File: Test2DVertexBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 86265ms, 88.70% of 97253ms total Dropped 1112 nodes (cum <= 486.26ms) flat flat% sum% cum cum% 0 0% 0% 96761ms 99.49% __libc_start_call_main 0 0% 0% 96761ms 99.49% __libc_start_main_impl 0 0% 0% 96761ms 99.49% _start 0 0% 0% 96743ms 99.48% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 96743ms 99.48% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 96743ms 99.48% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 96743ms 99.48% main 0 0% 0% 96703ms 99.43% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 96703ms 99.43% CxxTest::TestRunner::runTest (inline) 0 0% 0% 96703ms 99.43% Test2DVertexCryptRepresentativeSimulation::Test2DVertexCryptRepresentativeSimulationForProfiling 2ms 0.0021% 0.0021% 96696ms 99.43% AbstractCellBasedSimulation::Solve 10ms 0.01% 0.012% 45004ms 46.28% OffLatticeSimulation::UpdateCellLocationsAndTopology 20ms 0.021% 0.033% 42480ms 43.68% ForwardEulerNumericalMethod::UpdateAllNodePositions 122ms 0.13% 0.16% 41417ms 42.59% AbstractNumericalMethod::ComputeForcesIncludingDamping 0 0% 0.16% 38722ms 39.82% AbstractCellBasedSimulation::UpdateCellPopulation 530ms 0.54% 0.7% 29962ms 30.81% NagaiHondaForce::AddForceContribution 2ms 0.0021% 0.71% 24227ms 24.91% VertexBasedCellPopulation::Update 1ms 0.001% 0.71% 24108ms 24.79% MutableVertexMesh::ReMesh 14660ms 15.07% 15.78% 22970ms 23.62% Cylindrical2dVertexMesh::GetVectorFromAtoB 83ms 0.085% 15.87% 17487ms 17.98% Cell::ReadyToDivide 52ms 0.053% 15.92% 16332ms 16.79% AbstractPhaseBasedCellCycleModel::ReadyToDivide 130ms 0.13% 16.05% 14172ms 14.57% CellPropertyCollection::GetPropertiesType (inline) 418ms 0.43% 16.48% 13966ms 14.36% boost::numeric::ublas::c_vector::c_vector (partial-inline) 128ms 0.13% 16.61% 13876ms 14.27% SimpleWntCellCycleModel::UpdateCellCyclePhase 345ms 0.35% 16.97% 12372ms 12.72% boost::numeric::ublas::vector_assign (inline) 169ms 0.17% 17.14% 12072ms 12.41% MutableVertexMesh::CheckForIntersections 3579ms 3.68% 20.82% 11691ms 12.02% __dynamic_cast 73ms 0.075% 20.90% 11593ms 11.92% AbstractCellProperty::IsSubType (inline) 241ms 0.25% 21.15% 10987ms 11.30% VertexBasedCellPopulation::GetDampingConstant 77ms 0.079% 21.23% 10492ms 10.79% AbstractTargetAreaModifier::UpdateTargetAreas 58ms 0.06% 21.28% 10377ms 10.67% SimpleTargetAreaModifier::UpdateTargetAreaOfCell 33ms 0.034% 21.32% 10236ms 10.53% AbstractCellBasedSimulation::DoCellBirth 2620ms 2.69% 24.01% 9288ms 9.55% boost::numeric::ublas::indexing_vector_assign 75ms 0.077% 24.09% 9026ms 9.28% Cell::GetMutationState 430ms 0.44% 24.53% 8896ms 9.15% VertexMesh::GetNextEdgeGradientOfElementAtNode 746ms 0.77% 25.30% 8875ms 9.13% VertexMesh::ElementIncludesPoint 32ms 0.033% 25.33% 8726ms 8.97% VertexBasedCellPopulation::GetLocationOfCellCentre 427ms 0.44% 25.77% 8184ms 8.42% VertexMesh::GetCentroidOfElement 15ms 0.015% 25.79% 7460ms 7.67% MutableVertexMesh::RemoveDeletedNodesAndElements 514ms 0.53% 26.31% 7405ms 7.61% std::map::operator[] (partial-inline) 1435ms 1.48% 27.79% 7205ms 7.41% AbstractMesh::GetDistanceBetweenNodes (partial-inline) 118ms 