File: Test3dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 56393ms, 87.73% of 64278ms total Dropped 859 nodes (cum <= 321.39ms) flat flat% sum% cum cum% 0 0% 0% 64218ms 99.91% __libc_start_call_main 0 0% 0% 64218ms 99.91% __libc_start_main_impl 0 0% 0% 64218ms 99.91% _start 0 0% 0% 64204ms 99.88% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 64204ms 99.88% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 64204ms 99.88% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 64204ms 99.88% main 0 0% 0% 64167ms 99.83% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 64167ms 99.83% CxxTest::TestRunner::runTest (inline) 0 0% 0% 64167ms 99.83% Test3dTissueRepresentativeSimulation::Test3DHoneycombMeshWithGhostNodes 0 0% 0% 63919ms 99.44% AbstractCellBasedSimulation::Solve 0 0% 0% 54824ms 85.29% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 54773ms 85.21% MeshBasedCellPopulation::Update 0 0% 0% 33256ms 51.74% MeshBasedCellPopulation::CreateVoronoiTessellation (inline) 0 0% 0% 33256ms 51.74% MeshBasedCellPopulation::TessellateIfNeeded 311ms 0.48% 0.48% 28967ms 45.07% VertexMesh::VertexMesh 0 0% 0.48% 17534ms 27.28% MutableMesh::ReMesh 0 0% 0.48% 12818ms 19.94% tetgen::tetrahedralize 3ms 0.0047% 0.49% 12684ms 19.73% tetgen::tetgenmesh::delaunizevertices 8ms 0.012% 0.5% 12677ms 19.72% tetgen::tetgenmesh::incrflipdelaunay 598ms 0.93% 1.43% 12648ms 19.68% TetrahedralMesh::EdgeIterator::operator++ 549ms 0.85% 2.29% 11179ms 17.39% tetgen::tetgenmesh::lawson 35ms 0.054% 2.34% 11064ms 17.21% std::set::insert (inline) 210ms 0.33% 2.67% 10554ms 16.42% std::_Rb_tree::_M_insert_unique 453ms 0.7% 3.37% 10163ms 15.81% VertexElement::AddFace 3101ms 4.82% 8.20% 9329ms 14.51% std::_Rb_tree::_M_lower_bound (inline) 226ms 0.35% 8.55% 8667ms 13.48% std::_Rb_tree::find (inline) 0 0% 8.55% 8136ms 12.66% std::set::count (inline) 260ms 0.4% 8.95% 6336ms 9.86% std::_Rb_tree::_M_insert_ (inline) 6043ms 9.40% 18.35% 6043ms 9.40% std::_Rb_tree_increment 223ms 0.35% 18.70% 6026ms 9.37% operator new 108ms 0.17% 18.87% 5971ms 9.29% std::less::operator() (inline) 5918ms 9.21% 28.07% 5918ms 9.21% std::operator< (inline) 1092ms 1.70% 29.77% 5721ms 8.90% __GI___libc_malloc 0 0% 29.77% 5457ms 8.49% OffLatticeSimulation::UpdateCellLocationsAndTopology 1ms 0.0016% 29.78% 5320ms 8.28% ForwardEulerNumericalMethod::UpdateAllNodePositions 6ms 0.0093% 29.78% 5294ms 8.24% AbstractNumericalMethod::ComputeForcesIncludingDamping 7ms 0.011% 29.80% 5022ms 7.81% std::set_intersection (inline) 272ms 0.42% 30.22% 5015ms 7.80% std::__set_intersection 45ms 0.07% 30.29% 4878ms 7.59% std::__new_allocator::allocate (inline) 0 0% 30.29% 4861ms 7.56% std::allocator_traits::allocate (inline) 5ms 0.0078% 30.30% 4690ms 7.30% std::_Rb_tree::~_Rb_tree (inline) 1941ms 3.02% 33.32% 4684ms 7.29% std::_Rb_tree::_M_erase 0 0% 33.32% 4628ms 7.20% std::set::~set (inline) 28ms 0.044% 33.36% 4453ms 6.93% Node::AddElement 1248ms 1.94% 35.30% 4442ms 6.91% __GI___libc_free 8ms 0.012% 35.31% 4389ms 6.83% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 1ms 0.0016% 35.32% 4373ms 6.80% MeshBasedCellPopulation::UpdateNodePairs 1217ms 1.89% 37.21% 4323ms 6.73% std::_Rb_tree::_M_get_insert_unique_pos 3156ms 4.91% 42.12% 4316ms 6.71% _int_malloc 