Re: [Nek5000-users] Running MOAB example

11 Sep 2013

      Aha, good catch.

Iulian, could you backport the imesh_freememory function?  Thanks.

- tim

On 09/11/2013 11:33 AM, Vijay S. Mahadevan wrote:
...
The linker error is because of your version mismatch. You need to
update your moab to the latest version. I see you are using v4.6 now.
You should be able to use the dev version from
https://bitbucket.org/fathomteam/moab with git or download the newer
patch from https://trac.mcs.anl.gov/projects/ITAPS/wiki/MOAB.
Tim, can we create a new patched version of the release for download.
I spoke to Rajeev about this some time back but we need to decide what
fixes to backport.
Vijay
On Wed, Sep 11, 2013 at 11:20 AM,  <[email protected]> wrote:
...
Yes , I am using gnu, and whwen I add USR_LFLAGS="-lmpi_cxx -lstdc++,
I get this,
makenek - automatic build tool for Nek5000
generating makefile ...
mpif77 -c  -O2 -fdefault-real-8 -x f77-cpp-input -fcray-pointer -DMOAB
-DPTRSIZE8 -DMPI -DLONGINT8 -DUNDERSCORE -DGLOBAL_LONG_LONG
-I/home/amirreza/nek5_svn/amirreza_test/examples/moab
-I/home/amirreza/nek5_svn/trunk/nek -I./
/home/amirreza/nek5_svn/amirreza_test/examples/moab/pipe.f
-I/home/amirreza/nek5_svn/trunk/nek/3rd_party
-I/home/amirreza/Amirreza/moab-4.6.0/gcc/include  -o obj/pipe.o
mpif77 -o nek5000  obj/pipe.o obj/drive.o obj/drive1.o obj/drive2.o
obj/plan4.o obj/bdry.o obj/coef.o obj/conduct.o obj/connect1.o
obj/connect2.o obj/dssum.o obj/edgec.o obj/eigsolv.o obj/gauss.o
obj/genxyz.o obj/navier1.o obj/makeq.o obj/navier0.o obj/navier2.o
obj/navier3.o obj/navier4.o obj/prepost.o obj/speclib.o obj/map2.o
obj/turb.o obj/mvmesh.o obj/ic.o obj/ssolv.o obj/planx.o obj/math.o
obj/mxm_wrapper.o obj/hmholtz.o obj/gfdm_par.o obj/gfdm_op.o
obj/gfdm_solve.o obj/subs1.o obj/subs2.o obj/genbox.o obj/gmres.o obj/hsmg.o
obj/convect.o obj/induct.o obj/perturb.o obj/navier5.o obj/navier6.o
obj/navier7.o obj/navier8.o obj/fast3d.o obj/fasts.o obj/calcz.o obj/byte.o
obj/chelpers.o obj/byte_mpi.o obj/postpro.o obj/cvode_driver.o
obj/nek_comm.o obj/init_plugin.o obj/setprop.o obj/qthermal.o
obj/cvode_aux.o obj/makeq_aux.o obj/papi.o obj/ssygv.o obj/dsygv.o
obj/nek_in_situ.o obj/mxm_std.o obj/blas.o obj/moab.o obj/imeshutil.o
obj/imeshcutil.o obj/comm_mpi.o obj/singlmesh.o obj/jl_gs.o obj/jl_sort.o
obj/jl_sarray_transfer.o obj/jl_sarray_sort.o obj/jl_gs_local.o
obj/jl_crystal.o obj/jl_comm.o obj/jl_tensor.o obj/jl_fail.o
obj/jl_fcrystal.o obj/jl_findpts.o obj/jl_findpts_local.o obj/jl_obbox.o
obj/jl_poly.o obj/jl_lob_bnd.o obj/jl_findpts_el_3.o obj/jl_findpts_el_2.o
obj/jl_sparse_cholesky.o obj/jl_xxt.o obj/jl_fcrs.o
-L/home/amirreza/Amirreza/netcdf-4.1.3/gcc/lib
-L/home/amirreza/Amirreza/zlib-1.2.5/gcc/lib
-L/home/amirreza/Amirreza/szip-2.1/gcc/lib
-L/home/amirreza/Amirreza/hdf5-1.8.11/lib
-L/home/amirreza/Amirreza/moab-4.6.0/gcc/lib
-L/home/amirreza/Amirreza/moab-4.6.0/gcc/lib -liMesh -lMOAB -lnetcdf  -lhdf5
-lsz   -lm  -lmpi_cxx -lstdc++
obj/moab.o: In function `nekmoab_intbc_':
moab.f:(.text+0xe9d): undefined reference to `imesh_freememory_'
moab.f:(.text+0xece): undefined reference to `imesh_freememory_'
moab.f:(.text+0xee4): undefined reference to `imesh_freememory_'
moab.f:(.text+0xf05): undefined reference to `imesh_freememory_'
obj/moab.o: In function `nekmoab_bc_':
moab.f:(.text+0x1306): undefined reference to `imesh_freememory_'
collect2: ld returned 1 exit status
make: *** [nek5000] Error 1
Thanks,
Ami
On Wed, Sep 11, 2013 at 12:05 PM, <[email protected]> wrote:
...
It depends which compiler you're using.  Are you using gnu?
Please send complete compile output.
- tim
On 09/11/2013 10:11 AM, [email protected] 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, <[email protected]
<mailto:[email protected]>> 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, [email protected].__gov
<mailto:[email protected]> 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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        steadfast, because he trusts in you."               Isaiah 26:3
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               ([email protected] <mailto:[email protected]>)
(telecommuting from UW-Madison)
       phone (gvoice): (608) 354-1459 <tel:%28608%29%20354-1459>      1500
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--
================================================================
"You will keep in perfect peace him whose mind is
   steadfast, because he trusts in you."               Isaiah 26:3
Tim Tautges            Argonne National Laboratory
          ([email protected])      (telecommuting from UW-Madison)
  phone (gvoice): (608) 354-1459      1500 Engineering Dr.
             fax: (608) 263-4499      Madison, WI 53706
_______________________________________________
Nek5000-users mailing list
[email protected]
https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users
_______________________________________________
Nek5000-users mailing list
[email protected]
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
          ([email protected])      (telecommuting from UW-Madison)
  phone (gvoice): (608) 354-1459      1500 Engineering Dr.
             fax: (608) 263-4499      Madison, WI 53706

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