File: Test2DMeshBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 16993ms, 86.28% of 19695ms total Dropped 750 nodes (cum <= 98.47ms) flat flat% sum% cum cum% 0 0% 0% 19653ms 99.79% __libc_start_call_main 0 0% 0% 19653ms 99.79% __libc_start_main_impl 0 0% 0% 19653ms 99.79% _start 0 0% 0% 19636ms 99.70% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 19636ms 99.70% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 19636ms 99.70% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 19636ms 99.70% main 0 0% 0% 19600ms 99.52% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 19600ms 99.52% CxxTest::TestRunner::runTest (inline) 0 0% 0% 19600ms 99.52% Test2DCryptRepresentativeSimulation::TestRepresentativeSimulationForProfiling 1ms 0.0051% 0.0051% 19574ms 99.39% AbstractCellBasedSimulation::Solve 0 0% 0.0051% 15246ms 77.41% AbstractCellBasedSimulation::UpdateCellPopulation 1ms 0.0051% 0.01% 10117ms 51.37% AbstractCellBasedSimulation::DoCellBirth 3ms 0.015% 0.025% 10023ms 50.89% Cell::ReadyToDivide 4ms 0.02% 0.046% 9945ms 50.50% AbstractPhaseBasedCellCycleModel::ReadyToDivide 0 0% 0.046% 9804ms 49.78% AbstractWntOdeBasedCellCycleModel::UpdateCellCyclePhase 8ms 0.041% 0.086% 9796ms 49.74% AbstractOdeBasedPhaseBasedCellCycleModel::UpdateCellCyclePhase 2ms 0.01% 0.096% 9784ms 49.68% CellCycleModelOdeHandler::SolveOdeToTime 82ms 0.42% 0.51% 9624ms 48.87% AbstractOneStepIvpOdeSolver::InternalSolve 892ms 4.53% 5.04% 8836ms 44.86% RungeKutta4IvpOdeSolver::CalculateNextYValue 3307ms 16.79% 21.83% 7751ms 39.36% WntCellCycleOdeSystem::EvaluateYDerivatives 2ms 0.01% 21.84% 5036ms 25.57% MeshBasedCellPopulation::Update 130ms 0.66% 22.50% 4492ms 22.81% AbstractCellProperty::IsType (inline) 2ms 0.01% 22.51% 3902ms 19.81% Cylindrical2dMesh::ReMesh 618ms 3.14% 25.65% 3252ms 16.51% AbstractCellProperty::IsSame 423ms 2.15% 27.80% 2634ms 13.37% std::type_info::operator== (inline) 0 0% 27.80% 2423ms 12.30% OffLatticeSimulation::UpdateCellLocationsAndTopology 2172ms 11.03% 38.83% 2172ms 11.03% __strcmp_avx2 1ms 0.0051% 38.83% 2104ms 10.68% ForwardEulerNumericalMethod::UpdateAllNodePositions 0 0% 38.83% 2065ms 10.48% MutableMesh::ReMesh 3ms 0.015% 38.85% 2059ms 10.45% AbstractNumericalMethod::ComputeForcesIncludingDamping 0 0% 38.85% 1903ms 9.66% AbstractCellPopulation::WriteResultsToFiles 790ms 4.01% 42.86% 1863ms 9.46% std::_Rb_tree::_M_lower_bound (inline) 160ms 0.81% 43.67% 1650ms 8.38% TetrahedralMesh::EdgeIterator::operator++ 54ms 0.27% 43.95% 1351ms 6.86% std::_Rb_tree::find (inline) 0 0% 43.95% 1091ms 5.54% MeshBasedCellPopulation::UpdateNodePairs 4ms 0.02% 43.97% 1090ms 5.53% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 15ms 0.076% 44.04% 1049ms 5.33% TetrahedralMesh::ImportFromMesher 41ms 0.21% 44.25% 994ms 5.05% operator new 11ms 0.056% 44.31% 976ms 4.96% MeshBasedCellPopulation::SpringIterator::operator++ 9ms 0.046% 44.35% 950ms 4.82% std::set::insert (inline) 231ms 1.17% 45.52% 945ms 4.80% __GI___libc_malloc 6ms 0.03% 45.55% 941ms 