File: Test3dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 65823ms, 87.92% of 74867ms total Dropped 890 nodes (cum <= 374.33ms) flat flat% sum% cum cum% 0 0% 0% 74802ms 99.91% __libc_start_call_main 0 0% 0% 74802ms 99.91% __libc_start_main_impl 0 0% 0% 74802ms 99.91% _start 0 0% 0% 74785ms 99.89% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 74785ms 99.89% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 74785ms 99.89% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 74785ms 99.89% main 0 0% 0% 74744ms 99.84% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 74744ms 99.84% CxxTest::TestRunner::runTest (inline) 0 0% 0% 74744ms 99.84% Test3dTissueRepresentativeSimulation::Test3DHoneycombMeshWithGhostNodes 0 0% 0% 74437ms 99.43% AbstractCellBasedSimulation::Solve 0 0% 0% 62891ms 84.00% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 62837ms 83.93% MeshBasedCellPopulation::Update 0 0% 0% 39520ms 52.79% MeshBasedCellPopulation::CreateVoronoiTessellation (inline) 0 0% 0% 39520ms 52.79% MeshBasedCellPopulation::TessellateIfNeeded 322ms 0.43% 0.43% 33983ms 45.39% VertexMesh::VertexMesh 0 0% 0.43% 18608ms 24.85% MutableMesh::ReMesh 537ms 0.72% 1.15% 14708ms 19.65% TetrahedralMesh::EdgeIterator::operator++ 0 0% 1.15% 12971ms 17.33% tetgen::tetrahedralize 2ms 0.0027% 1.15% 12834ms 17.14% tetgen::tetgenmesh::delaunizevertices 7ms 0.0093% 1.16% 12825ms 17.13% tetgen::tetgenmesh::incrflipdelaunay 21ms 0.028% 1.19% 12622ms 16.86% std::set::insert (inline) 196ms 0.26% 1.45% 12119ms 16.19% std::_Rb_tree::_M_insert_unique 493ms 0.66% 2.11% 11362ms 15.18% tetgen::tetgenmesh::lawson 501ms 0.67% 2.78% 11162ms 14.91% VertexElement::AddFace 3028ms 4.04% 6.82% 11030ms 14.73% std::_Rb_tree::_M_lower_bound (inline) 241ms 0.32% 7.14% 10090ms 13.48% std::_Rb_tree::find (inline) 0 0% 7.14% 9550ms 12.76% std::set::count (inline) 8703ms 11.62% 18.77% 8703ms 11.62% std::_Rb_tree_increment 106ms 0.14% 18.91% 7440ms 9.94% std::less::operator() (inline) 7392ms 9.87% 28.78% 7392ms 9.87% std::operator< (inline) 207ms 0.28% 29.06% 7180ms 9.59% operator new 297ms 0.4% 29.46% 7026ms 9.38% std::_Rb_tree::_M_insert_ (inline) 1085ms 1.45% 30.91% 6902ms 9.22% __GI___libc_malloc 5ms 0.0067% 30.91% 6332ms 8.46% std::set_intersection (inline) 328ms 0.44% 31.35% 6327ms 8.45% std::__set_intersection 1ms 0.0013% 31.35% 6292ms 8.40% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 31.35% 6104ms 8.15% ForwardEulerNumericalMethod::UpdateAllNodePositions 6ms 0.008% 31.36% 6081ms 8.12% AbstractNumericalMethod::ComputeForcesIncludingDamping 13ms 0.017% 31.38% 5726ms 7.65% std::_Rb_tree::~_Rb_tree (inline) 43ms 0.057% 31.43% 5720ms 7.64% Node::AddElement 2555ms 3.41% 34.85% 5712ms 7.63% std::_Rb_tree::_M_erase 47ms 0.063% 34.91% 5677ms 7.58% std::__new_allocator::allocate (inline) 0 0% 34.91% 5658ms 7.56% std::allocator_traits::allocate (inline) 0 0% 34.91% 5639ms 7.53% std::set::~set (inline) 0 0% 34.91% 5585ms 7.46% VertexMesh::~VertexMesh 158ms 0.21% 35.12% 5483ms 7.32% std::_Rb_tree_const_iterator::operator++ (inline) 3954ms 5.28% 40.40% 5446ms 7.27% _int_malloc 1482ms 1.98% 