File: Test2DMeshBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 16512ms, 84.59% of 19519ms total Dropped 784 nodes (cum <= 97.59ms) flat flat% sum% cum cum% 0 0% 0% 19475ms 99.77% __libc_start_call_main 0 0% 0% 19475ms 99.77% __libc_start_main_impl 0 0% 0% 19475ms 99.77% _start 0 0% 0% 19453ms 99.66% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 19453ms 99.66% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 19453ms 99.66% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 19453ms 99.66% main 0 0% 0% 19411ms 99.45% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 19411ms 99.45% CxxTest::TestRunner::runTest (inline) 0 0% 0% 19411ms 99.45% Test2DCryptRepresentativeSimulation::TestRepresentativeSimulationForProfiling 1ms 0.0051% 0.0051% 19386ms 99.32% AbstractCellBasedSimulation::Solve 0 0% 0.0051% 14773ms 75.69% AbstractCellBasedSimulation::UpdateCellPopulation 1ms 0.0051% 0.01% 9282ms 47.55% AbstractCellBasedSimulation::DoCellBirth 3ms 0.015% 0.026% 9174ms 47.00% Cell::ReadyToDivide 8ms 0.041% 0.067% 9109ms 46.67% AbstractPhaseBasedCellCycleModel::ReadyToDivide 0 0% 0.067% 8957ms 45.89% AbstractWntOdeBasedCellCycleModel::UpdateCellCyclePhase 7ms 0.036% 0.1% 8946ms 45.83% AbstractOdeBasedPhaseBasedCellCycleModel::UpdateCellCyclePhase 2ms 0.01% 0.11% 8937ms 45.79% CellCycleModelOdeHandler::SolveOdeToTime 70ms 0.36% 0.47% 8745ms 44.80% AbstractOneStepIvpOdeSolver::InternalSolve 987ms 5.06% 5.53% 7839ms 40.16% RungeKutta4IvpOdeSolver::CalculateNextYValue 2833ms 14.51% 20.04% 6645ms 34.04% WntCellCycleOdeSystem::EvaluateYDerivatives 0 0% 20.04% 5390ms 27.61% MeshBasedCellPopulation::Update 2ms 0.01% 20.05% 4135ms 21.18% Cylindrical2dMesh::ReMesh 55ms 0.28% 20.33% 3807ms 19.50% AbstractCellProperty::IsType (inline) 2ms 0.01% 20.34% 2581ms 13.22% OffLatticeSimulation::UpdateCellLocationsAndTopology 327ms 1.68% 22.02% 2476ms 12.69% AbstractCellProperty::IsSame 0 0% 22.02% 2294ms 11.75% MutableMesh::ReMesh 1ms 0.0051% 22.02% 2262ms 11.59% ForwardEulerNumericalMethod::UpdateAllNodePositions 8ms 0.041% 22.07% 2213ms 11.34% AbstractNumericalMethod::ComputeForcesIncludingDamping 221ms 1.13% 23.20% 2149ms 11.01% std::type_info::operator== (inline) 2088ms 10.70% 33.90% 2088ms 10.70% __strcmp_avx2 0 0% 33.90% 2027ms 10.38% AbstractCellPopulation::WriteResultsToFiles 829ms 4.25% 38.14% 1867ms 9.57% std::_Rb_tree::_M_lower_bound (inline) 169ms 0.87% 39.01% 1681ms 8.61% TetrahedralMesh::EdgeIterator::operator++ 65ms 0.33% 39.34% 1357ms 6.95% std::_Rb_tree::find (inline) 0 0% 39.34% 1198ms 6.14% MeshBasedCellPopulation::UpdateNodePairs 9ms 0.046% 39.39% 1151ms 5.90% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 17ms 0.087% 39.47% 1148ms 5.88% TetrahedralMesh::ImportFromMesher 51ms 0.26% 39.74% 1129ms 5.78% operator new 255ms 1.31% 41.04% 1058ms 5.42% __GI___libc_malloc 18ms 0.092% 41.13% 1053ms 5.39% MeshBasedCellPopulation::SpringIterator::operator++ 10ms 0.051% 41.19% 1027ms 5.26% std::set::insert (inline) 13ms 0.067% 41.25% 1017ms 5.21% std::_Rb_tree::_M_insert_unique 49ms 0.25% 41.50% 1000ms 5.12% std::__new_allocator::allocate (inline) 0 0% 41.50% 997ms 