September 2013 - Nek5000-users - mailman3.cels.anl.gov

Re: [Nek5000-users] Vorticity
by nek5000-users＠lists.mcs.anl.gov 11 Oct '16

11 Oct '16

Hi, Thanks for your quick reply. Just I wanna know if I can use the interpolated values of velocity at some arbitrary points in the domain (not necessarily the grid points) as the input arguments to theses subroutines. Regards, Alireza Quoting nek5000-users-request(a)lists.mcs.anl.gov: > Send Nek5000-users mailing list submissions to > nek5000-users(a)lists.mcs.anl.gov > > To subscribe or unsubscribe via the World Wide Web, visit > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > or, via email, send a message with subject or body 'help' to > nek5000-users-request(a)lists.mcs.anl.gov > > You can reach the person managing the list at > nek5000-users-owner(a)lists.mcs.anl.gov > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Nek5000-users digest..." > > > Today's Topics: > > 1. Vorticity (nek5000-users(a)lists.mcs.anl.gov) > 2. Re: Vorticity (nek5000-users(a)lists.mcs.anl.gov) > 3. Re: Vorticity (nek5000-users(a)lists.mcs.anl.gov) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 13 Jul 2011 17:55:35 -0400 > From: nek5000-users(a)lists.mcs.anl.gov > Subject: [Nek5000-users] Vorticity > To: nek5000-users(a)lists.mcs.anl.gov > Message-ID: <20110713175535.1042430oct81vz2v(a)webmail.vt.edu> > Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes"; > format="flowed" > > Hi, > > I need to calculate the vorticity vector and the rate of strain tensor > at any arbitrary point in the domain. I wonder if these values are > computed somewhere in the code or if I should interpolate them in the > usr file. I appreciate any kind of help. > > Thanks in advance, > > > Regards, > Alireza Karimi > > > > ------------------------------ > > Message: 2 > Date: Wed, 13 Jul 2011 17:09:48 -0500 (CDT) > From: nek5000-users(a)lists.mcs.anl.gov > Subject: Re: [Nek5000-users] Vorticity > To: nek5000-users(a)lists.mcs.anl.gov > Message-ID: <Pine.LNX.4.64.1107131704140.26989(a)jacobi.mcs.anl.gov> > Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed > > Hi Alireza, > > For vorticity computation, you can call > > call comp_vort3(vort,work1,work2,vx,vy,vz) > > from userchk with the appropriate definitions of vorticity and work arrays > like > > common /scren/ vort (lx1,ly1,lz1,lelv,3) ! x y z components > $ , work1(lx1,ly1,lz1,lelv) > $ , work2(lx1,ly1,lz1,lelv) > > Let me check what we have for the calculation of strain tensor. > Best, > Aleks > > > On Wed, 13 Jul 2011, nek5000-users(a)lists.mcs.anl.gov wrote: > >> Hi, >> >> I need to calculate the vorticity vector and the rate of strain >> tensor at any >> arbitrary point in the domain. I wonder if these values are computed >> somewhere in the code or if I should interpolate them in the usr file. I >> appreciate any kind of help. >> >> Thanks in advance, >> >> >> Regards, >> Alireza Karimi >> >> _______________________________________________ >> Nek5000-users mailing list >> Nek5000-users(a)lists.mcs.anl.gov >> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > > ------------------------------ > > Message: 3 > Date: Wed, 13 Jul 2011 23:59:08 -0500 (CDT) > From: nek5000-users(a)lists.mcs.anl.gov > Subject: Re: [Nek5000-users] Vorticity > To: nek5000-users(a)lists.mcs.anl.gov > Message-ID: > <600285192.94128.1310619548370.JavaMail.root(a)zimbra.anl.gov> > Content-Type: text/plain; charset=utf-8 > > Hi Alireza, > > > For a strain stress computation you can call subroutine comp_sij > > call comp_sij(sij,nij,vx,vy,vz > $ ,ur,us,ut,vr,vs,vt,wr,ws,wt) > > > (navier5.f:2225) with nij=6 for 3D somewhere from userchk once you > declare the stress component array sij and arrays with local > coordinate r-s-t derivatives of velocity components > > common /csij/ > $ sij(lx1*ly1*lz1,6,lelv) ! 6 components > $ ,ur (lx1*ly1*lz1) > ... > $ ,wt (lx1*ly1*lz1) > > > Best, > Aleks > > > > > > > ----- Original Message ----- > From: nek5000-users(a)lists.mcs.anl.gov > To: nek5000-users(a)lists.mcs.anl.gov > Sent: Wednesday, July 13, 2011 5:09:48 PM > Subject: Re: [Nek5000-users] Vorticity > > Hi Alireza, > > For vorticity computation, you can call > > call comp_vort3(vort,work1,work2,vx,vy,vz) > > from userchk with the appropriate definitions of vorticity and work arrays > like > > common /scren/ vort (lx1,ly1,lz1,lelv,3) ! x y z components > $ , work1(lx1,ly1,lz1,lelv) > $ , work2(lx1,ly1,lz1,lelv) > > Let me check what we have for the calculation of strain tensor. > Best, > Aleks > > > On Wed, 13 Jul 2011, nek5000-users(a)lists.mcs.anl.gov wrote: > >> Hi, >> >> I need to calculate the vorticity vector and the rate of strain >> tensor at any >> arbitrary point in the domain. I wonder if these values are computed >> somewhere in the code or if I should interpolate them in the usr file. I >> appreciate any kind of help. >> >> Thanks in advance, >> >> >> Regards, >> Alireza Karimi >> >> _______________________________________________ >> Nek5000-users mailing list >> Nek5000-users(a)lists.mcs.anl.gov >> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > _______________________________________________ > Nek5000-users mailing list > Nek5000-users(a)lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > > ------------------------------ > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users(a)lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > > End of Nek5000-users Digest, Vol 29, Issue 2 > ******************************************** > -- Alireza Karimi PhD Candidate Department of Engineering Science and Mechanics Virginia Polytechnic Institute and State University Blacksburg, VA 24061

