File: Test2DMeshBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 16506ms, 83.50% of 19767ms total Dropped 803 nodes (cum <= 98.83ms) flat flat% sum% cum cum% 0 0% 0% 19718ms 99.75% __libc_start_call_main 0 0% 0% 19718ms 99.75% __libc_start_main_impl 0 0% 0% 19718ms 99.75% _start 0 0% 0% 19697ms 99.65% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 19697ms 99.65% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 19697ms 99.65% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 19697ms 99.65% main 0 0% 0% 19660ms 99.46% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 19660ms 99.46% CxxTest::TestRunner::runTest (inline) 0 0% 0% 19660ms 99.46% Test2DCryptRepresentativeSimulation::TestRepresentativeSimulationForProfiling 0 0% 0% 19634ms 99.33% AbstractCellBasedSimulation::Solve 0 0% 0% 15207ms 76.93% AbstractCellBasedSimulation::UpdateCellPopulation 4ms 0.02% 0.02% 9968ms 50.43% AbstractCellBasedSimulation::DoCellBirth 1ms 0.0051% 0.025% 9865ms 49.91% Cell::ReadyToDivide 5ms 0.025% 0.051% 9794ms 49.55% AbstractPhaseBasedCellCycleModel::ReadyToDivide 0 0% 0.051% 9661ms 48.87% AbstractWntOdeBasedCellCycleModel::UpdateCellCyclePhase 9ms 0.046% 0.096% 9656ms 48.85% AbstractOdeBasedPhaseBasedCellCycleModel::UpdateCellCyclePhase 1ms 0.0051% 0.1% 9644ms 48.79% CellCycleModelOdeHandler::SolveOdeToTime 70ms 0.35% 0.46% 9488ms 48.00% AbstractOneStepIvpOdeSolver::InternalSolve 871ms 4.41% 4.86% 8680ms 43.91% RungeKutta4IvpOdeSolver::CalculateNextYValue 3563ms 18.02% 22.89% 7591ms 38.40% WntCellCycleOdeSystem::EvaluateYDerivatives 0 0% 22.89% 5119ms 25.90% MeshBasedCellPopulation::Update 88ms 0.45% 23.33% 4065ms 20.56% AbstractCellProperty::IsType (inline) 8ms 0.04% 23.37% 3949ms 19.98% Cylindrical2dMesh::ReMesh 587ms 2.97% 26.34% 2821ms 14.27% AbstractCellProperty::IsSame 0 0% 26.34% 2438ms 12.33% OffLatticeSimulation::UpdateCellLocationsAndTopology 416ms 2.10% 28.45% 2234ms 11.30% std::type_info::operator== (inline) 1ms 0.0051% 28.45% 2119ms 10.72% MutableMesh::ReMesh 0 0% 28.45% 2111ms 10.68% ForwardEulerNumericalMethod::UpdateAllNodePositions 11ms 0.056% 28.51% 2069ms 10.47% AbstractNumericalMethod::ComputeForcesIncludingDamping 1ms 0.0051% 28.51% 1985ms 10.04% AbstractCellPopulation::WriteResultsToFiles 823ms 4.16% 32.68% 1879ms 9.51% std::_Rb_tree::_M_lower_bound (inline) 1773ms 8.97% 41.65% 1773ms 8.97% __strcmp_avx2 165ms 0.83% 42.48% 1703ms 8.62% TetrahedralMesh::EdgeIterator::operator++ 69ms 0.35% 42.83% 1437ms 7.27% std::_Rb_tree::find (inline) 1ms 0.0051% 42.83% 1144ms 5.79% MeshBasedCellPopulation::UpdateNodePairs 2ms 0.01% 42.84% 1119ms 5.66% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 55ms 0.28% 43.12% 1095ms 5.54% operator new 20ms 0.1% 43.22% 1080ms 5.46% TetrahedralMesh::ImportFromMesher 10ms 0.051% 43.27% 1053ms 5.33% std::set::insert (inline) 15ms 0.076% 43.35% 1042ms 5.27% std::_Rb_tree::_M_insert_unique 6ms 0.03% 43.38% 1029ms 