin/ld: /opt/petsc/linux-c-opt/lib/libpetsc.so: undefined reference to `std::__throw_length_error(char const*)'
/usr/bin/ld: /opt/petsc/linux-c-opt/lib/libpetsc.so: undefined reference to `std::ostream::put(char)'
/usr/bin/ld: /opt/petsc/linux-c-opt/lib/libpetsc.so: undefined reference to `std::__throw_out_of_range_fmt(char const*, ...)'
/usr/bin/ld: /opt/petsc/linux-c-opt/lib/libpetsc.so: undefined reference to `std::__glibcxx_assert_fail(char const*, int, char const*, char const*)'
/usr/bin/ld: /opt/petsc/linux-c-opt/lib/libpetsc.so: undefined reference to `operator new[](unsigned long, std::nothrow_t const&)'
/usr/bin/ld: /opt/petsc/linux-c-opt/lib/libpetsc.so: undefined reference to `__cxa_end_catch'
/usr/bin/ld: /opt/petsc/linux-c-opt/lib/libpetsc.so: undefined reference to `std::__throw_bad_array_new_length()'
/usr/bin/ld: /opt/petsc/linux-c-opt/lib/libpetsc.so: undefined reference to `vtable for std::basic_ios<char, std::char_traits<char> >'
/usr/bin/ld: /opt/petsc/linux-c-opt/lib/libpetsc.so: undefined reference to `std::__detail::_Prime_rehash_policy::_M_need_rehash(unsigned long, unsigned long, unsigned long) const'
/usr/bin/ld: /opt/petsc/linux-c-opt/lib/libpetsc.so: undefined reference to `__gxx_personality_v0'
/usr/bin/ld: /opt/petsc/linux-c-opt/lib/libpetsc.so: undefined reference to `operator delete[](void*)'
/usr/bin/ld: /opt/petsc/linux-c-opt/lib/libpetsc.so: undefined reference to `std::__throw_bad_alloc()'
collect2: error: ld returned 1 exit status
make: *** [makefile:2: checklink] Error 1
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ERROR: Unable to link with PETSc
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