<div dir="ltr"><div><div>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=$LD_LIBRARY_PATH:/usr/lib64/openmpi/lib/, it gives me fatal error like this<br>
[amirreza@biofluids moab]$ ./nek5000 pipe<br>Fatal error in PMPI_Comm_dup: Invalid communicator, error stack:<br>PMPI_Comm_dup(175): MPI_Comm_dup(comm=0x0, new_comm=0x7fff496883ac) failed<br>PMPI_Comm_dup(133): Invalid communicator<br>
<br></div>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!<br><br></div>Thanks,<br>Ami<br></div><div class="gmail_extra"><br><br>
<div class="gmail_quote">On Thu, Sep 12, 2013 at 2:49 PM, <span dir="ltr"><<a href="mailto:nek5000-users@lists.mcs.anl.gov" target="_blank">nek5000-users@lists.mcs.anl.gov</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
If you HDF5 and NetCDF are configured as shared libraries, make sure<br>
their library paths are included in LD_LIBRARY_PATH. e.g.,<br>
<br>
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/home/amirreza/Amirreza/hdf5-1.8.11/lib<br>
<br>
Also check<br>
<br>
ldd ./nek5000<br>
<br>
to make sure that all the necessary libraries are being resolved<br>
correctly before attempting to run the code again.<br>
<br>
Vijay<br>
<div class="HOEnZb"><div class="h5"><br>
On Thu, Sep 12, 2013 at 1:43 PM, <<a href="mailto:nek5000-users@lists.mcs.anl.gov">nek5000-users@lists.mcs.anl.gov</a>> wrote:<br>
> Hi All,<br>
><br>
> After fixing MOAB, I successully compiled MOAB example but when I tried<br>
> ./nek pipe, it gave me this error<br>
><br>
> mv: cannot stat `pipe.log': No such file or directory<br>
> ./nek5000: error while loading shared libraries: libhdf5.so.8: cannot open<br>
> shared object file: No such file or directory<br>
><br>
> real 0m0.001s<br>
> user 0m0.000s<br>
> sys 0m0.000s<br>
><br>
> can any one tell me what is the problem? FYI, I am using hdf5-1.8.11 with<br>
> zlib-1.2.5 and szip-2.1.<br>
><br>
> Thanks,<br>
> Ami<br>
><br>
><br>
> On Wed, Sep 11, 2013 at 1:30 PM, <<a href="mailto:nek5000-users@lists.mcs.anl.gov">nek5000-users@lists.mcs.anl.gov</a>> wrote:<br>
>><br>
>><br>
>><br>
>> On 09/11/2013 12:10 PM, Iulian Grindeanu wrote:<br>
>>><br>
>>><br>
>>><br>
>>><br>
>>> ------------------------------------------------------------------------------------------------------------------------<br>
>>><br>
>>><br>
>>> Aha, good catch.<br>
>>><br>
>>> Iulian, could you backport the imesh_freememory function? Thanks.<br>
>>><br>
>>> Hello,<br>
>>> The Version 4.6 was released on February 11. The link to the tar ball is<br>
>>> in the web page.<br>
>>> <a href="http://trac.mcs.anl.gov/projects/ITAPS/wiki/MOAB" target="_blank">http://trac.mcs.anl.gov/projects/ITAPS/wiki/MOAB</a><br>
>>><br>
>>> <a href="http://ftp.mcs.anl.gov/pub/fathom/moab-4.6.0.tar.gz" target="_blank">http://ftp.mcs.anl.gov/pub/fathom/moab-4.6.0.tar.gz</a><br>
>>> (so this is the official release 4.6)<br>
>>><br>
>>> The current Version4.6 branch, in the git repository, already has the<br>
>>> free memory function backported.<br>
>>> That tarball is updated nightly, and you can get it from this link (on<br>
>>> the moab wiki page too)<br>
>>><br>
>>> <a href="http://ftp.mcs.anl.gov/pub/fathom/moab-4.6-nightly.tar.gz" target="_blank">http://ftp.mcs.anl.gov/pub/fathom/moab-4.6-nightly.tar.gz</a><br>
>>><br>
>>> Is this what they need?<br>
>>><br>
>><br>
>> Ok, yes, that's what they need, thanks.<br>
>><br>
>> - tim<br>
>><br>
>><br>
>>> Thanks,<br>
>>> Iulian<br>
>>><br>
>>> - tim<br>
>>><br>
>>> On 09/11/2013 11:33 AM, Vijay S. Mahadevan wrote:<br>
>>> > The linker error is because of your version mismatch. You need to<br>
>>> > update your moab to the latest version. I see you are using v4.6<br>
>>> now.<br>
>>> > You should be able to use the dev version from<br>
>>> > <a href="https://bitbucket.org/fathomteam/moab" target="_blank">https://bitbucket.org/fathomteam/moab</a> with git or download the<br>
>>> newer<br>
