[Nek5000-users] Running MOAB example
nek5000-users at lists.mcs.anl.gov
nek5000-users at lists.mcs.anl.gov
Fri Sep 13 10:06:24 CDT 2013
Hi Ami,
It is better to run Nek with scripts
http://nek5000.mcs.anl.gov/index.php/Scripts
or to be specific, in your case with a appropriate parallel script like nekbmpi
Also make sure that you could run other examples in parallel (or alternatively have a MOAB build for serial execution).
Aleks
----- Original Message -----
From: nek5000-users at lists.mcs.anl.gov
To: nek5000-users at lists.mcs.anl.gov
Sent: Friday, September 13, 2013 9:39:26 AM
Subject: Re: [Nek5000-users] Running MOAB example
I added this hdf5 library, but thereis one not founded library (libmpi_cxx.so.1) abd when I set it with export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/lib64/openmpi/lib/, it gives me fatal error like this
[amirreza at biofluids moab]$ ./nek5000 pipe
Fatal error in PMPI_Comm_dup: Invalid communicator, error stack:
PMPI_Comm_dup(175): MPI_Comm_dup(comm=0x0, new_comm=0x7fff496883ac) failed
PMPI_Comm_dup(133): Invalid communicator
what should I do now? I checked this library and I just have it in /usr/local/lib/ and /usr/lib64/openmpi/lib/ which both of them not working!
Thanks,
Ami
On Thu, Sep 12, 2013 at 2:49 PM, < nek5000-users at lists.mcs.anl.gov > wrote:
If you HDF5 and NetCDF are configured as shared libraries, make sure
their library paths are included in LD_LIBRARY_PATH. e.g.,
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/home/amirreza/Amirreza/hdf5-1.8.11/lib
Also check
ldd ./nek5000
to make sure that all the necessary libraries are being resolved
correctly before attempting to run the code again.
Vijay
On Thu, Sep 12, 2013 at 1:43 PM, < nek5000-users at lists.mcs.anl.gov > wrote:
> Hi All,
>
> After fixing MOAB, I successully compiled MOAB example but when I tried
> ./nek pipe, it gave me this error
>
> mv: cannot stat `pipe.log': No such file or directory
> ./nek5000: error while loading shared libraries: libhdf5.so.8: cannot open
> shared object file: No such file or directory
>
> real 0m0.001s
> user 0m0.000s
> sys 0m0.000s
>
> can any one tell me what is the problem? FYI, I am using hdf5-1.8.11 with
> zlib-1.2.5 and szip-2.1.
>
> Thanks,
> Ami
>
>
> On Wed, Sep 11, 2013 at 1:30 PM, < nek5000-users at lists.mcs.anl.gov > wrote:
>>
>>
>>
>> On 09/11/2013 12:10 PM, Iulian Grindeanu wrote:
>>>
>>>
>>>
>>>
>>> ------------------------------------------------------------------------------------------------------------------------
>>>
>>>
>>> Aha, good catch.
>>>
>>> Iulian, could you backport the imesh_freememory function? Thanks.
>>>
>>> Hello,
>>> The Version 4.6 was released on February 11. The link to the tar ball is
>>> in the web page.
>>> http://trac.mcs.anl.gov/projects/ITAPS/wiki/MOAB
>>>
>>> http://ftp.mcs.anl.gov/pub/fathom/moab-4.6.0.tar.gz
>>> (so this is the official release 4.6)
>>>
>>> The current Version4.6 branch, in the git repository, already has the
>>> free memory function backported.
>>> That tarball is updated nightly, and you can get it from this link (on
>>> the moab wiki page too)
>>>
>>> http://ftp.mcs.anl.gov/pub/fathom/moab-4.6-nightly.tar.gz
>>>
>>> Is this what they need?
>>>
>>
>> Ok, yes, that's what they need, thanks.
>>
>> - tim
>>
>>
>>> Thanks,
>>> Iulian
>>>
>>> - 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,
>>> < nek5000-users at lists.mcs.anl.gov > 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,
>>> < nek5000-users at lists.mcs.anl.gov > 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, 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
>>> >>>
>>> >>> _______________________________________________
>>> >>> Nek5000-users mailing list
>>> >>> Nek5000-users at lists.mcs.anl.gov
>>> >>> 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
>>>
>>>
>>
>> --
>> ================================================================
>> "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
>>
>> _______________________________________________
>> Nek5000-users mailing list
>> Nek5000-users at lists.mcs.anl.gov
>> 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
>
_______________________________________________
Nek5000-users mailing list
Nek5000-users at lists.mcs.anl.gov
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
More information about the Nek5000-users
mailing list