File: Test2DMeshBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 16765ms, 84.87% of 19753ms total Dropped 787 nodes (cum <= 98.77ms) flat flat% sum% cum cum% 0 0% 0% 19708ms 99.77% __libc_start_call_main 0 0% 0% 19708ms 99.77% __libc_start_main_impl 0 0% 0% 19708ms 99.77% _start 0 0% 0% 19688ms 99.67% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 19688ms 99.67% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 19688ms 99.67% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 19688ms 99.67% main 0 0% 0% 19651ms 99.48% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 19651ms 99.48% CxxTest::TestRunner::runTest (inline) 0 0% 0% 19651ms 99.48% Test2DCryptRepresentativeSimulation::TestRepresentativeSimulationForProfiling 0 0% 0% 19624ms 99.35% AbstractCellBasedSimulation::Solve 0 0% 0% 15174ms 76.82% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 9968ms 50.46% AbstractCellBasedSimulation::DoCellBirth 3ms 0.015% 0.015% 9890ms 50.07% Cell::ReadyToDivide 5ms 0.025% 0.041% 9814ms 49.68% AbstractPhaseBasedCellCycleModel::ReadyToDivide 3ms 0.015% 0.056% 9687ms 49.04% AbstractWntOdeBasedCellCycleModel::UpdateCellCyclePhase 12ms 0.061% 0.12% 9679ms 49.00% AbstractOdeBasedPhaseBasedCellCycleModel::UpdateCellCyclePhase 2ms 0.01% 0.13% 9666ms 48.93% CellCycleModelOdeHandler::SolveOdeToTime 63ms 0.32% 0.45% 9471ms 47.95% AbstractOneStepIvpOdeSolver::InternalSolve 877ms 4.44% 4.89% 8674ms 43.91% RungeKutta4IvpOdeSolver::CalculateNextYValue 3597ms 18.21% 23.10% 7567ms 38.31% WntCellCycleOdeSystem::EvaluateYDerivatives 0 0% 23.10% 5108ms 25.86% MeshBasedCellPopulation::Update 84ms 0.43% 23.52% 4033ms 20.42% AbstractCellProperty::IsType (inline) 9ms 0.046% 23.57% 3951ms 20.00% Cylindrical2dMesh::ReMesh 556ms 2.81% 26.38% 2743ms 13.89% AbstractCellProperty::IsSame 1ms 0.0051% 26.39% 2428ms 12.29% OffLatticeSimulation::UpdateCellLocationsAndTopology 427ms 2.16% 28.55% 2187ms 11.07% std::type_info::operator== (inline) 0 0% 28.55% 2141ms 10.84% MutableMesh::ReMesh 1ms 0.0051% 28.55% 2113ms 10.70% ForwardEulerNumericalMethod::UpdateAllNodePositions 10ms 0.051% 28.60% 2072ms 10.49% AbstractNumericalMethod::ComputeForcesIncludingDamping 0 0% 28.60% 2017ms 10.21% AbstractCellPopulation::WriteResultsToFiles 830ms 4.20% 32.81% 1892ms 9.58% std::_Rb_tree::_M_lower_bound (inline) 1716ms 8.69% 41.49% 1716ms 8.69% __strcmp_avx2 138ms 0.7% 42.19% 1706ms 8.64% TetrahedralMesh::EdgeIterator::operator++ 59ms 0.3% 42.49% 1415ms 7.16% std::_Rb_tree::find (inline) 0 0% 42.49% 1133ms 5.74% MeshBasedCellPopulation::UpdateNodePairs 9ms 0.046% 42.54% 1127ms 5.71% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 58ms 0.29% 42.83% 1099ms 5.56% operator new 14ms 0.071% 42.90% 1088ms 5.51% TetrahedralMesh::ImportFromMesher 246ms 1.25% 44.15% 1029ms 5.21% __GI___libc_malloc 5ms 0.025% 44.17% 997ms 5.05% std::set::insert (inline) 9ms 0.046% 44.22% 994ms 5.03% MeshBasedCellPopulation::SpringIterator::operator++ 10ms 0.051% 44.27% 992ms 