>>> > patch from <a href="https://trac.mcs.anl.gov/projects/ITAPS/wiki/MOAB" target="_blank">https://trac.mcs.anl.gov/projects/ITAPS/wiki/MOAB</a>.<br>
>>> ><br>
>>> > Tim, can we create a new patched version of the release for<br>
>>> download.<br>
>>> > I spoke to Rajeev about this some time back but we need to decide<br>
>>> what<br>
>>> > fixes to backport.<br>
>>> ><br>
>>> > Vijay<br>
>>> ><br>
>>> > On Wed, Sep 11, 2013 at 11:20 AM,<br>
>>> <<a href="mailto:nek5000-users@lists.mcs.anl.gov">nek5000-users@lists.mcs.anl.gov</a>> wrote:<br>
>>> >><br>
>>> >> Yes , I am using gnu, and whwen I add USR_LFLAGS="-lmpi_cxx<br>
>>> -lstdc++,<br>
>>> >> I get this,<br>
>>> >> makenek - automatic build tool for Nek5000<br>
>>> >> generating makefile ...<br>
>>> >> mpif77 -c -O2 -fdefault-real-8 -x f77-cpp-input -fcray-pointer<br>
>>> -DMOAB<br>
>>> >> -DPTRSIZE8 -DMPI -DLONGINT8 -DUNDERSCORE -DGLOBAL_LONG_LONG<br>
>>> >> -I/home/amirreza/nek5_svn/amirreza_test/examples/moab<br>
>>> >> -I/home/amirreza/nek5_svn/trunk/nek -I./<br>
>>> >> /home/amirreza/nek5_svn/amirreza_test/examples/moab/pipe.f<br>
>>> >> -I/home/amirreza/nek5_svn/trunk/nek/3rd_party<br>
>>> >> -I/home/amirreza/Amirreza/moab-4.6.0/gcc/include -o obj/pipe.o<br>
>>> >> mpif77 -o nek5000 obj/pipe.o obj/drive.o obj/drive1.o<br>
>>> obj/drive2.o<br>
>>> >> obj/plan4.o obj/bdry.o obj/coef.o obj/conduct.o obj/connect1.o<br>
>>> >> obj/connect2.o obj/dssum.o obj/edgec.o obj/eigsolv.o obj/gauss.o<br>
>>> >> obj/genxyz.o obj/navier1.o obj/makeq.o obj/navier0.o<br>
>>> obj/navier2.o<br>
>>> >> obj/navier3.o obj/navier4.o obj/prepost.o obj/speclib.o<br>
>>> obj/map2.o<br>
>>> >> obj/turb.o obj/mvmesh.o obj/ic.o obj/ssolv.o obj/planx.o<br>
>>> obj/math.o<br>
>>> >> obj/mxm_wrapper.o obj/hmholtz.o obj/gfdm_par.o obj/gfdm_op.o<br>
>>> >> obj/gfdm_solve.o obj/subs1.o obj/subs2.o obj/genbox.o obj/gmres.o<br>
>>> obj/hsmg.o<br>
>>> >> obj/convect.o obj/induct.o obj/perturb.o obj/navier5.o<br>
>>> obj/navier6.o<br>
>>> >> obj/navier7.o obj/navier8.o obj/fast3d.o obj/fasts.o obj/calcz.o<br>
>>> obj/byte.o<br>
>>> >> obj/chelpers.o obj/byte_mpi.o obj/postpro.o obj/cvode_driver.o<br>
>>> >> obj/nek_comm.o obj/init_plugin.o obj/setprop.o obj/qthermal.o<br>
>>> >> obj/cvode_aux.o obj/makeq_aux.o obj/papi.o obj/ssygv.o<br>
>>> obj/dsygv.o<br>
>>> >> obj/nek_in_situ.o obj/mxm_std.o obj/blas.o obj/moab.o<br>
>>> obj/imeshutil.o<br>
>>> >> obj/imeshcutil.o obj/comm_mpi.o obj/singlmesh.o obj/jl_gs.o<br>
>>> obj/jl_sort.o<br>
>>> >> obj/jl_sarray_transfer.o obj/jl_sarray_sort.o obj/jl_gs_local.o<br>
>>> >> obj/jl_crystal.o obj/jl_comm.o obj/jl_tensor.o obj/jl_fail.o<br>
>>> >> obj/jl_fcrystal.o obj/jl_findpts.o obj/jl_findpts_local.o<br>
>>> obj/jl_obbox.o<br>
>>> >> obj/jl_poly.o obj/jl_lob_bnd.o obj/jl_findpts_el_3.o<br>
>>> obj/jl_findpts_el_2.o<br>
>>> >> obj/jl_sparse_cholesky.o obj/jl_xxt.o obj/jl_fcrs.o<br>
>>> >> -L/home/amirreza/Amirreza/netcdf-4.1.3/gcc/lib<br>
>>> >> -L/home/amirreza/Amirreza/zlib-1.2.5/gcc/lib<br>
>>> >> -L/home/amirreza/Amirreza/szip-2.1/gcc/lib<br>
>>> >> -L/home/amirreza/Amirreza/hdf5-1.8.11/lib<br>
>>> >> -L/home/amirreza/Amirreza/moab-4.6.0/gcc/lib<br>
>>> >> -L/home/amirreza/Amirreza/moab-4.6.0/gcc/lib -liMesh -lMOAB<br>
>>> -lnetcdf -lhdf5<br>
>>> >> -lsz -lm -lmpi_cxx -lstdc++<br>
>>> >> obj/moab.o: In function `nekmoab_intbc_':<br>
>>> >> moab.f:(.text+0xe9d): undefined reference to `imesh_freememory_'<br>
>>> >> moab.f:(.text+0xece): undefined reference to `imesh_freememory_'<br>
>>> >> moab.f:(.text+0xee4): undefined reference to `imesh_freememory_'<br>
>>> >> moab.f:(.text+0xf05): undefined reference to `imesh_freememory_'<br>
>>> >> obj/moab.o: In function `nekmoab_bc_':<br>
>>> >> moab.f:(.text+0x1306): undefined reference to `imesh_freememory_'<br>
>>> >><br>
>>> >> collect2: ld returned 1 exit status<br>
>>> >> make: *** [nek5000] Error 1<br>
>>> >><br>
>>> >> Thanks,<br>
>>> >> Ami<br>
>>> >><br>
>>> >><br>
>>> >> On Wed, Sep 11, 2013 at 12:05 PM,<br>
