File: Test2DMeshBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 17753ms, 85.25% of 20825ms total Dropped 842 nodes (cum <= 104.12ms) flat flat% sum% cum cum% 0 0% 0% 20775ms 99.76% __libc_start_call_main 0 0% 0% 20775ms 99.76% __libc_start_main_impl 0 0% 0% 20775ms 99.76% _start 0 0% 0% 20755ms 99.66% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 20755ms 99.66% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 20755ms 99.66% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 20755ms 99.66% main 0 0% 0% 20714ms 99.47% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 20714ms 99.47% CxxTest::TestRunner::runTest (inline) 0 0% 0% 20714ms 99.47% Test2DCryptRepresentativeSimulation::TestRepresentativeSimulationForProfiling 1ms 0.0048% 0.0048% 20686ms 99.33% AbstractCellBasedSimulation::Solve 0 0% 0.0048% 15876ms 76.24% AbstractCellBasedSimulation::UpdateCellPopulation 2ms 0.0096% 0.014% 10140ms 48.69% AbstractCellBasedSimulation::DoCellBirth 16ms 0.077% 0.091% 10007ms 48.05% Cell::ReadyToDivide 10ms 0.048% 0.14% 9857ms 47.33% AbstractPhaseBasedCellCycleModel::ReadyToDivide 0 0% 0.14% 9710ms 46.63% AbstractWntOdeBasedCellCycleModel::UpdateCellCyclePhase 17ms 0.082% 0.22% 9696ms 46.56% AbstractOdeBasedPhaseBasedCellCycleModel::UpdateCellCyclePhase 2ms 0.0096% 0.23% 9677ms 46.47% CellCycleModelOdeHandler::SolveOdeToTime 67ms 0.32% 0.55% 9451ms 45.38% AbstractOneStepIvpOdeSolver::InternalSolve 852ms 4.09% 4.64% 8641ms 41.49% RungeKutta4IvpOdeSolver::CalculateNextYValue 3584ms 17.21% 21.85% 7584ms 36.42% WntCellCycleOdeSystem::EvaluateYDerivatives 0 0% 21.85% 5616ms 26.97% MeshBasedCellPopulation::Update 7ms 0.034% 21.89% 4404ms 21.15% Cylindrical2dMesh::ReMesh 88ms 0.42% 22.31% 4091ms 19.64% AbstractCellProperty::IsType (inline) 639ms 3.07% 25.38% 2878ms 13.82% AbstractCellProperty::IsSame 0 0% 25.38% 2643ms 12.69% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 25.38% 2514ms 12.07% MutableMesh::ReMesh 0 0% 25.38% 2352ms 11.29% ForwardEulerNumericalMethod::UpdateAllNodePositions 8ms 0.038% 25.42% 2300ms 11.04% AbstractNumericalMethod::ComputeForcesIncludingDamping 459ms 2.20% 27.62% 2239ms 10.75% std::type_info::operator== (inline) 1ms 0.0048% 27.63% 2160ms 10.37% AbstractCellPopulation::WriteResultsToFiles 845ms 4.06% 31.68% 1892ms 9.09% std::_Rb_tree::_M_lower_bound (inline) 1739ms 8.35% 40.03% 1739ms 8.35% __strcmp_avx2 164ms 0.79% 40.82% 1738ms 8.35% TetrahedralMesh::EdgeIterator::operator++ 66ms 0.32% 41.14% 1411ms 6.78% std::_Rb_tree::find (inline) 15ms 0.072% 41.21% 1312ms 6.30% TetrahedralMesh::ImportFromMesher 2ms 0.0096% 41.22% 1166ms 5.60% MeshBasedCellPopulation::UpdateNodePairs 65ms 0.31% 41.53% 1163ms 5.58% operator new 6ms 0.029% 41.56% 1154ms 5.54% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 219ms 1.05% 42.61% 1092ms 5.24% __GI___libc_malloc 17ms 0.082% 42.69% 1043ms 5.01% MeshBasedCellPopulation::SpringIterator::operator++ 51ms 0.24% 42.94% 1020ms 4.90% std::__new_allocator::allocate (inline) 13ms 0.062% 43.00% 1020ms 4.90% std::set::insert (inline) 0 0% 43.00% 1010ms 4.85% std::allocator_traits::allocate (inline) 15ms 0.072% 43.07% 1007ms 4.84% std::_Rb_tree::_M_insert_unique 