0.12% 27.91% 6372ms 6.55% SimpleWntCellCycleModel::GetWntLevel 6354ms 6.53% 34.45% 6354ms 6.53% __strcmp_avx2 157ms 0.16% 34.61% 6196ms 6.37% WntConcentration::GetWntLevel 6070ms 6.24% 40.85% 6070ms 6.24% boost::numeric::ublas::c_vector::operator() 2464ms 2.53% 43.38% 5852ms 6.02% std::_Rb_tree::_M_lower_bound (inline) 2683ms 2.76% 46.14% 5658ms 5.82% __cxxabiv1::__si_class_type_info::__do_dyncast 165ms 0.17% 46.31% 5615ms 5.77% NagaiHondaForce::GetAdhesionParameter 24ms 0.025% 46.33% 5476ms 5.63% MutableVertexMesh::RemoveDeletedNodes 37ms 0.038% 46.37% 5315ms 5.47% EdgeHelper::RemoveDeletedEdges 33ms 0.034% 46.41% 5055ms 5.20% EdgeHelper::UpdateEdgesMapKey 361ms 0.37% 46.78% 4875ms 5.01% std::__new_allocator::allocate (inline) 1495ms 1.54% 48.32% 4800ms 4.94% boost::numeric::ublas::c_vector::operator[] (inline) 442ms 0.45% 48.77% 4715ms 4.85% operator new 0 0% 48.77% 4641ms 4.77% std::_Rb_tree::lower_bound (inline) 0 0% 48.77% 4641ms 4.77% std::map::lower_bound (inline) 194ms 0.2% 48.97% 4582ms 4.71% MutableElement::ResetIndex 0 0% 48.97% 4389ms 4.51% std::set::insert (inline) 0 0% 48.97% 4373ms 4.50% std::allocator_traits::allocate (inline) 0 0% 48.97% 4294ms 4.42% std::_Rb_tree::_M_create_node (inline) 0 0% 48.97% 4252ms 4.37% AbstractCellBasedSimulation::DoCellRemoval (inline) 1748ms 1.80% 50.77% 4160ms 4.28% __GI___libc_malloc 48ms 0.049% 50.82% 4057ms 4.17% Cell::GetCellProliferativeType 23ms 0.024% 50.84% 4030ms 4.14% std::set_intersection (inline) 369ms 0.38% 51.22% 4007ms 4.12% std::__set_intersection 3981ms 4.09% 55.31% 3981ms 4.09% boost::numeric::ublas::same_impl_ex 0 0% 55.31% 3911ms 4.02% std::_Rb_tree::_M_get_node (inline) 93ms 0.096% 55.41% 3864ms 3.97% AbstractCellPopulation::GetCellUsingLocationIndex 959ms 0.99% 56.39% 3760ms 3.87% std::_Rb_tree::_M_erase 577ms 0.59% 56.99% 3649ms 3.75% std::_Rb_tree::_M_insert_ (inline) 56ms 0.058% 57.05% 3516ms 3.62% AbstractCellProperty::IsType (inline) 4ms 0.0041% 57.05% 3499ms 3.60% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 365ms 0.38% 57.42% 3444ms 3.54% std::_Rb_tree_const_iterator::operator++ (inline) 1383ms 1.42% 58.85% 3434ms 3.53% __GI___libc_free 0 0% 58.85% 3388ms 3.48% std::_Rb_tree::_M_drop_node (inline) 830ms 0.85% 59.70% 3330ms 3.42% AbstractElement::GetNodeLocation 48ms 0.049% 59.75% 3210ms 3.30% Cell::SetCellProliferativeType 151ms 0.16% 59.90% 3147ms 3.24% std::__new_allocator::deallocate (inline) 0 0% 59.90% 3120ms 3.21% std::allocator_traits::deallocate (inline) 0 0% 59.90% 3109ms 3.20% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 59.90% 3063ms 3.15% std::_Rb_tree::_M_put_node (inline) 2929ms 3.01% 62.92% 2929ms 3.01% std::_Rb_tree_increment 39ms 0.04% 62.96% 2912ms 2.99% std::_Rb_tree::erase 190ms 0.2% 63.15% 2889ms 2.97% std::_Rb_tree::~_Rb_tree (inline) 2862ms 2.94% 66.09% 2862ms 2.94% std::_Rb_tree::_S_right (inline) 593ms 0.61% 66.70% 2807ms 2.89% boost::numeric::ublas::vector_binary::size (inline) 0 0% 66.70% 2648ms 2.72% std::_Rb_tree::_M_insert_unique 0 0% 66.70% 2588ms 2.66% std::set::~set (inline) 229ms 0.24% 66.94% 2560ms 2.63% VertexMesh::GetAreaGradientOfElementAtNode 