File: Test2DVertexBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 71807ms, 87.17% of 82377ms total Dropped 1029 nodes (cum <= 411.88ms) flat flat% sum% cum cum% 0 0% 0% 82057ms 99.61% __libc_start_call_main 0 0% 0% 82057ms 99.61% __libc_start_main_impl 0 0% 0% 82057ms 99.61% _start 0 0% 0% 82041ms 99.59% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 82041ms 99.59% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 82041ms 99.59% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 82041ms 99.59% main 0 0% 0% 81998ms 99.54% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 81998ms 99.54% CxxTest::TestRunner::runTest (inline) 0 0% 0% 81998ms 99.54% Test2DVertexCryptRepresentativeSimulation::Test2DVertexCryptRepresentativeSimulationForProfiling 2ms 0.0024% 0.0024% 81992ms 99.53% AbstractCellBasedSimulation::Solve 15ms 0.018% 0.021% 42804ms 51.96% OffLatticeSimulation::UpdateCellLocationsAndTopology 15ms 0.018% 0.039% 40212ms 48.81% ForwardEulerNumericalMethod::UpdateAllNodePositions 84ms 0.1% 0.14% 39338ms 47.75% AbstractNumericalMethod::ComputeForcesIncludingDamping 272ms 0.33% 0.47% 30559ms 37.10% NagaiHondaForce::AddForceContribution 0 0% 0.47% 29515ms 35.83% AbstractCellBasedSimulation::UpdateCellPopulation 11487ms 13.94% 14.42% 18275ms 22.18% Cylindrical2dVertexMesh::GetVectorFromAtoB 3ms 0.0036% 14.42% 18225ms 22.12% VertexBasedCellPopulation::Update 1ms 0.0012% 14.42% 18124ms 22.00% MutableVertexMesh::ReMesh 47ms 0.057% 14.48% 13154ms 15.97% Cell::ReadyToDivide 82ms 0.1% 14.58% 12324ms 14.96% AbstractPhaseBasedCellCycleModel::ReadyToDivide 255ms 0.31% 14.89% 11164ms 13.55% NagaiHondaForce::GetAdhesionParameter 359ms 0.44% 15.32% 10752ms 13.05% boost::numeric::ublas::c_vector::c_vector (partial-inline) 113ms 0.14% 15.46% 10575ms 12.84% SimpleWntCellCycleModel::UpdateCellCyclePhase 98ms 0.12% 15.58% 10035ms 12.18% CellPropertyCollection::GetPropertiesType (inline) 213ms 0.26% 15.84% 9598ms 11.65% boost::numeric::ublas::vector_assign (inline) 117ms 0.14% 15.98% 9304ms 11.29% MutableVertexMesh::CheckForIntersections 2404ms 2.92% 18.90% 8551ms 10.38% __dynamic_cast 68ms 0.083% 18.98% 8526ms 10.35% AbstractCellProperty::IsSubType (inline) 59ms 0.072% 19.05% 8394ms 10.19% VertexBasedCellPopulation::GetDampingConstant 19ms 0.023% 19.07% 7732ms 9.39% AbstractCellBasedSimulation::DoCellBirth 37ms 0.045% 19.12% 7697ms 9.34% AbstractTargetAreaModifier::UpdateTargetAreas 47ms 0.057% 19.18% 7611ms 9.24% SimpleTargetAreaModifier::UpdateTargetAreaOfCell 886ms 1.08% 20.25% 7391ms 8.97% std::__new_allocator::allocate (inline) 2267ms 2.75% 23.00% 7369ms 8.95% boost::numeric::ublas::indexing_vector_assign 296ms 0.36% 23.36% 7314ms 8.88% VertexMesh::GetNextEdgeGradientOfElementAtNode 941ms 1.14% 24.51% 7012ms 8.51% std::_Rb_tree::_M_erase 0 0% 24.51% 6998ms 8.50% std::_Rb_tree::_M_create_node (inline) 0 0% 24.51% 6976ms 8.47% std::allocator_traits::allocate (inline) 674ms 0.82% 25.32% 6791ms 8.24% VertexMesh::ElementIncludesPoint 20ms 0.024% 25.35% 6658ms 8.08% VertexBasedCellPopulation::GetLocationOfCellCentre 572ms 0.69% 26.04% 6477ms 7.86% operator new 180ms 0.22% 26.26% 6456ms 7.84% std::_Rb_tree::~_Rb_tree (inline) 0 0% 