>>> <<a href="mailto:nek5000-users@lists.mcs.anl.gov">nek5000-users@lists.mcs.anl.gov</a>> wrote:<br>
>>> >>><br>
>>> >>> It depends which compiler you're using. Are you using gnu?<br>
>>> >>><br>
>>> >>> Please send complete compile output.<br>
>>> >>><br>
>>> >>> - tim<br>
>>> >>><br>
>>> >>><br>
>>> >>> On 09/11/2013 10:11 AM, <a href="mailto:nek5000-users@lists.mcs.anl.gov">nek5000-users@lists.mcs.anl.gov</a> wrote:<br>
>>> >>>><br>
>>> >>>> Thanks for your answer, to make sure I have added libraries to<br>
>>> makenek<br>
>>> >>>> ''USR_LFLAGS="-lmpi_cxx -lstdc++" which I'm<br>
>>> >>>> getting same error,so you mean I need to add appropriate<br>
>>> fortran library<br>
>>> >>>> to USR_LFLAGS?<br>
>>> >>>><br>
>>> >>>> Thanks,<br>
>>> >>>> Ami<br>
>>> >>>><br>
>>> >>>><br>
>>> >>>> On Wed, Sep 11, 2013 at 10:47 AM,<br>
>>> <<a href="mailto:nek5000-users@lists.mcs.anl.gov">nek5000-users@lists.mcs.anl.gov</a><br>
>>> >>>> <mailto:<a href="mailto:nek5000-users@lists.mcs.anl.gov">nek5000-users@lists.mcs.anl.gov</a>>> wrote:<br>
>>> >>>><br>
>>> >>>> Hi Ami,<br>
>>> >>>> That's the C++ runtime. You have two options:<br>
>>> >>>> 1. Link with the C++ compiler; in this case, you'll have<br>
>>> to<br>
>>> >>>> explicitly add the fortran runtime libraries to the link<br>
>>> >>>> statement, which is most easily done by adding it to<br>
>>> USR_LFLAGS in<br>
>>> >>>> makenek. Compiler documents often tell you which<br>
>>> >>>> libraries implement the fortran runtime, usually in a<br>
>>> section about<br>
>>> >>>> inter-language linking.<br>
>>> >>>><br>
>>> >>>> 2. Add the C++ std libs to USR_LFLAGS. The<br>
>>> trunk/nek/makenek file<br>
>>> >>>> has a few examples of this method for<br>
>>> >>>> gnu/intel/pgi. Sometimes, like on BG/x, it can be<br>
>>> difficult to<br>
>>> >>>> figure out what all comprises the C++ runtime, which<br>
>>> >>>> is why I list 1. above.<br>
>>> >>>><br>
>>> >>>> - tim<br>
>>> >>>><br>
>>> >>>><br>
>>> >>>> On 09/11/2013 09:31 AM, nek5000-users@lists.mcs.anl.__gov<br>
>>> >>>> <mailto:<a href="mailto:nek5000-users@lists.mcs.anl.gov">nek5000-users@lists.mcs.anl.gov</a>> wrote:<br>
>>> >>>><br>
>>> >>>> Hello Neks,<br>
>>> >>>><br>
>>> >>>> I am trying to run MOAB example with nek5000, but all<br>
>>> the time<br>
>>> >>>> which I am running, it gives me set of undefined<br>
>>> >>>> reference error. I put an error with last part of my<br>
>>> ./makenek<br>
>>> >>>> pipe log below.<br>
>>> >>>> What is wrong with my work?<br>
>>> >>>><br>
>>> >>>> IODebugTrack.cpp:(.text+0xb74)__: undefined reference<br>
>>> to<br>
>>> >>>> `std::basic_ostream<char, std::char_traits<char> >&<br>
>>> >>>><br>
>>> >>>> std::operator<< <std::char_traits<char><br>
>>> >>>>> (std::basic_ostream<char, std::char_traits<char> >&, char<br>
>>> const*)'<br>
>>> >>>> IODebugTrack.cpp:(.text+0xb7f)__: undefined reference<br>
>>> to<br>
>>> >>>> `std::basic_ostream<char, std::char_traits<char><br>
>>> >>>> >::operator<<(unsigned long)'<br>
>>> >>>> IODebugTrack.cpp:(.text+0xb8c)__: undefined reference<br>
>>> to<br>
>>> >>>> `std::basic_ostream<char, std::char_traits<char> >&<br>
>>> >>>><br>
>>> >>>> std::operator<< <std::char_traits<char><br>
>>> >>>>> (std::basic_ostream<char, std::char_traits<char> >&, char<br>
>>> const*)'<br>
>>> >>>> IODebugTrack.cpp:(.text+0xb97)__: undefined reference<br>
>>> to<br>
>>> >>>> `std::basic_ostream<char, std::char_traits<char><br>
>>> >>>> >::operator<<(unsigned long)'<br>
>>> >>>> IODebugTrack.cpp:(.text+0xbd3)__: undefined reference<br>
>>> to<br>
>>> >>>> `std::basic_ostream<char, std::char_traits<char> >&<br>
>>> >>>><br>
>>> >>>> std::operator<< <std::char_traits<char><br>
>>> >>>>> (std::basic_ostream<char, std::char_traits<char> >&, char<br>
>>> const*)'<br>
>>> >>>> IODebugTrack.cpp:(.text+0xbde)__: undefined reference<br>
>>> to<br>
>>> >>>> `std::basic_ostream<char, std::char_traits<char><br>
>>> >>>> >::operator<<(unsigned long)'<br>
