[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 
> 
_______________________________________________ 
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