From: Vinicius C. R. <vin...@co...> - 2018-06-05 19:04:18
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Sorry about that, I should have imagined... Well, exception and stack trace from a fresh run in the text dump below. I managed to reproduce it in a quite smaller code, what would be the best way to share, paste it into an email or through git repository? Thanks, VCR ------------------------------------------------------------ -------------------------------------------------- exception /usr/include/c++/5/debug/vector:409:error: attempt to subscript container with out-of-bounds index 0, but container only holds 0 elements. Objects involved in the operation: sequence "this" @ 0x0x7ffd71e0cd70 { type = NSt7__debug6vectorIjSaIjEEE; } [jurenux:04135] *** Process received signal *** [jurenux:04135] Signal: Aborted (6) [jurenux:04135] Signal code: (-6) [jurenux:04135] [ 0] /lib/x86_64-linux-gnu/libpthread.so.0(+0x11390)[ 0x7f8e82b59390] [jurenux:04135] [ 1] /lib/x86_64-linux-gnu/libc.so.6(gsignal+0x38)[ 0x7f8e7eb93428] [jurenux:04135] [ 2] /lib/x86_64-linux-gnu/libc.so. 6(abort+0x16a)[0x7f8e7eb9502a] [jurenux:04135] [ 3] /usr/lib/x86_64-linux-gnu/libstdc++.so.6(_ZNK11__gnu_ debug16_Error_formatter8_M_errorEv+0x155)[0x7f8e83306f95] [jurenux:04135] [ 4] /home/vinicius/Workspace/poisson/bin/poisson-dbg(_ ZNSt7__debug6vectorIjSaIjEEixEm+0xdc)[0x4a766e] [jurenux:04135] [ 5] /opt/libmesh/libmesh-1.2.0/lib/libmesh_dbg.so.0(+ 0x16b47fc)[0x7f8e8141e7fc] [jurenux:04135] [ 6] /opt/libmesh/libmesh-1.2.0/lib/libmesh_dbg.so.0(_ ZN7libMesh2FEILj2ELNS_8FEFamilyE0EE19compute_constraintsERNS_ 14DofConstraintsERNS_6DofMapEjPKNS_4ElemE+0x34)[0x7f8e8141f2d6] [jurenux:04135] [ 7] /opt/libmesh/libmesh-1.2.0/lib/libmesh_dbg.so.0(_ ZN7libMesh11FEInterface19compute_constraintsERNS_14DofConstraintsERNS_ 6DofMapEjPKNS_4ElemE+0x1a4)[0x7f8e813f8f62] [jurenux:04135] [ 8] /opt/libmesh/libmesh-1.2.0/lib/libmesh_dbg.so.0(+ 0x144b359)[0x7f8e811b5359] [jurenux:04135] [ 9] /opt/libmesh/libmesh-1.2.0/lib/libmesh_dbg.so.0(+ 0x146fdd6)[0x7f8e811d9dd6] [jurenux:04135] [10] /opt/libmesh/libmesh-1.2.0/lib/libmesh_dbg.so.0(+ 0x147452f)[0x7f8e811de52f] [jurenux:04135] [11] /usr/lib/x86_64-linux-gnu/libgomp.so.1(GOMP_parallel+ 0x3f)[0x7f8e7ad7fcbf] [jurenux:04135] [12] /opt/libmesh/libmesh-1.2.0/lib/libmesh_dbg.so.0(+ 0x146f491)[0x7f8e811d9491] [jurenux:04135] [13] /opt/libmesh/libmesh-1.2.0/lib/libmesh_dbg.so.0(_ ZN7libMesh6DofMap22create_dof_constraintsERKNS_8MeshBaseEd+ 0x870)[0x7f8e811b6722] [jurenux:04135] [14] /opt/libmesh/libmesh-1.2.0/lib/libmesh_dbg.so.0(_ ZN7libMesh6System18reinit_constraintsEv+0x42)[0x7f8e81b60b44] [jurenux:04135] [15] /opt/libmesh/libmesh-1.2.0/lib/libmesh_dbg.so.0(_ ZN7libMesh6System9init_dataEv+0xee)[0x7f8e81b5ffc8] [jurenux:04135] [16] /opt/libmesh/libmesh-1.2.0/lib/libmesh_dbg.so.0(_ ZN7libMesh14ExplicitSystem9init_dataEv+0x24)[0x7f8e81b27db6] [jurenux:04135] [17] /opt/libmesh/libmesh-1.2.0/lib/libmesh_dbg.so.0(_ ZN7libMesh14ImplicitSystem9init_dataEv+0x28)[0x7f8e81b475f4] [jurenux:04135] [18] /opt/libmesh/libmesh-1.2.0/lib/libmesh_dbg.so.0(_ ZN7libMesh20LinearImplicitSystem9init_dataEv+0x18)[0x7f8e81b52a2a] [jurenux:04135] [19] /opt/libmesh/libmesh-1.2.0/lib/libmesh_dbg.so.0(_ ZN7libMesh6System4initEv+0xff)[0x7f8e81b5fe89] [jurenux:04135] [20] /opt/libmesh/libmesh-1.2.0/lib/libmesh_dbg.so.0(_ ZN7libMesh15EquationSystems4initEv+0x348)[0x7f8e81b13cb6] [jurenux:04135] [21] /home/vinicius/Workspace/poisson/bin/poisson-dbg[ 