26.26% 6428ms 7.80% std::_Rb_tree::_M_get_node (inline) 352ms 0.43% 26.69% 6406ms 7.78% VertexMesh::GetCentroidOfElement 75ms 0.091% 26.78% 6400ms 7.77% Cell::GetMutationState 0 0% 26.78% 6329ms 7.68% std::_Rb_tree::_M_drop_node (inline) 0 0% 26.78% 6234ms 7.57% std::_Rb_tree::_Alloc_node::operator() (inline) 167ms 0.2% 26.98% 6159ms 7.48% std::__new_allocator::deallocate (inline) 0 0% 26.98% 6149ms 7.46% std::allocator_traits::deallocate (inline) 0 0% 26.98% 6117ms 7.43% std::set::~set (inline) 0 0% 26.98% 6089ms 7.39% std::_Rb_tree::_M_put_node (inline) 1842ms 2.24% 29.22% 5787ms 7.03% __GI___libc_free 2189ms 2.66% 31.88% 5746ms 6.98% __GI___libc_malloc 1081ms 1.31% 33.19% 5740ms 6.97% AbstractMesh::GetDistanceBetweenNodes (partial-inline) 14ms 0.017% 33.20% 5609ms 6.81% MutableVertexMesh::RemoveDeletedNodesAndElements 361ms 0.44% 33.64% 5415ms 6.57% std::map::operator[] (partial-inline) 157ms 0.19% 33.83% 5360ms 6.51% std::_Rb_tree::_Rb_tree (partial-inline) 585ms 0.71% 34.54% 5019ms 6.09% std::_Rb_tree::_M_copy (inline) 25ms 0.03% 34.57% 4956ms 6.02% std::set::set (inline) 4896ms 5.94% 40.52% 4896ms 5.94% __strcmp_evex 101ms 0.12% 40.64% 4820ms 5.85% SimpleWntCellCycleModel::GetWntLevel 4800ms 5.83% 46.47% 4800ms 5.83% boost::numeric::ublas::c_vector::operator() 118ms 0.14% 46.61% 4666ms 5.66% WntConcentration::GetWntLevel 582ms 0.71% 47.32% 4251ms 5.16% std::_Rb_tree::_M_clone_node (inline) 1825ms 2.22% 49.53% 4205ms 5.10% std::_Rb_tree::_M_lower_bound (inline) 1597ms 1.94% 51.47% 4169ms 5.06% boost::numeric::ublas::c_vector::operator[] (inline) 3591ms 4.36% 55.83% 3924ms 4.76% _int_free 0 0% 55.83% 3893ms 4.73% std::set::insert (inline) 13ms 0.016% 55.85% 3843ms 4.67% MutableVertexMesh::RemoveDeletedNodes 2163ms 2.63% 58.47% 3834ms 4.65% __cxxabiv1::__si_class_type_info::__do_dyncast 27ms 0.033% 58.50% 3708ms 4.50% EdgeHelper::RemoveDeletedEdges 2ms 0.0024% 58.51% 3548ms 4.31% AbstractCellBasedSimulation::DoCellRemoval (inline) 155ms 0.19% 58.69% 3474ms 4.22% MutableElement::ResetIndex 0 0% 58.69% 3470ms 4.21% std::_Rb_tree::lower_bound (inline) 0 0% 58.69% 3470ms 4.21% std::map::lower_bound (inline) 24ms 0.029% 58.72% 3453ms 4.19% EdgeHelper::UpdateEdgesMapKey 373ms 0.45% 59.18% 3304ms 4.01% std::_Rb_tree::_M_insert_ (inline) 90ms 0.11% 59.29% 3278ms 3.98% std::set_intersection (inline) 176ms 0.21% 59.50% 3188ms 3.87% std::__set_intersection 95ms 0.12% 59.61% 3184ms 3.87% AbstractCellPopulation::GetCellUsingLocationIndex 32ms 0.039% 59.65% 2947ms 3.58% Cell::GetCellProliferativeType 2889ms 3.51% 63.16% 2889ms 3.51% boost::numeric::ublas::same_impl_ex 40ms 0.049% 63.21% 2783ms 3.38% AbstractCellProperty::IsType (inline) 11ms 0.013% 63.22% 2662ms 3.23% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 0 0% 63.22% 2454ms 2.98% std::insert_iterator::operator= (inline) 1649ms 2.00% 65.22% 2382ms 2.89% _int_malloc 40ms 0.049% 65.27% 2316ms 2.81% Cell::SetCellProliferativeType 687ms 0.83% 66.11% 2284ms 2.77% AbstractElement::GetNodeLocation 39ms 0.047% 66.15% 2208ms 2.68% std::_Rb_tree::erase 2ms 0.0024% 66.16% 2127ms 2.58% std::_Rb_tree::_M_insert_unique_ (inline) 179ms 0.22% 66.37% 2055ms 2.49% VertexMesh::GetAreaGradientOfElementAtNode 