0 0% 43.07% 858ms 4.12% std::set::count (inline) 1ms 0.0048% 43.08% 839ms 4.03% triangulate 431ms 2.07% 45.15% 783ms 3.76% _int_malloc 2ms 0.0096% 45.16% 779ms 3.74% MeshBasedCellPopulationWithGhostNodes::AcceptCellWritersAcrossPopulation 2ms 0.0096% 45.17% 762ms 3.66% AbstractTwoBodyInteractionForce::AddForceContribution 0 0% 45.17% 754ms 3.62% delaunay 2ms 0.0096% 45.18% 753ms 3.62% divconqdelaunay 53ms 0.25% 45.43% 735ms 3.53% std::map::operator[] (partial-inline) 15ms 0.072% 45.50% 726ms 3.49% CellPopulationElementWriter::Visit 711ms 3.41% 48.92% 711ms 3.41% std::_Rb_tree::_S_right (inline) 12ms 0.058% 48.97% 702ms 3.37% CellPropertyCollection::GetPropertiesType (inline) 259ms 1.24% 50.22% 690ms 3.31% __dynamic_cast 0 0% 50.22% 665ms 3.19% std::_Rb_tree::_M_create_node (inline) 636ms 3.05% 53.27% 650ms 3.12% WntCellCycleOdeSystem::CalculateStoppingEvent 31ms 0.15% 53.42% 645ms 3.10% AbstractVariableSizeTwoBodyInteractionForce::CalculateForceBetweenNodes 13ms 0.062% 53.48% 641ms 3.08% std::less::operator() (inline) 15ms 0.072% 53.56% 639ms 3.07% AbstractCellPopulation::GetCellUsingLocationIndex 0 0% 53.56% 638ms 3.06% std::_Rb_tree::_M_get_node (inline) 24ms 0.12% 53.67% 628ms 3.02% std::_Rb_tree::_M_insert_ (inline) 628ms 3.02% 56.69% 628ms 3.02% std::operator< (inline) 6ms 0.029% 56.72% 618ms 2.97% MeshBasedCellPopulation::AcceptCellWriter 0 0% 56.72% 587ms 2.82% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 56.72% 576ms 2.77% std::_Rb_tree::lower_bound (inline) 0 0% 56.72% 576ms 2.77% std::map::lower_bound (inline) 3ms 0.014% 56.73% 550ms 2.64% AbstractCellProperty::IsSubType (inline) 3ms 0.014% 56.74% 548ms 2.63% Element::Element 0 0% 56.74% 545ms 2.62% std::map::find (inline) 11ms 0.053% 56.80% 536ms 2.57% Cylindrical2dMesh::ReconstructCylindricalMesh 68ms 0.33% 57.12% 501ms 2.41% std::ostream::_M_insert 0 0% 57.12% 501ms 2.41% std::ostream::operator<< (inline) 10ms 0.048% 57.17% 491ms 2.36% MutableMesh::ReIndex 198ms 0.95% 58.12% 484ms 2.32% __GI___libc_free 7ms 0.034% 58.16% 475ms 2.28% Element::RegisterWithNodes (inline) 7ms 0.034% 58.19% 472ms 2.27% Node::AddElement 319ms 1.53% 59.72% 465ms 2.23% AbstractCellMutationState::AbstractCellMutationState 172ms 0.83% 60.55% 453ms 2.18% std::_Rb_tree::_M_erase 13ms 0.062% 60.61% 436ms 2.09% Cylindrical2dMesh::CorrectNonPeriodicMesh 19ms 0.091% 60.70% 411ms 1.97% std::_Rb_tree::~_Rb_tree (inline) 5ms 0.024% 60.73% 406ms 1.95% Cell::GetMutationState 5ms 0.024% 60.75% 391ms 1.88% divconqrecurse 4ms 0.019% 60.77% 382ms 1.83% std::set::erase (inline) 10ms 0.048% 60.82% 381ms 1.83% std::_Rb_tree::erase 55ms 0.26% 61.08% 379ms 1.82% TetrahedralMesh::Clear 16ms 0.077% 61.16% 379ms 1.82% std::__new_allocator::deallocate (inline) 0 0% 61.16% 379ms 1.82% std::set::~set (inline) 99ms 0.48% 61.63% 378ms 1.82% mergehulls 0 0% 61.63% 377ms 1.81% std::allocator_traits::deallocate (inline) 3ms 0.014% 61.65% 374ms 1.80% std::_Vector_base::_M_allocate (inline) 9ms 0.043% 61.69% 373ms 1.79% Node::RemoveElement 135ms 0.65% 62.34% 364ms 1.75% std::_Rb_tree::_M_get_insert_unique_pos 1ms 0.0048% 62.34% 340ms 1.63% TetrahedralMesh::RefreshJacobianCachedData 4ms 0.019% 