0 0% 42.12% 4303ms 6.69% VertexMesh::~VertexMesh 192ms 0.3% 42.42% 4254ms 6.62% std::_Rb_tree_const_iterator::operator++ (inline) 11ms 0.017% 42.43% 4208ms 6.55% MeshBasedCellPopulation::SpringIterator::operator++ 0 0% 42.43% 3965ms 6.17% std::_Rb_tree::_M_create_node (inline) 0 0% 42.43% 3948ms 6.14% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 42.43% 3918ms 6.10% std::_Rb_tree::_M_get_node (inline) 3883ms 6.04% 48.48% 3883ms 6.04% std::_Rb_tree::_S_right (inline) 133ms 0.21% 48.68% 3831ms 5.96% std::__new_allocator::deallocate (inline) 0 0% 48.68% 3815ms 5.94% std::allocator_traits::deallocate (inline) 8ms 0.012% 48.69% 3783ms 5.89% TetrahedralMesh::ImportFromMesher 110ms 0.17% 48.87% 3518ms 5.47% tetgen::tetgenmesh::insphere_sos 0 0% 48.87% 3444ms 5.36% AbstractCellPopulation::WriteResultsToFiles 82ms 0.13% 48.99% 3391ms 5.28% MutableElement::AddNode 3089ms 4.81% 53.80% 3390ms 5.27% tetgen::insphere 1147ms 1.78% 55.58% 3190ms 4.96% _int_free 171ms 0.27% 55.85% 2851ms 4.44% Node::~Node 213ms 0.33% 56.18% 2686ms 4.18% VertexMesh::Clear 215ms 0.33% 56.52% 2678ms 4.17% tetgen::tetgenmesh::flip23 3ms 0.0047% 56.52% 2282ms 3.55% MeshBasedCellPopulationWithGhostNodes::WriteVtkResultsToFile 225ms 0.35% 56.87% 2265ms 3.52% VertexMesh::GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex 2211ms 3.44% 60.31% 2211ms 3.44% std::_Rb_tree_insert_and_rebalance 2194ms 3.41% 63.72% 2194ms 3.41% Node::GetIndex 0 0% 63.72% 2072ms 3.22% std::_Rb_tree_iterator::operator++ (inline) 1405ms 2.19% 65.91% 2042ms 3.18% malloc_consolidate 25ms 0.039% 65.95% 1931ms 3.00% std::_Vector_base::_M_deallocate (inline) 0 0% 65.95% 1927ms 3.00% std::_Rb_tree::_M_drop_node (inline) 0 0% 65.95% 1909ms 2.97% std::_Rb_tree::_M_put_node (inline) 3ms 0.0047% 65.95% 1833ms 2.85% Element::Element 173ms 0.27% 66.22% 1824ms 2.84% tetgen::tetgenmesh::flip32 0 0% 66.22% 1810ms 2.82% std::vector::~vector (inline) 7ms 0.011% 66.23% 1784ms 2.78% _int_free_maybe_consolidate 1ms 0.0016% 66.23% 1754ms 2.73% std::_Vector_base::~_Vector_base (inline) 221ms 0.34% 66.58% 1515ms 2.36% TetrahedralMesh::Clear 3ms 0.0047% 66.58% 1513ms 2.35% Element::RegisterWithNodes (inline) 1464ms 2.28% 68.86% 1464ms 2.28% unlink_chunk 1338ms 2.08% 70.94% 1434ms 2.23% tetgen::orient3d 1ms 0.0016% 70.94% 1364ms 2.12% VertexMesh::GenerateVerticesFromElementCircumcentres 148ms 0.23% 71.17% 1311ms 2.04% tetgen::tetgenmesh::enqueueflipface 44ms 0.068% 71.24% 1246ms 1.94% tetgen::tetgenmesh::locate 56ms 0.087% 71.33% 1184ms 1.84% std::map::operator[] 85ms 0.13% 71.46% 1153ms 1.79% tetgen::tetgenmesh::preciselocate 56ms 0.087% 71.55% 1138ms 1.77% std::vector::_M_realloc_insert 968ms 1.51% 73.05% 1090ms 1.70% AbstractElement::GetNodeGlobalIndex 0 0% 73.05% 1067ms 1.66% std::_Rb_tree::lower_bound (inline) 0 0% 73.05% 1067ms 1.66% std::map::lower_bound (inline) 103ms 0.16% 73.21% 964ms 1.50% std::vector::push_back (inline) 3ms 0.0047% 73.22% 946ms 1.47% std::_Vector_base::_M_allocate (inline) 0 0% 73.22% 923ms 1.44% VoronoiDataWriter::Visit 2ms 0.0031% 73.22% 905ms 1.41% TetrahedralMesh::RefreshJacobianCachedData 836ms 1.30% 74.52% 836ms 1.30% tetgen::tetgenmesh::triface::triface 367ms 0.57% 75.09% 798ms 1.24% AbstractElement::GetNodeLocation 