[Nek5000-users] Running MOAB example

[nek5000-users at lists.mcs.anl.gov]

Hello Neks,

I am trying to run MOAB example with nek5000, but all the time which I am
running, it gives me set of undefined reference error. I put an error with
last part of my ./makenek pipe log below.
What is wrong with my work?

IODebugTrack.cpp:(.text+0xb74): undefined reference to
`std::basic_ostream<char, std::char_traits<char> >& std::operator<<
<std::char_traits<char> >(std::basic_ostream<char, std::char_traits<char>
>&, char const*)'
IODebugTrack.cpp:(.text+0xb7f): undefined reference to
`std::basic_ostream<char, std::char_traits<char> >::operator<<(unsigned
long)'
IODebugTrack.cpp:(.text+0xb8c): undefined reference to
`std::basic_ostream<char, std::char_traits<char> >& std::operator<<
<std::char_traits<char> >(std::basic_ostream<char, std::char_traits<char>
>&, char const*)'
IODebugTrack.cpp:(.text+0xb97): undefined reference to
`std::basic_ostream<char, std::char_traits<char> >::operator<<(unsigned
long)'
IODebugTrack.cpp:(.text+0xbd3): undefined reference to
`std::basic_ostream<char, std::char_traits<char> >& std::operator<<
<std::char_traits<char> >(std::basic_ostream<char, std::char_traits<char>
>&, char const*)'
IODebugTrack.cpp:(.text+0xbde): undefined reference to
`std::basic_ostream<char, std::char_traits<char> >::operator<<(unsigned
long)'
IODebugTrack.cpp:(.text+0xbeb): undefined reference to
`std::basic_ostream<char, std::char_traits<char> >& std::operator<<
<std::char_traits<char> >(std::basic_ostream<char, std::char_traits<char>
>&, char const*)'
IODebugTrack.cpp:(.text+0xbf6): undefined reference to
`std::basic_ostream<char, std::char_traits<char> >::operator<<(unsigned
long)'
IODebugTrack.cpp:(.text+0xc03): undefined reference to
`std::basic_ostream<char, std::char_traits<char> >& std::operator<<
<std::char_traits<char> >(std::basic_ostream<char, std::char_traits<char>
>&, char const*)'
IODebugTrack.cpp:(.text+0xc0e): undefined reference to
`std::basic_ostream<char, std::char_traits<char> >::operator<<(unsigned
long)'
IODebugTrack.cpp:(.text+0xc1b): undefined reference to
`std::basic_ostream<char, std::char_traits<char> >& std::operator<<
<std::char_traits<char> >(std::basic_ostream<char, std::char_traits<char>
>&, char const*)'
IODebugTrack.cpp:(.text+0xc26): undefined reference to
`std::basic_ostream<char, std::char_traits<char> >::operator<<(unsigned
long)'
IODebugTrack.cpp:(.text+0xc33): undefined reference to
`std::basic_ostream<char, std::char_traits<char> >& std::operator<<
<std::char_traits<char> >(std::basic_ostream<char, std::char_traits<char>
>&, char const*)'
IODebugTrack.cpp:(.text+0xc38): undefined reference to
`std::basic_ostream<char, std::char_traits<char> >& std::endl<char,
std::char_traits<char> >(std::basic_ostream<char, std::char_traits<char>
>&)'
IODebugTrack.cpp:(.text+0xc40): undefined reference to
`std::basic_ostream<char, std::char_traits<char>
>::operator<<(std::basic_ostream<char, std::char_traits<char> >&
(*)(std::basic_ostream<char, std::char_traits<char> >&))'
IODebugTrack.cpp:(.text+0xc50): undefined reference to
`std::basic_ostream<char, std::char_traits<char> >::flush()'
/home/amirreza/Amirreza/moab-4.6.0/gcc/lib/libMOAB.a(IODebugTrack.o): In
function `moab::IODebugTrack::all_reduce()':
IODebugTrack.cpp:(.text+0xd08): undefined reference to `MPI_Comm_size'
IODebugTrack.cpp:(.text+0xdfe): undefined reference to `MPI_Gather'
IODebugTrack.cpp:(.text+0x1080): undefined reference to `MPI_Gatherv'
/home/amirreza/Amirreza/moab-4.6.0/gcc/lib/libMOAB.a(IODebugTrack.o): In
function `__static_initialization_and_destruction_0(int, int)':
IODebugTrack.cpp:(.text+0x1221): undefined reference to
