File: Test2DMeshBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 16747ms, 85.00% of 19702ms total Dropped 760 nodes (cum <= 98.51ms) flat flat% sum% cum cum% 0 0% 0% 19655ms 99.76% __libc_start_call_main 0 0% 0% 19655ms 99.76% __libc_start_main_impl 0 0% 0% 19655ms 99.76% _start 0 0% 0% 19635ms 99.66% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 19635ms 99.66% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 19635ms 99.66% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 19635ms 99.66% main 0 0% 0% 19599ms 99.48% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 19599ms 99.48% CxxTest::TestRunner::runTest (inline) 0 0% 0% 19599ms 99.48% Test2DCryptRepresentativeSimulation::TestRepresentativeSimulationForProfiling 0 0% 0% 19571ms 99.34% AbstractCellBasedSimulation::Solve 0 0% 0% 15140ms 76.84% AbstractCellBasedSimulation::UpdateCellPopulation 3ms 0.015% 0.015% 9976ms 50.63% AbstractCellBasedSimulation::DoCellBirth 1ms 0.0051% 0.02% 9886ms 50.18% Cell::ReadyToDivide 4ms 0.02% 0.041% 9813ms 49.81% AbstractPhaseBasedCellCycleModel::ReadyToDivide 6ms 0.03% 0.071% 9698ms 49.22% AbstractWntOdeBasedCellCycleModel::UpdateCellCyclePhase 15ms 0.076% 0.15% 9684ms 49.15% AbstractOdeBasedPhaseBasedCellCycleModel::UpdateCellCyclePhase 4ms 0.02% 0.17% 9667ms 49.07% CellCycleModelOdeHandler::SolveOdeToTime 75ms 0.38% 0.55% 9505ms 48.24% AbstractOneStepIvpOdeSolver::InternalSolve 866ms 4.40% 4.94% 8710ms 44.21% RungeKutta4IvpOdeSolver::CalculateNextYValue 3584ms 18.19% 23.13% 7612ms 38.64% WntCellCycleOdeSystem::EvaluateYDerivatives 1ms 0.0051% 23.14% 5068ms 25.72% MeshBasedCellPopulation::Update 80ms 0.41% 23.55% 4091ms 20.76% AbstractCellProperty::IsType (inline) 4ms 0.02% 23.57% 3898ms 19.78% Cylindrical2dMesh::ReMesh 564ms 2.86% 26.43% 2848ms 14.46% AbstractCellProperty::IsSame 0 0% 26.43% 2451ms 12.44% OffLatticeSimulation::UpdateCellLocationsAndTopology 440ms 2.23% 28.66% 2284ms 11.59% std::type_info::operator== (inline) 0 0% 28.66% 2145ms 10.89% MutableMesh::ReMesh 0 0% 28.66% 2140ms 10.86% ForwardEulerNumericalMethod::UpdateAllNodePositions 9ms 0.046% 28.71% 2098ms 10.65% AbstractNumericalMethod::ComputeForcesIncludingDamping 0 0% 28.71% 1972ms 10.01% AbstractCellPopulation::WriteResultsToFiles 810ms 4.11% 32.82% 1815ms 9.21% std::_Rb_tree::_M_lower_bound (inline) 1770ms 8.98% 41.80% 1770ms 8.98% __strcmp_avx2 162ms 0.82% 42.63% 1672ms 8.49% TetrahedralMesh::EdgeIterator::operator++ 56ms 0.28% 42.91% 1331ms 6.76% std::_Rb_tree::find (inline) 2ms 0.01% 42.92% 1128ms 5.73% MeshBasedCellPopulation::UpdateNodePairs 9ms 0.046% 42.97% 1113ms 5.65% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 15ms 0.076% 43.04% 1052ms 5.34% TetrahedralMesh::ImportFromMesher 56ms 0.28% 43.33% 1024ms 5.20% operator new 8ms 0.041% 43.37% 1001ms 5.08% MeshBasedCellPopulation::SpringIterator::operator++ 9ms 0.046% 43.41% 968ms 4.91% std::set::insert (inline) 13ms 0.066% 43.48% 959ms 