0x4ca273] [jurenux:04135] [22] /lib/x86_64-linux-gnu/libc.so. 6(__libc_start_main+0xf0)[0x7f8e7eb7e830] [jurenux:04135] [23] /home/vinicius/Workspace/poisson/bin/poisson-dbg[ 0x4845e9] [jurenux:04135] *** End of error message *** ------------------------------------------------------------ -------------------------------------------------- stack __GI_raise (sig=6, sig@entry=6) __GI_abort () __gnu_debug::_Error_formatter::_M_error() const () std::__debug::vector<unsigned int, std::allocator<unsigned int> >::operator[] (this=0x7fffffffcb70, __n=0) libMesh::(anonymous namespace)::lagrange_compute_constraints (constraints=@0xb60b78: {<std::__debug::map<unsigned int, std::__debug::map<unsigned int, double, std::less<unsigned int>, libMesh::Threads::scalable_allocator<std::pair<unsigned int const, double> > >, std::less<unsigned int>, libMesh::Threads::scalable_allocator<std::pair<unsigned int const, std::__debug::map<unsigned int, double, std::less<unsigned int>, libMesh::Threads::scalable_allocator<std::pair<unsigned int const, double> > > > > >> = std::__debug::map with 0 elements, <No data fields>}, dof_map=@0xb60820: {<libMesh::ReferenceCountedObject<libMesh::DofMap>> = {<libMesh::ReferenceCounter> = {static _counts = <optimized out>, static _n_objects = {val = 0, smutex = {slock = 0}}, static _mutex = {slock = 1}, static _enable_print_counter = true}, <No data fields>}, <libMesh::ParallelObject> = {_vptr.ParallelObject = 0x7ffff704b890 <vtable for libMesh::DofMap+16>, _communicator = @0x7fffffffd6e8}, _dof_coupling = 0x0, _variables = std::__debug::vector of length 1, capacity 1 = {{_sys = 0xc26700, _name = \"u\", _active_subdomains = std::__debug::set with 2 elements, _number = 0, _first_scalar_number = 0, _type = {order = {_order = 1}, family = libMesh::LAGRANGE}}}, _variable_groups = std::__debug::vector of length 1, capacity 1 = {{<libMesh::Variable> = {_sys = 0xc26700, _name = \"var_group\", _active_subdomains = std::__debug::set with 2 elements, _number = 0, _first_scalar_number = 0, _type = {order = {_order = 1}, family = libMesh::LAGRANGE}}, _names = std::__debug::vector of length 1, capacity 1 = {\"u\"}}}, _sys_number = 0, _mesh = @0x7fffffffd9a0, _matrices = std::__debug::vector of length 0, capacity 0, _first_df = std::__debug::vector of length 1, capacity 1 = {0}, _end_df = std::__debug::vector of length 1, capacity 1 = {785}, _first_scalar_df = std::__debug::vector of length 1, capacity 1 = {4294967295}, _send_list = std::__debug::vector of length 0, capacity 0, _augment_sparsity_pattern = 0x0, _extra_sparsity_function = 0x0, _extra_sparsity_context = 0x0, _augment_send_list = 0x0, _extra_send_list_function = 0x0, _extra_send_list_context = 0x0, _default_coupling = std::unique_ptr<libMesh::DefaultCoupling> containing 0xb7ee10, _default_evaluating = std::unique_ptr<libMesh::DefaultCoupling> containing 0xb82e60, _algebraic_ghosting_functors = std::__debug::set with 1 elements, _coupling_functors = std::__debug::set with 1 elements, need_full_sparsity_pattern = false, _sp = std::unique_ptr<libMesh::SparsityPattern::Build> containing 0x0, _n_nz = 0x0, _n_oz = 0x0, _n_dfs = 785, _n_SCALAR_dofs = 0, _n_old_dfs = 0, _first_old_df = std::__debug::vector of length 0, capacity 0, _end_old_df = std::__debug::vector of length 0, capacity 0, _first_old_scalar_df = std::__debug::vector of length 0, capacity 0, _dof_constraints = {<std::__debug::map<unsigned int, std::__debug::map<unsigned int, double, std::less<unsigned