4.78% std::_Rb_tree::_M_insert_unique 26ms 0.13% 45.69% 853ms 4.33% std::__new_allocator::allocate (inline) 0 0% 45.69% 851ms 4.32% std::allocator_traits::allocate (inline) 0 0% 45.69% 799ms 4.06% std::set::count (inline) 2ms 0.01% 45.70% 765ms 3.88% triangulate 4ms 0.02% 45.72% 735ms 3.73% MeshBasedCellPopulationWithGhostNodes::AcceptCellWritersAcrossPopulation 64ms 0.32% 46.04% 714ms 3.63% std::map::operator[] (partial-inline) 709ms 3.60% 49.64% 709ms 3.60% std::_Rb_tree::_S_right (inline) 1ms 0.0051% 49.65% 698ms 3.54% AbstractTwoBodyInteractionForce::AddForceContribution 0 0% 49.65% 688ms 3.49% delaunay 2ms 0.01% 49.66% 687ms 3.49% divconqdelaunay 5ms 0.025% 49.68% 684ms 3.47% CellPopulationElementWriter::Visit 373ms 1.89% 51.58% 647ms 3.29% _int_malloc 25ms 0.13% 51.70% 636ms 3.23% std::less::operator() (inline) 611ms 3.10% 54.81% 611ms 3.10% std::operator< (inline) 594ms 3.02% 57.82% 604ms 3.07% WntCellCycleOdeSystem::CalculateStoppingEvent 14ms 0.071% 57.89% 601ms 3.05% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 172ms 0.87% 58.77% 589ms 2.99% __dynamic_cast 5ms 0.025% 58.79% 586ms 2.98% MeshBasedCellPopulation::AcceptCellWriter 0 0% 58.79% 574ms 2.91% std::_Rb_tree::lower_bound (inline) 0 0% 58.79% 574ms 2.91% std::map::lower_bound (inline) 15ms 0.076% 58.87% 559ms 2.84% AbstractCellPopulation::GetCellUsingLocationIndex 0 0% 58.87% 553ms 2.81% std::_Rb_tree::_M_create_node (inline) 30ms 0.15% 59.02% 548ms 2.78% std::_Rb_tree::_M_insert_ (inline) 0 0% 59.02% 545ms 2.77% std::map::find (inline) 10ms 0.051% 59.07% 541ms 2.75% CellPropertyCollection::GetPropertiesType (inline) 385ms 1.95% 61.03% 538ms 2.73% AbstractCellMutationState::AbstractCellMutationState 7ms 0.036% 61.06% 525ms 2.67% MutableMesh::ReIndex 0 0% 61.06% 518ms 2.63% std::_Rb_tree::_M_get_node (inline) 14ms 0.071% 61.13% 517ms 2.63% Cylindrical2dMesh::CorrectNonPeriodicMesh 4ms 0.02% 61.15% 512ms 2.60% Element::Element 0 0% 61.15% 511ms 2.59% std::_Rb_tree::_Alloc_node::operator() (inline) 63ms 0.32% 61.47% 493ms 2.50% std::ostream::_M_insert 0 0% 61.47% 493ms 2.50% std::ostream::operator<< (inline) 13ms 0.066% 61.54% 476ms 2.42% Cylindrical2dMesh::ReconstructCylindricalMesh 9ms 0.046% 61.58% 451ms 2.29% Element::RegisterWithNodes (inline) 9ms 0.046% 61.63% 435ms 2.21% Node::AddElement 6ms 0.03% 61.66% 425ms 2.16% AbstractCellProperty::IsSubType (inline) 139ms 0.71% 62.37% 401ms 2.04% __GI___libc_free 137ms 0.7% 63.06% 387ms 1.96% std::_Rb_tree::_M_get_insert_unique_pos 7ms 0.036% 63.10% 382ms 1.94% std::_Rb_tree::erase 0 0% 63.10% 381ms 1.93% std::set::erase (inline) 16ms 0.081% 63.18% 380ms 1.93% Node::RemoveElement 10ms 0.051% 63.23% 346ms 1.76% Cylindrical2dMesh::GenerateVectorsOfElementsStraddlingPeriodicBoundaries 25ms 0.13% 63.36% 339ms 1.72% Element::ResetIndex 1ms 0.0051% 63.36% 334ms 1.70% std::_Vector_base::_M_allocate (inline) 21ms 0.11% 63.47% 330ms 1.68% divconqrecurse 11ms 0.056% 63.52% 327ms 1.66% std::__new_allocator::deallocate (inline) 107ms 0.54% 