>>> >>>> IODebugTrack.cpp:(.text+0xbeb)__: undefined reference<br>
>>> to<br>
>>> >>>> `std::basic_ostream<char, std::char_traits<char> >&<br>
>>> >>>><br>
>>> >>>> std::operator<< <std::char_traits<char><br>
>>> >>>>> (std::basic_ostream<char, std::char_traits<char> >&, char<br>
>>> const*)'<br>
>>> >>>> IODebugTrack.cpp:(.text+0xbf6)__: undefined reference<br>
>>> to<br>
>>> >>>> `std::basic_ostream<char, std::char_traits<char><br>
>>> >>>> >::operator<<(unsigned long)'<br>
>>> >>>> IODebugTrack.cpp:(.text+0xc03)__: undefined reference<br>
>>> to<br>
>>> >>>> `std::basic_ostream<char, std::char_traits<char> >&<br>
>>> >>>><br>
>>> >>>> std::operator<< <std::char_traits<char><br>
>>> >>>>> (std::basic_ostream<char, std::char_traits<char> >&, char<br>
>>> const*)'<br>
>>> >>>> IODebugTrack.cpp:(.text+0xc0e)__: undefined reference<br>
>>> to<br>
>>> >>>> `std::basic_ostream<char, std::char_traits<char><br>
>>> >>>> >::operator<<(unsigned long)'<br>
>>> >>>> IODebugTrack.cpp:(.text+0xc1b)__: undefined reference<br>
>>> to<br>
>>> >>>> `std::basic_ostream<char, std::char_traits<char> >&<br>
>>> >>>><br>
>>> >>>> std::operator<< <std::char_traits<char><br>
>>> >>>>> (std::basic_ostream<char, std::char_traits<char> >&, char<br>
>>> const*)'<br>
>>> >>>> IODebugTrack.cpp:(.text+0xc26)__: undefined reference<br>
>>> to<br>
>>> >>>> `std::basic_ostream<char, std::char_traits<char><br>
>>> >>>> >::operator<<(unsigned long)'<br>
>>> >>>> IODebugTrack.cpp:(.text+0xc33)__: undefined reference<br>
>>> to<br>
>>> >>>> `std::basic_ostream<char, std::char_traits<char> >&<br>
>>> >>>><br>
>>> >>>> std::operator<< <std::char_traits<char><br>
>>> >>>>> (std::basic_ostream<char, std::char_traits<char> >&, char<br>
>>> const*)'<br>
>>> >>>> IODebugTrack.cpp:(.text+0xc38)__: undefined reference<br>
>>> to<br>
>>> >>>> `std::basic_ostream<char, std::char_traits<char> >&<br>
>>> >>>><br>
>>> >>>> std::endl<char, std::char_traits<char><br>
>>> >(std::basic_ostream<char,<br>
>>> >>>> std::char_traits<char> >&)'<br>
>>> >>>> IODebugTrack.cpp:(.text+0xc40)__: undefined reference<br>
>>> to<br>
>>> >>>> `std::basic_ostream<char, std::char_traits<char><br>
>>> >>>> >::operator<<(std::basic___ostream<char,<br>
>>> std::char_traits<char><br>
>>> >>>>> & (*)(std::basic_ostream<char,<br>
>>> >>>> std::char_traits<char> >&))'<br>
>>> >>>> IODebugTrack.cpp:(.text+0xc50)__: undefined reference<br>
>>> to<br>
>>> >>>> `std::basic_ostream<char, std::char_traits<char><br>
>>> >>>> >::flush()'<br>
>>> >>>><br>
>>> >>>><br>
>>> /home/amirreza/Amirreza/moab-__4.6.0/gcc/lib/libMOAB.a(__IODebugTrack.o): In<br>
>>> >>>> function<br>
>>> >>>> `moab::IODebugTrack::all___reduce()':<br>
>>> >>>> IODebugTrack.cpp:(.text+0xd08)__: undefined reference<br>
>>> to<br>
>>> >>>> `MPI_Comm_size'<br>
>>> >>>> IODebugTrack.cpp:(.text+0xdfe)__: undefined reference<br>
>>> to<br>
>>> >>>> `MPI_Gather'<br>
>>> >>>> IODebugTrack.cpp:(.text+__0x1080): undefined reference<br>
>>> to<br>
>>> >>>> `MPI_Gatherv'<br>
>>> >>>><br>
>>> >>>><br>
>>> /home/amirreza/Amirreza/moab-__4.6.0/gcc/lib/libMOAB.a(__IODebugTrack.o): In<br>
>>> >>>> function<br>
>>> >>>> `__static_initialization_and___destruction_0(int,<br>
>>> int)':<br>
>>> >>>> IODebugTrack.cpp:(.text+__0x1221): undefined reference<br>
>>> to<br>
>>> >>>> `std::ios_base::Init::Init()'<br>
>>> >>>> IODebugTrack.cpp:(.text+__0x1226): undefined reference<br>
>>> to<br>
>>> >>>> `std::ios_base::Init::~Init()'<br>
>>> >>>><br>
>>> >>>><br>
>>> /home/amirreza/Amirreza/moab-__4.6.0/gcc/lib/libMOAB.a(__IODebugTrack.o): In<br>
>>> >>>> function<br>
>>> >>>> `std::list<moab::IODebugTrack:__:DRange,<br>
>>> >>>> std::allocator<moab::__IODebugTrack::DRange><br>
>>> >>>>><br>
>>> ::_M_insert(std::_List___iterator<moab::IODebugTrack::__DRange>,<br>
>>> >>>> moab::IODebugTrack::DRange const&)':<br>
>>> >>>><br>
>>> >>>><br>
>>><br>
