File: Test3dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 66990ms, 87.19% of 76835ms total Dropped 866 nodes (cum <= 384.18ms) flat flat% sum% cum cum% 0 0% 0% 76777ms 99.92% __libc_start_call_main 0 0% 0% 76777ms 99.92% __libc_start_main_impl 0 0% 0% 76777ms 99.92% _start 0 0% 0% 76760ms 99.90% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 76760ms 99.90% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 76760ms 99.90% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 76760ms 99.90% main 0 0% 0% 76718ms 99.85% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 76718ms 99.85% CxxTest::TestRunner::runTest (inline) 0 0% 0% 76718ms 99.85% Test3dTissueRepresentativeSimulation::Test3DHoneycombMeshWithGhostNodes 0 0% 0% 76419ms 99.46% AbstractCellBasedSimulation::Solve 0 0% 0% 64797ms 84.33% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 64739ms 84.26% MeshBasedCellPopulation::Update 0 0% 0% 41225ms 53.65% MeshBasedCellPopulation::CreateVoronoiTessellation (inline) 0 0% 0% 41225ms 53.65% MeshBasedCellPopulation::TessellateIfNeeded 355ms 0.46% 0.46% 35286ms 45.92% VertexMesh::VertexMesh 0 0% 0.46% 18764ms 24.42% MutableMesh::ReMesh 525ms 0.68% 1.15% 14840ms 19.31% TetrahedralMesh::EdgeIterator::operator++ 18ms 0.023% 1.17% 13056ms 16.99% std::set::insert (inline) 0 0% 1.17% 12926ms 16.82% tetgen::tetrahedralize 1ms 0.0013% 1.17% 12794ms 16.65% tetgen::tetgenmesh::delaunizevertices 7ms 0.0091% 1.18% 12787ms 16.64% tetgen::tetgenmesh::incrflipdelaunay 205ms 0.27% 1.45% 12543ms 16.32% std::_Rb_tree::_M_insert_unique 531ms 0.69% 2.14% 11374ms 14.80% VertexElement::AddFace 595ms 0.77% 2.91% 11333ms 14.75% tetgen::tetgenmesh::lawson 3165ms 4.12% 7.03% 11279ms 14.68% std::_Rb_tree::_M_lower_bound (inline) 253ms 0.33% 7.36% 10289ms 13.39% std::_Rb_tree::find (inline) 0 0% 7.36% 9707ms 12.63% std::set::count (inline) 9059ms 11.79% 19.15% 9059ms 11.79% std::_Rb_tree_increment 105ms 0.14% 19.29% 7481ms 9.74% std::less::operator() (inline) 7434ms 9.68% 28.96% 7434ms 9.68% std::operator< (inline) 207ms 0.27% 29.23% 7376ms 9.60% operator new 246ms 0.32% 29.55% 7207ms 9.38% std::_Rb_tree::_M_insert_ (inline) 1176ms 1.53% 31.08% 7121ms 9.27% __GI___libc_malloc 2ms 0.0026% 31.08% 6694ms 8.71% std::set_intersection (inline) 357ms 0.46% 31.55% 6692ms 8.71% std::__set_intersection 2ms 0.0026% 31.55% 6333ms 8.24% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 31.55% 6153ms 8.01% ForwardEulerNumericalMethod::UpdateAllNodePositions 4ms 0.0052% 31.56% 6128ms 7.98% AbstractNumericalMethod::ComputeForcesIncludingDamping 30ms 0.039% 31.60% 6025ms 7.84% Node::AddElement 0 0% 31.60% 5986ms 7.79% VertexMesh::~VertexMesh 12ms 0.016% 31.61% 5864ms 7.63% std::_Rb_tree::~_Rb_tree (inline) 2634ms 3.43% 35.04% 5849ms 7.61% std::_Rb_tree::_M_erase 203ms 0.26% 35.30% 5824ms 7.58% std::_Rb_tree_const_iterator::operator++ (inline) 41ms 0.053% 35.36% 5802ms 7.55% std::__new_allocator::allocate (inline) 0 0% 35.36% 5782ms 7.53% std::set::~set (inline) 0 0% 35.36% 5772ms 7.51% std::allocator_traits::allocate (inline) 4102ms 5.34% 40.70% 5602ms 7.29% _int_malloc 1499ms 