5.02% std::_Rb_tree::_M_insert_unique 40ms 0.2% 44.47% 977ms 4.95% std::__new_allocator::allocate (inline) 0 0% 44.47% 972ms 4.92% std::allocator_traits::allocate (inline) 0 0% 44.47% 893ms 4.52% std::set::count (inline) 0 0% 44.47% 797ms 4.03% triangulate 8ms 0.041% 44.51% 757ms 3.83% MeshBasedCellPopulationWithGhostNodes::AcceptCellWritersAcrossPopulation 0 0% 44.51% 719ms 3.64% delaunay 4ms 0.02% 44.53% 717ms 3.63% divconqdelaunay 54ms 0.27% 44.80% 703ms 3.56% std::map::operator[] (partial-inline) 7ms 0.035% 44.84% 697ms 3.53% CellPopulationElementWriter::Visit 404ms 2.05% 46.88% 694ms 3.51% _int_malloc 2ms 0.01% 46.89% 683ms 3.46% AbstractTwoBodyInteractionForce::AddForceContribution 672ms 3.40% 50.30% 672ms 3.40% std::_Rb_tree::_S_right (inline) 22ms 0.11% 50.41% 669ms 3.39% std::less::operator() (inline) 647ms 3.28% 53.68% 647ms 3.28% std::operator< (inline) 0 0% 53.68% 637ms 3.22% std::_Rb_tree::_M_create_node (inline) 27ms 0.14% 53.82% 622ms 3.15% std::_Rb_tree::_M_insert_ (inline) 611ms 3.09% 56.91% 620ms 3.14% WntCellCycleOdeSystem::CalculateStoppingEvent 0 0% 56.91% 615ms 3.11% std::_Rb_tree::_M_get_node (inline) 3ms 0.015% 56.93% 605ms 3.06% MeshBasedCellPopulation::AcceptCellWriter 166ms 0.84% 57.77% 588ms 2.98% __dynamic_cast 0 0% 57.77% 581ms 2.94% std::_Rb_tree::_Alloc_node::operator() (inline) 22ms 0.11% 57.88% 571ms 2.89% AbstractCellPopulation::GetCellUsingLocationIndex 16ms 0.081% 57.96% 565ms 2.86% AbstractVariableSizeTwoBodyInteractionForce::CalculateForceBetweenNodes 0 0% 57.96% 562ms 2.85% std::_Rb_tree::lower_bound (inline) 0 0% 57.96% 562ms 2.85% std::map::lower_bound (inline) 2ms 0.01% 57.97% 551ms 2.79% CellPropertyCollection::GetPropertiesType (inline) 3ms 0.015% 57.99% 541ms 2.74% Element::Element 9ms 0.046% 58.03% 527ms 2.67% MutableMesh::ReIndex 353ms 1.79% 59.82% 520ms 2.63% AbstractCellMutationState::AbstractCellMutationState 0 0% 59.82% 520ms 2.63% std::map::find (inline) 14ms 0.071% 59.89% 496ms 2.51% Cylindrical2dMesh::ReconstructCylindricalMesh 13ms 0.066% 59.96% 484ms 2.45% Cylindrical2dMesh::CorrectNonPeriodicMesh 7ms 0.035% 59.99% 482ms 2.44% Element::RegisterWithNodes (inline) 1ms 0.0051% 60.00% 479ms 2.42% std::ostream::operator<< (inline) 68ms 0.34% 60.34% 478ms 2.42% std::ostream::_M_insert 11ms 0.056% 60.40% 475ms 2.40% Node::AddElement 155ms 0.78% 61.18% 454ms 2.30% __GI___libc_free 4ms 0.02% 61.20% 431ms 2.18% AbstractCellProperty::IsSubType (inline) 4ms 0.02% 61.22% 392ms 1.98% std::set::erase (inline) 15ms 0.076% 61.30% 390ms 1.97% std::_Rb_tree::erase 16ms 0.081% 61.38% 387ms 1.96% Node::RemoveElement 122ms 0.62% 62.00% 366ms 1.85% std::_Rb_tree::_M_erase 13ms 0.066% 62.06% 361ms 1.83% divconqrecurse 4ms 0.02% 62.08% 361ms 1.83% std::_Vector_base::_M_allocate (inline) 138ms 0.7% 62.78% 360ms 1.82% std::_Rb_tree::_M_get_insert_unique_pos 22ms 0.11% 62.89% 357ms 1.81% Element::ResetIndex 8ms 0.041% 62.93% 353ms 1.79% std::__new_allocator::deallocate (inline) 0 0% 62.93% 347ms 