`std::ios_base::Init::Init()'
IODebugTrack.cpp:(.text+0x1226): undefined reference to
`std::ios_base::Init::~Init()'
/home/amirreza/Amirreza/moab-4.6.0/gcc/lib/libMOAB.a(IODebugTrack.o): In
function `std::list<moab::IODebugTrack::DRange,
std::allocator<moab::IODebugTrack::DRange>
>::_M_insert(std::_List_iterator<moab::IODebugTrack::DRange>,
moab::IODebugTrack::DRange const&)':
IODebugTrack.cpp:(.text._ZNSt4listIN4moab12IODebugTrack6DRangeESaIS2_EE9_M_insertESt14_List_iteratorIS2_ERKS2_[std::list<moab::IODebugTrack::DRange,
std::allocator<moab::IODebugTrack::DRange>
>::_M_insert(std::_List_iterator<moab::IODebugTrack::DRange>,
moab::IODebugTrack::DRange const&)]+0x3a): undefined reference to
`std::__detail::_List_node_base::_M_hook(std::__detail::_List_node_base*)'
/home/amirreza/Amirreza/moab-4.6.0/gcc/lib/libMOAB.a(IODebugTrack.o): In
function
`__gnu_cxx::new_allocator<std::_List_node<moab::IODebugTrack::DRange>
>::deallocate(std::_List_node<moab::IODebugTrack::DRange>*, unsigned long)':
IODebugTrack.cpp:(.text._ZN9__gnu_cxx13new_allocatorISt10_List_nodeIN4moab12IODebugTrack6DRangeEEE10deallocateEPS5_m[__gnu_cxx::new_allocator<std::_List_node<moab::IODebugTrack::DRange>
>::deallocate(std::_List_node<moab::IODebugTrack::DRange>*, unsigned
long)]+0x1c): undefined reference to `operator delete(void*)'
/home/amirreza/Amirreza/moab-4.6.0/gcc/lib/libMOAB.a(IODebugTrack.o): In
function
`__gnu_cxx::new_allocator<moab::IODebugTrack::DRange>::allocate(unsigned
long, void const*)':
IODebugTrack.cpp:(.text._ZN9__gnu_cxx13new_allocatorIN4moab12IODebugTrack6DRangeEE8allocateEmPKv[__gnu_cxx::new_allocator<moab::IODebugTrack::DRange>::allocate(unsigned
long, void const*)]+0x2c): undefined reference to `std::__throw_bad_alloc()'
IODebugTrack.cpp:(.text._ZN9__gnu_cxx13new_allocatorIN4moab12IODebugTrack6DRangeEE8allocateEmPKv[__gnu_cxx::new_allocator<moab::IODebugTrack::DRange>::allocate(unsigned
long, void const*)]+0x45): undefined reference to `operator new(unsigned
long)'
/home/amirreza/Amirreza/moab-4.6.0/gcc/lib/libMOAB.a(IODebugTrack.o): In
function
`__gnu_cxx::new_allocator<moab::IODebugTrack::DRange>::deallocate(moab::IODebugTrack::DRange*,
unsigned long)':
IODebugTrack.cpp:(.text._ZN9__gnu_cxx13new_allocatorIN4moab12IODebugTrack6DRangeEE10deallocateEPS3_m[__gnu_cxx::new_allocator<moab::IODebugTrack::DRange>::deallocate(moab::IODebugTrack::DRange*,
unsigned long)]+0x1c): undefined reference to `operator delete(void*)'
/home/amirreza/Amirreza/moab-4.6.0/gcc/lib/libMOAB.a(IODebugTrack.o): In
function
`__gnu_cxx::new_allocator<std::_List_node<moab::IODebugTrack::DRange>
>::allocate(unsigned long, void const*)':
IODebugTrack.cpp:(.text._ZN9__gnu_cxx13new_allocatorISt10_List_nodeIN4moab12IODebugTrack6DRangeEEE8allocateEmPKv[__gnu_cxx::new_allocator<std::_List_node<moab::IODebugTrack::DRange>
>::allocate(unsigned long, void const*)]+0x2c): undefined reference to
`std::__throw_bad_alloc()'
IODebugTrack.cpp:(.text._ZN9__gnu_cxx13new_allocatorISt10_List_nodeIN4moab12IODebugTrack6DRangeEEE8allocateEmPKv[__gnu_cxx::new_allocator<std::_List_node<moab::IODebugTrack::DRange>
>::allocate(unsigned long, void const*)]+0x46): undefined reference to
`operator new(unsigned long)'
/home/amirreza/Amirreza/moab-4.6.0/gcc/lib/libMOAB.a(IODebugTrack.o):(.eh_frame+0x24b):
undefined reference to `__gxx_personality_v0'
/home/amirreza/Amirreza/moab-4.6.0/gcc/lib/libMOAB.a(OrientedBox.o): In
function `moab::operator<<(std::basic_ostream<char, std::char_traits<char>
>&, moab::OrientedBox const&)':
OrientedBox.cpp:(.text+0x97): undefined reference to
`std::basic_ostream<char, std::char_traits<char> >& std::operator<<
<std::char_traits<char> >(std::basic_ostream<char, std::char_traits<char>