1 3

Error in generalev
by nek5000-users＠lists.mcs.anl.gov 02 Jul '14

02 Jul '14

Hello Neks, I've recently come across an error I haven't seen before. It occurs in the routine "generalev" at the beginning of my run. It looks like the matrix "a" and "b" being fed to the routine have an Infinity or NaN at position (0,0). Are there any ideas of what could cause this type of error? I have attached the logfile to this email. Thanks, -- Josh Camp "All that is necessary for the triumph of evil is that good men do nothing" -- Edmund Burke

1 11

Linearized Nek: Compute only the right-hand side
by nek5000-users＠lists.mcs.anl.gov 21 Jan '14

21 Jan '14

Hi Nek's, Given a random initial vector u and the Jacobian matrix of the linearized Navier-Stokes, I would like to calculate the matrix-vector product J * u. In Nek, that would consists in calculating only the right hand side of the equations, that is: RHS = ( -U.grad(u) - u.grad(U) - grad(p) + 1/Re Lap(u) ; div(u) ) I have a few questions on how to compute those different terms in userchk (Nek is used in post-process mode): - I would tend to use convop() for the convection terms, however I'm not sure whereas it would output the strong or weak form (and I need the strong one obviously)? - Same question regarding grad(p) and div(u) if I use opgradt() and opdiv() to calculate them? Last but not least, for the Laplacian I've read a previous mail where it is said that it can be computed using a sequence of wgradm1() and vec_dssum() so I guess I kown how to compute at the strong form for it. Sincerely, -- Jean-Christophe

1 4

neuman bc for the normal velocity component
by nek5000-users＠lists.mcs.anl.gov 23 Oct '13

23 Oct '13

Dear Nekians, I'm relatively new to nek. I would like to compute the flow of a boundary layer and I would like to impose the following boundary condition on the top (2D) boundary, which is parallel to the wall: u = U_base and dv/dy = - dU_base/dx, where U_base is the known inviscid base flow. The velocity component u is parallel to the boundary, whereas v is normal. I tried to use 'ON ' but this did not give the result I was expecting (Am I doing smth. wrong?). At the boundary nodes u was equal to U_base, but at the very next node u was completly different (and v was of course completly wrong). Thanks for any help Joris

1 4

Compilation Error on BG/Q
by nek5000-users＠lists.mcs.anl.gov 15 Oct '13

15 Oct '13

Hi neks! On the BG/Q in Jï¿½lich we encounter several errors while compiling nek5000 (Revision: 853). Please find attached the compiler output, the makenek script and the makefile. The installed compiler versions are "IBM XL C/C++ for Blue Gene, V12.1" and "IBM XL Fortran for Blue Gene, V14.1". Did you come across similar problems on your BG/Q runs? Do you have any hint how I can fix this? Thanks in advance Fabian

1 5

ParaView with Nek5000
by nek5000-users＠lists.mcs.anl.gov 25 Sep '13

25 Sep '13

Dear Nek users, I'm trying to use ParaView 3.98 in order to visualize the results of a Nek5000 simulation. Starting from the output files .fld, I first create the metatada file .nek5000 (the same which can be used with VisIt). When I open this file in Paraview 3.98 all the .fld files are loaded, but the problem is that I can see only the first of these files, while the others are not visualized. Can anyone explain me the procedure to solve this problem? Thanks a lot. Matteo