677ms 0.7% 67.64% 2513ms 2.58% AbstractCellProperty::IsSame 0 0% 67.64% 2483ms 2.55% boost::numeric::ublas::c_vector::operator-= (inline) 0 0% 67.64% 2457ms 2.53% AbstractCellPopulation::WriteResultsToFiles 49ms 0.05% 67.69% 2431ms 2.50% CellPropertyCollection::HasProperty 29ms 0.03% 67.72% 2387ms 2.45% Cell::GetCellData 100ms 0.1% 67.82% 2385ms 2.45% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 0 0% 67.82% 2354ms 2.42% boost::numeric::ublas::c_vector::assign (inline) 0 0% 67.82% 2334ms 2.40% Cell::HasCellProperty (inline) 1ms 0.001% 67.82% 2321ms 2.39% AbstractCellPopulation::Iterator::operator++ (inline) 234ms 0.24% 68.06% 2300ms 2.36% AbstractCellPopulation::Iterator::IsRealCell (inline) 107ms 0.11% 68.17% 2278ms 2.34% VertexMesh::GetVolumeOfElement 35ms 0.036% 68.21% 2192ms 2.25% std::_Rb_tree::_M_emplace_hint_unique 0 0% 68.21% 2157ms 2.22% std::insert_iterator::operator= (inline) 1828ms 1.88% 70.09% 2046ms 2.10% _int_free 0 0% 70.09% 2007ms 2.06% VertexBasedCellPopulation::WriteVtkResultsToFile 1ms 0.001% 70.09% 1992ms 2.05% VertexBasedCellPopulation::WriteCellVtkResultsToFile 1301ms 1.34% 71.43% 1952ms 2.01% std::_Rb_tree::equal_range (inline) 3ms 0.0031% 71.43% 1924ms 1.98% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 71.43% 1924ms 1.98% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 68ms 0.07% 71.50% 1911ms 1.96% MutableVertexMesh::CheckForSwapsFromShortEdges 474ms 0.49% 71.99% 1836ms 1.89% std::type_info::operator== (inline) 1ms 0.001% 71.99% 1798ms 1.85% VertexMeshWriter::WriteVtkUsingMesh 20ms 0.021% 72.01% 1768ms 1.82% VertexBasedCellPopulation::IsCellAssociatedWithADeletedLocation 5ms 0.0051% 72.01% 1741ms 1.79% std::_Rb_tree::_M_insert_unique_ (inline) 29ms 0.03% 72.04% 1701ms 1.75% VertexMesh::GetSurfaceAreaOfElement 190ms 0.2% 72.24% 1655ms 1.70% CellPropertyCollection::AddProperty 25ms 0.026% 72.26% 1562ms 1.61% AbstractCellPopulation::GetLocationIndexUsingCell 97ms 0.1% 72.36% 1555ms 1.60% VertexBasedCellPopulation::GetElementCorrespondingToCell (inline) 1022ms 1.05% 73.41% 1542ms 1.59% _int_malloc 42ms 0.043% 73.46% 1523ms 1.57% Node::RemoveElement 21ms 0.022% 73.48% 1496ms 1.54% std::set::erase (inline) 131ms 0.13% 73.61% 1482ms 1.52% boost::numeric::ublas::vector_reference::operator() (inline) 0 0% 73.61% 1380ms 1.42% boost::numeric::ublas::vector_binary::operator() (inline) 11ms 0.011% 73.62% 1379ms 1.42% std::set::set (inline) 50ms 0.051% 73.68% 1366ms 1.40% std::_Rb_tree::_Rb_tree 0 0% 73.68% 1287ms 1.32% boost::numeric::ublas::norm_2 (inline) 542ms 0.56% 74.23% 1275ms 1.31% boost::numeric::ublas::vector_norm_2::apply (partial-inline) 1229ms 1.26% 75.50% 1229ms 1.26% Node::rGetLocation 65ms 0.067% 75.56% 1228ms 1.26% std::less::operator() (inline) 1223ms 1.26% 76.82% 1223ms 1.26% std::_Rb_tree_insert_and_rebalance 1ms 0.001% 76.82% 1222ms 1.26% OffLatticeSimulation::ApplyBoundaries 96ms 0.099% 76.92% 1188ms 1.22% std::_Rb_tree::_M_copy (inline) 0 0% 76.92% 1185ms 1.22% std::_Rb_tree::_Auto_node::_Auto_node (inline) 916ms 0.94% 77.86% 1163ms 1.20% std::operator< (inline) 94ms 0.097% 77.96% 1161ms 