1.76% std::allocator_traits::deallocate (inline) 21ms 0.11% 63.04% 341ms 1.73% std::_Rb_tree::~_Rb_tree (inline) 11ms 0.056% 63.09% 339ms 1.72% Cylindrical2dMesh::GenerateVectorsOfElementsStraddlingPeriodicBoundaries 95ms 0.48% 63.58% 338ms 1.71% mergehulls 328ms 1.66% 65.24% 328ms 1.66% std::type_info::name (inline) 131ms 0.66% 65.90% 324ms 1.64% __cxxabiv1::__si_class_type_info::__do_dyncast 0 0% 65.90% 319ms 1.61% std::_Rb_tree::_M_drop_node (inline) 5ms 0.025% 65.92% 318ms 1.61% Cell::GetCellProliferativeType 7ms 0.035% 65.96% 304ms 1.54% LegacyCellProliferativeTypesWriter::VisitCell 1ms 0.0051% 65.96% 304ms 1.54% NodeLocationWriter::Visit 0 0% 65.96% 304ms 1.54% std::set::~set (inline) 244ms 1.24% 67.20% 299ms 1.51% _int_free 5ms 0.025% 67.23% 287ms 1.45% AbstractCellPopulation::GetLocationIndexUsingCell 0 0% 67.23% 283ms 1.43% std::_Rb_tree::_M_put_node (inline) 6ms 0.03% 67.26% 280ms 1.42% Cell::GetMutationState 275ms 1.39% 68.65% 275ms 1.39% std::vector::operator[] (inline) 14ms 0.071% 68.72% 268ms 1.36% AbstractTetrahedralElement::CalculateJacobian 0 0% 68.72% 266ms 1.35% AbstractCellPopulation::Iterator::operator++ (inline) 8ms 0.041% 68.76% 266ms 1.35% std::vector::push_back (inline) 13ms 0.066% 68.82% 265ms 1.34% std::_Rb_tree::_Rb_tree (partial-inline) 31ms 0.16% 68.98% 264ms 1.34% AbstractCellPopulation::Iterator::IsRealCell (inline) 22ms 0.11% 69.09% 264ms 1.34% std::num_put::_M_insert_float 5ms 0.025% 69.12% 261ms 1.32% AbstractCellPopulation::IsCellAttachedToLocationIndex 40ms 0.2% 69.32% 250ms 1.27% ApcTwoHitCellMutationState::ApcTwoHitCellMutationState 16ms 0.081% 69.40% 250ms 1.27% std::vector::_M_realloc_insert 2ms 0.01% 69.41% 241ms 1.22% std::set::set (inline) 8ms 0.041% 69.45% 235ms 1.19% std::_Rb_tree::_M_erase_aux (inline) 61ms 0.31% 69.76% 234ms 1.18% ApcOneHitCellMutationState::ApcOneHitCellMutationState 0 0% 69.76% 227ms 1.15% TetrahedralMesh::RefreshJacobianCachedData 10ms 0.051% 69.81% 226ms 1.14% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 47ms 0.24% 70.05% 226ms 1.14% BetaCateninOneHitCellMutationState::BetaCateninOneHitCellMutationState 20ms 0.1% 70.15% 226ms 1.14% std::_Rb_tree::_M_copy (inline) 217ms 1.10% 71.25% 217ms 1.10% [libchaste_cell_based.so] 0 0% 71.25% 213ms 1.08% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 1ms 0.0051% 71.25% 212ms 1.07% alternateaxes 201ms 1.02% 72.27% 211ms 1.07% vertexmedian 6ms 0.03% 72.30% 207ms 1.05% std::__cxx11::collate::do_transform 60ms 0.3% 72.61% 203ms 1.03% std::_Rb_tree::_M_clone_node (inline) 13ms 0.066% 72.67% 199ms 1.01% Element::MarkAsDeleted 149ms 0.75% 73.43% 198ms 1.00% AbstractElement::GetNodeGlobalIndex 9ms 0.046% 73.47% 198ms 1.00% AbstractTetrahedralElement::CalculateInverseJacobian 0 0% 73.47% 198ms 1.00% ___vsnprintf 0 0% 73.47% 198ms 1.00% __vsnprintf_internal (inline) 23ms 0.12% 73.59% 194ms 0.98% __printf_buffer 138ms 0.7% 74.29% 194ms 0.98% malloc_consolidate 9ms 0.046% 74.33% 193ms 0.98% AbstractTetrahedralElement::RefreshJacobian 