1 3

Re: [Nek5000-users] Running MOAB example
by nek5000-users＠lists.mcs.anl.gov 13 Sep '13

13 Sep '13

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(a)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(a)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(a)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(a)lists.mcs.anl.gov > >>>> <mailto:[email protected]>> 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(a)lists.mcs.anl.__gov > >>>> <mailto:[email protected]> 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(a)lists.mcs.anl.__gov > >>>> <mailto:[email protected]> > >>>> 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(a)mcs.anl.gov <mailto:[email protected]>) > >>>> (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(a)lists.mcs.anl.__gov > >>>> <mailto:[email protected]> > >>>> https://lists.mcs.anl.gov/__mailman/listinfo/nek5000-users > >>>> <https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users> > >>>> > >>>> > >>>> > >>>> > >>>> > >>>> _______________________________________________ > >>>> Nek5000-users mailing list > >>>> Nek5000-users(a)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(a)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(a)lists.mcs.anl.gov > >>> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > >> > >> > >> > >> _______________________________________________ > >> Nek5000-users mailing list > >> Nek5000-users(a)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(a)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(a)mcs.anl.gov) (telecommuting from UW-Madison) phone (gvoice): (608) 354-1459 1500 Engineering Dr. fax: (608) 263-4499 Madison, WI 53706

1 5

Re: [Nek5000-users] Running MOAB example
by nek5000-users＠lists.mcs.anl.gov 11 Sep '13

11 Sep '13

> http://ftp.mcs.anl.gov/pub/fathom/moab-4.6-nightly.tar.gz > > Is this what they need? Yes. But can you also replace the link to moab-4.6.0.tar.gz with the nightly and rename with a patch number like: 4.6.1. That should give better tractability for future version related queries. Vijay On Wed, Sep 11, 2013 at 12:10 PM, Iulian Grindeanu <iulian(a)mcs.anl.gov> 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? > > 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(a)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(a)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(a)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(a)lists.mcs.anl.gov >>>>> <mailto:[email protected]>> 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(a)lists.mcs.anl.__gov >>>>> <mailto:[email protected]> 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(a)lists.mcs.anl.__gov >>>>> <mailto:[email protected]> >>>>> 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(a)mcs.anl.gov <mailto:[email protected]>) >>>>> (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(a)lists.mcs.anl.__gov >>>>> <mailto:[email protected]> >>>>> https://lists.mcs.anl.gov/__mailman/listinfo/nek5000-users >>>>> <https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> _______________________________________________ >>>>> Nek5000-users mailing list >>>>> Nek5000-users(a)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(a)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(a)lists.mcs.anl.gov >>>> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >>> >>> >>> >>> _______________________________________________ >>> Nek5000-users mailing list >>> Nek5000-users(a)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(a)mcs.anl.gov) (telecommuting from UW-Madison) > phone (gvoice): (608) 354-1459 1500 Engineering Dr. > fax: (608) 263-4499 Madison, WI 53706 > >

1 0

Re: [Nek5000-users] Running MOAB example
by nek5000-users＠lists.mcs.anl.gov 11 Sep '13

11 Sep '13

1 0

Re: [Nek5000-users] Running MOAB example
by nek5000-users＠lists.mcs.anl.gov 11 Sep '13

11 Sep '13

Aha, good catch. Iulian, could you backport the imesh_freememory function? Thanks. - 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(a)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(a)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(a)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(a)lists.mcs.anl.gov >>>> <mailto:[email protected]>> 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(a)lists.mcs.anl.__gov >>>> <mailto:[email protected]> 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(a)lists.mcs.anl.__gov >>>> <mailto:[email protected]> >>>> 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(a)mcs.anl.gov <mailto:[email protected]>) >>>> (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(a)lists.mcs.anl.__gov >>>> <mailto:[email protected]> >>>> https://lists.mcs.anl.gov/__mailman/listinfo/nek5000-users >>>> <https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users> >>>> >>>> >>>> >>>> >>>> >>>> _______________________________________________ >>>> Nek5000-users mailing list >>>> Nek5000-users(a)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(a)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(a)lists.mcs.anl.gov >>> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >> >> >> >> _______________________________________________ >> Nek5000-users mailing list >> Nek5000-users(a)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(a)mcs.anl.gov) (telecommuting from UW-Madison) phone (gvoice): (608) 354-1459 1500 Engineering Dr. fax: (608) 263-4499 Madison, WI 53706

1 0