File: Test3dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 46612ms, 86.03% of 54179ms total Dropped 856 nodes (cum <= 270.89ms) flat flat% sum% cum cum% 0 0% 0% 54122ms 99.89% __libc_start_call_main 0 0% 0% 54122ms 99.89% __libc_start_main_impl 0 0% 0% 54122ms 99.89% _start 0 0% 0% 54108ms 99.87% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 54108ms 99.87% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 54108ms 99.87% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 54108ms 99.87% main 0 0% 0% 54074ms 99.81% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 54074ms 99.81% CxxTest::TestRunner::runTest (inline) 0 0% 0% 54074ms 99.81% Test3dTissueRepresentativeSimulation::Test3DHoneycombMeshWithGhostNodes 0 0% 0% 53822ms 99.34% AbstractCellBasedSimulation::Solve 0 0% 0% 45211ms 83.45% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 45175ms 83.38% MeshBasedCellPopulation::Update 0 0% 0% 24970ms 46.09% MeshBasedCellPopulation::CreateVoronoiTessellation (inline) 0 0% 0% 24970ms 46.09% MeshBasedCellPopulation::TessellateIfNeeded 188ms 0.35% 0.35% 22386ms 41.32% VertexMesh::VertexMesh 0 0% 0.35% 16563ms 30.57% MutableMesh::ReMesh 0 0% 0.35% 12878ms 23.77% tetgen::tetrahedralize 0 0% 0.35% 12745ms 23.52% tetgen::tetgenmesh::delaunizevertices 7ms 0.013% 0.36% 12741ms 23.52% tetgen::tetgenmesh::incrflipdelaunay 546ms 1.01% 1.37% 11320ms 20.89% tetgen::tetgenmesh::lawson 617ms 1.14% 2.51% 11099ms 20.49% TetrahedralMesh::EdgeIterator::operator++ 24ms 0.044% 2.55% 9151ms 16.89% std::set::insert (inline) 327ms 0.6% 3.15% 8722ms 16.10% VertexElement::AddFace 249ms 0.46% 3.61% 8666ms 16.00% std::_Rb_tree::_M_insert_unique 2957ms 5.46% 9.07% 8440ms 15.58% std::_Rb_tree::_M_lower_bound (inline) 226ms 0.42% 9.49% 7953ms 14.68% std::_Rb_tree::find (inline) 0 0% 9.49% 7413ms 13.68% std::set::count (inline) 103ms 0.19% 9.68% 5368ms 9.91% std::less::operator() (inline) 5313ms 9.81% 19.49% 5313ms 9.81% std::operator< (inline) 273ms 0.5% 19.99% 5166ms 9.54% std::_Rb_tree::_M_insert_ (inline) 1ms 0.0018% 19.99% 4959ms 9.15% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 19.99% 4850ms 8.95% ForwardEulerNumericalMethod::UpdateAllNodePositions 3ms 0.0055% 20.00% 4813ms 8.88% AbstractNumericalMethod::ComputeForcesIncludingDamping 212ms 0.39% 20.39% 4396ms 8.11% operator new 4301ms 7.94% 28.33% 4301ms 7.94% std::_Rb_tree_increment 1100ms 2.03% 30.36% 4104ms 7.57% __GI___libc_malloc 2ms 0.0037% 30.36% 3972ms 7.33% MeshBasedCellPopulation::UpdateNodePairs 4ms 0.0074% 30.37% 3938ms 7.27% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 11ms 0.02% 30.39% 3841ms 7.09% MeshBasedCellPopulation::SpringIterator::operator++ 41ms 0.076% 30.46% 3816ms 7.04% std::__new_allocator::allocate (inline) 0 0% 30.46% 3799ms 7.01% std::allocator_traits::allocate (inline) 4ms 0.0074% 30.47% 3754ms 6.93% std::_Rb_tree::~_Rb_tree (inline) 1366ms 2.52% 32.99% 3748ms 6.92% std::_Rb_tree::_M_erase 0 0% 32.99% 3704ms 6.84% std::set::~set (inline) 1227ms 2.26% 35.26% 3565ms 6.58% std::_Rb_tree::_M_get_insert_unique_pos 0 0% 35.26% 3510ms 6.48% AbstractCellPopulation::WriteResultsToFiles 120ms 0.22% 35.48% 3423ms 6.32% tetgen::tetgenmesh::insphere_sos 1022ms 1.89% 37.37% 3368ms 6.22% __GI___libc_free 2994ms 5.53% 42.89% 3292ms 