4.87% std::_Rb_tree::_M_insert_unique 219ms 1.11% 44.59% 949ms 4.82% __GI___libc_malloc 31ms 0.16% 44.75% 916ms 4.65% std::__new_allocator::allocate (inline) 0 0% 44.75% 910ms 4.62% std::allocator_traits::allocate (inline) 0 0% 44.75% 844ms 4.28% triangulate 0 0% 44.75% 809ms 4.11% std::set::count (inline) 0 0% 44.75% 763ms 3.87% delaunay 6ms 0.03% 44.78% 763ms 3.87% divconqdelaunay 0 0% 44.78% 730ms 3.71% MeshBasedCellPopulationWithGhostNodes::AcceptCellWritersAcrossPopulation 66ms 0.33% 45.11% 715ms 3.63% std::map::operator[] (partial-inline) 4ms 0.02% 45.13% 711ms 3.61% CellPopulationElementWriter::Visit 2ms 0.01% 45.14% 689ms 3.50% AbstractTwoBodyInteractionForce::AddForceContribution 689ms 3.50% 48.64% 689ms 3.50% std::_Rb_tree::_S_right (inline) 347ms 1.76% 50.40% 636ms 3.23% _int_malloc 22ms 0.11% 50.51% 609ms 3.09% AbstractCellPopulation::GetCellUsingLocationIndex 4ms 0.02% 50.53% 595ms 3.02% MeshBasedCellPopulation::AcceptCellWriter 178ms 0.9% 51.44% 595ms 3.02% __dynamic_cast 18ms 0.091% 51.53% 595ms 3.02% std::less::operator() (inline) 583ms 2.96% 54.49% 590ms 2.99% WntCellCycleOdeSystem::CalculateStoppingEvent 0 0% 54.49% 588ms 2.98% std::_Rb_tree::_M_create_node (inline) 25ms 0.13% 54.61% 587ms 2.98% std::_Rb_tree::_M_insert_ (inline) 577ms 2.93% 57.54% 577ms 2.93% std::operator< (inline) 27ms 0.14% 57.68% 576ms 2.92% AbstractVariableSizeTwoBodyInteractionForce::CalculateForceBetweenNodes 2ms 0.01% 57.69% 570ms 2.89% CellPropertyCollection::GetPropertiesType (inline) 0 0% 57.69% 567ms 2.88% std::_Rb_tree::lower_bound (inline) 0 0% 57.69% 567ms 2.88% std::map::lower_bound (inline) 0 0% 57.69% 560ms 2.84% std::_Rb_tree::_M_get_node (inline) 5ms 0.025% 57.71% 535ms 2.72% Element::Element 0 0% 57.71% 531ms 2.70% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 57.71% 514ms 2.61% std::map::find (inline) 17ms 0.086% 57.80% 502ms 2.55% Cylindrical2dMesh::ReconstructCylindricalMesh 3ms 0.015% 57.82% 488ms 2.48% std::ostream::operator<< (inline) 74ms 0.38% 58.19% 484ms 2.46% std::ostream::_M_insert 353ms 1.79% 59.98% 480ms 2.44% AbstractCellMutationState::AbstractCellMutationState 7ms 0.036% 60.02% 477ms 2.42% MutableMesh::ReIndex 16ms 0.081% 60.10% 465ms 2.36% Cylindrical2dMesh::CorrectNonPeriodicMesh 8ms 0.041% 60.14% 465ms 2.36% Element::RegisterWithNodes (inline) 1ms 0.0051% 60.15% 461ms 2.34% AbstractCellProperty::IsSubType (inline) 8ms 0.041% 60.19% 452ms 2.29% Node::AddElement 177ms 0.9% 61.09% 432ms 2.19% __GI___libc_free 15ms 0.076% 61.16% 375ms 1.90% std::__new_allocator::deallocate (inline) 0 0% 61.16% 371ms 1.88% std::allocator_traits::deallocate (inline) 118ms 0.6% 61.76% 370ms 1.88% std::_Rb_tree::_M_erase 139ms 0.71% 62.47% 359ms 1.82% std::_Rb_tree::_M_get_insert_unique_pos 20ms 0.1% 62.57% 358ms 1.82% divconqrecurse 5ms 0.025% 62.59% 357ms 1.81% std::_Rb_tree::erase 0 0% 62.59% 356ms 1.81% std::set::erase (inline) 10ms 0.051% 62.64% 351ms 