>>> IODebugTrack.cpp:(.text.___ZNSt4listIN4moab12IODebugTrack__6DRangeESaIS2_EE9_M___insertESt14_List_iteratorIS2___ERKS2_[std::list<moab::__IODebugTrack::DRange,<br>
>>> >>>> std::allocator<moab::__IODebugTrack::DRange><br>
>>> >>>>><br>
>>> ::_M_insert(std::_List___iterator<moab::IODebugTrack::__DRange>,<br>
>>> >>>><br>
>>> >>>> moab::IODebugTrack::DRange const&)]+0x3a): undefined<br>
>>> reference to<br>
>>> >>>><br>
>>> >>>><br>
>>> `std::__detail::_List_node___base::_M_hook(std::__detail::___List_node_base*)'<br>
>>> >>>><br>
>>> >>>><br>
>>> /home/amirreza/Amirreza/moab-__4.6.0/gcc/lib/libMOAB.a(__IODebugTrack.o): In<br>
>>> >>>> function<br>
>>> >>>><br>
>>> >>>><br>
>>> `__gnu_cxx::new_allocator<std:__:_List_node<moab::__IODebugTrack::DRange><br>
>>> >>>><br>
>>> >::deallocate(std::_List_node<__moab::IODebugTrack::DRange>*,<br>
>>> >>>> unsigned long)':<br>
>>> >>>><br>
>>> >>>><br>
>>><br>
>>> IODebugTrack.cpp:(.text._ZN9____gnu_cxx13new_allocatorISt10___List___nodeIN4moab12IODebugTrack6DRan__geEEE10deallocateEPS5_m[__gnu___cxx::new_allocator<std::_List___node<moab::IODebugTrack::__DRange><br>
>>> >>>><br>
>>> >::deallocate(std::_List_node<__moab::IODebugTrack::DRange>*,<br>
>>> >>>> unsigned long)]+0x1c): undefined reference to<br>
>>> >>>> `operator<br>
>>> >>>> delete(void*)'<br>
>>> >>>><br>
>>> >>>><br>
>>> /home/amirreza/Amirreza/moab-__4.6.0/gcc/lib/libMOAB.a(__IODebugTrack.o): In<br>
>>> >>>> function<br>
>>> >>>><br>
>>> >>>><br>
>>> `__gnu_cxx::new_allocator<__moab::IODebugTrack::DRange>::__allocate(unsigned<br>
>>> >>>> long, void const*)':<br>
>>> >>>><br>
>>> >>>><br>
>>><br>
>>> IODebugTrack.cpp:(.text._ZN9____gnu_cxx13new___allocatorIN4moab12IODebugTrack__6DRangeEE8allocateEmPKv[__gnu___cxx::new_allocator<moab::__IODebugTrack::DRange>::__allocate(unsigned<br>
>>> >>>><br>
>>> >>>> long, void const*)]+0x2c): undefined reference to<br>
>>> >>>> `std::__throw_bad_alloc()'<br>
>>> >>>><br>
>>> >>>><br>
>>><br>
>>> IODebugTrack.cpp:(.text._ZN9____gnu_cxx13new___allocatorIN4moab12IODebugTrack__6DRangeEE8allocateEmPKv[__gnu___cxx::new_allocator<moab::__IODebugTrack::DRange>::__allocate(unsigned<br>
>>> >>>><br>
>>> >>>> long, void const*)]+0x45): undefined reference to<br>
>>> `operator<br>
>>> >>>> new(unsigned long)'<br>
>>> >>>><br>
>>> >>>><br>
>>> /home/amirreza/Amirreza/moab-__4.6.0/gcc/lib/libMOAB.a(__IODebugTrack.o): In<br>
>>> >>>> function<br>
>>> >>>><br>
>>> >>>><br>
>>> `__gnu_cxx::new_allocator<__moab::IODebugTrack::DRange>::__deallocate(moab::IODebugTrack:__:DRange*,<br>
>>> >>>> unsigned<br>
>>> >>>> long)':<br>
>>> >>>><br>
>>> >>>><br>
>>><br>
>>> IODebugTrack.cpp:(.text._ZN9____gnu_cxx13new___allocatorIN4moab12IODebugTrack__6DRangeEE10deallocateEPS3_m[____gnu_cxx::new_allocator<moab::__IODebugTrack::DRange>::__deallocate(moab::IODebugTrack:__:DRange*,<br>
>>> >>>><br>
>>> >>>> unsigned long)]+0x1c): undefined reference to<br>
>>> `operator<br>
>>> >>>> delete(void*)'<br>
>>> >>>><br>
>>> >>>><br>
>>> /home/amirreza/Amirreza/moab-__4.6.0/gcc/lib/libMOAB.a(__IODebugTrack.o): In<br>
>>> >>>> function<br>
>>> >>>><br>
>>> >>>><br>
>>> `__gnu_cxx::new_allocator<std:__:_List_node<moab::__IODebugTrack::DRange><br>
>>> >>>>> ::allocate(unsigned long, void const*)':<br>
>>> >>>><br>
>>> >>>><br>
>>><br>
>>> IODebugTrack.cpp:(.text._ZN9____gnu_cxx13new_allocatorISt10___List___nodeIN4moab12IODebugTrack6DRan__geEEE8allocateEmPKv[__gnu_cxx:__:new_allocator<std::_List___node<moab::IODebugTrack::__DRange><br>
>>> >>>><br>
>>> >>>> >::allocate(unsigned long, void const*)]+0x2c):<br>
>>> undefined<br>
>>> >>>> reference to `std::__throw_bad_alloc()'<br>
>>> >>>><br>
>>> >>>><br>
>>><br>
>>> IODebugTrack.cpp:(.text._ZN9____gnu_cxx13new_allocatorISt10___List___nodeIN4moab12IODebugTrack6DRan__geEEE8allocateEmPKv[__gnu_cxx:__:new_allocator<std::_List___node<moab::IODebugTrack::__DRange><br>
>>> >>>><br>
>>> >>>> >::allocate(unsigned long, void const*)]+0x46):<br>
>>> undefined<br>
>>> >>>> reference to `operator new(unsigned long)'<br>