5.11% std::allocator_traits::allocate (inline) 0 0% 41.50% 894ms 4.58% triangulate 0 0% 41.50% 817ms 4.19% delaunay 6ms 0.031% 41.53% 817ms 4.19% divconqdelaunay 0 0% 41.53% 811ms 4.15% std::set::count (inline) 68ms 0.35% 41.88% 754ms 3.86% std::map::operator[] (partial-inline) 6ms 0.031% 41.91% 751ms 3.85% MeshBasedCellPopulationWithGhostNodes::AcceptCellWritersAcrossPopulation 0 0% 41.91% 742ms 3.80% AbstractTwoBodyInteractionForce::AddForceContribution 400ms 2.05% 43.96% 727ms 3.72% _int_malloc 8ms 0.041% 44.00% 725ms 3.71% CellPopulationElementWriter::Visit 721ms 3.69% 47.70% 721ms 3.69% std::_Rb_tree::_S_right (inline) 708ms 3.63% 51.32% 708ms 3.63% WntCellCycleOdeSystem::CalculateStoppingEvent 197ms 1.01% 52.33% 667ms 3.42% __dynamic_cast 0 0% 52.33% 667ms 3.42% std::_Rb_tree::_M_create_node (inline) 23ms 0.12% 52.45% 661ms 3.39% AbstractCellPopulation::GetCellUsingLocationIndex 22ms 0.11% 52.56% 644ms 3.30% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 0 0% 52.56% 642ms 3.29% std::_Rb_tree::_M_get_node (inline) 21ms 0.11% 52.67% 637ms 3.26% std::_Rb_tree::_M_insert_ (inline) 0 0% 52.67% 603ms 3.09% std::_Rb_tree::_Alloc_node::operator() (inline) 3ms 0.015% 52.69% 602ms 3.08% CellPropertyCollection::GetPropertiesType (inline) 0 0% 52.69% 592ms 3.03% std::_Rb_tree::lower_bound (inline) 0 0% 52.69% 592ms 3.03% std::map::lower_bound (inline) 4ms 0.02% 52.71% 582ms 2.98% Element::Element 6ms 0.031% 52.74% 578ms 2.96% MeshBasedCellPopulation::AcceptCellWriter 8ms 0.041% 52.78% 572ms 2.93% std::less::operator() (inline) 564ms 2.89% 55.67% 564ms 2.89% std::operator< (inline) 0 0% 55.67% 543ms 2.78% std::map::find (inline) 5ms 0.026% 55.69% 535ms 2.74% MutableMesh::ReIndex 10ms 0.051% 55.75% 517ms 2.65% Element::RegisterWithNodes (inline) 10ms 0.051% 55.80% 501ms 2.57% Node::AddElement 3ms 0.015% 55.81% 491ms 2.52% AbstractCellProperty::IsSubType (inline) 17ms 0.087% 55.90% 486ms 2.49% Cylindrical2dMesh::CorrectNonPeriodicMesh 9ms 0.046% 55.95% 481ms 2.46% Cylindrical2dMesh::ReconstructCylindricalMesh 1ms 0.0051% 55.95% 478ms 2.45% std::ostream::operator<< (inline) 65ms 0.33% 56.28% 475ms 2.43% std::ostream::_M_insert 126ms 0.65% 56.93% 454ms 2.33% __GI___libc_free 123ms 0.63% 57.56% 399ms 2.04% std::_Rb_tree::_M_erase 260ms 1.33% 58.89% 393ms 2.01% AbstractCellMutationState::AbstractCellMutationState 15ms 0.077% 58.97% 388ms 1.99% Node::RemoveElement 3ms 0.015% 58.98% 386ms 1.98% std::set::erase (inline) 8ms 0.041% 59.02% 384ms 1.97% std::_Rb_tree::erase 30ms 0.15% 59.18% 381ms 1.95% std::_Rb_tree::~_Rb_tree (inline) 15ms 0.077% 59.26% 379ms 1.94% divconqrecurse 12ms 0.061% 59.32% 368ms 1.89% std::__new_allocator::deallocate (inline) 160ms 0.82% 60.14% 367ms 1.88% std::_Rb_tree::_M_get_insert_unique_pos 0 0% 60.14% 362ms 1.85% std::allocator_traits::deallocate (inline) 91ms 0.47% 60.60% 355ms 1.82% mergehulls 0 0% 60.60% 355ms 1.82% std::_Vector_base::_M_allocate (inline) 169ms 0.87% 61.47% 351ms 1.80% __cxxabiv1::__si_class_type_info::__do_dyncast 23ms 0.12% 61.59% 348ms 1.78% Element::ResetIndex 0 0% 61.59% 347ms 1.78% std::set::~set (inline) 0 0% 61.59% 