File: Test3dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 44652ms, 85.85% of 52010ms total Dropped 822 nodes (cum <= 260.05ms) flat flat% sum% cum cum% 0 0% 0% 51935ms 99.86% __libc_start_call_main 0 0% 0% 51935ms 99.86% __libc_start_main_impl 0 0% 0% 51935ms 99.86% _start 0 0% 0% 51921ms 99.83% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 51921ms 99.83% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 51921ms 99.83% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 51921ms 99.83% main 0 0% 0% 51886ms 99.76% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 51886ms 99.76% CxxTest::TestRunner::runTest (inline) 0 0% 0% 51886ms 99.76% Test3dTissueRepresentativeSimulation::Test3DHoneycombMeshWithGhostNodes 0 0% 0% 51639ms 99.29% AbstractCellBasedSimulation::Solve 0 0% 0% 43410ms 83.46% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 43369ms 83.39% MeshBasedCellPopulation::Update 0 0% 0% 23797ms 45.75% MeshBasedCellPopulation::CreateVoronoiTessellation (inline) 0 0% 0% 23797ms 45.75% MeshBasedCellPopulation::TessellateIfNeeded 174ms 0.33% 0.33% 21344ms 41.04% VertexMesh::VertexMesh 0 0% 0.33% 15991ms 30.75% MutableMesh::ReMesh 0 0% 0.33% 12641ms 24.30% tetgen::tetrahedralize 3ms 0.0058% 0.34% 12507ms 24.05% tetgen::tetgenmesh::delaunizevertices 9ms 0.017% 0.36% 12500ms 24.03% tetgen::tetgenmesh::incrflipdelaunay 530ms 1.02% 1.38% 11054ms 21.25% tetgen::tetgenmesh::lawson 556ms 1.07% 2.45% 10879ms 20.92% TetrahedralMesh::EdgeIterator::operator++ 33ms 0.063% 2.51% 8591ms 16.52% std::set::insert (inline) 333ms 0.64% 3.15% 8587ms 16.51% VertexElement::AddFace 3077ms 5.92% 9.07% 8515ms 16.37% std::_Rb_tree::_M_lower_bound (inline) 216ms 0.42% 9.48% 8094ms 15.56% std::_Rb_tree::_M_insert_unique 253ms 0.49% 9.97% 8028ms 15.44% std::_Rb_tree::find (inline) 0 0% 9.97% 7494ms 14.41% std::set::count (inline) 117ms 0.22% 10.19% 5334ms 10.26% std::less::operator() (inline) 5292ms 10.17% 20.37% 5292ms 10.17% std::operator< (inline) 291ms 0.56% 20.93% 4908ms 9.44% std::_Rb_tree::_M_insert_ (inline) 0 0% 20.93% 4874ms 9.37% OffLatticeSimulation::UpdateCellLocationsAndTopology 1ms 0.0019% 20.93% 4766ms 9.16% ForwardEulerNumericalMethod::UpdateAllNodePositions 0 0% 20.93% 4741ms 9.12% AbstractNumericalMethod::ComputeForcesIncludingDamping 208ms 0.4% 21.33% 4183ms 8.04% operator new 3ms 0.0058% 21.33% 3914ms 7.53% MeshBasedCellPopulation::UpdateNodePairs 1021ms 1.96% 23.30% 3898ms 7.49% __GI___libc_malloc 6ms 0.012% 23.31% 3867ms 7.44% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 12ms 0.023% 23.33% 3794ms 7.29% MeshBasedCellPopulation::SpringIterator::operator++ 3761ms 7.23% 30.56% 3761ms 7.23% std::_Rb_tree_increment 38ms 0.073% 30.64% 3708ms 7.13% std::__new_allocator::allocate (inline) 0 0% 30.64% 3686ms 7.09% std::allocator_traits::allocate (inline) 7ms 0.013% 30.65% 3609ms 6.94% std::_Rb_tree::~_Rb_tree (inline) 1223ms 2.35% 33.00% 3601ms 6.92% std::_Rb_tree::_M_erase 0 0% 33.00% 3564ms 6.85% std::set::~set (inline) 118ms 0.23% 33.23% 3478ms 6.69% tetgen::tetgenmesh::insphere_sos 3059ms 5.88% 39.11% 3346ms 6.43% tetgen::insphere 1150ms 2.21% 41.32% 3278ms 6.30% std::_Rb_tree::_M_get_insert_unique_pos 0 0% 41.32% 3219ms 6.19% AbstractCellPopulation::WriteResultsToFiles 899ms 1.73% 43.05% 3170ms 