int>, libMesh::Threads::scalable_allocator<std::pair<unsigned int const, double> > >, std::less<unsigned int>, libMesh::Threads::scalable_allocator<std::pair<unsigned int const, std::__debug::map<unsigned int, double, std::less<unsigned int>, libMesh::Threads::scalable_allocator<std::pair<unsigned int const, double> > > > > >> = std::__debug::map with 0 elements, <No data fields>}, _stashed_dof_constraints = {<std::__debug::map<unsigned int, std::__debug::map<unsigned int, double, std::less<unsigned int>, libMesh::Threads::scalable_allocator<std::pair<unsigned int const, double> > >, std::less<unsigned int>, libMesh::Threads::scalable_allocator<std::pair<unsigned int const, std::__debug::map<unsigned int, double, std::less<unsigned int>, libMesh::Threads::scalable_allocator<std::pair<unsigned int const, double> > > > > >> = std::__debug::map with 0 elements, <No data fields>}, _primal_constraint_values = {<std::__debug::map<unsigned int, double, std::less<unsigned int>, libMesh::Threads::scalable_allocator<std::pair<unsigned int const, double> > >> = std::__debug::map with 0 elements, <No data fields>}, _adjoint_constraint_values = {<std::__debug::map<unsigned int, libMesh::DofConstraintValueMap, std::less<unsigned int>, libMesh::Threads::scalable_allocator<std::pair<unsigned int const, libMesh::DofConstraintValueMap> > >> = std::__debug::map with 0 elements, <No data fields>}, _periodic_boundaries = std::unique_ptr<libMesh::PeriodicBoundaries> containing 0xc23d00, _dirichlet_boundaries = std::unique_ptr<libMesh::DirichletBoundaries> containing 0xc23c20, _adjoint_dirichlet_boundaries = std::__debug::vector of length 0, capacity 0, _implicit_neighbor_dofs_initialized = false, _implicit_neighbor_dofs = false}, variable_number=0, elem=0xc38160, Dim=2) libMesh::FE<2u, (libMesh::FEFamily)0>::compute_constraints (constraints=@0xb60b78: {<std::__debug::map<unsigned int, std::__debug::map<unsigned int, double, std::less<unsigned int>, libMesh::Threads::scalable_allocator<std::pair<unsigned int const, double> > >, std::less<unsigned int>, libMesh::Threads::scalable_allocator<std::pair<unsigned int const, std::__debug::map<unsigned int, double, std::less<unsigned int>, libMesh::Threads::scalable_allocator<std::pair<unsigned int const, double> > > > > >> = std::__debug::map with 0 elements, <No data fields>}, dof_map=@0xb60820: {<libMesh::ReferenceCountedObject<libMesh::DofMap>> = {<libMesh::ReferenceCounter> = {static _counts = <optimized out>, static _n_objects = {val = 0, smutex = {slock = 0}}, static _mutex = {slock = 1}, static _enable_print_counter = true}, <No data fields>}, <libMesh::ParallelObject> = {_vptr.ParallelObject = 0x7ffff704b890 <vtable for libMesh::DofMap+16>, _communicator = @0x7fffffffd6e8}, _dof_coupling = 0x0, _variables = std::__debug::vector of length 1, capacity 1 = {{_sys = 0xc26700, _name = \"u\", _active_subdomains = std::__debug::set with 2 elements, _number = 0, _first_scalar_number = 0, _type = {order = {_order = 1}, family = libMesh::LAGRANGE}}}, _variable_groups = std::__debug::vector of length 1, capacity 1 = {{<libMesh::Variable> = {_sys = 0xc26700, _name = \"var_group\", _active_subdomains = std::__debug::set with 2 elements, _number = 0, _first_scalar_number = 0, _type = {order = {_order = 1}, family = libMesh::LAGRANGE}}, _names = std::__debug::vector of length 1, capacity 1 = {\"u\"}}}, _sys_number = 0, _mesh = @0x7fffffffd9a0, _matrices = std::__debug::vector of length 0, capacity 0, _first_df = std::__debug::vector of