[Nek5000-users] Running MOAB example
nek5000-users at lists.mcs.anl.gov
nek5000-users at lists.mcs.anl.gov
Fri Sep 13 09:39:26 CDT 2013
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.govwrote:
> >>> >>>>
> >>> >>>> 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
>
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