762ms 1.19% 76.28% 762ms 1.19% Node::rGetLocation 7ms 0.011% 76.29% 753ms 1.17% AbstractTetrahedralElement::CalculateInverseJacobian 746ms 1.16% 77.45% 746ms 1.16% tetgen::tetgenmesh::oppo 2ms 0.0031% 77.45% 724ms 1.13% AbstractTwoBodyInteractionForce::AddForceContribution 701ms 1.09% 78.54% 701ms 1.09% AbstractElement::IsDeleted 20ms 0.031% 78.58% 680ms 1.06% AbstractTetrahedralElement::CalculateJacobian 10ms 0.016% 78.59% 671ms 1.04% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 22ms 0.034% 78.63% 659ms 1.03% boost::numeric::ublas::vector_assign (inline) 12ms 0.019% 78.64% 644ms 1.00% boost::numeric::ublas::c_vector::c_vector (inline) 348ms 0.54% 79.19% 637ms 0.99% tetgen::tetgenmesh::fnextself 635ms 0.99% 80.17% 635ms 0.99% [libchaste_mesh.so] 51ms 0.079% 80.25% 631ms 0.98% __atan2 14ms 0.022% 80.27% 619ms 0.96% Element::CalculateCircumsphere 601ms 0.94% 81.21% 601ms 0.94% tetgen::tetgenmesh::triface::operator= 471ms 0.73% 81.94% 580ms 0.9% __ieee754_atan2_fma 544ms 0.85% 82.79% 544ms 0.85% std::vector::size (inline) 0 0% 82.79% 530ms 0.82% std::set::find (inline) 0 0% 82.79% 526ms 0.82% boost::numeric::ublas::inner_prod (inline) 3ms 0.0047% 82.79% 524ms 0.82% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 47ms 0.073% 82.87% 522ms 0.81% AbstractTetrahedralElement::RefreshJacobian 27ms 0.042% 82.91% 521ms 0.81% boost::numeric::ublas::vector_scalar_binary::evaluate 342ms 0.53% 83.44% 488ms 0.76% tetgen::tetgenmesh::sym 5ms 0.0078% 83.45% 485ms 0.75% CellPropertyCollection::GetPropertiesType (inline) 0 0% 83.45% 483ms 0.75% std::insert_iterator::operator= (inline) 1ms 0.0016% 83.45% 461ms 0.72% Cell::GetCellId 66ms 0.1% 83.55% 458ms 0.71% tetgen::tetgenmesh::enextfnext 0 0% 83.55% 437ms 0.68% std::_Rb_tree::_M_insert_unique_ (inline) 188ms 0.29% 83.85% 432ms 0.67% boost::numeric::ublas::vector_inner_prod::apply (inline) 430ms 0.67% 84.51% 430ms 0.67% boost::numeric::ublas::c_vector::operator() 44ms 0.068% 84.58% 420ms 0.65% tetgen::tetgenmesh::enext2fnext 15ms 0.023% 84.61% 417ms 0.65% std::_Rb_tree_iterator::operator-- (inline) 15ms 0.023% 84.63% 411ms 0.64% VertexMesh::CalculateUnitNormalToFaceWithArea 287ms 0.45% 85.08% 410ms 0.64% tetgen::tetgenmesh::bond 111ms 0.17% 85.25% 408ms 0.63% boost::numeric::ublas::indexing_vector_assign 4ms 0.0062% 85.25% 404ms 0.63% AbstractCellProperty::IsSubType (inline) 63ms 0.098% 85.35% 400ms 0.62% __dynamic_cast 0 0% 85.35% 398ms 0.62% VertexMeshWriter::WriteVtkUsingMesh 212ms 0.33% 85.68% 390ms 0.61% AbstractTetrahedralMesh::GetElement 387ms 0.6% 86.28% 387ms 0.6% std::_Rb_tree_decrement 26ms 0.04% 86.33% 380ms 0.59% tetgen::tetgenmesh::queue::push 0 0% 86.33% 376ms 0.58% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 1ms 0.0016% 86.33% 367ms 0.57% boost::numeric::ublas::c_vector::operator= (inline) 366ms 0.57% 86.90% 366ms 0.57% tetgen::tetgenmesh::org 261ms 0.41% 87.30% 353ms 0.55% tetgen::tetgenmesh::link::add 58ms 0.09% 87.39% 338ms 0.53% boost::numeric::ublas::vector_reference::operator() (inline) 74ms 0.12% 87.51% 336ms 0.52% tetgen::tetgenmesh::queue::pop 5ms 0.0078% 87.52% 333ms 0.52% VertexElement::~VertexElement 2ms 0.0031% 87.52% 328ms 0.51% VertexMesh::GetVolumeOfElement 138ms 0.21% 87.73% 324ms 0.5% Inverse