5.21% MeshBasedCellPopulation::SpringIterator::operator++ 217ms 1.10% 44.48% 1025ms 5.19% __GI___libc_malloc 37ms 0.19% 44.67% 969ms 4.90% std::__new_allocator::allocate (inline) 0 0% 44.67% 965ms 4.88% std::allocator_traits::allocate (inline) 0 0% 44.67% 875ms 4.43% std::set::count (inline) 1ms 0.0051% 44.67% 798ms 4.04% triangulate 3ms 0.015% 44.69% 742ms 3.75% MeshBasedCellPopulationWithGhostNodes::AcceptCellWritersAcrossPopulation 0 0% 44.69% 722ms 3.65% delaunay 1ms 0.0051% 44.69% 722ms 3.65% divconqdelaunay 409ms 2.07% 46.76% 717ms 3.63% _int_malloc 42ms 0.21% 46.97% 676ms 3.42% std::map::operator[] (partial-inline) 24ms 0.12% 47.09% 673ms 3.40% std::_Rb_tree::_M_insert_ (inline) 0 0% 47.09% 672ms 3.40% std::_Rb_tree::_M_create_node (inline) 669ms 3.38% 50.48% 669ms 3.38% std::_Rb_tree::_S_right (inline) 6ms 0.03% 50.51% 666ms 3.37% CellPopulationElementWriter::Visit 19ms 0.096% 50.60% 657ms 3.32% std::less::operator() (inline) 1ms 0.0051% 50.61% 648ms 3.28% AbstractTwoBodyInteractionForce::AddForceContribution 0 0% 50.61% 641ms 3.24% std::_Rb_tree::_M_get_node (inline) 627ms 3.17% 53.78% 639ms 3.23% WntCellCycleOdeSystem::CalculateStoppingEvent 638ms 3.23% 57.01% 638ms 3.23% std::operator< (inline) 180ms 0.91% 57.92% 617ms 3.12% __dynamic_cast 0 0% 57.92% 607ms 3.07% std::_Rb_tree::_Alloc_node::operator() (inline) 2ms 0.01% 57.93% 600ms 3.04% MeshBasedCellPopulation::AcceptCellWriter 5ms 0.025% 57.96% 592ms 2.99% CellPropertyCollection::GetPropertiesType (inline) 24ms 0.12% 58.08% 560ms 2.83% AbstractCellPopulation::GetCellUsingLocationIndex 0 0% 58.08% 559ms 2.83% std::map::find (inline) 29ms 0.15% 58.22% 555ms 2.81% AbstractVariableSizeTwoBodyInteractionForce::CalculateForceBetweenNodes 8ms 0.04% 58.26% 553ms 2.80% Element::Element 17ms 0.086% 58.35% 547ms 2.77% MutableMesh::ReIndex 0 0% 58.35% 538ms 2.72% std::_Rb_tree::lower_bound (inline) 0 0% 58.35% 538ms 2.72% std::map::lower_bound (inline) 8ms 0.04% 58.39% 519ms 2.63% Element::RegisterWithNodes (inline) 3ms 0.015% 58.41% 517ms 2.62% std::ostream::operator<< (inline) 67ms 0.34% 58.74% 514ms 2.60% std::ostream::_M_insert 14ms 0.071% 58.82% 503ms 2.54% Cylindrical2dMesh::CorrectNonPeriodicMesh 12ms 0.061% 58.88% 503ms 2.54% Node::AddElement 349ms 1.77% 60.64% 493ms 2.49% AbstractCellMutationState::AbstractCellMutationState 6ms 0.03% 60.67% 491ms 2.48% Cylindrical2dMesh::ReconstructCylindricalMesh 5ms 0.025% 60.70% 475ms 2.40% AbstractCellProperty::IsSubType (inline) 140ms 0.71% 61.41% 397ms 2.01% __GI___libc_free 5ms 0.025% 61.43% 374ms 1.89% std::_Rb_tree::erase 1ms 0.0051% 61.44% 374ms 1.89% std::set::erase (inline) 9ms 0.046% 61.48% 368ms 1.86% Node::RemoveElement 24ms 0.12% 61.60% 367ms 1.86% Element::ResetIndex 13ms 0.066% 61.67% 357ms 1.81% divconqrecurse 145ms 0.73% 62.40% 355ms 1.80% std::_Rb_tree::_M_get_insert_unique_pos 6ms 0.03% 62.43% 351ms 1.78% Cylindrical2dMesh::GenerateVectorsOfElementsStraddlingPeriodicBoundaries 104ms 0.53% 62.96% 336ms 