64.07% 325ms 1.65% std::_Rb_tree::_M_erase 0 0% 64.07% 321ms 1.63% std::allocator_traits::deallocate (inline) 1ms 0.0051% 64.07% 308ms 1.56% NodeLocationWriter::Visit 308ms 1.56% 65.64% 308ms 1.56% std::type_info::name (inline) 6ms 0.03% 65.67% 307ms 1.56% LegacyCellProliferativeTypesWriter::VisitCell 142ms 0.72% 66.39% 307ms 1.56% __cxxabiv1::__si_class_type_info::__do_dyncast 33ms 0.17% 66.55% 307ms 1.56% std::_Rb_tree::~_Rb_tree (inline) 4ms 0.02% 66.58% 306ms 1.55% AbstractCellPopulation::GetLocationIndexUsingCell 4ms 0.02% 66.60% 304ms 1.54% Cell::GetCellProliferativeType 91ms 0.46% 67.06% 304ms 1.54% mergehulls 6ms 0.03% 67.09% 280ms 1.42% Cell::GetMutationState 0 0% 67.09% 279ms 1.42% std::set::~set (inline) 0 0% 67.09% 277ms 1.41% std::_Rb_tree::_M_drop_node (inline) 0 0% 67.09% 275ms 1.40% AbstractCellPopulation::Iterator::operator++ (inline) 28ms 0.14% 67.23% 271ms 1.38% AbstractCellPopulation::Iterator::IsRealCell (inline) 13ms 0.066% 67.30% 270ms 1.37% std::num_put::_M_insert_float 15ms 0.076% 67.37% 270ms 1.37% std::vector::push_back (inline) 28ms 0.14% 67.51% 267ms 1.36% AbstractTetrahedralElement::CalculateJacobian 210ms 1.07% 68.58% 261ms 1.33% _int_free 0 0% 68.58% 247ms 1.25% std::_Rb_tree::_M_put_node (inline) 11ms 0.056% 68.64% 247ms 1.25% std::vector::_M_realloc_insert 10ms 0.051% 68.69% 245ms 1.24% std::_Rb_tree::_Rb_tree (partial-inline) 72ms 0.37% 69.05% 241ms 1.22% ApcOneHitCellMutationState::ApcOneHitCellMutationState 5ms 0.025% 69.08% 237ms 1.20% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 231ms 1.17% 70.25% 233ms 1.18% std::vector::operator[] (inline) 2ms 0.01% 70.26% 232ms 1.18% alternateaxes 5ms 0.025% 70.29% 229ms 1.16% AbstractCellPopulation::IsCellAttachedToLocationIndex 209ms 1.06% 71.35% 229ms 1.16% vertexmedian 44ms 0.22% 71.57% 228ms 1.16% ApcTwoHitCellMutationState::ApcTwoHitCellMutationState 14ms 0.071% 71.64% 228ms 1.16% std::_Rb_tree::_M_erase_aux (inline) 1ms 0.0051% 71.65% 227ms 1.15% TetrahedralMesh::RefreshJacobianCachedData 5ms 0.025% 71.67% 227ms 1.15% std::__cxx11::collate::do_transform 40ms 0.2% 71.88% 224ms 1.14% BetaCateninOneHitCellMutationState::BetaCateninOneHitCellMutationState 3ms 0.015% 71.89% 223ms 1.13% std::set::set (inline) 4ms 0.02% 71.91% 219ms 1.11% ___vsnprintf 1ms 0.0051% 71.92% 216ms 1.10% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 0 0% 71.92% 215ms 1.09% __vsnprintf_internal (inline) 28ms 0.14% 72.06% 210ms 1.07% __printf_buffer 17ms 0.086% 72.15% 209ms 1.06% std::_Rb_tree::_M_copy (inline) 155ms 0.79% 72.93% 206ms 1.05% AbstractElement::GetNodeGlobalIndex 0 0% 72.93% 205ms 1.04% OffLatticeSimulation::ApplyBoundaries 6ms 0.03% 72.96% 199ms 1.01% AbstractTetrahedralElement::CalculateInverseJacobian 13ms 0.066% 73.03% 195ms 0.99% Element::MarkAsDeleted 192ms 0.97% 74.00% 192ms 0.97% [libchaste_cell_based.so] 58ms 0.29% 74.30% 191ms 0.97% std::_Rb_tree::_M_clone_node (inline) 28ms 0.14% 74.44% 189ms 0.96% AbstractTetrahedralElement::RefreshJacobian 136ms 0.69% 