File: Test3dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 44006ms, 85.39% of 51535ms total Dropped 841 nodes (cum <= 257.68ms) flat flat% sum% cum cum% 0 0% 0% 51497ms 99.93% __libc_start_call_main 0 0% 0% 51497ms 99.93% __libc_start_main_impl 0 0% 0% 51497ms 99.93% _start 0 0% 0% 51482ms 99.90% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 51482ms 99.90% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 51482ms 99.90% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 51482ms 99.90% main 0 0% 0% 51447ms 99.83% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 51447ms 99.83% CxxTest::TestRunner::runTest (inline) 0 0% 0% 51447ms 99.83% Test3dTissueRepresentativeSimulation::Test3DHoneycombMeshWithGhostNodes 0 0% 0% 51250ms 99.45% AbstractCellBasedSimulation::Solve 1ms 0.0019% 0.0019% 42706ms 82.87% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0.0019% 42644ms 82.75% MeshBasedCellPopulation::Update 0 0% 0.0019% 25790ms 50.04% MeshBasedCellPopulation::CreateVoronoiTessellation (inline) 0 0% 0.0019% 25790ms 50.04% MeshBasedCellPopulation::TessellateIfNeeded 209ms 0.41% 0.41% 23278ms 45.17% VertexMesh::VertexMesh 0 0% 0.41% 13174ms 25.56% MutableMesh::ReMesh 478ms 0.93% 1.34% 11362ms 22.05% TetrahedralMesh::EdgeIterator::operator++ 0 0% 1.34% 9975ms 19.36% tetgen::tetrahedralize 2ms 0.0039% 1.34% 9864ms 19.14% tetgen::tetgenmesh::delaunizevertices 5ms 0.0097% 1.35% 9859ms 19.13% tetgen::tetgenmesh::incrflipdelaunay 31ms 0.06% 1.41% 9779ms 18.98% std::set::insert (inline) 141ms 0.27% 1.68% 9269ms 17.99% std::_Rb_tree::_M_insert_unique 250ms 0.49% 2.17% 9176ms 17.81% VertexElement::AddFace 3810ms 7.39% 9.56% 8900ms 17.27% std::_Rb_tree::_M_lower_bound (inline) 480ms 0.93% 10.49% 8713ms 16.91% tetgen::tetgenmesh::lawson 168ms 0.33% 10.82% 8595ms 16.68% std::_Rb_tree::find (inline) 0 0% 10.82% 8084ms 15.69% std::set::count (inline) 295ms 0.57% 11.39% 6041ms 11.72% std::_Rb_tree::_M_insert_ (inline) 180ms 0.35% 11.74% 5843ms 11.34% operator new 1908ms 3.70% 15.44% 5610ms 10.89% __GI___libc_malloc 58ms 0.11% 15.55% 5072ms 9.84% std::__new_allocator::allocate (inline) 0 0% 15.55% 5045ms 9.79% std::allocator_traits::allocate (inline) 0 0% 15.55% 5015ms 9.73% OffLatticeSimulation::UpdateCellLocationsAndTopology 1ms 0.0019% 15.56% 4873ms 9.46% ForwardEulerNumericalMethod::UpdateAllNodePositions 2ms 0.0039% 15.56% 4857ms 9.42% AbstractNumericalMethod::ComputeForcesIncludingDamping 4612ms 8.95% 24.51% 4612ms 8.95% std::_Rb_tree_increment 65ms 0.13% 24.64% 4521ms 8.77% std::less::operator() (inline) 4516ms 8.76% 33.40% 4516ms 8.76% std::operator< (inline) 0 0% 33.40% 4175ms 8.10% std::_Rb_tree::_M_create_node (inline) 0 0% 33.40% 4159ms 8.07% std::_Rb_tree::_M_get_node (inline) 0 0% 33.40% 4132ms 8.02% std::_Rb_tree::_Alloc_node::operator() (inline) 1ms 0.0019% 33.40% 3977ms 7.72% MeshBasedCellPopulation::UpdateNodePairs 5ms 0.0097% 33.41% 3951ms 7.67% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 27ms 0.052% 33.46% 3885ms 7.54% MeshBasedCellPopulation::SpringIterator::operator++ 672ms 1.30% 34.77% 3867ms 7.50% __GI___libc_free 