File: Test2DMeshBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 16245ms, 83.64% of 19422ms total Dropped 794 nodes (cum <= 97.11ms) flat flat% sum% cum cum% 0 0% 0% 19379ms 99.78% __libc_start_call_main 0 0% 0% 19379ms 99.78% __libc_start_main_impl 0 0% 0% 19379ms 99.78% _start 0 0% 0% 19358ms 99.67% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 19358ms 99.67% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 19358ms 99.67% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 19358ms 99.67% main 0 0% 0% 19310ms 99.42% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 19310ms 99.42% CxxTest::TestRunner::runTest (inline) 0 0% 0% 19310ms 99.42% Test2DCryptRepresentativeSimulation::TestRepresentativeSimulationForProfiling 1ms 0.0051% 0.0051% 19282ms 99.28% AbstractCellBasedSimulation::Solve 0 0% 0.0051% 14686ms 75.62% AbstractCellBasedSimulation::UpdateCellPopulation 2ms 0.01% 0.015% 9266ms 47.71% AbstractCellBasedSimulation::DoCellBirth 4ms 0.021% 0.036% 9173ms 47.23% Cell::ReadyToDivide 5ms 0.026% 0.062% 9094ms 46.82% AbstractPhaseBasedCellCycleModel::ReadyToDivide 2ms 0.01% 0.072% 8947ms 46.07% AbstractWntOdeBasedCellCycleModel::UpdateCellCyclePhase 10ms 0.051% 0.12% 8937ms 46.01% AbstractOdeBasedPhaseBasedCellCycleModel::UpdateCellCyclePhase 2ms 0.01% 0.13% 8924ms 45.95% CellCycleModelOdeHandler::SolveOdeToTime 74ms 0.38% 0.51% 8776ms 45.19% AbstractOneStepIvpOdeSolver::InternalSolve 1005ms 5.17% 5.69% 7865ms 40.50% RungeKutta4IvpOdeSolver::CalculateNextYValue 2825ms 14.55% 20.23% 6676ms 34.37% WntCellCycleOdeSystem::EvaluateYDerivatives 0 0% 20.23% 5298ms 27.28% MeshBasedCellPopulation::Update 2ms 0.01% 20.25% 4066ms 20.94% Cylindrical2dMesh::ReMesh 61ms 0.31% 20.56% 3850ms 19.82% AbstractCellProperty::IsType (inline) 0 0% 20.56% 2580ms 13.28% OffLatticeSimulation::UpdateCellLocationsAndTopology 345ms 1.78% 22.34% 2511ms 12.93% AbstractCellProperty::IsSame 0 0% 22.34% 2269ms 11.68% ForwardEulerNumericalMethod::UpdateAllNodePositions 0 0% 22.34% 2247ms 11.57% MutableMesh::ReMesh 12ms 0.062% 22.40% 2224ms 11.45% AbstractNumericalMethod::ComputeForcesIncludingDamping 205ms 1.06% 23.45% 2166ms 11.15% std::type_info::operator== (inline) 2093ms 10.78% 34.23% 2093ms 10.78% __strcmp_avx2 2ms 0.01% 34.24% 2009ms 10.34% AbstractCellPopulation::WriteResultsToFiles 790ms 4.07% 38.31% 1848ms 9.51% std::_Rb_tree::_M_lower_bound (inline) 145ms 0.75% 39.05% 1679ms 8.64% TetrahedralMesh::EdgeIterator::operator++ 56ms 0.29% 39.34% 1385ms 7.13% std::_Rb_tree::find (inline) 0 0% 39.34% 1198ms 6.17% MeshBasedCellPopulation::UpdateNodePairs 3ms 0.015% 39.36% 1148ms 5.91% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 18ms 0.093% 39.45% 1100ms 5.66% TetrahedralMesh::ImportFromMesher 11ms 0.057% 39.51% 1069ms 5.50% MeshBasedCellPopulation::SpringIterator::operator++ 40ms 0.21% 39.71% 1047ms 5.39% operator new 11ms 0.057% 39.77% 1008ms 5.19% std::set::insert (inline) 227ms 1.17% 40.94% 998ms 5.14% __GI___libc_malloc 11ms 0.057% 40.99% 997ms 5.13% std::_Rb_tree::_M_insert_unique 33ms 0.17% 41.16% 900ms 4.63% std::__new_allocator::allocate (inline) 0 0% 41.16% 894ms 4.60% std::allocator_traits::allocate (inline) 0 0% 41.16% 889ms 4.58% triangulate 0 0% 41.16% 836ms 4.30% std::set::count (inline) 1ms 0.0051% 41.17% 801ms 4.12% delaunay 4ms 0.021% 41.19% 800ms 4.12% divconqdelaunay 2ms 0.01% 41.20% 744ms 3.83% AbstractTwoBodyInteractionForce::AddForceContribution 2ms 0.01% 41.21% 731ms 3.76% MeshBasedCellPopulationWithGhostNodes::AcceptCellWritersAcrossPopulation 712ms 3.67% 44.88% 712ms 3.67% std::_Rb_tree::_S_right (inline) 5ms 0.026% 44.90% 708ms 3.65% CellPopulationElementWriter::Visit 705ms 3.63% 48.53% 705ms 3.63% WntCellCycleOdeSystem::CalculateStoppingEvent 369ms 1.90% 50.43% 680ms 3.50% _int_malloc 55ms 0.28% 50.72% 676ms 3.48% std::map::operator[] (partial-inline) 201ms 1.03% 51.75% 661ms 3.40% __dynamic_cast 19ms 0.098% 51.85% 648ms 3.34% std::less::operator() (inline) 629ms 3.24% 55.09% 629ms 3.24% std::operator< (inline) 32ms 0.16% 55.25% 627ms 3.23% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 36ms 0.19% 55.44% 608ms 3.13% std::_Rb_tree::_M_insert_ (inline) 0 0% 55.44% 590ms 3.04% std::_Rb_tree::_M_create_node (inline) 4ms 0.021% 55.46% 586ms 3.02% CellPropertyCollection::GetPropertiesType (inline) 5ms 0.026% 55.48% 583ms 3.00% MeshBasedCellPopulation::AcceptCellWriter 0 0% 55.48% 568ms 2.92% std::_Rb_tree::_M_get_node (inline) 25ms 0.13% 55.61% 564ms 2.90% AbstractCellPopulation::GetCellUsingLocationIndex 11ms 0.057% 55.67% 559ms 2.88% Element::Element 0 0% 55.67% 545ms 2.81% std::_Rb_tree::lower_bound (inline) 0 0% 55.67% 545ms 2.81% std::map::lower_bound (inline) 0 0% 55.67% 543ms 2.80% std::map::find (inline) 0 0% 55.67% 538ms 2.77% std::_Rb_tree::_Alloc_node::operator() (inline) 10ms 0.051% 55.72% 519ms 2.67% MutableMesh::ReIndex 14ms 0.072% 55.79% 509ms 2.62% Cylindrical2dMesh::ReconstructCylindricalMesh 12ms 0.062% 55.85% 506ms 2.61% Element::RegisterWithNodes (inline) 15ms 0.077% 55.93% 496ms 2.55% Cylindrical2dMesh::CorrectNonPeriodicMesh 9ms 0.046% 55.98% 492ms 2.53% Node::AddElement 0 0% 55.98% 486ms 2.50% AbstractCellProperty::IsSubType (inline) 0 0% 55.98% 465ms 2.39% std::ostream::operator<< (inline) 65ms 0.33% 56.31% 463ms 2.38% std::ostream::_M_insert 142ms 0.73% 57.04% 424ms 2.18% __GI___libc_free 266ms 1.37% 58.41% 423ms 2.18% AbstractCellMutationState::AbstractCellMutationState 15ms 0.077% 58.49% 379ms 1.95% std::_Rb_tree::erase 132ms 0.68% 59.17% 378ms 1.95% std::_Rb_tree::_M_get_insert_unique_pos 1ms 0.0051% 59.18% 377ms 1.94% std::set::erase (inline) 14ms 0.072% 59.25% 375ms 1.93% Node::RemoveElement 18ms 0.093% 59.34% 375ms 1.93% divconqrecurse 43ms 0.22% 59.56% 354ms 1.82% Element::ResetIndex 119ms 0.61% 60.17% 350ms 1.80% mergehulls 17ms 0.088% 60.26% 347ms 1.79% std::__new_allocator::deallocate (inline) 0 0% 60.26% 340ms 1.75% std::allocator_traits::deallocate (inline) 96ms 0.49% 60.76% 338ms 1.74% std::_Rb_tree::_M_erase 171ms 0.88% 61.64% 328ms 1.69% __cxxabiv1::__si_class_type_info::__do_dyncast 2ms 0.01% 61.65% 328ms 1.69% std::_Vector_base::_M_allocate (inline) 9ms 0.046% 61.69% 320ms 