1.19% std::_Rb_tree::find (inline) 98ms 0.1% 78.06% 1121ms 1.15% std::_Rb_tree::_M_erase_aux (partial-inline) 447ms 0.46% 78.52% 1088ms 1.12% std::_Rb_tree::_M_clone_node (inline) 1ms 0.001% 78.52% 1068ms 1.10% std::_Rb_tree::clear (inline) 30ms 0.031% 78.55% 1056ms 1.09% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 0 0% 78.55% 1050ms 1.08% std::map::clear (inline) 24ms 0.025% 78.58% 1039ms 1.07% CellPropertyRegistry::Get 146ms 0.15% 78.73% 1014ms 1.04% boost::detail::shared_count::~shared_count (inline) 0 0% 78.73% 1014ms 1.04% boost::shared_ptr::~shared_ptr (inline) 993ms 1.02% 79.75% 993ms 1.02% std::vector::size (inline) 422ms 0.43% 80.18% 992ms 1.02% Edge::GetMapIndex 0 0% 80.18% 966ms 0.99% std::map::find (inline) 951ms 0.98% 81.16% 951ms 0.98% [libchaste_cell_based.so] 947ms 0.97% 82.13% 947ms 0.97% [libchaste_mesh.so] 0 0% 82.13% 938ms 0.96% boost::numeric::ublas::c_vector::assign_temporary (inline) 8ms 0.0082% 82.14% 938ms 0.96% boost::numeric::ublas::c_vector::swap 73ms 0.075% 82.22% 930ms 0.96% std::swap_ranges (inline) 28ms 0.029% 82.25% 896ms 0.92% boost::numeric::ublas::detail::expression_type_check (inline) 858ms 0.88% 83.13% 858ms 0.88% std::swap (inline) 1ms 0.001% 83.13% 857ms 0.88% VertexMeshWriter::MakeVtkMesh 167ms 0.17% 83.30% 857ms 0.88% boost::numeric::ublas::detail::equals 0 0% 83.30% 857ms 0.88% std::iter_swap (inline) 849ms 0.87% 84.17% 851ms 0.88% boost::detail::sp_counted_base::release 0 0% 84.17% 777ms 0.8% tcache_get (inline) 777ms 0.8% 84.97% 777ms 0.8% tcache_get_n (inline) 106ms 0.11% 85.08% 774ms 0.8% MutableElement::GetNodeLocalIndex 24ms 0.025% 85.11% 755ms 0.78% MutableElement::RegisterWithEdges (inline) 755ms 0.78% 85.88% 755ms 0.78% Node::GetIndex 143ms 0.15% 86.03% 755ms 0.78% boost::shared_ptr::shared_ptr (inline) 33ms 0.034% 86.06% 744ms 0.77% Edge::AddElement 99ms 0.1% 86.16% 721ms 0.74% boost::numeric::ublas::c_vector::operator= (inline) 0 0% 86.16% 700ms 0.72% CellPropertyCollection::~CellPropertyCollection (inline) 6ms 0.0062% 86.17% 694ms 0.71% T2SwapCellKiller::CheckAndLabelCellsForApoptosisOrDeath 0 0% 86.17% 693ms 0.71% std::_Rb_tree::_Auto_node::_M_insert (inline) 26ms 0.027% 86.20% 693ms 0.71% std::_Rb_tree::_M_insert_node (inline) 0 0% 86.20% 637ms 0.65% boost::numeric::ublas::norm_inf (inline) 326ms 0.34% 86.53% 637ms 0.65% boost::numeric::ublas::vector_norm_inf::apply (inline) 583ms 0.6% 87.13% 612ms 0.63% boost::detail::shared_count::shared_count (inline) 0 0% 87.13% 606ms 0.62% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 0 0% 87.13% 605ms 0.62% vtkPolygon::New 1ms 0.001% 87.13% 605ms 0.62% vtkPolygon::vtkPolygon 600ms 0.62% 87.75% 600ms 0.62% boost::shared_ptr::operator-> (inline) 313ms 0.32% 88.07% 599ms 0.62% std::_Rb_tree::_M_get_insert_hint_unique_pos (partial-inline) 27ms 0.028% 88.10% 590ms 0.61% MutableElement::RegisterWithNodes (inline) 26ms 0.027% 88.13% 564ms 0.58% Node::AddElement 38ms 0.039% 88.17% 540ms 0.56% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 88.17% 540ms 0.56% boost::numeric::ublas::vector::vector (inline) 521ms 0.54% 88.70% 521ms 0.54% [libstdc++.so.6.0.33]