62.36% 334ms 1.60% Cell::GetCellProliferativeType 24ms 0.12% 62.48% 332ms 1.59% std::_Rb_tree::_Rb_tree (partial-inline) 169ms 0.81% 63.29% 329ms 1.58% __cxxabiv1::__si_class_type_info::__do_dyncast 2ms 0.0096% 63.30% 326ms 1.57% NodeLocationWriter::Visit 0 0% 63.30% 324ms 1.56% std::_Rb_tree::_M_drop_node (inline) 20ms 0.096% 63.39% 319ms 1.53% AbstractTetrahedralElement::CalculateJacobian 0 0% 63.39% 317ms 1.52% AbstractCellPopulation::Iterator::operator++ (inline) 5ms 0.024% 63.42% 314ms 1.51% std::set::set (inline) 54ms 0.26% 63.68% 312ms 1.50% AbstractCellPopulation::Iterator::IsRealCell (inline) 312ms 1.50% 65.18% 312ms 1.50% std::type_info::name (inline) 4ms 0.019% 65.20% 310ms 1.49% AbstractCellPopulation::GetLocationIndexUsingCell 6ms 0.029% 65.22% 304ms 1.46% Cylindrical2dMesh::GenerateVectorsOfElementsStraddlingPeriodicBoundaries 20ms 0.096% 65.32% 304ms 1.46% Element::ResetIndex 0 0% 65.32% 301ms 1.45% std::_Rb_tree::_M_put_node (inline) 2ms 0.0096% 65.33% 288ms 1.38% LegacyCellProliferativeTypesWriter::VisitCell 1ms 0.0048% 65.33% 288ms 1.38% MeshBasedCellPopulation::GetDampingConstant 2ms 0.0096% 65.34% 287ms 1.38% AbstractCentreBasedCellPopulation::GetDampingConstant 219ms 1.05% 66.40% 285ms 1.37% _int_free 18ms 0.086% 66.48% 283ms 1.36% std::num_put::_M_insert_float 12ms 0.058% 66.54% 282ms 1.35% AbstractTetrahedralElement::CalculateInverseJacobian 25ms 0.12% 66.66% 278ms 1.33% std::_Rb_tree::_M_copy (inline) 13ms 0.062% 66.72% 262ms 1.26% std::vector::push_back (inline) 8ms 0.038% 66.76% 261ms 1.25% AbstractCellPopulation::IsCellAttachedToLocationIndex 28ms 0.13% 66.90% 254ms 1.22% AbstractTetrahedralElement::RefreshJacobian 102ms 0.49% 67.39% 251ms 1.21% std::_Rb_tree::_M_clone_node (inline) 247ms 1.19% 68.57% 247ms 1.19% std::vector::operator[] (inline) 22ms 0.11% 68.68% 243ms 1.17% std::vector::_M_realloc_insert 68ms 0.33% 69.00% 231ms 1.11% ApcOneHitCellMutationState::ApcOneHitCellMutationState 10ms 0.048% 69.05% 228ms 1.09% std::__cxx11::collate::do_transform 1ms 0.0048% 69.06% 227ms 1.09% CellPropertyCollection::HasProperty 44ms 0.21% 69.27% 226ms 1.09% BetaCateninOneHitCellMutationState::BetaCateninOneHitCellMutationState 6ms 0.029% 69.30% 225ms 1.08% std::_Rb_tree::_M_erase_aux (inline) 12ms 0.058% 69.35% 224ms 1.08% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 0 0% 69.35% 224ms 1.08% alternateaxes 0 0% 69.35% 223ms 1.07% Cell::HasCellProperty (inline) 210ms 1.01% 70.36% 222ms 1.07% vertexmedian 5ms 0.024% 70.39% 220ms 1.06% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 15ms 0.072% 70.46% 216ms 1.04% Element::MarkAsDeleted 169ms 0.81% 71.27% 212ms 1.02% malloc_consolidate 2ms 0.0096% 71.28% 207ms 0.99% ___vsnprintf 15ms 0.072% 71.35% 206ms 0.99% Node::~Node 0 0% 71.35% 205ms 0.98% __vsnprintf_internal (inline) 27ms 0.13% 71.48% 203ms 0.97% __printf_buffer 85ms 0.41% 71.89% 200ms 0.96% AbstractElement::GetNodeLocation 1ms 0.0048% 71.89% 200ms 0.96% CellProliferativeTypesWriter::VisitCell 199ms 0.96% 72.85% 199ms 0.96% [libchaste_cell_based.so] 38ms 0.18% 73.03% 192ms 0.92% ApcTwoHitCellMutationState::ApcTwoHitCellMutationState 146ms 0.7% 73.73% 187ms 