6.09% __GI___libc_free 0 0% 43.05% 3000ms 5.77% std::_Rb_tree::_M_create_node (inline) 0 0% 43.05% 2973ms 5.72% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 43.05% 2973ms 5.72% std::_Rb_tree::_M_get_node (inline) 145ms 0.28% 43.33% 2953ms 5.68% std::__new_allocator::deallocate (inline) 0 0% 43.33% 2933ms 5.64% std::allocator_traits::deallocate (inline) 7ms 0.013% 43.34% 2720ms 5.23% std::set_intersection (inline) 180ms 0.35% 43.69% 2713ms 5.22% std::__set_intersection 18ms 0.035% 43.72% 2619ms 5.04% TetrahedralMesh::ImportFromMesher 188ms 0.36% 44.08% 2616ms 5.03% tetgen::tetgenmesh::flip23 15ms 0.029% 44.11% 2608ms 5.01% Node::AddElement 1969ms 3.79% 47.90% 2539ms 4.88% _int_malloc 2514ms 4.83% 52.73% 2514ms 4.83% std::_Rb_tree::_S_right (inline) 0 0% 52.73% 2469ms 4.75% VertexMesh::~VertexMesh 1201ms 2.31% 55.04% 2269ms 4.36% _int_free 8ms 0.015% 55.06% 2160ms 4.15% MeshBasedCellPopulationWithGhostNodes::WriteVtkResultsToFile 202ms 0.39% 55.45% 2125ms 4.09% VertexMesh::GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex 175ms 0.34% 55.78% 2105ms 4.05% std::_Rb_tree_const_iterator::operator++ (inline) 80ms 0.15% 55.94% 1958ms 3.76% MutableElement::AddNode 2ms 0.0038% 55.94% 1933ms 3.72% std::_Rb_tree_iterator::operator++ (inline) 0 0% 55.94% 1900ms 3.65% std::_Rb_tree::_M_drop_node (inline) 0 0% 55.94% 1885ms 3.62% std::_Rb_tree::_M_put_node (inline) 165ms 0.32% 56.26% 1847ms 3.55% tetgen::tetgenmesh::flip32 56ms 0.11% 56.36% 1728ms 3.32% Node::~Node 1712ms 3.29% 59.66% 1712ms 3.29% std::_Rb_tree_insert_and_rebalance 112ms 0.22% 59.87% 1669ms 3.21% VertexMesh::Clear 8ms 0.015% 59.89% 1442ms 2.77% Element::Element 1333ms 2.56% 62.45% 1425ms 2.74% tetgen::orient3d 180ms 0.35% 62.80% 1271ms 2.44% tetgen::tetgenmesh::enqueueflipface 28ms 0.054% 62.85% 1235ms 2.37% tetgen::tetgenmesh::locate 1207ms 2.32% 65.17% 1207ms 2.32% Node::GetIndex 88ms 0.17% 65.34% 1146ms 2.20% tetgen::tetgenmesh::preciselocate 7ms 0.013% 65.35% 1104ms 2.12% Element::RegisterWithNodes (inline) 11ms 0.021% 65.37% 1059ms 2.04% std::_Vector_base::_M_deallocate (inline) 57ms 0.11% 65.48% 1058ms 2.03% std::map::operator[] 0 0% 65.48% 1014ms 1.95% std::vector::~vector (inline) 625ms 1.20% 66.69% 1006ms 1.93% malloc_consolidate 55ms 0.11% 66.79% 964ms 1.85% std::vector::_M_realloc_insert 939ms 1.81% 68.60% 939ms 1.81% tetgen::tetgenmesh::triface::triface 0 0% 68.60% 937ms 1.80% std::_Rb_tree::lower_bound (inline) 0 0% 68.60% 937ms 1.80% std::map::lower_bound (inline) 101ms 0.19% 68.79% 899ms 1.73% TetrahedralMesh::Clear 1ms 0.0019% 68.79% 893ms 1.72% std::_Vector_base::~_Vector_base (inline) 7ms 0.013% 68.81% 877ms 1.69% _int_free_maybe_consolidate 0 0% 68.81% 846ms 1.63% VoronoiDataWriter::Visit 98ms 0.19% 68.99% 796ms 1.53% std::vector::push_back (inline) 5ms 0.0096% 69.00% 745ms 1.43% VertexMesh::GenerateVerticesFromElementCircumcentres 1ms 0.0019% 69.01% 731ms 1.41% AbstractTwoBodyInteractionForce::AddForceContribution 9ms 0.017% 69.02% 722ms 1.39% std::_Vector_base::_M_allocate (inline) 720ms 1.38% 70.41% 720ms 1.38% tetgen::tetgenmesh::oppo 718ms 1.38% 71.79% 718ms 1.38% unlink_chunk 12ms 0.023% 71.81% 710ms 1.37% boost::numeric::ublas::vector_assign (inline) 0 0% 71.81% 707ms 1.36% TetrahedralMesh::RefreshJacobianCachedData 700ms 1.35% 73.16% 700ms 