1.95% 42.65% 5561ms 7.24% __GI___libc_free 5550ms 7.22% 49.87% 5550ms 7.22% std::_Rb_tree::_S_right (inline) 1306ms 1.70% 51.57% 5463ms 7.11% std::_Rb_tree::_M_get_insert_unique_pos 3ms 0.0039% 51.57% 5130ms 6.68% MeshBasedCellPopulation::UpdateNodePairs 6ms 0.0078% 51.58% 5107ms 6.65% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 0 0% 51.58% 5097ms 6.63% AbstractCellPopulation::WriteResultsToFiles 8ms 0.01% 51.59% 4912ms 6.39% MeshBasedCellPopulation::SpringIterator::operator++ 142ms 0.18% 51.78% 4856ms 6.32% std::__new_allocator::deallocate (inline) 0 0% 51.78% 4832ms 6.29% std::allocator_traits::deallocate (inline) 13ms 0.017% 51.79% 4670ms 6.08% TetrahedralMesh::ImportFromMesher 0 0% 51.79% 4621ms 6.01% std::_Rb_tree::_M_create_node (inline) 0 0% 51.79% 4583ms 5.96% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 51.79% 4569ms 5.95% std::_Rb_tree::_M_get_node (inline) 61ms 0.079% 51.87% 4532ms 5.90% MutableElement::AddNode 1230ms 1.60% 53.47% 4061ms 5.29% _int_free 274ms 0.36% 53.83% 3789ms 4.93% Node::~Node 235ms 0.31% 54.14% 3723ms 4.85% VertexMesh::GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex 288ms 0.37% 54.51% 3562ms 4.64% VertexMesh::Clear 0 0% 54.51% 3517ms 4.58% std::_Rb_tree_iterator::operator++ (inline) 101ms 0.13% 54.64% 3512ms 4.57% tetgen::tetgenmesh::insphere_sos 2ms 0.0026% 54.65% 3503ms 4.56% MeshBasedCellPopulationWithGhostNodes::WriteVtkResultsToFile 3120ms 4.06% 58.71% 3399ms 4.42% tetgen::insphere 2883ms 3.75% 62.46% 2883ms 3.75% Node::GetIndex 1927ms 2.51% 64.97% 2871ms 3.74% malloc_consolidate 220ms 0.29% 65.25% 2750ms 3.58% tetgen::tetgenmesh::flip23 13ms 0.017% 65.27% 2709ms 3.53% std::_Vector_base::_M_deallocate (inline) 0 0% 65.27% 2580ms 3.36% std::vector::~vector (inline) 8ms 0.01% 65.28% 2545ms 3.31% _int_free_maybe_consolidate 1ms 0.0013% 65.28% 2539ms 3.30% std::_Vector_base::~_Vector_base (inline) 2492ms 3.24% 68.52% 2492ms 3.24% std::_Rb_tree_insert_and_rebalance 3ms 0.0039% 68.53% 2416ms 3.14% Element::Element 0 0% 68.53% 2147ms 2.79% std::_Rb_tree::_M_drop_node (inline) 0 0% 68.53% 2136ms 2.78% std::_Rb_tree::_M_put_node (inline) 3ms 0.0039% 68.53% 2017ms 2.63% Element::RegisterWithNodes (inline) 2013ms 2.62% 71.15% 2013ms 2.62% unlink_chunk 147ms 0.19% 71.34% 1930ms 2.51% tetgen::tetgenmesh::flip32 2ms 0.0026% 71.35% 1911ms 2.49% VertexMesh::GenerateVerticesFromElementCircumcentres 258ms 0.34% 71.68% 1758ms 2.29% TetrahedralMesh::Clear 65ms 0.085% 71.77% 1570ms 2.04% std::map::operator[] 0 0% 71.77% 1416ms 1.84% std::_Rb_tree::lower_bound (inline) 0 0% 71.77% 1416ms 1.84% std::map::lower_bound (inline) 1333ms 1.73% 73.50% 1406ms 1.83% tetgen::orient3d 67ms 0.087% 73.59% 1372ms 1.79% std::vector::_M_realloc_insert 216ms 0.28% 73.87% 1336ms 1.74% tetgen::tetgenmesh::enqueueflipface 0 0% 73.87% 1321ms 1.72% VoronoiDataWriter::Visit 1165ms 1.52% 75.39% 1308ms 1.70% AbstractElement::GetNodeGlobalIndex 29ms 0.038% 75.42% 1248ms 1.62% tetgen::tetgenmesh::locate 6ms 0.0078% 75.43% 1209ms 1.57% std::_Vector_base::_M_allocate (inline) 530ms 0.69% 76.12% 1170ms 1.52% AbstractElement::GetNodeLocation 100ms 