0.9% AbstractElement::GetNodeGlobalIndex 0 0% 73.73% 187ms 0.9% OffLatticeSimulation::ApplyBoundaries 187ms 0.9% 74.63% 187ms 0.9% unlink_chunk 177ms 0.85% 75.48% 177ms 0.85% std::_Rb_tree_insert_and_rebalance 4ms 0.019% 75.50% 169ms 0.81% AbstractTetrahedralElement::AbstractTetrahedralElement 11ms 0.053% 75.55% 166ms 0.8% non-virtual thunk to WntCellCycleModel::AdjustOdeParameters(double) 162ms 0.78% 76.33% 162ms 0.78% incircle 1ms 0.0048% 76.34% 161ms 0.77% __printf_fp_spec (inline) 160ms 0.77% 77.10% 160ms 0.77% Node::GetIndex 10ms 0.048% 77.15% 160ms 0.77% __printf_fp_l_buffer 101ms 0.48% 77.64% 152ms 0.73% std::_Rb_tree::equal_range (inline) 147ms 0.71% 78.34% 147ms 0.71% std::vector::size (inline) 1ms 0.0048% 78.35% 146ms 0.7% AbstractCellBasedWriter::OpenOutputFileForAppend 3ms 0.014% 78.36% 146ms 0.7% boost::numeric::ublas::vector_assign (inline) 70ms 0.34% 78.70% 145ms 0.7% __printf_fp_buffer_1 9ms 0.043% 78.74% 142ms 0.68% MeshBasedCellPopulationWithGhostNodes::CalculateForceBetweenGhostNodes 3ms 0.014% 78.76% 142ms 0.68% OutputFileHandler::OpenOutputFile 142ms 0.68% 79.44% 142ms 0.68% std::_Rb_tree_increment 0 0% 79.44% 139ms 0.67% std::vector::resize (inline) 2ms 0.0096% 79.45% 138ms 0.66% std::vector::_M_default_append 10ms 0.048% 79.50% 136ms 0.65% boost::numeric::ublas::c_vector::c_vector (inline) 9ms 0.043% 79.54% 136ms 0.65% std::_Rb_tree_const_iterator::operator++ (inline) 2ms 0.0096% 79.55% 131ms 0.63% WntCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel 119ms 0.57% 80.12% 128ms 0.61% vertexsort 39ms 0.19% 80.31% 127ms 0.61% ApcTwoHitCellMutationState::~ApcTwoHitCellMutationState (inline) 124ms 0.6% 80.90% 124ms 0.6% boost::shared_ptr::operator-> (inline) 0 0% 80.90% 123ms 0.59% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 37ms 0.18% 81.08% 123ms 0.59% ApcOneHitCellMutationState::~ApcOneHitCellMutationState (inline) 0 0% 81.08% 123ms 0.59% NodeMap::NodeMap 75ms 0.36% 81.44% 122ms 0.59% Cylindrical2dMesh::GetVectorFromAtoB 121ms 0.58% 82.02% 121ms 0.58% AbstractCellProperty::~AbstractCellProperty 5ms 0.024% 82.05% 119ms 0.57% MeshBasedCellPopulation::SpringsEnd (inline) 0 0% 82.05% 117ms 0.56% AbstractCellBasedSimulation::DoCellRemoval (inline) 116ms 0.56% 82.60% 116ms 0.56% AbstractElement::IsDeleted 31ms 0.15% 82.75% 116ms 0.56% TetrahedralMesh::EdgesEnd 3ms 0.014% 82.77% 115ms 0.55% Cylindrical2dMesh::CreateMirrorNodes 3ms 0.014% 82.78% 115ms 0.55% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 37ms 0.18% 82.96% 113ms 0.54% boost::numeric::ublas::indexing_vector_assign 48ms 0.23% 83.19% 112ms 0.54% BetaCateninOneHitCellMutationState::~BetaCateninOneHitCellMutationState (inline) 110ms 0.53% 83.72% 110ms 0.53% counterclockwise 34ms 0.16% 83.88% 109ms 0.52% std::_Vector_base::_M_deallocate (inline) 1ms 0.0048% 83.88% 107ms 0.51% CryptSimulationBoundaryCondition::ImposeBoundaryCondition 44ms 0.21% 84.10% 107ms 0.51% std::__ostream_insert 106ms 0.51% 84.61% 106ms 0.51% [libchaste_mesh.so] 3ms 0.014% 84.62% 106ms 0.51% std::_Rb_tree::_M_emplace_hint_unique 26ms 0.12% 84.74% 106ms 0.51% std::num_put::_M_insert_int 105ms 0.5% 85.25% 105ms 0.5% AbstractCellMutationState::~AbstractCellMutationState