1.78% Node::RemoveElement 1ms 0.0051% 62.65% 351ms 1.78% std::_Vector_base::_M_allocate (inline) 345ms 1.75% 64.40% 345ms 1.75% std::type_info::name (inline) 30ms 0.15% 64.55% 344ms 1.75% std::_Rb_tree::~_Rb_tree (inline) 90ms 0.46% 65.01% 332ms 1.69% mergehulls 27ms 0.14% 65.15% 327ms 1.66% Element::ResetIndex 0 0% 65.15% 316ms 1.60% std::_Rb_tree::_M_drop_node (inline) 6ms 0.03% 65.18% 309ms 1.57% Cell::GetCellProliferativeType 0 0% 65.18% 304ms 1.54% std::set::~set (inline) 152ms 0.77% 65.95% 303ms 1.54% __cxxabiv1::__si_class_type_info::__do_dyncast 2ms 0.01% 65.96% 297ms 1.51% Cell::GetMutationState 0 0% 65.96% 293ms 1.49% NodeLocationWriter::Visit 0 0% 65.96% 289ms 1.47% std::_Rb_tree::_M_put_node (inline) 5ms 0.025% 65.98% 285ms 1.45% LegacyCellProliferativeTypesWriter::VisitCell 7ms 0.036% 66.02% 275ms 1.40% Cylindrical2dMesh::GenerateVectorsOfElementsStraddlingPeriodicBoundaries 5ms 0.025% 66.04% 262ms 1.33% AbstractCellPopulation::IsCellAttachedToLocationIndex 39ms 0.2% 66.24% 261ms 1.32% AbstractCellPopulation::Iterator::IsRealCell (inline) 0 0% 66.24% 260ms 1.32% AbstractCellPopulation::Iterator::operator++ (inline) 12ms 0.061% 66.30% 259ms 1.31% std::num_put::_M_insert_float 258ms 1.31% 67.61% 259ms 1.31% std::vector::operator[] (inline) 9ms 0.046% 67.66% 256ms 1.30% alternateaxes 17ms 0.086% 67.74% 256ms 1.30% std::_Rb_tree::_Rb_tree (partial-inline) 215ms 1.09% 68.84% 254ms 1.29% _int_free 5ms 0.025% 68.86% 253ms 1.28% AbstractCellPopulation::GetLocationIndexUsingCell 10ms 0.051% 68.91% 245ms 1.24% AbstractTetrahedralElement::CalculateJacobian 230ms 1.17% 70.08% 244ms 1.24% vertexmedian 15ms 0.076% 70.16% 241ms 1.22% std::vector::push_back (inline) 1ms 0.0051% 70.16% 238ms 1.21% std::set::set (inline) 63ms 0.32% 70.48% 231ms 1.17% ApcOneHitCellMutationState::ApcOneHitCellMutationState 1ms 0.0051% 70.49% 230ms 1.17% TetrahedralMesh::RefreshJacobianCachedData 29ms 0.15% 70.63% 223ms 1.13% std::_Rb_tree::_M_copy (inline) 9ms 0.046% 70.68% 220ms 1.12% std::vector::_M_realloc_insert 3ms 0.015% 70.69% 215ms 1.09% std::__cxx11::collate::do_transform 10ms 0.051% 70.74% 214ms 1.09% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 32ms 0.16% 70.91% 214ms 1.09% BetaCateninOneHitCellMutationState::BetaCateninOneHitCellMutationState 14ms 0.071% 70.98% 210ms 1.07% std::_Rb_tree::_M_erase_aux (inline) 24ms 0.12% 71.10% 207ms 1.05% AbstractTetrahedralElement::RefreshJacobian 45ms 0.23% 71.33% 206ms 1.05% ApcTwoHitCellMutationState::ApcTwoHitCellMutationState 3ms 0.015% 71.34% 204ms 1.04% MeshBasedCellPopulation::GetDampingConstant 3ms 0.015% 71.36% 204ms 1.04% ___vsnprintf 0 0% 71.36% 201ms 1.02% AbstractCentreBasedCellPopulation::GetDampingConstant 0 0% 71.36% 201ms 1.02% __vsnprintf_internal (inline) 14ms 0.071% 71.43% 197ms 1% AbstractTetrahedralElement::CalculateInverseJacobian 14ms 0.071% 71.50% 197ms 1% __printf_buffer 3ms 0.015% 71.52% 192ms 0.97% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 