0 0% 74.33% 193ms 0.98% OffLatticeSimulation::ApplyBoundaries 2ms 0.01% 74.34% 189ms 0.96% CellProliferativeTypesWriter::VisitCell 20ms 0.1% 74.44% 184ms 0.93% TetrahedralMesh::Clear 1ms 0.0051% 74.45% 179ms 0.91% MeshBasedCellPopulation::GetDampingConstant 0 0% 74.45% 178ms 0.9% AbstractCentreBasedCellPopulation::GetDampingConstant 2ms 0.01% 74.46% 172ms 0.87% AbstractTetrahedralElement::AbstractTetrahedralElement 167ms 0.85% 75.31% 167ms 0.85% std::_Rb_tree_insert_and_rebalance 73ms 0.37% 75.67% 164ms 0.83% AbstractElement::GetNodeLocation 5ms 0.025% 75.70% 164ms 0.83% CellPropertyCollection::HasProperty 0 0% 75.70% 161ms 0.82% Cell::HasCellProperty (inline) 8ms 0.041% 75.74% 161ms 0.82% __printf_fp_l_buffer 0 0% 75.74% 161ms 0.82% __printf_fp_spec (inline) 151ms 0.76% 76.50% 151ms 0.76% Node::GetIndex 6ms 0.03% 76.54% 151ms 0.76% non-virtual thunk to WntCellCycleModel::AdjustOdeParameters(double) 76ms 0.38% 76.92% 150ms 0.76% __printf_fp_buffer_1 150ms 0.76% 77.68% 150ms 0.76% incircle 97ms 0.49% 78.17% 147ms 0.74% std::_Rb_tree::equal_range (inline) 5ms 0.025% 78.20% 144ms 0.73% MeshBasedCellPopulationWithGhostNodes::CalculateForceBetweenGhostNodes 2ms 0.01% 78.21% 143ms 0.72% MeshBasedCellPopulation::SpringsEnd (inline) 140ms 0.71% 78.91% 140ms 0.71% unlink_chunk 46ms 0.23% 79.15% 137ms 0.69% ApcTwoHitCellMutationState::~ApcTwoHitCellMutationState (inline) 0 0% 79.15% 134ms 0.68% boost::numeric::ublas::vector_assign (inline) 127ms 0.64% 79.79% 132ms 0.67% vertexsort 48ms 0.24% 80.03% 131ms 0.66% BetaCateninOneHitCellMutationState::~BetaCateninOneHitCellMutationState (inline) 37ms 0.19% 80.22% 130ms 0.66% TetrahedralMesh::EdgesEnd (partial-inline) 75ms 0.38% 80.60% 128ms 0.65% Cylindrical2dMesh::GetVectorFromAtoB 0 0% 80.60% 126ms 0.64% AbstractCellBasedWriter::OpenOutputFileForAppend 125ms 0.63% 81.23% 125ms 0.63% AbstractCellProperty::~AbstractCellProperty 0 0% 81.23% 124ms 0.63% OutputFileHandler::OpenOutputFile 124ms 0.63% 81.86% 124ms 0.63% std::vector::size (inline) 43ms 0.22% 82.08% 121ms 0.61% std::__ostream_insert 1ms 0.0051% 82.08% 119ms 0.6% WntCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel 6ms 0.03% 82.11% 118ms 0.6% boost::numeric::ublas::c_vector::c_vector (inline) 117ms 0.59% 82.71% 117ms 0.59% AbstractCellMutationState::~AbstractCellMutationState 36ms 0.18% 82.89% 109ms 0.55% ApcOneHitCellMutationState::~ApcOneHitCellMutationState (inline) 14ms 0.071% 82.96% 109ms 0.55% std::_Rb_tree_const_iterator::operator++ (inline) 0 0% 82.96% 106ms 0.54% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 31ms 0.16% 83.12% 106ms 0.54% boost::numeric::ublas::indexing_vector_assign 106ms 0.54% 83.65% 106ms 0.54% std::_Rb_tree_rebalance_for_erase 104ms 0.53% 84.18% 104ms 0.53% std::_Rb_tree_increment 11ms 0.056% 84.24% 103ms 0.52% Node::~Node 0 0% 84.24% 102ms 0.52% Cell::SetCellProliferativeType 101ms 0.51% 84.75% 101ms 0.51% [libchaste_mesh.so] 25ms 0.13% 84.87% 100ms 0.51% std::num_put::_M_insert_int