470ms 0.57% 66.94% 2032ms 2.47% boost::numeric::ublas::vector_binary::size (inline) 0 0% 66.94% 2018ms 2.45% boost::numeric::ublas::c_vector::operator-= (inline) 496ms 0.6% 67.55% 2000ms 2.43% AbstractCellProperty::IsSame 0 0% 67.55% 1949ms 2.37% AbstractCellPopulation::WriteResultsToFiles 1948ms 2.36% 69.91% 1948ms 2.36% std::_Rb_tree::_S_right (inline) 0 0% 69.91% 1944ms 2.36% boost::numeric::ublas::c_vector::assign (inline) 14ms 0.017% 69.93% 1924ms 2.34% CellPropertyCollection::HasProperty 0 0% 69.93% 1859ms 2.26% Cell::HasCellProperty (inline) 201ms 0.24% 70.17% 1794ms 2.18% std::_Rb_tree_const_iterator::operator++ (inline) 63ms 0.076% 70.25% 1770ms 2.15% VertexMesh::GetVolumeOfElement 4ms 0.0049% 70.25% 1766ms 2.14% std::_Rb_tree::_M_insert_unique 17ms 0.021% 70.27% 1696ms 2.06% Cell::GetCellData 1ms 0.0012% 70.28% 1661ms 2.02% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 70.28% 1661ms 2.02% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 47ms 0.057% 70.33% 1653ms 2.01% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 3ms 0.0036% 70.34% 1633ms 1.98% AbstractCellPopulation::Iterator::operator++ (inline) 121ms 0.15% 70.48% 1612ms 1.96% AbstractCellPopulation::Iterator::IsRealCell (inline) 0 0% 70.48% 1593ms 1.93% VertexBasedCellPopulation::WriteVtkResultsToFile 1ms 0.0012% 70.48% 1586ms 1.93% VertexBasedCellPopulation::WriteCellVtkResultsToFile 31ms 0.038% 70.52% 1545ms 1.88% std::_Rb_tree::_M_emplace_hint_unique 339ms 0.41% 70.93% 1504ms 1.83% std::type_info::operator== (inline) 54ms 0.066% 71.00% 1459ms 1.77% MutableVertexMesh::CheckForSwapsFromShortEdges 0 0% 71.00% 1439ms 1.75% VertexMeshWriter::WriteVtkUsingMesh 952ms 1.16% 72.15% 1437ms 1.74% std::_Rb_tree::equal_range (inline) 1400ms 1.70% 73.85% 1400ms 1.70% std::_Rb_tree_increment 23ms 0.028% 73.88% 1243ms 1.51% VertexBasedCellPopulation::IsCellAssociatedWithADeletedLocation 30ms 0.036% 73.92% 1186ms 1.44% VertexMesh::GetSurfaceAreaOfElement 37ms 0.045% 73.96% 1112ms 1.35% Node::RemoveElement 23ms 0.028% 73.99% 1105ms 1.34% AbstractCellPopulation::GetLocationIndexUsingCell 10ms 0.012% 74.00% 1077ms 1.31% std::set::erase (inline) 65ms 0.079% 74.08% 1076ms 1.31% VertexBasedCellPopulation::GetElementCorrespondingToCell (inline) 40ms 0.049% 74.13% 1076ms 1.31% boost::numeric::ublas::vector_reference::operator() (inline) 2ms 0.0024% 74.13% 1059ms 1.29% OffLatticeSimulation::ApplyBoundaries 105ms 0.13% 74.26% 1033ms 1.25% CellPropertyCollection::AddProperty 0 0% 74.26% 1019ms 1.24% boost::numeric::ublas::vector_binary::operator() (inline) 0 0% 74.26% 1017ms 1.23% boost::numeric::ublas::norm_2 (inline) 1ms 0.0012% 74.26% 1013ms 1.23% tcache_get (inline) 1012ms 1.23% 75.49% 1012ms 1.23% tcache_get_n (inline) 434ms 0.53% 76.02% 1010ms 1.23% boost::numeric::ublas::vector_norm_2::apply (partial-inline) 986ms 1.20% 77.21% 986ms 1.20% [libchaste_cell_based.so] 47ms 0.057% 77.27% 967ms 1.17% std::less::operator() (inline) 753ms 0.91% 78.19% 920ms 1.12% std::operator< (inline) 13ms 0.016% 78.20% 896ms 1.09% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 56ms 0.068% 78.27% 868ms 1.05% std::_Rb_tree::_M_erase_aux (partial-inline) 18ms 0.022% 