>>> >>>><br>
>>> >>>><br>
>>> /home/amirreza/Amirreza/moab-__4.6.0/gcc/lib/libMOAB.a(__IODebugTrack.o):(.eh_frame+__0x24b):<br>
>>> >>>> undefined reference to<br>
>>> >>>> `__gxx_personality_v0'<br>
>>> >>>><br>
>>> >>>><br>
>>> /home/amirreza/Amirreza/moab-__4.6.0/gcc/lib/libMOAB.a(__OrientedBox.o): In<br>
>>> >>>> function<br>
>>> >>>> `moab::operator<<(std::basic___ostream<char,<br>
>>> >>>> std::char_traits<char> >&, moab::OrientedBox const&)':<br>
>>> >>>><br>
>>> >>>> OrientedBox.cpp:(.text+0x97): undefined reference to<br>
>>> >>>> `std::basic_ostream<char, std::char_traits<char> >&<br>
>>> >>>> std::operator<<<br>
>>> >>>> <std::char_traits<char> >(std::basic_ostream<char,<br>
>>> >>>> std::char_traits<char> >&, char const*)'<br>
>>> >>>> OrientedBox.cpp:(.text+0xaf): undefined reference to<br>
>>> >>>> `std::basic_ostream<char, std::char_traits<char> >&<br>
>>> >>>> std::operator<<<br>
>>> >>>> <std::char_traits<char> >(std::basic_ostream<char,<br>
>>> >>>> std::char_traits<char> >&, char const*)'<br>
>>> >>>> OrientedBox.cpp:(.text+0xbc): undefined reference to<br>
>>> >>>> `std::basic_ostream<char, std::char_traits<char><br>
>>> >>>> >::operator<<(double)'<br>
>>> >>>> OrientedBox.cpp:(.text+0xc9): undefined reference to<br>
>>> >>>> `std::basic_ostream<char, std::char_traits<char> >&<br>
>>> >>>> std::operator<<<br>
>>> >>>> <std::char_traits<char> >(std::basic_ostream<char,<br>
>>> >>>> std::char_traits<char> >&, char const*)'<br>
>>> >>>> OrientedBox.cpp:(.text+0xe1): undefined reference to<br>
>>> >>>> `std::basic_ostream<char, std::char_traits<char> >&<br>
>>> >>>> std::operator<<<br>
>>> >>>> <std::char_traits<char> >(std::basic_ostream<char,<br>
>>> >>>> std::char_traits<char> >&, char const*)'<br>
>>> >>>> OrientedBox.cpp:(.text+0xee): undefined reference to<br>
>>> >>>> `std::basic_ostream<char, std::char_traits<char><br>
>>> >>>> >::operator<<(double)'<br>
>>> >>>> OrientedBox.cpp:(.text+0xfb): undefined reference to<br>
>>> >>>> `std::basic_ostream<char, std::char_traits<char> >&<br>
>>> >>>> std::operator<<<br>
>>> >>>> <std::char_traits<char> >(std::basic_ostream<char,<br>
>>> >>>> std::char_traits<char> >&, char const*)'<br>
>>> >>>> OrientedBox.cpp:(.text+0x113): undefined reference to<br>
>>> >>>> `std::basic_ostream<char, std::char_traits<char> >&<br>
>>> >>>> std::operator<< <std::char_traits<char><br>
>>> >>>>> (std::basic_ostream<char, std::char_traits<char> >&, char<br>
>>> const*)'<br>
>>> >>>> OrientedBox.cpp:(.text+0x120): undefined reference to<br>
>>> >>>> `std::basic_ostream<char, std::char_traits<char><br>
>>> >>>> >::operator<<(double)'<br>
>>> >>>><br>
>>> >>>><br>
>>> /home/amirreza/Amirreza/moab-__4.6.0/gcc/lib/libMOAB.a(__OrientedBox.o): In<br>
>>> >>>> function<br>
>>> >>>> `__static_initialization_and___destruction_0(int,<br>
>>> int)':<br>
>>> >>>> OrientedBox.cpp:(.text+0x3aaf)__: undefined reference<br>
>>> to<br>
>>> >>>> `std::ios_base::Init::Init()'<br>
>>> >>>> OrientedBox.cpp:(.text+0x3ab4)__: undefined reference<br>
>>> to<br>
>>> >>>> `std::ios_base::Init::~Init()'<br>
>>> >>>><br>
>>> >>>><br>
>>> /home/amirreza/Amirreza/moab-__4.6.0/gcc/lib/libMOAB.a(__OrientedBox.o): In<br>
>>> >>>> function `moab::ErrorCode<br>
>>> >>>> moab::EigenDecomp<moab::__Matrix3,<br>
>>> moab::CartVect>(moab::Matrix3<br>
>>> >>>> const&, double*, moab::CartVect*)':<br>
>>> >>>><br>
>>> >>>><br>
>>><br>
>>> OrientedBox.cpp:(.text.___ZN4moab11EigenDecompINS___7Matrix3ENS_8CartVectEEENS___9ErrorCodeERKT_PdPT0_[moab::__ErrorCode<br>
>>> >>>> moab::EigenDecomp<moab::__Matrix3,<br>
>>> moab::CartVect>(moab::Matrix3<br>
>>> >>>> const&, double*, moab::CartVect*)]+0xb7f):<br>
>>> >>>><br>
>>> >>>> undefined<br>
>>> >>>> reference to `std::cerr'<br>
>>> >>>><br>
>>> >>>><br>
>>><br>
>>> OrientedBox.cpp:(.text.___ZN4moab11EigenDecompINS___7Matrix3ENS_8CartVectEEENS___9ErrorCodeERKT_PdPT0_[moab::__ErrorCode<br>
>>> >>>> moab::EigenDecomp<moab::__Matrix3,<br>
