[Nek5000-users] Running MOAB example
nek5000-users at lists.mcs.anl.gov
nek5000-users at lists.mcs.anl.gov
Fri Sep 13 10:04:02 CDT 2013
Check that you don't have multiple installations of the MPI library
installed and in the path. And make sure that you consistently use
only one version of MPI in all your libraries. The error might be
because HDF or MOAB was not configured with your system version of
OpenMPI. Check all your configuration options again.
Vijay
On Fri, Sep 13, 2013 at 9:39 AM, <nek5000-users at lists.mcs.anl.gov> wrote:
> 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
>
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