1.70% mergehulls 12ms 0.061% 63.02% 336ms 1.70% std::__new_allocator::deallocate (inline) 0 0% 63.02% 332ms 1.68% std::allocator_traits::deallocate (inline) 105ms 0.53% 63.55% 331ms 1.67% std::_Rb_tree::_M_erase 6ms 0.03% 63.58% 327ms 1.65% Cell::GetCellProliferativeType 2ms 0.01% 63.59% 326ms 1.65% std::_Vector_base::_M_allocate (inline) 0 0% 63.59% 325ms 1.64% NodeLocationWriter::Visit 173ms 0.88% 64.47% 319ms 1.61% __cxxabiv1::__si_class_type_info::__do_dyncast 311ms 1.57% 66.04% 311ms 1.57% std::type_info::name (inline) 3ms 0.015% 66.05% 310ms 1.57% Cell::GetMutationState 21ms 0.11% 66.16% 310ms 1.57% std::_Rb_tree::~_Rb_tree (inline) 3ms 0.015% 66.18% 308ms 1.56% LegacyCellProliferativeTypesWriter::VisitCell 1ms 0.0051% 66.18% 294ms 1.49% AbstractCellPopulation::Iterator::operator++ (inline) 0 0% 66.18% 292ms 1.48% std::_Rb_tree::_M_drop_node (inline) 22ms 0.11% 66.29% 291ms 1.47% std::num_put::_M_insert_float 47ms 0.24% 66.53% 290ms 1.47% AbstractCellPopulation::Iterator::IsRealCell (inline) 3ms 0.015% 66.55% 287ms 1.45% AbstractCellPopulation::GetLocationIndexUsingCell 25ms 0.13% 66.67% 286ms 1.45% std::_Rb_tree::_Rb_tree (partial-inline) 0 0% 66.67% 283ms 1.43% std::set::~set (inline) 281ms 1.42% 68.09% 283ms 1.43% std::vector::operator[] (inline) 0 0% 68.09% 265ms 1.34% std::_Rb_tree::_M_put_node (inline) 2ms 0.01% 68.10% 259ms 1.31% std::set::set (inline) 203ms 1.03% 69.13% 257ms 1.30% _int_free 6ms 0.03% 69.16% 253ms 1.28% std::vector::push_back (inline) 4ms 0.02% 69.18% 244ms 1.23% AbstractCellPopulation::IsCellAttachedToLocationIndex 43ms 0.22% 69.40% 243ms 1.23% ApcTwoHitCellMutationState::ApcTwoHitCellMutationState 10ms 0.051% 69.45% 239ms 1.21% std::_Rb_tree::_M_erase_aux (inline) 3ms 0.015% 69.46% 238ms 1.20% alternateaxes 18ms 0.091% 69.56% 238ms 1.20% std::vector::_M_realloc_insert 16ms 0.081% 69.64% 235ms 1.19% AbstractTetrahedralElement::CalculateJacobian 26ms 0.13% 69.77% 234ms 1.18% std::_Rb_tree::_M_copy (inline) 214ms 1.08% 70.85% 234ms 1.18% vertexmedian 12ms 0.061% 70.91% 229ms 1.16% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 5ms 0.025% 70.94% 225ms 1.14% std::__cxx11::collate::do_transform 4ms 0.02% 70.96% 217ms 1.10% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 64ms 0.32% 71.28% 217ms 1.10% ApcOneHitCellMutationState::ApcOneHitCellMutationState 0 0% 71.28% 217ms 1.10% TetrahedralMesh::RefreshJacobianCachedData 35ms 0.18% 71.46% 213ms 1.08% BetaCateninOneHitCellMutationState::BetaCateninOneHitCellMutationState 1ms 0.0051% 71.46% 213ms 1.08% ___vsnprintf 0 0% 71.46% 212ms 1.07% __vsnprintf_internal (inline) 1ms 0.0051% 71.47% 209ms 1.06% AbstractCentreBasedCellPopulation::GetDampingConstant 0 0% 71.47% 209ms 1.06% MeshBasedCellPopulation::GetDampingConstant 68ms 0.34% 71.81% 206ms 1.04% std::_Rb_tree::_M_clone_node (inline) 23ms 0.12% 71.93% 205ms 1.04% __printf_buffer 201ms 1.02% 72.94% 201ms 1.02% [libchaste_cell_based.so] 0 0% 72.94% 198ms 