>>> moab::CartVect>(moab::Matrix3<br>
>>> >>>> const&, double*, moab::CartVect*)]+0xb84):<br>
>>> >>>><br>
>>> >>>> undefined<br>
>>> >>>> reference to `std::basic_ostream<char,<br>
>>> std::char_traits<char> >&<br>
>>> >>>> std::operator<< <std::char_traits<char><br>
>>> >>>> >(std::basic_ostream<char, std::char_traits<char><br>
>>> >&, char<br>
>>> >>>> const*)'<br>
>>> >>>><br>
>>> >>>><br>
>>><br>
>>> OrientedBox.cpp:(.text.___ZN4moab11EigenDecompINS___7Matrix3ENS_8CartVectEEENS___9ErrorCodeERKT_PdPT0_[moab::__ErrorCode<br>
>>> >>>> moab::EigenDecomp<moab::__Matrix3,<br>
>>> moab::CartVect>(moab::Matrix3<br>
>>> >>>> const&, double*, moab::CartVect*)]+0xb89):<br>
>>> >>>><br>
>>> >>>> undefined<br>
>>> >>>> reference to `std::basic_ostream<char,<br>
>>> std::char_traits<char> >&<br>
>>> >>>> std::endl<char, std::char_traits<char><br>
>>> >>>> >(std::basic_ostream<char, std::char_traits<char><br>
>>> >&)'<br>
>>> >>>><br>
>>> >>>><br>
>>><br>
>>> OrientedBox.cpp:(.text.___ZN4moab11EigenDecompINS___7Matrix3ENS_8CartVectEEENS___9ErrorCodeERKT_PdPT0_[moab::__ErrorCode<br>
>>> >>>> moab::EigenDecomp<moab::__Matrix3,<br>
>>> moab::CartVect>(moab::Matrix3<br>
>>> >>>> const&, double*, moab::CartVect*)]+0xb91):<br>
>>> >>>> undefined<br>
>>> >>>> reference to `std::basic_ostream<char,<br>
>>> std::char_traits<char><br>
>>> >>>>> ::operator<<(std::basic___ostream<char,<br>
>>> >>>><br>
>>> >>>> std::char_traits<char> >& (*)(std::basic_ostream<char,<br>
>>> >>>> std::char_traits<char> >&))'<br>
>>> >>>><br>
>>> >>>><br>
>>> /home/amirreza/Amirreza/moab-__4.6.0/gcc/lib/libMOAB.a(__OrientedBox.o):(.eh_frame+__0x22f):<br>
>>> >>>> undefined reference to<br>
>>> >>>><br>
>>> >>>> `__gxx_personality_v0'<br>
>>> >>>> collect2: ld returned 1 exit status<br>
>>> >>>> make: *** [nek5000] Error 1<br>
>>> >>>><br>
>>> >>>> Thanks,<br>
>>> >>>> Ami<br>
>>> >>>><br>
>>> >>>><br>
>>> >>>> _________________________________________________<br>
>>> >>>> Nek5000-users mailing list<br>
>>> >>>> Nek5000-users@lists.mcs.anl.__gov<br>
>>> >>>> <mailto:<a href="mailto:Nek5000-users@lists.mcs.anl.gov">Nek5000-users@lists.mcs.anl.gov</a>><br>
>>> >>>><br>
>>> <a href="https://lists.mcs.anl.gov/__mailman/listinfo/nek5000-users" target="_blank">https://lists.mcs.anl.gov/__mailman/listinfo/nek5000-users</a><br>
>>> >>>><br>
>>> <<a href="https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users" target="_blank">https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users</a>><br>
>>> >>>><br>
>>> >>>><br>
>>> >>>> --<br>
>>> >>>><br>
>>> ==============================__==============================__====<br>
>>> >>>><br>
>>> >>>> "You will keep in perfect peace him whose mind is<br>
>>> >>>> steadfast, because he trusts in you."<br>
>>> Isaiah 26:3<br>
>>> >>>><br>
>>> >>>> Tim Tautges Argonne National<br>
>>> Laboratory<br>
>>> >>>> (<a href="mailto:tautges@mcs.anl.gov">tautges@mcs.anl.gov</a><br>
>>> <mailto:<a href="mailto:tautges@mcs.anl.gov">tautges@mcs.anl.gov</a>>)<br>
>>> >>>> (telecommuting from UW-Madison)<br>
>>> >>>> phone (gvoice): <a href="tel:%28608%29%20354-1459" value="+16083541459">(608) 354-1459</a><br>
>>> <tel:%28608%29%20354-1459> 1500<br>
>>> >>>> Engineering Dr.<br>
>>> >>>> fax: <a href="tel:%28608%29%20263-4499" value="+16082634499">(608) 263-4499</a><br>
>>> <tel:%28608%29%20263-4499><br>
>>> >>>> Madison, WI 53706<br>
>>> >>>><br>
>>> >>>> _________________________________________________<br>
>>> >>>> Nek5000-users mailing list<br>
>>> >>>> Nek5000-users@lists.mcs.anl.__gov<br>
>>> >>>> <mailto:<a href="mailto:Nek5000-users@lists.mcs.anl.gov">Nek5000-users@lists.mcs.anl.gov</a>><br>
>>> >>>> <a href="https://lists.mcs.anl.gov/__mailman/listinfo/nek5000-users" target="_blank">https://lists.mcs.anl.gov/__mailman/listinfo/nek5000-users</a><br>
>>> >>>> <<a href="https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users" target="_blank">https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users</a>><br>