345ms 1.77% std::_Rb_tree::_M_drop_node (inline) 260ms 1.33% 62.92% 328ms 1.68% _int_free 5ms 0.026% 62.94% 322ms 1.65% Cell::GetMutationState 4ms 0.02% 62.96% 316ms 1.62% Cell::GetCellProliferativeType 5ms 0.026% 62.99% 309ms 1.58% alternateaxes 291ms 1.49% 64.48% 304ms 1.56% vertexmedian 0 0% 64.48% 299ms 1.53% std::_Rb_tree::_M_put_node (inline) 9ms 0.046% 64.53% 297ms 1.52% Cylindrical2dMesh::GenerateVectorsOfElementsStraddlingPeriodicBoundaries 297ms 1.52% 66.05% 297ms 1.52% [libchaste_cell_based.so] 295ms 1.51% 67.56% 296ms 1.52% std::vector::operator[] (inline) 7ms 0.036% 67.60% 292ms 1.50% AbstractCellPopulation::GetLocationIndexUsingCell 20ms 0.1% 67.70% 285ms 1.46% std::_Rb_tree::_Rb_tree (partial-inline) 0 0% 67.70% 284ms 1.45% AbstractCellPopulation::Iterator::operator++ (inline) 2ms 0.01% 67.71% 284ms 1.45% LegacyCellProliferativeTypesWriter::VisitCell 36ms 0.18% 67.89% 280ms 1.43% AbstractCellPopulation::Iterator::IsRealCell (inline) 0 0% 67.89% 269ms 1.38% NodeLocationWriter::Visit 10ms 0.051% 67.94% 269ms 1.38% std::vector::push_back (inline) 2ms 0.01% 67.95% 264ms 1.35% std::set::set (inline) 21ms 0.11% 68.06% 263ms 1.35% AbstractTetrahedralElement::CalculateJacobian 7ms 0.036% 68.10% 261ms 1.34% AbstractCellPopulation::IsCellAttachedToLocationIndex 29ms 0.15% 68.25% 249ms 1.28% std::num_put::_M_insert_float 12ms 0.061% 68.31% 249ms 1.28% std::vector::_M_realloc_insert 16ms 0.082% 68.39% 235ms 1.20% std::_Rb_tree::_M_erase_aux (inline) 74ms 0.38% 68.77% 234ms 1.20% ApcOneHitCellMutationState::ApcOneHitCellMutationState 24ms 0.12% 68.89% 234ms 1.20% std::_Rb_tree::_M_copy (inline) 95ms 0.49% 69.38% 232ms 1.19% ApcTwoHitCellMutationState::ApcTwoHitCellMutationState 4ms 0.02% 69.40% 225ms 1.15% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 101ms 0.52% 69.92% 221ms 1.13% BetaCateninOneHitCellMutationState::BetaCateninOneHitCellMutationState 1ms 0.0051% 69.92% 221ms 1.13% MeshBasedCellPopulation::GetDampingConstant 1ms 0.0051% 69.93% 220ms 1.13% AbstractCentreBasedCellPopulation::GetDampingConstant 1ms 0.0051% 69.93% 220ms 1.13% TetrahedralMesh::RefreshJacobianCachedData 17ms 0.087% 70.02% 218ms 1.12% TetrahedralMesh::Clear 152ms 0.78% 70.80% 214ms 1.10% AbstractElement::GetNodeGlobalIndex 5ms 0.026% 70.82% 210ms 1.08% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 13ms 0.067% 70.89% 209ms 1.07% Element::MarkAsDeleted 150ms 0.77% 71.66% 204ms 1.05% malloc_consolidate 70ms 0.36% 72.02% 202ms 1.03% std::_Rb_tree::_M_clone_node (inline) 0 0% 72.02% 199ms 1.02% OffLatticeSimulation::ApplyBoundaries 25ms 0.13% 72.15% 197ms 1.01% AbstractTetrahedralElement::RefreshJacobian 6ms 0.031% 72.18% 191ms 0.98% AbstractTetrahedralElement::AbstractTetrahedralElement 11ms 0.056% 72.23% 191ms 0.98% AbstractTetrahedralElement::CalculateInverseJacobian 2ms 0.01% 72.24% 191ms 0.98% std::__cxx11::collate::do_transform 0 0% 72.24% 185ms 0.95% ___vsnprintf 1ms 0.0051% 72.25% 185ms 0.95% __vsnprintf_internal (inline) 19ms 0.097% 72.34% 184ms 0.94% __printf_buffer 1ms 0.0051% 72.35% 174ms 0.89% CellProliferativeTypesWriter::VisitCell 172ms 0.88% 73.23% 172ms 