6.08% tetgen::insphere 0 0% 42.89% 3123ms 5.76% std::_Rb_tree::_M_create_node (inline) 0 0% 42.89% 3099ms 5.72% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 42.89% 3092ms 5.71% std::_Rb_tree::_M_get_node (inline) 2ms 0.0037% 42.89% 2999ms 5.54% std::set_intersection (inline) 243ms 0.45% 43.34% 2997ms 5.53% std::__set_intersection 20ms 0.037% 43.38% 2964ms 5.47% TetrahedralMesh::ImportFromMesher 31ms 0.057% 43.44% 2960ms 5.46% Node::AddElement 110ms 0.2% 43.64% 2960ms 5.46% std::__new_allocator::deallocate (inline) 0 0% 43.64% 2942ms 5.43% std::allocator_traits::deallocate (inline) 203ms 0.37% 44.02% 2795ms 5.16% tetgen::tetgenmesh::flip23 2753ms 5.08% 49.10% 2753ms 5.08% std::_Rb_tree::_S_right (inline) 2064ms 3.81% 52.91% 2716ms 5.01% _int_malloc 0 0% 52.91% 2604ms 4.81% VertexMesh::~VertexMesh 191ms 0.35% 53.26% 2444ms 4.51% VertexMesh::GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex 3ms 0.0055% 53.26% 2384ms 4.40% MeshBasedCellPopulationWithGhostNodes::WriteVtkResultsToFile 1213ms 2.24% 55.50% 2342ms 4.32% _int_free 176ms 0.32% 55.83% 2341ms 4.32% std::_Rb_tree_const_iterator::operator++ (inline) 85ms 0.16% 55.98% 2279ms 4.21% MutableElement::AddNode 2ms 0.0037% 55.99% 2262ms 4.18% std::_Rb_tree_iterator::operator++ (inline) 105ms 0.19% 56.18% 1934ms 3.57% Node::~Node 1880ms 3.47% 59.65% 1880ms 3.47% std::_Rb_tree_insert_and_rebalance 0 0% 59.65% 1837ms 3.39% std::_Rb_tree::_M_drop_node (inline) 0 0% 59.65% 1828ms 3.37% std::_Rb_tree::_M_put_node (inline) 162ms 0.3% 59.95% 1818ms 3.36% tetgen::tetgenmesh::flip32 149ms 0.28% 60.23% 1762ms 3.25% VertexMesh::Clear 3ms 0.0055% 60.23% 1455ms 2.69% Element::Element 1353ms 2.50% 62.73% 1443ms 2.66% tetgen::orient3d 1244ms 2.30% 65.03% 1244ms 2.30% Node::GetIndex 146ms 0.27% 65.29% 1223ms 2.26% TetrahedralMesh::Clear 162ms 0.3% 65.59% 1220ms 2.25% tetgen::tetgenmesh::enqueueflipface 25ms 0.046% 65.64% 1210ms 2.23% tetgen::tetgenmesh::locate 3ms 0.0055% 65.65% 1148ms 2.12% Element::RegisterWithNodes (inline) 95ms 0.18% 65.82% 1144ms 2.11% tetgen::tetgenmesh::preciselocate 11ms 0.02% 65.84% 1125ms 2.08% std::_Vector_base::_M_deallocate (inline) 677ms 1.25% 67.09% 1078ms 1.99% malloc_consolidate 0 0% 67.09% 1036ms 1.91% std::vector::~vector (inline) 57ms 0.11% 67.20% 1020ms 1.88% std::map::operator[] 53ms 0.098% 67.29% 978ms 1.81% std::vector::_M_realloc_insert 1ms 0.0018% 67.30% 936ms 1.73% std::_Vector_base::~_Vector_base (inline) 2ms 0.0037% 67.30% 912ms 1.68% _int_free_maybe_consolidate 0 0% 67.30% 896ms 1.65% std::_Rb_tree::lower_bound (inline) 0 0% 67.30% 896ms 1.65% std::map::lower_bound (inline) 0 0% 67.30% 895ms 1.65% VoronoiDataWriter::Visit 496ms 0.92% 68.21% 820ms 1.51% tetgen::tetgenmesh::fnextself 809ms 1.49% 69.71% 809ms 1.49% tetgen::tetgenmesh::triface::triface 809ms 1.49% 71.20% 809ms 1.49% unlink_chunk 10ms 0.018% 71.22% 779ms 1.44% VertexMesh::GenerateVerticesFromElementCircumcentres 100ms 0.18% 71.40% 777ms 1.43% std::vector::push_back (inline) 0 0% 71.40% 726ms 1.34% AbstractTwoBodyInteractionForce::AddForceContribution 4ms 0.0074% 71.41% 711ms 1.31% std::_Vector_base::_M_allocate (inline) 709ms 1.31% 72.72% 709ms 1.31% [libchaste_mesh.so] 1ms 0.0018% 72.72% 705ms 1.30% TetrahedralMesh::RefreshJacobianCachedData 113ms 0.21% 72.93% 695ms 