42.38% 5323ms 7.11% __GI___libc_free 1302ms 1.74% 44.12% 5220ms 6.97% std::_Rb_tree::_M_get_insert_unique_pos 5205ms 6.95% 51.07% 5205ms 6.95% std::_Rb_tree::_S_right (inline) 6ms 0.008% 51.08% 5101ms 6.81% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 0 0% 51.08% 5092ms 6.80% MeshBasedCellPopulation::UpdateNodePairs 0 0% 51.08% 5067ms 6.77% AbstractCellPopulation::WriteResultsToFiles 14ms 0.019% 51.10% 4881ms 6.52% MeshBasedCellPopulation::SpringIterator::operator++ 134ms 0.18% 51.28% 4624ms 6.18% std::__new_allocator::deallocate (inline) 0 0% 51.28% 4592ms 6.13% std::_Rb_tree::_M_create_node (inline) 0 0% 51.28% 4580ms 6.12% std::allocator_traits::deallocate (inline) 3ms 0.004% 51.28% 4551ms 6.08% TetrahedralMesh::ImportFromMesher 0 0% 51.28% 4542ms 6.07% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 51.28% 4533ms 6.05% std::_Rb_tree::_M_get_node (inline) 62ms 0.083% 51.37% 4299ms 5.74% MutableElement::AddNode 1268ms 1.69% 53.06% 3837ms 5.13% _int_free 232ms 0.31% 53.37% 3678ms 4.91% VertexMesh::GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex 222ms 0.3% 53.67% 3638ms 4.86% Node::~Node 95ms 0.13% 53.79% 3615ms 4.83% tetgen::tetgenmesh::insphere_sos 3219ms 4.30% 58.09% 3509ms 4.69% tetgen::insphere 4ms 0.0053% 58.10% 3484ms 4.65% MeshBasedCellPopulationWithGhostNodes::WriteVtkResultsToFile 2ms 0.0027% 58.10% 3478ms 4.65% std::_Rb_tree_iterator::operator++ (inline) 273ms 0.36% 58.47% 3411ms 4.56% VertexMesh::Clear 2849ms 3.81% 62.27% 2849ms 3.81% Node::GetIndex 192ms 0.26% 62.53% 2772ms 3.70% tetgen::tetgenmesh::flip23 1745ms 2.33% 64.86% 2604ms 3.48% malloc_consolidate 27ms 0.036% 64.89% 2474ms 3.30% std::_Vector_base::_M_deallocate (inline) 0 0% 64.89% 2329ms 3.11% std::vector::~vector (inline) 3ms 0.004% 64.90% 2328ms 3.11% Element::Element 2314ms 3.09% 67.99% 2314ms 3.09% std::_Rb_tree_insert_and_rebalance 0 0% 67.99% 2283ms 3.05% std::_Vector_base::~_Vector_base (inline) 3ms 0.004% 67.99% 2280ms 3.05% _int_free_maybe_consolidate 0 0% 67.99% 2140ms 2.86% std::_Rb_tree::_M_drop_node (inline) 0 0% 67.99% 2133ms 2.85% std::_Rb_tree::_M_put_node (inline) 8ms 0.011% 68.00% 1980ms 2.64% Element::RegisterWithNodes (inline) 1919ms 2.56% 70.57% 1919ms 2.56% unlink_chunk 178ms 0.24% 70.80% 1826ms 2.44% tetgen::tetgenmesh::flip32 264ms 0.35% 71.16% 1778ms 2.37% TetrahedralMesh::Clear 8ms 0.011% 71.17% 1735ms 2.32% VertexMesh::GenerateVerticesFromElementCircumcentres 52ms 0.069% 71.24% 1488ms 1.99% std::map::operator[] 1348ms 1.80% 73.04% 1443ms 1.93% tetgen::orient3d 1251ms 1.67% 74.71% 1373ms 1.83% AbstractElement::GetNodeGlobalIndex 69ms 0.092% 74.80% 1349ms 1.80% std::vector::_M_realloc_insert 0 0% 74.80% 1336ms 1.78% std::_Rb_tree::lower_bound (inline) 0 0% 74.80% 1336ms 1.78% std::map::lower_bound (inline) 210ms 0.28% 75.08% 1328ms 1.77% tetgen::tetgenmesh::enqueueflipface 0 0% 75.08% 1303ms 1.74% VoronoiDataWriter::Visit 41ms 0.055% 75.14% 1261ms 1.68% tetgen::tetgenmesh::locate 95ms 0.13% 75.26% 1158ms 1.55% tetgen::tetgenmesh::preciselocate 5ms 0.0067% 75.27% 1130ms 1.51% std::_Vector_base::_M_allocate (inline) 141ms 0.19% 75.46% 1096ms 