1ms 0.0051% 71.52% 191ms 0.97% CellProliferativeTypesWriter::VisitCell 60ms 0.3% 71.83% 191ms 0.97% std::_Rb_tree::_M_clone_node (inline) 138ms 0.7% 72.53% 190ms 0.96% malloc_consolidate 147ms 0.75% 73.27% 189ms 0.96% AbstractElement::GetNodeGlobalIndex 0 0% 73.27% 177ms 0.9% OffLatticeSimulation::ApplyBoundaries 15ms 0.076% 73.35% 176ms 0.89% Element::MarkAsDeleted 174ms 0.88% 74.23% 174ms 0.88% std::_Rb_tree_insert_and_rebalance 171ms 0.87% 75.10% 171ms 0.87% [libchaste_cell_based.so] 169ms 0.86% 75.96% 169ms 0.86% Node::GetIndex 6ms 0.03% 75.99% 168ms 0.85% __printf_fp_l_buffer 0 0% 75.99% 168ms 0.85% __printf_fp_spec (inline) 4ms 0.02% 76.01% 165ms 0.84% AbstractTetrahedralElement::AbstractTetrahedralElement 24ms 0.12% 76.13% 165ms 0.84% TetrahedralMesh::Clear 69ms 0.35% 76.48% 163ms 0.83% AbstractElement::GetNodeLocation 87ms 0.44% 76.92% 154ms 0.78% __printf_fp_buffer_1 3ms 0.015% 76.94% 151ms 0.77% CellPropertyCollection::HasProperty 55ms 0.28% 77.22% 149ms 0.76% ApcTwoHitCellMutationState::~ApcTwoHitCellMutationState (inline) 91ms 0.46% 77.68% 149ms 0.76% std::_Rb_tree::equal_range (inline) 43ms 0.22% 77.90% 148ms 0.75% ApcOneHitCellMutationState::~ApcOneHitCellMutationState (inline) 148ms 0.75% 78.65% 148ms 0.75% incircle 0 0% 78.65% 145ms 0.74% Cell::HasCellProperty (inline) 7ms 0.036% 78.68% 145ms 0.74% MeshBasedCellPopulationWithGhostNodes::CalculateForceBetweenGhostNodes 139ms 0.71% 79.39% 139ms 0.71% AbstractCellMutationState::~AbstractCellMutationState 4ms 0.02% 79.41% 138ms 0.7% MeshBasedCellPopulation::SpringsEnd (inline) 138ms 0.7% 80.11% 138ms 0.7% unlink_chunk 3ms 0.015% 80.12% 137ms 0.7% boost::numeric::ublas::vector_assign (inline) 119ms 0.6% 80.73% 135ms 0.69% vertexsort 2ms 0.01% 80.74% 134ms 0.68% non-virtual thunk to WntCellCycleModel::AdjustOdeParameters(double) 134ms 0.68% 81.42% 134ms 0.68% std::vector::size (inline) 132ms 0.67% 82.09% 132ms 0.67% AbstractCellProperty::~AbstractCellProperty 79ms 0.4% 82.49% 131ms 0.66% Cylindrical2dMesh::GetVectorFromAtoB 10ms 0.051% 82.54% 128ms 0.65% boost::numeric::ublas::c_vector::c_vector (inline) 30ms 0.15% 82.69% 126ms 0.64% TetrahedralMesh::EdgesEnd (partial-inline) 10ms 0.051% 82.74% 113ms 0.57% std::_Rb_tree_const_iterator::operator++ (inline) 110ms 0.56% 83.30% 110ms 0.56% AbstractElement::IsDeleted 27ms 0.14% 83.44% 110ms 0.56% BetaCateninOneHitCellMutationState::~BetaCateninOneHitCellMutationState (inline) 37ms 0.19% 83.63% 110ms 0.56% std::__ostream_insert 33ms 0.17% 83.79% 108ms 0.55% boost::numeric::ublas::indexing_vector_assign 108ms 0.55% 84.34% 108ms 0.55% std::_Rb_tree_increment 0 0% 84.34% 106ms 0.54% std::vector::resize (inline) 0 0% 84.34% 104ms 0.53% WntCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel 104ms 0.53% 84.87% 104ms 0.53% [libchaste_mesh.so] 0 0% 84.87% 104ms 0.53% std::vector::_M_default_append 26ms 0.13% 85.00% 103ms 0.52% std::num_put::_M_insert_int