209ms 0.41% 35.17% 3570ms 6.93% std::__set_intersection 0 0% 35.17% 3570ms 6.93% std::set_intersection (inline) 60ms 0.12% 35.29% 3461ms 6.72% std::__new_allocator::deallocate (inline) 0 0% 35.29% 3450ms 6.69% std::allocator_traits::deallocate (inline) 0 0% 35.29% 3388ms 6.57% AbstractCellPopulation::WriteResultsToFiles 1301ms 2.52% 37.81% 3384ms 6.57% std::_Rb_tree::_M_get_insert_unique_pos 9ms 0.017% 37.83% 3380ms 6.56% std::_Rb_tree::~_Rb_tree (inline) 831ms 1.61% 39.44% 3363ms 6.53% std::_Rb_tree::_M_erase 0 0% 39.44% 3347ms 6.49% std::set::~set (inline) 2748ms 5.33% 44.78% 3332ms 6.47% _int_malloc 1678ms 3.26% 48.03% 3179ms 6.17% _int_free 64ms 0.12% 48.16% 3038ms 5.90% Node::AddElement 235ms 0.46% 48.61% 2868ms 5.57% std::_Rb_tree_const_iterator::operator++ (inline) 2750ms 5.34% 53.95% 2750ms 5.34% std::_Rb_tree::_S_right (inline) 83ms 0.16% 54.11% 2666ms 5.17% tetgen::tetgenmesh::insphere_sos 2382ms 4.62% 58.73% 2550ms 4.95% tetgen::insphere 0 0% 58.73% 2529ms 4.91% VertexMesh::~VertexMesh 220ms 0.43% 59.16% 2466ms 4.79% std::_Rb_tree_iterator::operator++ (inline) 6ms 0.012% 59.17% 2458ms 4.77% VertexMesh::GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex 2ms 0.0039% 59.17% 2424ms 4.70% MeshBasedCellPopulationWithGhostNodes::WriteVtkResultsToFile 2ms 0.0039% 59.18% 2403ms 4.66% TetrahedralMesh::ImportFromMesher 34ms 0.066% 59.24% 2207ms 4.28% MutableElement::AddNode 0 0% 59.24% 2202ms 4.27% std::_Rb_tree::_M_drop_node (inline) 0 0% 59.24% 2177ms 4.22% std::_Rb_tree::_M_put_node (inline) 209ms 0.41% 59.65% 2100ms 4.07% tetgen::tetgenmesh::flip23 1829ms 3.55% 63.20% 1829ms 3.55% [libchaste_mesh.so] 1674ms 3.25% 66.45% 1674ms 3.25% std::_Rb_tree_insert_and_rebalance 3ms 0.0058% 66.45% 1499ms 2.91% VertexMesh::Clear 4ms 0.0078% 66.46% 1490ms 2.89% Element::Element 24ms 0.047% 66.51% 1472ms 2.86% Node::~Node 1351ms 2.62% 69.13% 1418ms 2.75% tetgen::orient3d 177ms 0.34% 69.47% 1380ms 2.68% tetgen::tetgenmesh::flip32 17ms 0.033% 69.50% 1290ms 2.50% std::_Vector_base::_M_deallocate (inline) 814ms 1.58% 71.08% 1270ms 2.46% malloc_consolidate 6ms 0.012% 71.10% 1226ms 2.38% Element::RegisterWithNodes (inline) 0 0% 71.10% 1188ms 2.31% std::vector::~vector (inline) 8ms 0.016% 71.11% 1140ms 2.21% _int_free_maybe_consolidate 0 0% 71.11% 1137ms 2.21% std::_Vector_base::~_Vector_base (inline) 1036ms 2.01% 73.12% 1036ms 2.01% Node::GetIndex 83ms 0.16% 73.28% 1012ms 1.96% std::map::operator[] 25ms 0.049% 73.33% 994ms 1.93% std::vector::_M_realloc_insert 24ms 0.047% 73.38% 974ms 1.89% tetgen::tetgenmesh::locate 71ms 0.14% 73.52% 924ms 1.79% tetgen::tetgenmesh::preciselocate 180ms 0.35% 73.86% 908ms 1.76% tetgen::tetgenmesh::enqueueflipface 1ms 0.0019% 73.87% 887ms 1.72% std::_Vector_base::_M_allocate (inline) 3ms 0.0058% 73.87% 864ms 1.68% VertexMesh::GenerateVerticesFromElementCircumcentres 0 0% 73.87% 831ms 1.61% std::_Rb_tree::lower_bound (inline) 0 0% 73.87% 831ms 1.61% std::map::lower_bound (inline) 55ms 0.11% 73.98% 790ms 1.53% std::vector::push_back (inline) 0 0% 73.98% 781ms 1.52% TetrahedralMesh::RefreshJacobianCachedData 780ms 1.51% 