>>> >>>><br>
>>> >>>><br>
>>> >>>><br>
>>> >>>><br>
>>> >>>><br>
>>> >>>> _______________________________________________<br>
>>> >>>> Nek5000-users mailing list<br>
>>> >>>> <a href="mailto:Nek5000-users@lists.mcs.anl.gov">Nek5000-users@lists.mcs.anl.gov</a><br>
>>> >>>> <a href="https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users" target="_blank">https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users</a><br>
>>> >>>><br>
>>> >>><br>
>>> >>> --<br>
>>> >>> ================================================================<br>
>>> >>> "You will keep in perfect peace him whose mind is<br>
>>> >>> steadfast, because he trusts in you." Isaiah<br>
>>> 26:3<br>
>>> >>><br>
>>> >>> Tim Tautges Argonne National Laboratory<br>
>>> >>> (<a href="mailto:tautges@mcs.anl.gov">tautges@mcs.anl.gov</a>) (telecommuting from<br>
>>> UW-Madison)<br>
>>> >>> phone (gvoice): <a href="tel:%28608%29%20354-1459" value="+16083541459">(608) 354-1459</a> 1500 Engineering Dr.<br>
>>> >>> fax: <a href="tel:%28608%29%20263-4499" value="+16082634499">(608) 263-4499</a> Madison, WI 53706<br>
>>> >>><br>
>>> >>> _______________________________________________<br>
>>> >>> Nek5000-users mailing list<br>
>>> >>> <a href="mailto:Nek5000-users@lists.mcs.anl.gov">Nek5000-users@lists.mcs.anl.gov</a><br>
>>> >>> <a href="https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users" target="_blank">https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users</a><br>
>>> >><br>
>>> >><br>
>>> >><br>
>>> >> _______________________________________________<br>
>>> >> Nek5000-users mailing list<br>
>>> >> <a href="mailto:Nek5000-users@lists.mcs.anl.gov">Nek5000-users@lists.mcs.anl.gov</a><br>
>>> >> <a href="https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users" target="_blank">https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users</a><br>
>>> >><br>
>>> ><br>
>>><br>
>>> --<br>
>>> ================================================================<br>
>>> "You will keep in perfect peace him whose mind is<br>
>>> steadfast, because he trusts in you." Isaiah 26:3<br>
>>><br>
>>> Tim Tautges Argonne National Laboratory<br>
>>> (<a href="mailto:tautges@mcs.anl.gov">tautges@mcs.anl.gov</a>) (telecommuting from UW-Madison)<br>
>>> phone (gvoice): <a href="tel:%28608%29%20354-1459" value="+16083541459">(608) 354-1459</a> 1500 Engineering Dr.<br>
>>> fax: <a href="tel:%28608%29%20263-4499" value="+16082634499">(608) 263-4499</a> Madison, WI 53706<br>
>>><br>
>>><br>
>><br>
>> --<br>
>> ================================================================<br>
>> "You will keep in perfect peace him whose mind is<br>
>> steadfast, because he trusts in you." Isaiah 26:3<br>
>><br>
>> Tim Tautges Argonne National Laboratory<br>
>> (<a href="mailto:tautges@mcs.anl.gov">tautges@mcs.anl.gov</a>) (telecommuting from UW-Madison)<br>
>> phone (gvoice): <a href="tel:%28608%29%20354-1459" value="+16083541459">(608) 354-1459</a> 1500 Engineering Dr.<br>
>> fax: <a href="tel:%28608%29%20263-4499" value="+16082634499">(608) 263-4499</a> Madison, WI 53706<br>
>><br>
>> _______________________________________________<br>
>> Nek5000-users mailing list<br>
>> <a href="mailto:Nek5000-users@lists.mcs.anl.gov">Nek5000-users@lists.mcs.anl.gov</a><br>
>> <a href="https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users" target="_blank">https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users</a><br>
><br>
><br>
><br>
> _______________________________________________<br>
> Nek5000-users mailing list<br>
> <a href="mailto:Nek5000-users@lists.mcs.anl.gov">Nek5000-users@lists.mcs.anl.gov</a><br>
> <a href="https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users" target="_blank">https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users</a><br>
><br>
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</div></div></blockquote></div><br></div>