78.29% 864ms 1.05% CellPropertyRegistry::Get 2ms 0.0024% 78.29% 852ms 1.03% T2SwapCellKiller::CheckAndLabelCellsForApoptosisOrDeath 816ms 0.99% 79.28% 816ms 0.99% std::_Rb_tree_insert_and_rebalance 0 0% 79.28% 803ms 0.97% boost::numeric::ublas::c_vector::assign_temporary (inline) 10ms 0.012% 79.30% 803ms 0.97% boost::numeric::ublas::c_vector::swap (inline) 2ms 0.0024% 79.30% 800ms 0.97% boost::numeric::ublas::detail::expression_type_check (inline) 65ms 0.079% 79.38% 793ms 0.96% std::swap_ranges (inline) 111ms 0.13% 79.51% 779ms 0.95% boost::numeric::ublas::detail::equals 90ms 0.11% 79.62% 770ms 0.93% boost::detail::shared_count::~shared_count (inline) 0 0% 79.62% 770ms 0.93% boost::shared_ptr::~shared_ptr (inline) 0 0% 79.62% 764ms 0.93% std::_Rb_tree::_Auto_node::_Auto_node (inline) 62ms 0.075% 79.70% 755ms 0.92% std::_Rb_tree::find (inline) 0 0% 79.70% 739ms 0.9% std::_Rb_tree::clear (inline) 0 0% 79.70% 729ms 0.88% std::map::clear (inline) 0 0% 79.70% 728ms 0.88% std::iter_swap (inline) 728ms 0.88% 80.58% 728ms 0.88% std::swap (inline) 712ms 0.86% 81.45% 712ms 0.86% Node::rGetLocation 0 0% 81.45% 688ms 0.84% VertexMeshWriter::MakeVtkMesh 649ms 0.79% 82.23% 666ms 0.81% boost::detail::sp_counted_base::release 0 0% 82.23% 644ms 0.78% boost::numeric::ublas::norm_inf (inline) 293ms 0.36% 82.59% 644ms 0.78% boost::numeric::ublas::vector_norm_inf::apply (inline) 0 0% 82.59% 642ms 0.78% std::map::find (inline) 193ms 0.23% 82.82% 620ms 0.75% std::__new_allocator::construct (inline) 0 0% 82.82% 620ms 0.75% std::allocator_traits::construct (inline) 619ms 0.75% 83.57% 619ms 0.75% std::vector::size (inline) 604ms 0.73% 84.31% 604ms 0.73% [libchaste_mesh.so] 69ms 0.084% 84.39% 602ms 0.73% boost::numeric::ublas::c_vector::operator= (inline) 191ms 0.23% 84.62% 593ms 0.72% boost::shared_ptr::shared_ptr (inline) 23ms 0.028% 84.65% 576ms 0.7% MutableElement::RegisterWithEdges (inline) 0 0% 84.65% 575ms 0.7% CellPropertyCollection::~CellPropertyCollection (inline) 572ms 0.69% 85.35% 572ms 0.69% [libstdc++.so.6.0.33] 0 0% 85.35% 570ms 0.69% std::_Rb_tree::_M_construct_node (inline) 24ms 0.029% 85.37% 564ms 0.68% Edge::AddElement 1ms 0.0012% 85.38% 546ms 0.66% std::_Vector_base::_M_allocate (inline) 265ms 0.32% 85.70% 545ms 0.66% Edge::GetMapIndex 284ms 0.34% 86.04% 544ms 0.66% std::_Rb_tree::_M_get_insert_hint_unique_pos (partial-inline) 0 0% 86.04% 511ms 0.62% std::_Rb_tree::_Auto_node::_M_insert (inline) 20ms 0.024% 86.07% 511ms 0.62% std::_Rb_tree::_M_insert_node (inline) 0 0% 86.07% 504ms 0.61% boost::numeric::ublas::scalar_traits::type_sqrt (inline) 111ms 0.13% 86.20% 498ms 0.6% MutableElement::GetNodeLocalIndex 3ms 0.0036% 86.20% 498ms 0.6% vtkPolygon::New 2ms 0.0024% 86.21% 495ms 0.6% vtkPolygon::vtkPolygon 5ms 0.0061% 86.21% 464ms 0.56% std::vector::_M_default_append (inline) 446ms 0.54% 86.75% 446ms 0.54% Node::GetIndex 19ms 0.023% 86.78% 434ms 0.53% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 86.78% 434ms 0.53% boost::numeric::ublas::vector::vector (inline) 0 0% 86.78% 434ms 0.53% std::map::map (inline) 32ms 0.039% 86.82% 431ms 0.52% MutableElement::RegisterWithNodes (inline) 290ms 0.35% 87.17% 412ms 0.5% malloc_consolidate