1.00% OffLatticeSimulation::ApplyBoundaries 198ms 1.00% 73.95% 198ms 1.00% std::_Rb_tree_insert_and_rebalance 152ms 0.77% 74.72% 191ms 0.97% AbstractElement::GetNodeGlobalIndex 3ms 0.015% 74.73% 185ms 0.94% CellProliferativeTypesWriter::VisitCell 129ms 0.65% 75.38% 181ms 0.92% malloc_consolidate 14ms 0.071% 75.45% 180ms 0.91% AbstractTetrahedralElement::CalculateInverseJacobian 27ms 0.14% 75.59% 176ms 0.89% AbstractTetrahedralElement::RefreshJacobian 176ms 0.89% 76.48% 176ms 0.89% Node::GetIndex 9ms 0.046% 76.53% 175ms 0.89% Element::MarkAsDeleted 14ms 0.071% 76.60% 166ms 0.84% TetrahedralMesh::Clear 2ms 0.01% 76.61% 164ms 0.83% __printf_fp_spec (inline) 4ms 0.02% 76.63% 163ms 0.82% AbstractTetrahedralElement::AbstractTetrahedralElement 10ms 0.051% 76.68% 162ms 0.82% __printf_fp_l_buffer 160ms 0.81% 77.49% 160ms 0.81% unlink_chunk 72ms 0.36% 77.85% 151ms 0.76% __printf_fp_buffer_1 1ms 0.0051% 77.86% 148ms 0.75% CellPropertyCollection::HasProperty 12ms 0.061% 77.92% 145ms 0.73% MeshBasedCellPopulationWithGhostNodes::CalculateForceBetweenGhostNodes 143ms 0.72% 78.64% 143ms 0.72% AbstractCellProperty::~AbstractCellProperty 0 0% 78.64% 143ms 0.72% Cell::HasCellProperty (inline) 49ms 0.25% 78.89% 135ms 0.68% ApcOneHitCellMutationState::~ApcOneHitCellMutationState (inline) 135ms 0.68% 79.57% 135ms 0.68% incircle 1ms 0.0051% 79.58% 134ms 0.68% boost::numeric::ublas::vector_assign (inline) 80ms 0.4% 79.98% 134ms 0.68% std::_Rb_tree::equal_range (inline) 70ms 0.35% 80.34% 133ms 0.67% AbstractElement::GetNodeLocation 132ms 0.67% 81.00% 132ms 0.67% std::vector::size (inline) 7ms 0.035% 81.04% 131ms 0.66% non-virtual thunk to WntCellCycleModel::AdjustOdeParameters(double) 3ms 0.015% 81.05% 127ms 0.64% MeshBasedCellPopulation::SpringsEnd (inline) 73ms 0.37% 81.42% 125ms 0.63% Cylindrical2dMesh::GetVectorFromAtoB 34ms 0.17% 81.60% 125ms 0.63% TetrahedralMesh::EdgesEnd 33ms 0.17% 81.76% 124ms 0.63% BetaCateninOneHitCellMutationState::~BetaCateninOneHitCellMutationState (inline) 2ms 0.01% 81.77% 124ms 0.63% WntCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel 1ms 0.0051% 81.78% 118ms 0.6% AbstractCellBasedSimulation::DoCellRemoval (inline) 108ms 0.55% 82.32% 118ms 0.6% vertexsort 117ms 0.59% 82.92% 117ms 0.59% std::_Rb_tree_rebalance_for_erase 0 0% 82.92% 116ms 0.59% AbstractCellBasedWriter::OpenOutputFileForAppend 0 0% 82.92% 115ms 0.58% OutputFileHandler::OpenOutputFile 38ms 0.19% 83.11% 112ms 0.57% ApcTwoHitCellMutationState::~ApcTwoHitCellMutationState (inline) 2ms 0.01% 83.12% 111ms 0.56% Cell::SetCellProliferativeType 2ms 0.01% 83.13% 111ms 0.56% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 30ms 0.15% 83.28% 110ms 0.56% boost::numeric::ublas::indexing_vector_assign 5ms 0.025% 83.31% 109ms 0.55% CryptSimulationBoundaryCondition::ImposeBoundaryCondition 10ms 0.051% 83.36% 109ms 0.55% boost::numeric::ublas::c_vector::c_vector (inline) 29ms 0.15% 83.50% 107ms 0.54% std::num_put::_M_insert_int