length 1, capacity 1 = {0}, _end_df = std::__debug::vector of length 1, capacity 1 = {785}, _first_scalar_df = std::__debug::vector of length 1, capacity 1 = {4294967295}, _send_list = std::__debug::vector of length 0, capacity 0, _augment_sparsity_pattern = 0x0, _extra_sparsity_function = 0x0, _extra_sparsity_context = 0x0, _augment_send_list = 0x0, _extra_send_list_function = 0x0, _extra_send_list_context = 0x0, _default_coupling = std::unique_ptr<libMesh::DefaultCoupling> containing 0xb7ee10, _default_evaluating = std::unique_ptr<libMesh::DefaultCoupling> containing 0xb82e60, _algebraic_ghosting_functors = std::__debug::set with 1 elements, _coupling_functors = std::__debug::set with 1 elements, need_full_sparsity_pattern = false, _sp = std::unique_ptr<libMesh::SparsityPattern::Build> containing 0x0, _n_nz = 0x0, _n_oz = 0x0, _n_dfs = 785, _n_SCALAR_dofs = 0, _n_old_dfs = 0, _first_old_df = std::__debug::vector of length 0, capacity 0, _end_old_df = std::__debug::vector of length 0, capacity 0, _first_old_scalar_df = std::__debug::vector of length 0, capacity 0, _dof_constraints = {<std::__debug::map<unsigned int, std::__debug::map<unsigned int, double, std::less<unsigned int>, libMesh::Threads::scalable_allocator<std::pair<unsigned int const, double> > >, std::less<unsigned int>, libMesh::Threads::scalable_allocator<std::pair<unsigned int const, std::__debug::map<unsigned int, double, std::less<unsigned int>, libMesh::Threads::scalable_allocator<std::pair<unsigned int const, double> > > > > >> = std::__debug::map with 0 elements, <No data fields>}, _stashed_dof_constraints = {<std::__debug::map<unsigned int, std::__debug::map<unsigned int, double, std::less<unsigned int>, libMesh::Threads::scalable_allocator<std::pair<unsigned int const, double> > >, std::less<unsigned int>, libMesh::Threads::scalable_allocator<std::pair<unsigned int const, std::__debug::map<unsigned int, double, std::less<unsigned int>, libMesh::Threads::scalable_allocator<std::pair<unsigned int const, double> > > > > >> = std::__debug::map with 0 elements, <No data fields>}, _primal_constraint_values = {<std::__debug::map<unsigned int, double, std::less<unsigned int>, libMesh::Threads::scalable_allocator<std::pair<unsigned int const, double> > >> = std::__debug::map with 0 elements, <No data fields>}, _adjoint_constraint_values = {<std::__debug::map<unsigned int, libMesh::DofConstraintValueMap, std::less<unsigned int>, libMesh::Threads::scalable_allocator<std::pair<unsigned int const, libMesh::DofConstraintValueMap> > >> = std::__debug::map with 0 elements, <No data fields>}, _periodic_boundaries = std::unique_ptr<libMesh::PeriodicBoundaries> containing 0xc23d00, _dirichlet_boundaries = std::unique_ptr<libMesh::DirichletBoundaries> containing 0xc23c20, _adjoint_dirichlet_boundaries = std::__debug::vector of length 0, capacity 0, _implicit_neighbor_dofs_initialized = false, _implicit_neighbor_dofs = false}, variable_number=0, elem=0xc38160) libMesh::FEInterface::compute_constraints (constraints=@0xb60b78: {<std::__debug::map<unsigned int, std::__debug::map<unsigned int, double, std::less<unsigned int>, libMesh::Threads::scalable_allocator<std::pair<unsigned int const, double> > >, std::less<unsigned int>, libMesh::Threads::scalable_allocator<std::pair<unsigned int const, std::__debug::map<unsigned int, double, std::less<unsigned int>, libMesh::Threads::scalable_allocator<std::pair<unsigned int const, double> > > > > >> = std::__debug::map with 0 elements, <No