[Nek5000-users] Running MOAB example
nek5000-users at lists.mcs.anl.gov
nek5000-users at lists.mcs.anl.gov
Wed Sep 11 11:05:44 CDT 2013
It depends which compiler you're using. Are you using gnu?
Please send complete compile output.
- tim
On 09/11/2013 10:11 AM, nek5000-users at lists.mcs.anl.gov wrote:
> 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 <mailto: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 <mailto: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
>
>
> _________________________________________________
> Nek5000-users mailing list
> Nek5000-users at lists.mcs.anl.__gov <mailto:Nek5000-users at lists.mcs.anl.gov>
> https://lists.mcs.anl.gov/__mailman/listinfo/nek5000-users
> <https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users>
>
>
> --
> ==============================__==============================__====
> "You will keep in perfect peace him whose mind is
> steadfast, because he trusts in you." Isaiah 26:3
>
> Tim Tautges Argonne National Laboratory
> (tautges at mcs.anl.gov <mailto:tautges at mcs.anl.gov>) (telecommuting from UW-Madison)
> phone (gvoice): (608) 354-1459 <tel:%28608%29%20354-1459> 1500 Engineering Dr.
> fax: (608) 263-4499 <tel:%28608%29%20263-4499> Madison, WI 53706
>
> _________________________________________________
> Nek5000-users mailing list
> Nek5000-users at lists.mcs.anl.__gov <mailto:Nek5000-users at lists.mcs.anl.gov>
> https://lists.mcs.anl.gov/__mailman/listinfo/nek5000-users <https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users>
>
>
>
>
> _______________________________________________
> Nek5000-users mailing list
> Nek5000-users at lists.mcs.anl.gov
> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users
>
--
================================================================
"You will keep in perfect peace him whose mind is
steadfast, because he trusts in you." Isaiah 26:3
Tim Tautges Argonne National Laboratory
(tautges at mcs.anl.gov) (telecommuting from UW-Madison)
phone (gvoice): (608) 354-1459 1500 Engineering Dr.
fax: (608) 263-4499 Madison, WI 53706
More information about the Nek5000-users
mailing list