1.65% Cylindrical2dMesh::GenerateVectorsOfElementsStraddlingPeriodicBoundaries 319ms 1.64% 63.34% 319ms 1.64% [libchaste_cell_based.so] 1ms 0.0051% 63.34% 310ms 1.60% Cell::GetCellProliferativeType 0 0% 63.34% 310ms 1.60% std::_Rb_tree::_M_drop_node (inline) 20ms 0.1% 63.44% 310ms 1.60% std::_Rb_tree::~_Rb_tree (inline) 12ms 0.062% 63.51% 303ms 1.56% AbstractCellPopulation::GetLocationIndexUsingCell 0 0% 63.51% 298ms 1.53% AbstractCellPopulation::Iterator::operator++ (inline) 3ms 0.015% 63.52% 297ms 1.53% Cell::GetMutationState 36ms 0.19% 63.71% 295ms 1.52% AbstractCellPopulation::Iterator::IsRealCell (inline) 1ms 0.0051% 63.71% 295ms 1.52% LegacyCellProliferativeTypesWriter::VisitCell 2ms 0.01% 63.72% 294ms 1.51% alternateaxes 275ms 1.42% 65.14% 291ms 1.50% vertexmedian 0 0% 65.14% 289ms 1.49% std::set::~set (inline) 285ms 1.47% 66.60% 286ms 1.47% std::vector::operator[] (inline) 3ms 0.015% 66.62% 280ms 1.44% NodeLocationWriter::Visit 235ms 1.21% 67.83% 280ms 1.44% _int_free 16ms 0.082% 67.91% 277ms 1.43% std::_Rb_tree::_Rb_tree (partial-inline) 0 0% 67.91% 275ms 1.42% std::_Rb_tree::_M_put_node (inline) 6ms 0.031% 67.94% 265ms 1.36% AbstractCellPopulation::IsCellAttachedToLocationIndex 0 0% 67.94% 250ms 1.29% std::set::set (inline) 12ms 0.062% 68.01% 245ms 1.26% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 13ms 0.067% 68.07% 245ms 1.26% std::vector::push_back (inline) 19ms 0.098% 68.17% 243ms 1.25% std::num_put::_M_insert_float 48ms 0.25% 68.42% 236ms 1.22% ApcOneHitCellMutationState::ApcOneHitCellMutationState 95ms 0.49% 68.91% 233ms 1.20% BetaCateninOneHitCellMutationState::BetaCateninOneHitCellMutationState 19ms 0.098% 69.00% 231ms 1.19% AbstractTetrahedralElement::CalculateJacobian 97ms 0.5% 69.50% 229ms 1.18% ApcTwoHitCellMutationState::ApcTwoHitCellMutationState 0 0% 69.50% 227ms 1.17% TetrahedralMesh::RefreshJacobianCachedData 11ms 0.057% 69.56% 220ms 1.13% std::_Rb_tree::_M_erase_aux (inline) 4ms 0.021% 69.58% 218ms 1.12% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 21ms 0.11% 69.69% 217ms 1.12% std::_Rb_tree::_M_copy (inline) 10ms 0.051% 69.74% 217ms 1.12% std::vector::_M_realloc_insert 12ms 0.062% 69.80% 212ms 1.09% Element::MarkAsDeleted 2ms 0.01% 69.81% 209ms 1.08% MeshBasedCellPopulation::GetDampingConstant 0 0% 69.81% 206ms 1.06% AbstractCentreBasedCellPopulation::GetDampingConstant 154ms 0.79% 70.61% 205ms 1.06% AbstractElement::GetNodeGlobalIndex 0 0% 70.61% 202ms 1.04% OffLatticeSimulation::ApplyBoundaries 3ms 0.015% 70.62% 194ms 1% AbstractTetrahedralElement::CalculateInverseJacobian 8ms 0.041% 70.66% 193ms 0.99% std::__cxx11::collate::do_transform 42ms 0.22% 70.88% 192ms 0.99% TetrahedralMesh::EdgesEnd (partial-inline) 66ms 0.34% 71.22% 189ms 0.97% std::_Rb_tree::_M_clone_node (inline) 188ms 0.97% 72.19% 188ms 0.97% Node::GetIndex 12ms 0.062% 72.25% 185ms 0.95% TetrahedralMesh::Clear 124ms 0.64% 72.89% 184ms 0.95% malloc_consolidate 0 0% 72.89% 182ms 0.94% ___vsnprintf 0 0% 72.89% 182ms 0.94% __vsnprintf_internal (inline) 15ms 0.077% 72.96% 179ms 0.92% __printf_buffer 3ms 0.015% 72.98% 172ms 0.89% CellProliferativeTypesWriter::VisitCell 