[Nek5000-users] Running MOAB example

Wed Sep 11 10:11:04 CDT 2013

Thanks for your answer, to make sure I have added libraries to makenek
''USR_LFLAGS="-lmpi_cxx -lstdc++" which I'm getting same error,so you mean
I need to add appropriate fortran library to USR_LFLAGS?

Thanks,
Ami

On Wed, Sep 11, 2013 at 10:47 AM, <nek5000-users at lists.mcs.anl.gov> wrote:

> Hi Ami,
>   That's the C++ runtime.  You have two options:
> 1. Link with the C++ compiler; in this case, you'll have to explicitly add
> the fortran runtime libraries to the link statement, which is most easily
> done by adding it to USR_LFLAGS in makenek.  Compiler documents often tell
> you which libraries implement the fortran runtime, usually in a section
> about inter-language linking.
>
> 2. Add the C++ std libs to USR_LFLAGS.  The trunk/nek/makenek file has a
> few examples of this method for gnu/intel/pgi.  Sometimes, like on BG/x, it
> can be difficult to figure out what all comprises the C++ runtime, which is
> why I list 1. above.
>
> - tim
>
>
> On 09/11/2013 09:31 AM, nek5000-users at lists.mcs.anl.**gov<nek5000-users at lists.mcs.anl.gov>wrote:
>
>> 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._**ZNSt4listIN4moab12IODebugTrack**
>> 6DRangeESaIS2_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_**
>> nodeIN4moab12IODebugTrack6DRan**geEEE10deallocateEPS5_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_**
>> allocatorIN4moab12IODebugTrack**6DRangeEE8allocateEmPKv[__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_**
>> allocatorIN4moab12IODebugTrack**6DRangeEE8allocateEmPKv[__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_**
>> allocatorIN4moab12IODebugTrack**6DRangeEE10deallocateEPS3_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_**
>> nodeIN4moab12IODebugTrack6DRan**geEEE8allocateEmPKv[__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_**
>> nodeIN4moab12IODebugTrack6DRan**geEEE8allocateEmPKv[__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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>>
>>
> --
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>   steadfast, because he trusts in you."               Isaiah 26:3
>
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>          (tautges at mcs.anl.gov)      (telecommuting from UW-Madison)
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