data fields>}, dof_map=@0xb60820: {<libMesh::ReferenceCountedObject<libMesh::DofMap>> = {<libMesh::ReferenceCounter> = {static _counts = <optimized out>, static _n_objects = {val = 0, smutex = {slock = 0}}, static _mutex = {slock = 1}, static _enable_print_counter = true}, <No data fields>}, <libMesh::ParallelObject> = {_vptr.ParallelObject = 0x7ffff704b890 <vtable for libMesh::DofMap+16>, _communicator = @0x7fffffffd6e8}, _dof_coupling = 0x0, _variables = std::__debug::vector of length 1, capacity 1 = {{_sys = 0xc26700, _name = \"u\", _active_subdomains = std::__debug::set with 2 elements, _number = 0, _first_scalar_number = 0, _type = {order = {_order = 1}, family = libMesh::LAGRANGE}}}, _variable_groups = std::__debug::vector of length 1, capacity 1 = {{<libMesh::Variable> = {_sys = 0xc26700, _name = \"var_group\", _active_subdomains = std::__debug::set with 2 elements, _number = 0, _first_scalar_number = 0, _type = {order = {_order = 1}, family = libMesh::LAGRANGE}}, _names = std::__debug::vector of length 1, capacity 1 = {\"u\"}}}, _sys_number = 0, _mesh = @0x7fffffffd9a0, _matrices = std::__debug::vector of length 0, capacity 0, _first_df = std::__debug::vector of length 1, capacity 1 = {0}, _end_df = std::__debug::vector of length 1, capacity 1 = {785}, _first_scalar_df = std::__debug::vector of length 1, capacity 1 = {4294967295}, _send_list = std::__debug::vector of length 0, capacity 0, _augment_sparsity_pattern = 0x0, _extra_sparsity_function = 0x0, _extra_sparsity_context = 0x0, _augment_send_list = 0x0, _extra_send_list_function = 0x0, _extra_send_list_context = 0x0, _default_coupling = std::unique_ptr<libMesh::DefaultCoupling> containing 0xb7ee10, _default_evaluating = std::unique_ptr<libMesh::DefaultCoupling> containing 0xb82e60, _algebraic_ghosting_functors = std::__debug::set with 1 elements, _coupling_functors = std::__debug::set with 1 elements, need_full_sparsity_pattern = false, _sp = std::unique_ptr<libMesh::SparsityPattern::Build> containing 0x0, _n_nz = 0x0, _n_oz = 0x0, _n_dfs = 785, _n_SCALAR_dofs = 0, _n_old_dfs = 0, _first_old_df = std::__debug::vector of length 0, capacity 0, _end_old_df = std::__debug::vector of length 0, capacity 0, _first_old_scalar_df = std::__debug::vector of length 0, capacity 0, _dof_constraints = {<std::__debug::map<unsigned int, std::__debug::map<unsigned int, double, std::less<unsigned int>, libMesh::Threads::scalable_allocator<std::pair<unsigned int const, double> > >, std::less<unsigned int>, libMesh::Threads::scalable_allocator<std::pair<unsigned int const, std::__debug::map<unsigned int, double, std::less<unsigned int>, libMesh::Threads::scalable_allocator<std::pair<unsigned int const, double> > > > > >> = std::__debug::map with 0 elements, <No data fields>}, _stashed_dof_constraints = {<std::__debug::map<unsigned int, std::__debug::map<unsigned int, double, std::less<unsigned int>, libMesh::Threads::scalable_allocator<std::pair<unsigned int const, double> > >, std::less<unsigned int>, libMesh::Threads::scalable_allocator<std::pair<unsigned int const, std::__debug::map<unsigned int, double, std::less<unsigned int>, libMesh::Threads::scalable_allocator<std::pair<unsigned int const, double> > > > > >> = std::__debug::map with 0 elements, <No data fields>}, _primal_constraint_values = {<std::__debug::map<unsigned int, double, std::less<unsigned int>, libMesh::Threads::scalable_allocator<std::pair<unsigned int const, double> > >> = std::__debug::map with 0 elements, <No