1.28% __atan2 693ms 1.28% 74.21% 693ms 1.28% tetgen::tetgenmesh::oppo 15ms 0.028% 74.24% 689ms 1.27% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 537ms 0.99% 75.23% 674ms 1.24% AbstractElement::GetNodeGlobalIndex 25ms 0.046% 75.27% 663ms 1.22% boost::numeric::ublas::vector_assign (inline) 10ms 0.018% 75.29% 651ms 1.20% AbstractTetrahedralElement::CalculateInverseJacobian 651ms 1.20% 76.49% 651ms 1.20% tetgen::tetgenmesh::triface::operator= 6ms 0.011% 76.51% 635ms 1.17% boost::numeric::ublas::c_vector::c_vector (inline) 5ms 0.0092% 76.51% 615ms 1.14% AbstractTetrahedralElement::CalculateJacobian 453ms 0.84% 77.35% 582ms 1.07% __ieee754_atan2_fma 0 0% 77.35% 537ms 0.99% std::set::find (inline) 45ms 0.083% 77.43% 522ms 0.96% tetgen::tetgenmesh::enext2fnext 209ms 0.39% 77.82% 516ms 0.95% AbstractElement::GetNodeLocation 40ms 0.074% 77.89% 502ms 0.93% tetgen::tetgenmesh::enextfnext 0 0% 77.89% 499ms 0.92% std::insert_iterator::operator= (inline) 0 0% 77.89% 487ms 0.9% boost::numeric::ublas::inner_prod (inline) 1ms 0.0018% 77.90% 485ms 0.9% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 34ms 0.063% 77.96% 484ms 0.89% boost::numeric::ublas::vector_scalar_binary::evaluate 313ms 0.58% 78.54% 467ms 0.86% tetgen::tetgenmesh::sym 38ms 0.07% 78.61% 442ms 0.82% AbstractTetrahedralElement::RefreshJacobian 18ms 0.033% 78.64% 439ms 0.81% Element::CalculateCircumsphere 0 0% 78.64% 434ms 0.8% std::_Rb_tree::_M_insert_unique_ (inline) 428ms 0.79% 79.43% 428ms 0.79% Node::rGetLocation 252ms 0.47% 79.89% 427ms 0.79% AbstractTetrahedralMesh::GetElement 101ms 0.19% 80.08% 423ms 0.78% boost::numeric::ublas::indexing_vector_assign 421ms 0.78% 80.86% 421ms 0.78% boost::numeric::ublas::c_vector::operator() 413ms 0.76% 81.62% 413ms 0.76% std::vector::size (inline) 3ms 0.0055% 81.63% 400ms 0.74% Cell::GetCellId 4ms 0.0074% 81.63% 394ms 0.73% CellPropertyCollection::GetPropertiesType (inline) 95ms 0.18% 81.81% 391ms 0.72% __dynamic_cast 173ms 0.32% 82.13% 389ms 0.72% boost::numeric::ublas::vector_inner_prod::apply (inline) 0 0% 82.13% 385ms 0.71% VertexMeshWriter::WriteVtkUsingMesh 6ms 0.011% 82.14% 385ms 0.71% boost::numeric::ublas::c_vector::operator= (inline) 21ms 0.039% 82.18% 381ms 0.7% tetgen::tetgenmesh::queue::push 380ms 0.7% 82.88% 380ms 0.7% tetgen::tetgenmesh::org 288ms 0.53% 83.41% 366ms 0.68% tetgen::tetgenmesh::bond 241ms 0.44% 83.86% 359ms 0.66% tetgen::tetgenmesh::link::add 20ms 0.037% 83.89% 358ms 0.66% std::_Rb_tree_iterator::operator-- (inline) 337ms 0.62% 84.51% 337ms 0.62% AbstractElement::IsDeleted 20ms 0.037% 84.55% 335ms 0.62% VertexMesh::CalculateUnitNormalToFaceWithArea 48ms 0.089% 84.64% 328ms 0.61% boost::numeric::ublas::vector_reference::operator() (inline) 2ms 0.0037% 84.64% 327ms 0.6% AbstractCellProperty::IsSubType (inline) 324ms 0.6% 85.24% 324ms 0.6% std::_Rb_tree_decrement 8ms 0.015% 85.26% 321ms 0.59% std::vector::insert (inline) 4ms 0.0074% 85.26% 304ms 0.56% AbstractTetrahedralElement::AbstractTetrahedralElement 112ms 0.21% 85.47% 299ms 0.55% Inverse 32ms 0.059% 85.53% 298ms 0.55% tetgen::insphereadapt 5ms 0.0092% 85.54% 296ms 0.55% VertexElement::~VertexElement 64ms 0.12% 85.66% 282ms 0.52% tetgen::tetgenmesh::queue::pop 204ms 0.38% 86.03% 276ms 0.51% boost::numeric::ublas::c_matrix::operator()