0.13% 76.25% 1169ms 1.52% tetgen::tetgenmesh::preciselocate 1166ms 1.52% 77.77% 1166ms 1.52% Node::rGetLocation 0 0% 77.77% 1141ms 1.49% TetrahedralMesh::RefreshJacobianCachedData 124ms 0.16% 77.93% 1120ms 1.46% std::vector::push_back (inline) 1039ms 1.35% 79.28% 1039ms 1.35% AbstractElement::IsDeleted 11ms 0.014% 79.30% 915ms 1.19% AbstractTetrahedralElement::CalculateInverseJacobian 24ms 0.031% 79.33% 905ms 1.18% AbstractTetrahedralElement::CalculateJacobian 894ms 1.16% 80.49% 894ms 1.16% tetgen::tetgenmesh::triface::triface 501ms 0.65% 81.14% 869ms 1.13% tetgen::tetgenmesh::fnextself 20ms 0.026% 81.17% 867ms 1.13% Element::CalculateCircumsphere 1ms 0.0013% 81.17% 768ms 1% AbstractTwoBodyInteractionForce::AddForceContribution 758ms 0.99% 82.16% 758ms 0.99% tetgen::tetgenmesh::oppo 21ms 0.027% 82.19% 743ms 0.97% boost::numeric::ublas::vector_assign (inline) 14ms 0.018% 82.20% 711ms 0.93% AbstractVariableSizeTwoBodyInteractionForce::CalculateForceBetweenNodes 47ms 0.061% 82.26% 709ms 0.92% AbstractTetrahedralElement::RefreshJacobian 16ms 0.021% 82.29% 702ms 0.91% boost::numeric::ublas::c_vector::c_vector (inline) 684ms 0.89% 83.18% 684ms 0.89% std::vector::size (inline) 648ms 0.84% 84.02% 648ms 0.84% [libchaste_mesh.so] 46ms 0.06% 84.08% 592ms 0.77% __atan2 0 0% 84.08% 576ms 0.75% std::set::find (inline) 53ms 0.069% 84.15% 571ms 0.74% tetgen::tetgenmesh::enextfnext 562ms 0.73% 84.88% 562ms 0.73% tetgen::tetgenmesh::triface::operator= 22ms 0.029% 84.91% 547ms 0.71% VertexMesh::CalculateUnitNormalToFaceWithArea 441ms 0.57% 85.48% 545ms 0.71% __ieee754_atan2_fma 0 0% 85.48% 525ms 0.68% std::insert_iterator::operator= (inline) 31ms 0.04% 85.52% 521ms 0.68% tetgen::tetgenmesh::enext2fnext 0 0% 85.52% 518ms 0.67% boost::numeric::ublas::inner_prod (inline) 0 0% 85.52% 517ms 0.67% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 2ms 0.0026% 85.52% 515ms 0.67% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 30ms 0.039% 85.56% 513ms 0.67% boost::numeric::ublas::vector_scalar_binary::evaluate 475ms 0.62% 86.18% 475ms 0.62% boost::numeric::ublas::c_vector::operator() 0 0% 86.18% 471ms 0.61% std::_Rb_tree::_M_insert_unique_ (inline) 7ms 0.0091% 86.19% 468ms 0.61% CellPropertyCollection::GetPropertiesType (inline) 141ms 0.18% 86.37% 457ms 0.59% boost::numeric::ublas::indexing_vector_assign 266ms 0.35% 86.72% 435ms 0.57% tetgen::tetgenmesh::sym 26ms 0.034% 86.75% 431ms 0.56% std::_Rb_tree_iterator::operator-- (inline) 2ms 0.0026% 86.76% 422ms 0.55% Cell::GetCellId 163ms 0.21% 86.97% 421ms 0.55% boost::numeric::ublas::vector_inner_prod::apply (inline) 0 0% 86.97% 409ms 0.53% VertexMeshWriter::WriteVtkUsingMesh 4ms 0.0052% 86.97% 404ms 0.53% boost::numeric::ublas::c_vector::operator= (inline) 91ms 0.12% 87.09% 403ms 0.52% __dynamic_cast 18ms 0.023% 87.12% 402ms 0.52% std::vector::insert (inline) 33ms 0.043% 87.16% 402ms 0.52% tetgen::tetgenmesh::queue::push 4ms 0.0052% 87.16% 399ms 0.52% AbstractTetrahedralElement::AbstractTetrahedralElement 7ms 0.0091% 87.17% 396ms 0.52% VertexElement::~VertexElement 10ms 0.013% 87.19% 386ms 0.5% VertexMesh::GetVolumeOfElement