75.13% 185ms 0.94% malloc_consolidate 1ms 0.0051% 75.14% 184ms 0.93% MeshBasedCellPopulation::GetDampingConstant 3ms 0.015% 75.15% 183ms 0.93% AbstractCentreBasedCellPopulation::GetDampingConstant 2ms 0.01% 75.16% 170ms 0.86% AbstractTetrahedralElement::AbstractTetrahedralElement 3ms 0.015% 75.18% 170ms 0.86% CellProliferativeTypesWriter::VisitCell 14ms 0.071% 75.25% 169ms 0.86% TetrahedralMesh::Clear 4ms 0.02% 75.27% 168ms 0.85% CellPropertyCollection::HasProperty 14ms 0.071% 75.34% 166ms 0.84% __printf_fp_l_buffer 0 0% 75.34% 166ms 0.84% __printf_fp_spec (inline) 0 0% 75.34% 162ms 0.82% Cell::HasCellProperty (inline) 108ms 0.55% 75.89% 155ms 0.79% std::_Rb_tree::equal_range (inline) 155ms 0.79% 76.67% 155ms 0.79% std::_Rb_tree_insert_and_rebalance 69ms 0.35% 77.02% 150ms 0.76% __printf_fp_buffer_1 65ms 0.33% 77.35% 149ms 0.76% AbstractElement::GetNodeLocation 142ms 0.72% 78.08% 142ms 0.72% std::vector::size (inline) 140ms 0.71% 78.79% 140ms 0.71% Node::GetIndex 4ms 0.02% 78.81% 139ms 0.71% MeshBasedCellPopulationWithGhostNodes::CalculateForceBetweenGhostNodes 133ms 0.68% 79.48% 133ms 0.68% AbstractCellProperty::~AbstractCellProperty 131ms 0.67% 80.15% 131ms 0.67% AbstractCellMutationState::~AbstractCellMutationState 5ms 0.025% 80.17% 131ms 0.67% WntCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel 48ms 0.24% 80.42% 130ms 0.66% ApcOneHitCellMutationState::~ApcOneHitCellMutationState (inline) 35ms 0.18% 80.59% 130ms 0.66% ApcTwoHitCellMutationState::~ApcTwoHitCellMutationState (inline) 128ms 0.65% 81.24% 128ms 0.65% incircle 25ms 0.13% 81.37% 126ms 0.64% BetaCateninOneHitCellMutationState::~BetaCateninOneHitCellMutationState (inline) 6ms 0.03% 81.40% 124ms 0.63% non-virtual thunk to WntCellCycleModel::AdjustOdeParameters(double) 4ms 0.02% 81.42% 122ms 0.62% boost::numeric::ublas::vector_assign (inline) 15ms 0.076% 81.50% 122ms 0.62% std::_Rb_tree_const_iterator::operator++ (inline) 117ms 0.59% 82.09% 117ms 0.59% unlink_chunk 71ms 0.36% 82.45% 115ms 0.58% Cylindrical2dMesh::GetVectorFromAtoB 26ms 0.13% 82.58% 113ms 0.57% std::num_put::_M_insert_int 101ms 0.51% 83.10% 113ms 0.57% vertexsort 112ms 0.57% 83.67% 112ms 0.57% std::_Rb_tree_increment 5ms 0.025% 83.69% 111ms 0.56% MeshBasedCellPopulation::SpringsEnd (inline) 9ms 0.046% 83.74% 109ms 0.55% boost::detail::shared_count::~shared_count (inline) 0 0% 83.74% 109ms 0.55% boost::shared_ptr::~shared_ptr (inline) 5ms 0.025% 83.76% 108ms 0.55% CryptSimulationBoundaryCondition::ImposeBoundaryCondition 108ms 0.55% 84.31% 108ms 0.55% boost::shared_ptr::operator-> (inline) 102ms 0.52% 84.83% 102ms 0.52% AbstractElement::IsDeleted 0 0% 84.83% 101ms 0.51% Cell::SetCellProliferativeType 27ms 0.14% 84.97% 101ms 0.51% TetrahedralMesh::EdgesEnd 3ms 0.015% 84.98% 101ms 0.51% boost::numeric::ublas::c_vector::c_vector (inline) 56ms 0.28% 85.27% 101ms 0.51% boost::shared_ptr::shared_ptr (inline) 100ms 0.51% 85.77% 100ms 0.51% [libchaste_mesh.so] 100ms 0.51% 86.28% 100ms 0.51% std::_Rb_tree_rebalance_for_erase