1.35% [libchaste_mesh.so] 17ms 0.033% 73.19% 692ms 1.33% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 332ms 0.64% 73.83% 686ms 1.32% tetgen::tetgenmesh::fnextself 17ms 0.033% 73.86% 668ms 1.28% boost::numeric::ublas::c_vector::c_vector (inline) 6ms 0.012% 73.87% 667ms 1.28% AbstractTetrahedralElement::CalculateInverseJacobian 522ms 1.00% 74.88% 664ms 1.28% AbstractElement::GetNodeGlobalIndex 13ms 0.025% 74.90% 618ms 1.19% AbstractTetrahedralElement::CalculateJacobian 43ms 0.083% 74.98% 576ms 1.11% __atan2 553ms 1.06% 76.05% 553ms 1.06% tetgen::tetgenmesh::triface::operator= 436ms 0.84% 76.89% 533ms 1.02% __ieee754_atan2_fma 0 0% 76.89% 530ms 1.02% std::set::find (inline) 231ms 0.44% 77.33% 508ms 0.98% AbstractElement::GetNodeLocation 0 0% 77.33% 505ms 0.97% std::insert_iterator::operator= (inline) 0 0% 77.33% 488ms 0.94% boost::numeric::ublas::inner_prod (inline) 38ms 0.073% 77.40% 486ms 0.93% tetgen::tetgenmesh::enext2fnext 4ms 0.0077% 77.41% 484ms 0.93% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 40ms 0.077% 77.49% 480ms 0.92% boost::numeric::ublas::vector_scalar_binary::evaluate 45ms 0.087% 77.57% 461ms 0.89% AbstractTetrahedralElement::RefreshJacobian 459ms 0.88% 78.46% 459ms 0.88% std::vector::size (inline) 125ms 0.24% 78.70% 458ms 0.88% boost::numeric::ublas::indexing_vector_assign 0 0% 78.70% 437ms 0.84% std::_Rb_tree::_M_insert_unique_ (inline) 18ms 0.035% 78.73% 433ms 0.83% Element::CalculateCircumsphere 424ms 0.82% 79.55% 424ms 0.82% boost::numeric::ublas::c_vector::operator() 256ms 0.49% 80.04% 422ms 0.81% tetgen::tetgenmesh::sym 33ms 0.063% 80.10% 421ms 0.81% tetgen::tetgenmesh::enextfnext 2ms 0.0038% 80.11% 409ms 0.79% Cell::GetCellId 6ms 0.012% 80.12% 408ms 0.78% CellPropertyCollection::GetPropertiesType (inline) 224ms 0.43% 80.55% 407ms 0.78% AbstractTetrahedralMesh::GetElement 91ms 0.17% 80.72% 397ms 0.76% __dynamic_cast 21ms 0.04% 80.76% 395ms 0.76% VertexMesh::CalculateUnitNormalToFaceWithArea 4ms 0.0077% 80.77% 390ms 0.75% boost::numeric::ublas::c_vector::operator= (inline) 162ms 0.31% 81.08% 388ms 0.75% boost::numeric::ublas::vector_inner_prod::apply (inline) 0 0% 81.08% 376ms 0.72% VertexMeshWriter::WriteVtkUsingMesh 372ms 0.72% 81.80% 372ms 0.72% Node::rGetLocation 31ms 0.06% 81.86% 367ms 0.71% tetgen::tetgenmesh::queue::push 257ms 0.49% 82.35% 350ms 0.67% tetgen::tetgenmesh::bond 27ms 0.052% 82.40% 346ms 0.67% std::_Rb_tree_iterator::operator-- (inline) 346ms 0.67% 83.07% 346ms 0.67% tetgen::tetgenmesh::org 3ms 0.0058% 83.07% 339ms 0.65% AbstractCellProperty::IsSubType (inline) 162ms 0.31% 83.39% 333ms 0.64% Inverse 236ms 0.45% 83.84% 333ms 0.64% tetgen::tetgenmesh::link::add 3ms 0.0058% 83.85% 331ms 0.64% AbstractTetrahedralElement::AbstractTetrahedralElement 58ms 0.11% 83.96% 320ms 0.62% boost::numeric::ublas::vector_reference::operator() (inline) 65ms 0.12% 84.08% 310ms 0.6% tetgen::tetgenmesh::queue::pop 306ms 0.59% 84.67% 306ms 0.59% std::_Rb_tree_decrement 0 0% 84.67% 297ms 0.57% tcache_get (inline) 297ms 0.57% 85.24% 297ms 0.57% tcache_get_n (inline) 7ms 0.013% 85.25% 293ms 0.56% VertexElement::~VertexElement 10ms 0.019% 85.27% 290ms 0.56% std::vector::insert (inline) 34ms 0.065% 85.34% 287ms 0.55% tetgen::insphereadapt 267ms 0.51% 85.85% 267ms 0.51% tetgen::tetgenmesh::pointmark