75.49% 780ms 1.51% unlink_chunk 0 0% 75.49% 779ms 1.51% VoronoiDataWriter::Visit 5ms 0.0097% 75.50% 707ms 1.37% AbstractTetrahedralElement::CalculateInverseJacobian 3ms 0.0058% 75.51% 687ms 1.33% AbstractTwoBodyInteractionForce::AddForceContribution 11ms 0.021% 75.53% 657ms 1.27% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 9ms 0.017% 75.55% 623ms 1.21% TetrahedralMesh::Clear 347ms 0.67% 76.22% 607ms 1.18% AbstractElement::GetNodeGlobalIndex 7ms 0.014% 76.23% 591ms 1.15% boost::numeric::ublas::vector_assign (inline) 365ms 0.71% 76.94% 564ms 1.09% tetgen::tetgenmesh::sym 9ms 0.017% 76.96% 554ms 1.07% AbstractTetrahedralElement::CalculateJacobian 3ms 0.0058% 76.97% 545ms 1.06% boost::numeric::ublas::c_vector::c_vector (inline) 0 0% 76.97% 524ms 1.02% std::insert_iterator::operator= (inline) 0 0% 76.97% 504ms 0.98% std::set::find (inline) 33ms 0.064% 77.03% 497ms 0.96% __atan2 255ms 0.49% 77.52% 487ms 0.94% AbstractElement::GetNodeLocation 472ms 0.92% 78.44% 472ms 0.92% tetgen::tetgenmesh::oppo 469ms 0.91% 79.35% 469ms 0.91% Node::rGetLocation 420ms 0.81% 80.16% 458ms 0.89% __ieee754_atan2_fma 0 0% 80.16% 446ms 0.87% std::_Rb_tree::_M_insert_unique_ (inline) 429ms 0.83% 81.00% 429ms 0.83% std::vector::size (inline) 15ms 0.029% 81.03% 421ms 0.82% Element::CalculateCircumsphere 27ms 0.052% 81.08% 417ms 0.81% AbstractTetrahedralElement::RefreshJacobian 45ms 0.087% 81.17% 416ms 0.81% std::_Rb_tree_iterator::operator-- (inline) 1ms 0.0019% 81.17% 368ms 0.71% Cell::GetCellId 6ms 0.012% 81.18% 368ms 0.71% CellPropertyCollection::GetPropertiesType (inline) 138ms 0.27% 81.45% 366ms 0.71% Inverse 348ms 0.68% 82.12% 348ms 0.68% std::_Rb_tree_decrement 0 0% 82.12% 332ms 0.64% VertexMeshWriter::WriteVtkUsingMesh 33ms 0.064% 82.19% 322ms 0.62% tetgen::tetgenmesh::enext2fnext 14ms 0.027% 82.21% 320ms 0.62% VertexMesh::CalculateUnitNormalToFaceWithArea 318ms 0.62% 82.83% 318ms 0.62% boost::numeric::ublas::c_vector::operator() 9ms 0.017% 82.85% 299ms 0.58% std::vector::insert (inline) 0 0% 82.85% 296ms 0.57% boost::numeric::ublas::inner_prod (inline) 14ms 0.027% 82.88% 296ms 0.57% boost::numeric::ublas::vector_scalar_binary::evaluate 0 0% 82.88% 296ms 0.57% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 229ms 0.44% 83.32% 294ms 0.57% tetgen::tetgenmesh::fnextself 77ms 0.15% 83.47% 293ms 0.57% boost::numeric::ublas::indexing_vector_assign 1ms 0.0019% 83.47% 292ms 0.57% tcache_get (inline) 291ms 0.56% 84.04% 291ms 0.56% tcache_get_n (inline) 290ms 0.56% 84.60% 290ms 0.56% tetgen::tetgenmesh::triface::triface 65ms 0.13% 84.72% 289ms 0.56% __dynamic_cast 3ms 0.0058% 84.73% 284ms 0.55% boost::numeric::ublas::c_vector::operator= (inline) 67ms 0.13% 84.86% 281ms 0.55% tetgen::tetgenmesh::queue::pop 20ms 0.039% 84.90% 280ms 0.54% tetgen::tetgenmesh::enextfnext 53ms 0.1% 85.00% 280ms 0.54% tetgen::tetgenmesh::queue::push 181ms 0.35% 85.35% 264ms 0.51% AbstractTetrahedralMesh::GetElement 4ms 0.0078% 85.36% 260ms 0.5% AbstractTetrahedralElement::AbstractTetrahedralElement 15ms 0.029% 85.39% 258ms 0.5% boost::numeric::ublas::vector_reference::operator() (inline)