1.46% std::vector::push_back (inline) 0 0% 75.46% 1062ms 1.42% TetrahedralMesh::RefreshJacobianCachedData 1059ms 1.41% 76.87% 1059ms 1.41% Node::rGetLocation 446ms 0.6% 77.47% 1026ms 1.37% AbstractElement::GetNodeLocation 1007ms 1.35% 78.81% 1007ms 1.35% AbstractElement::IsDeleted 3ms 0.004% 78.82% 858ms 1.15% AbstractTetrahedralElement::CalculateInverseJacobian 17ms 0.023% 78.84% 805ms 1.08% AbstractTetrahedralElement::CalculateJacobian 12ms 0.016% 78.86% 750ms 1.00% Element::CalculateCircumsphere 0 0% 78.86% 744ms 0.99% AbstractTwoBodyInteractionForce::AddForceContribution 477ms 0.64% 79.49% 744ms 0.99% tetgen::tetgenmesh::fnextself 741ms 0.99% 80.48% 741ms 0.99% tetgen::tetgenmesh::triface::triface 22ms 0.029% 80.51% 733ms 0.98% boost::numeric::ublas::vector_assign (inline) 710ms 0.95% 81.46% 710ms 0.95% tetgen::tetgenmesh::triface::operator= 18ms 0.024% 81.48% 693ms 0.93% AbstractVariableSizeTwoBodyInteractionForce::CalculateForceBetweenNodes 10ms 0.013% 81.50% 675ms 0.9% boost::numeric::ublas::c_vector::c_vector (inline) 664ms 0.89% 82.38% 664ms 0.89% tetgen::tetgenmesh::oppo 643ms 0.86% 83.24% 643ms 0.86% [libchaste_mesh.so] 41ms 0.055% 83.30% 642ms 0.86% AbstractTetrahedralElement::RefreshJacobian 50ms 0.067% 83.37% 633ms 0.85% __atan2 591ms 0.79% 84.15% 591ms 0.79% std::vector::size (inline) 478ms 0.64% 84.79% 583ms 0.78% __ieee754_atan2_fma 0 0% 84.79% 534ms 0.71% std::set::find (inline) 23ms 0.031% 84.82% 526ms 0.7% VertexMesh::CalculateUnitNormalToFaceWithArea 0 0% 84.82% 502ms 0.67% boost::numeric::ublas::inner_prod (inline) 58ms 0.077% 84.90% 502ms 0.67% tetgen::tetgenmesh::enextfnext 0 0% 84.90% 499ms 0.67% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 4ms 0.0053% 84.91% 498ms 0.67% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 34ms 0.045% 84.95% 494ms 0.66% boost::numeric::ublas::vector_scalar_binary::evaluate 0 0% 84.95% 494ms 0.66% std::insert_iterator::operator= (inline) 39ms 0.052% 85.00% 487ms 0.65% tetgen::tetgenmesh::enext2fnext 313ms 0.42% 85.42% 477ms 0.64% tetgen::tetgenmesh::sym 1ms 0.0013% 85.42% 456ms 0.61% std::_Rb_tree::_M_insert_unique_ (inline) 154ms 0.21% 85.63% 440ms 0.59% boost::numeric::ublas::indexing_vector_assign 16ms 0.021% 85.65% 423ms 0.57% std::vector::insert (inline) 422ms 0.56% 86.21% 422ms 0.56% tetgen::tetgenmesh::org 10ms 0.013% 86.23% 416ms 0.56% CellPropertyCollection::GetPropertiesType (inline) 415ms 0.55% 86.78% 415ms 0.55% boost::numeric::ublas::c_vector::operator() 6ms 0.008% 86.79% 414ms 0.55% boost::numeric::ublas::c_vector::operator= (inline) 6ms 0.008% 86.80% 409ms 0.55% VertexElement::~VertexElement 0 0% 86.80% 407ms 0.54% VertexMeshWriter::WriteVtkUsingMesh 293ms 0.39% 87.19% 405ms 0.54% tetgen::tetgenmesh::bond 17ms 0.023% 87.21% 400ms 0.53% std::_Rb_tree_iterator::operator-- (inline) 187ms 0.25% 87.46% 393ms 0.52% boost::numeric::ublas::vector_inner_prod::apply (inline) 216ms 0.29% 87.75% 388ms 0.52% AbstractTetrahedralMesh::GetElement 18ms 0.024% 87.77% 384ms 0.51% tetgen::tetgenmesh::queue::push 3ms 0.004% 87.78% 382ms 0.51% Cell::GetCellId 106ms 0.14% 87.92% 379ms 0.51% __dynamic_cast