0.88% std::vector::size (inline) 163ms 0.84% 74.07% 163ms 0.84% std::_Rb_tree_insert_and_rebalance 162ms 0.83% 74.90% 162ms 0.83% incircle 27ms 0.14% 75.03% 160ms 0.82% TetrahedralMesh::EdgesEnd (partial-inline) 3ms 0.015% 75.05% 159ms 0.81% MeshBasedCellPopulationWithGhostNodes::CalculateForceBetweenGhostNodes 158ms 0.81% 75.86% 158ms 0.81% Node::GetIndex 9ms 0.046% 75.91% 158ms 0.81% non-virtual thunk to WntCellCycleModel::AdjustOdeParameters(double) 10ms 0.051% 75.96% 156ms 0.8% MeshBasedCellPopulation::SpringsEnd (inline) 95ms 0.49% 76.44% 156ms 0.8% std::_Rb_tree::equal_range (inline) 3ms 0.015% 76.46% 155ms 0.79% __printf_fp_l_buffer 0 0% 76.46% 155ms 0.79% __printf_fp_spec (inline) 155ms 0.79% 77.25% 155ms 0.79% unlink_chunk 17ms 0.087% 77.34% 148ms 0.76% boost::detail::shared_count::~shared_count (inline) 0 0% 77.34% 148ms 0.76% boost::shared_ptr::~shared_ptr (inline) 53ms 0.27% 77.61% 146ms 0.75% AbstractElement::GetNodeLocation 54ms 0.28% 77.89% 146ms 0.75% ApcTwoHitCellMutationState::~ApcTwoHitCellMutationState (inline) 145ms 0.74% 78.63% 145ms 0.74% [libchaste_crypt.so] 64ms 0.33% 78.96% 145ms 0.74% __printf_fp_buffer_1 0 0% 78.96% 144ms 0.74% WntCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel 3ms 0.015% 78.97% 143ms 0.73% CellPropertyCollection::HasProperty 37ms 0.19% 79.16% 140ms 0.72% ApcOneHitCellMutationState::~ApcOneHitCellMutationState (inline) 0 0% 79.16% 139ms 0.71% Cell::HasCellProperty (inline) 2ms 0.01% 79.17% 136ms 0.7% boost::numeric::ublas::vector_assign (inline) 1ms 0.0051% 79.18% 134ms 0.69% AbstractCellBasedWriter::OpenOutputFileForAppend 84ms 0.43% 79.61% 134ms 0.69% Cylindrical2dMesh::GetVectorFromAtoB 133ms 0.68% 80.29% 133ms 0.68% AbstractCellMutationState::~AbstractCellMutationState 87ms 0.45% 80.74% 133ms 0.68% TetrahedralMesh::EdgeIterator::EdgeIterator (partial-inline) 0 0% 80.74% 131ms 0.67% OutputFileHandler::OpenOutputFile 17ms 0.087% 80.82% 131ms 0.67% boost::numeric::ublas::c_vector::c_vector (inline) 123ms 0.63% 81.45% 128ms 0.66% boost::detail::sp_counted_base::release 45ms 0.23% 81.68% 127ms 0.65% BetaCateninOneHitCellMutationState::~BetaCateninOneHitCellMutationState (inline) 5ms 0.026% 81.71% 127ms 0.65% Cell::SetCellProliferativeType 3ms 0.015% 81.73% 127ms 0.65% Node::~Node 14ms 0.072% 81.80% 125ms 0.64% MeshBasedCellPopulation::SpringIterator::SpringIterator 22ms 0.11% 81.91% 117ms 0.6% std::num_put::_M_insert_int 30ms 0.15% 82.06% 116ms 0.59% boost::numeric::ublas::indexing_vector_assign 0 0% 82.06% 115ms 0.59% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 114ms 0.58% 82.65% 114ms 0.58% std::type_info::name (inline) 108ms 0.55% 83.20% 114ms 0.58% vertexsort 4ms 0.02% 83.22% 110ms 0.56% CryptSimulationBoundaryCondition::ImposeBoundaryCondition 43ms 0.22% 83.44% 101ms 0.52% boost::shared_ptr::shared_ptr (inline) 59ms 0.3% 83.74% 100ms 0.51% TimeStepper::AdvanceOneTimeStep 100ms 0.51% 84.26% 100ms 0.51% std::_Rb_tree_increment 40ms 0.2% 84.46% 98ms 0.5% AbstractTetrahedralMesh::GetElement 4ms 0.02% 84.48% 98ms 0.5% std::_Rb_tree_const_iterator::operator++ (inline) 22ms 0.11% 84.59% 98ms 0.5% std::__ostream_insert