data fields>}, _adjoint_constraint_values = {<std::__debug::map<unsigned int, libMesh::DofConstraintValueMap, std::less<unsigned int>, libMesh::Threads::scalable_allocator<std::pair<unsigned int const, libMesh::DofConstraintValueMap> > >> = std::__debug::map with 0 elements, <No data fields>}, _periodic_boundaries = std::unique_ptr<libMesh::PeriodicBoundaries> containing 0xc23d00, _dirichlet_boundaries = std::unique_ptr<libMesh::DirichletBoundaries> containing 0xc23c20, _adjoint_dirichlet_boundaries = std::__debug::vector of length 0, capacity 0, _implicit_neighbor_dofs_initialized = false, _implicit_neighbor_dofs = false}, variable_number=0, elem=0xc38160) (anonymous namespace)::ComputeConstraints::operator() (this=0x7fffffffd110, range=@0xd231c0: {_end = , _begin = , _last = 5156, _first = 0, _grainsize = 1000, _objs = 0x0, _should_release = false}) libMesh::Threads::run_body<libMesh::StoredRange<libMesh:: MeshBase::const_element_iterator, libMesh::Elem const*>, (anonymous namespace)::ComputeConstraints> (args=0xc37500) libMesh::Threads::parallel_for<libMesh::StoredRange< libMesh::MeshBase::const_element_iterator, libMesh::Elem const*>, (anonymous namespace)::ComputeConstraints> () GOMP_parallel () libMesh::Threads::parallel_for<libMesh::StoredRange< libMesh::MeshBase::const_element_iterator, libMesh::Elem const*>, (anonymous namespace)::ComputeConstraints> (range=@0x7fffffffcfc0: {_end = , _begin = , _last = 5156, _first = 0, _grainsize = 1000, _objs = 0xd0d540, _should_release = true}, body=@0x7fffffffd110: {_constraints = @0xb60b78, _dof_map = @0xb60820, _periodic_boundaries = @0xc23d00, _mesh = @0x7fffffffd9a0, _variable_number = 0}) libMesh::DofMap::create_dof_constraints (this=0xb60820, mesh=@0x7fffffffd9a0: {<libMesh::ParallelObject> = {_vptr.ParallelObject = 0x539ac8 <vtable for libMesh::Mesh+16>, _communicator = @0x7fffffffd6e8}, boundary_info = std::unique_ptr<libMesh::BoundaryInfo> containing 0xb60400, _n_parts = 1, _is_prepared = true, _point_locator = std::unique_ptr<libMesh::PointLocatorBase> containing 0x0, _count_lower_dim_elems_in_point_locator = true, _partitioner = std::unique_ptr<libMesh::Partitioner> containing 0x7bd690, _skip_partitioning = false, _skip_renumber_nodes_and_elements = false, _allow_remote_element_removal = true, _block_id_to_name = std::__debug::map with 1 elements, _elem_dims = std::__debug::set with 1 elements, _spatial_dimension = 2 '\\002', _default_ghosting = std::unique_ptr<libMesh::GhostingFunctor> containing 0x9973d0, _ghosting_functors = std::__debug::set with 3 elements}, time=0) libMesh::System::reinit_constraints (this=0xc26700) libMesh::System::init_data (this=0xc26700) libMesh::ExplicitSystem::init_data (this=0xc26700) libMesh::ImplicitSystem::init_data (this=0xc26700) libMesh::LinearImplicitSystem::init_data (this=0xc26700) libMesh::System::init (this=0xc26700) libMesh::EquationSystems::init (this=0x7fffffffd800) main (argc=1, argv=0x7fffffffdfe8) 2018-06-05 9:23 GMT-03:00 Roy Stogner <roy...@ic...>: > > On Mon, 4 Jun 2018, Vinicius C. Reis wrote: > > The exception is thrown from within EquationSystems.init(). I'll do some >> cleanup and get back with a somewhat more concise reproduction. I've >> attached two text files with the exception and the stack trace. >> > > I'm afraid the attachments got stripped by the mailing list, so John's > the only one who has them. Assuming the exception and trace are short > enough could you post them inline? > > Thanks, > --- > Roy > |