27ms 0.14% 73.12% 171ms 0.88% AbstractTetrahedralElement::RefreshJacobian 17ms 0.088% 73.21% 169ms 0.87% MeshBasedCellPopulationWithGhostNodes::CalculateForceBetweenGhostNodes 169ms 0.87% 74.08% 169ms 0.87% unlink_chunk 4ms 0.021% 74.10% 166ms 0.85% boost::numeric::ublas::vector_assign (inline) 163ms 0.84% 74.94% 163ms 0.84% std::_Rb_tree_insert_and_rebalance 4ms 0.021% 74.96% 162ms 0.83% CellPropertyCollection::HasProperty 3ms 0.015% 74.97% 159ms 0.82% AbstractTetrahedralElement::AbstractTetrahedralElement 0 0% 74.97% 159ms 0.82% Cell::HasCellProperty (inline) 157ms 0.81% 75.78% 157ms 0.81% [libchaste_crypt.so] 7ms 0.036% 75.82% 155ms 0.8% MeshBasedCellPopulation::SpringsEnd (inline) 94ms 0.48% 76.30% 155ms 0.8% std::_Rb_tree::equal_range 154ms 0.79% 77.09% 154ms 0.79% std::vector::size (inline) 7ms 0.036% 77.13% 153ms 0.79% __printf_fp_l_buffer 0 0% 77.13% 153ms 0.79% __printf_fp_spec (inline) 152ms 0.78% 77.91% 152ms 0.78% AbstractCellMutationState::~AbstractCellMutationState 147ms 0.76% 78.67% 147ms 0.76% incircle 48ms 0.25% 78.92% 146ms 0.75% BetaCateninOneHitCellMutationState::~BetaCateninOneHitCellMutationState (inline) 100ms 0.51% 79.43% 146ms 0.75% TetrahedralMesh::EdgeIterator::EdgeIterator 10ms 0.051% 79.48% 146ms 0.75% boost::numeric::ublas::c_vector::c_vector (inline) 142ms 0.73% 80.21% 142ms 0.73% std::type_info::name (inline) 0 0% 80.21% 140ms 0.72% AbstractCellBasedWriter::OpenOutputFileForAppend 3ms 0.015% 80.23% 140ms 0.72% WntCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel 76ms 0.39% 80.62% 139ms 0.72% Cylindrical2dMesh::GetVectorFromAtoB 0 0% 80.62% 139ms 0.72% OutputFileHandler::OpenOutputFile 73ms 0.38% 81.00% 134ms 0.69% __printf_fp_buffer_1 46ms 0.24% 81.23% 133ms 0.68% ApcTwoHitCellMutationState::~ApcTwoHitCellMutationState (inline) 57ms 0.29% 81.53% 131ms 0.67% AbstractElement::GetNodeLocation 38ms 0.2% 81.72% 129ms 0.66% boost::numeric::ublas::indexing_vector_assign 37ms 0.19% 81.91% 128ms 0.66% ApcOneHitCellMutationState::~ApcOneHitCellMutationState (inline) 0 0% 81.91% 122ms 0.63% AbstractCellBasedSimulation::DoCellRemoval (inline) 1ms 0.0051% 81.92% 121ms 0.62% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 115ms 0.59% 82.51% 121ms 0.62% vertexsort 0 0% 82.51% 119ms 0.61% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 71ms 0.37% 82.88% 117ms 0.6% TimeStepper::AdvanceOneTimeStep 16ms 0.082% 82.96% 116ms 0.6% boost::detail::shared_count::~shared_count (inline) 0 0% 82.96% 116ms 0.6% boost::shared_ptr::~shared_ptr (inline) 7ms 0.036% 82.99% 116ms 0.6% non-virtual thunk to WntCellCycleModel::AdjustOdeParameters(double) 28ms 0.14% 83.14% 116ms 0.6% std::__ostream_insert 3ms 0.015% 83.15% 112ms 0.58% CryptSimulationBoundaryCondition::ImposeBoundaryCondition 1ms 0.0051% 83.16% 111ms 0.57% Cell::SetCellProliferativeType 14ms 0.072% 83.23% 111ms 0.57% Node::~Node 12ms 0.062% 83.29% 109ms 0.56% MeshBasedCellPopulation::SpringIterator::SpringIterator 52ms 0.27% 83.56% 108ms 0.56% boost::shared_ptr::shared_ptr (inline) 16ms 0.082% 83.64% 105ms 0.54% std::num_put::_M_insert_int