>&, char const*)'
OrientedBox.cpp:(.text+0xaf): undefined reference to
`std::basic_ostream<char, std::char_traits<char> >& std::operator<<
<std::char_traits<char> >(std::basic_ostream<char, std::char_traits<char>
>&, char const*)'
OrientedBox.cpp:(.text+0xbc): undefined reference to
`std::basic_ostream<char, std::char_traits<char> >::operator<<(double)'
OrientedBox.cpp:(.text+0xc9): undefined reference to
`std::basic_ostream<char, std::char_traits<char> >& std::operator<<
<std::char_traits<char> >(std::basic_ostream<char, std::char_traits<char>
>&, char const*)'
OrientedBox.cpp:(.text+0xe1): undefined reference to
`std::basic_ostream<char, std::char_traits<char> >& std::operator<<
<std::char_traits<char> >(std::basic_ostream<char, std::char_traits<char>
>&, char const*)'
OrientedBox.cpp:(.text+0xee): undefined reference to
`std::basic_ostream<char, std::char_traits<char> >::operator<<(double)'
OrientedBox.cpp:(.text+0xfb): undefined reference to
`std::basic_ostream<char, std::char_traits<char> >& std::operator<<
<std::char_traits<char> >(std::basic_ostream<char, std::char_traits<char>
>&, char const*)'
OrientedBox.cpp:(.text+0x113): undefined reference to
`std::basic_ostream<char, std::char_traits<char> >& std::operator<<
<std::char_traits<char> >(std::basic_ostream<char, std::char_traits<char>
>&, char const*)'
OrientedBox.cpp:(.text+0x120): undefined reference to
`std::basic_ostream<char, std::char_traits<char> >::operator<<(double)'
/home/amirreza/Amirreza/moab-4.6.0/gcc/lib/libMOAB.a(OrientedBox.o): In
function `__static_initialization_and_destruction_0(int, int)':
OrientedBox.cpp:(.text+0x3aaf): undefined reference to
`std::ios_base::Init::Init()'
OrientedBox.cpp:(.text+0x3ab4): undefined reference to
`std::ios_base::Init::~Init()'
/home/amirreza/Amirreza/moab-4.6.0/gcc/lib/libMOAB.a(OrientedBox.o): In
function `moab::ErrorCode moab::EigenDecomp<moab::Matrix3,
moab::CartVect>(moab::Matrix3 const&, double*, moab::CartVect*)':
OrientedBox.cpp:(.text._ZN4moab11EigenDecompINS_7Matrix3ENS_8CartVectEEENS_9ErrorCodeERKT_PdPT0_[moab::ErrorCode
moab::EigenDecomp<moab::Matrix3, moab::CartVect>(moab::Matrix3 const&,
double*, moab::CartVect*)]+0xb7f): undefined reference to `std::cerr'
OrientedBox.cpp:(.text._ZN4moab11EigenDecompINS_7Matrix3ENS_8CartVectEEENS_9ErrorCodeERKT_PdPT0_[moab::ErrorCode
moab::EigenDecomp<moab::Matrix3, moab::CartVect>(moab::Matrix3 const&,
double*, moab::CartVect*)]+0xb84): undefined reference to
`std::basic_ostream<char, std::char_traits<char> >& std::operator<<
<std::char_traits<char> >(std::basic_ostream<char, std::char_traits<char>
>&, char const*)'
OrientedBox.cpp:(.text._ZN4moab11EigenDecompINS_7Matrix3ENS_8CartVectEEENS_9ErrorCodeERKT_PdPT0_[moab::ErrorCode
moab::EigenDecomp<moab::Matrix3, moab::CartVect>(moab::Matrix3 const&,
double*, moab::CartVect*)]+0xb89): undefined reference to
`std::basic_ostream<char, std::char_traits<char> >& std::endl<char,
std::char_traits<char> >(std::basic_ostream<char, std::char_traits<char>
>&)'
OrientedBox.cpp:(.text._ZN4moab11EigenDecompINS_7Matrix3ENS_8CartVectEEENS_9ErrorCodeERKT_PdPT0_[moab::ErrorCode
moab::EigenDecomp<moab::Matrix3, moab::CartVect>(moab::Matrix3 const&,
double*, moab::CartVect*)]+0xb91): undefined reference to
`std::basic_ostream<char, std::char_traits<char>
>::operator<<(std::basic_ostream<char, std::char_traits<char> >&
(*)(std::basic_ostream<char, std::char_traits<char> >&))'
/home/amirreza/Amirreza/moab-4.6.0/gcc/lib/libMOAB.a(OrientedBox.o):(.eh_frame+0x22f):
undefined reference to `__gxx_personality_v0'
collect2: ld returned 1 exit status
make: *** [nek5000] Error 1

Thanks,
Ami
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