File: Test2dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 6613ms, 85.34% of 7749ms total Dropped 535 nodes (cum <= 38.74ms) flat flat% sum% cum cum% 0 0% 0% 7715ms 99.56% __libc_start_call_main 0 0% 0% 7715ms 99.56% __libc_start_main_impl 0 0% 0% 7715ms 99.56% _start 0 0% 0% 7698ms 99.34% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 7698ms 99.34% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 7698ms 99.34% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 7698ms 99.34% main 0 0% 0% 7662ms 98.88% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 7662ms 98.88% CxxTest::TestRunner::runTest (inline) 0 0% 0% 7662ms 98.88% Test2DMonolayerRepresentativeSimulation::Test2DMonolayerRepresentativeSimulationForProfiling 0 0% 0% 7660ms 98.85% AbstractCellBasedSimulation::Solve 0 0% 0% 3604ms 46.51% AbstractCellBasedSimulation::UpdateCellPopulation 3ms 0.039% 0.039% 3171ms 40.92% MeshBasedCellPopulation::Update 0 0% 0.039% 2528ms 32.62% AbstractCellPopulation::WriteResultsToFiles 0 0% 0.039% 1608ms 20.75% MeshBasedCellPopulation::UpdateNodePairs 0 0% 0.039% 1524ms 19.67% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 0.039% 1491ms 19.24% MutableMesh::ReMesh 29ms 0.37% 0.41% 1392ms 17.96% MeshBasedCellPopulation::SpringIterator::operator++ 1ms 0.013% 0.43% 1352ms 17.45% ForwardEulerNumericalMethod::UpdateAllNodePositions 3ms 0.039% 0.46% 1302ms 16.80% AbstractNumericalMethod::ComputeForcesIncludingDamping 123ms 1.59% 2.05% 1138ms 14.69% TetrahedralMesh::EdgeIterator::operator++ 13ms 0.17% 2.22% 982ms 12.67% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 1ms 0.013% 2.23% 938ms 12.10% AbstractTwoBodyInteractionForce::AddForceContribution 434ms 5.60% 7.83% 888ms 11.46% std::_Rb_tree::_M_lower_bound (inline) 35ms 0.45% 8.28% 861ms 11.11% GeneralisedLinearSpringForce::CalculateForceBetweenNodes (partial-inline) 190ms 2.45% 10.74% 849ms 10.96% __dynamic_cast 9ms 0.12% 10.85% 823ms 10.62% CellPopulationElementWriter::Visit 0 0% 10.85% 812ms 10.48% CellPropertyCollection::GetPropertiesType (inline) 16ms 0.21% 11.06% 789ms 10.18% MeshBasedCellPopulation::AcceptCellWriter 16ms 0.21% 11.27% 777ms 10.03% AbstractCellPopulation::GetCellUsingLocationIndex 1ms 0.013% 11.28% 754ms 9.73% TetrahedralMesh::ImportFromMesher 37ms 0.48% 11.76% 728ms 9.39% operator new 10ms 0.13% 11.89% 689ms 8.89% AbstractCellProperty::IsSubType (inline) 253ms 3.26% 15.15% 678ms 8.75% __GI___libc_malloc 12ms 0.15% 15.31% 666ms 8.59% std::set::insert (inline) 17ms 0.22% 15.52% 654ms 8.44% std::_Rb_tree::_M_insert_unique 18ms 0.23% 15.76% 619ms 7.99% std::__new_allocator::allocate (inline) 0 0% 15.76% 615ms 7.94% std::allocator_traits::allocate (inline) 84ms 1.08% 16.84% 575ms 7.42% std::_Rb_tree::~_Rb_tree (inline) 1ms 0.013% 16.85% 548ms 7.07% triangulate 0 0% 16.85% 536ms 6.92% std::set::~set (inline) 0 0% 16.85% 535ms 6.90% std::ostream::operator<< (inline) 79ms 1.02% 17.87% 534ms 6.89% std::ostream::_M_insert 8ms 0.1% 17.98% 530ms 6.84% LegacyCellProliferativeTypesWriter::VisitCell 20ms 0.26% 18.23% 526ms 6.79% std::_Rb_tree::find (inline) 516ms 6.66% 24.89% 516ms 6.66% __strcmp_evex 4ms 0.052% 24.95% 509ms 6.57% Cell::GetCellProliferativeType 49ms 0.63% 25.58% 506ms 6.53% std::map::operator[] (partial-inline) 61ms 0.79% 26.36% 491ms 6.34% std::_Rb_tree::_M_erase 0 0% 26.36% 488ms 6.30% std::set::count (inline) 0 0% 26.36% 481ms 6.21% std::_Rb_tree::_M_create_node (inline) 0 0% 26.36% 472ms 6.09% delaunay 2ms 0.026% 26.39% 472ms 6.09% divconqdelaunay 0 0% 26.39% 472ms 6.09% std::_Rb_tree::_M_get_node (inline) 0 0% 26.39% 451ms 5.82% std::_Rb_tree::_Alloc_node::operator() (inline) 196ms 2.53% 28.92% 443ms 5.72% __cxxabiv1::__si_class_type_info::__do_dyncast 0 0% 28.92% 423ms 5.46% std::_Rb_tree::_M_drop_node (inline) 2ms 0.026% 28.95% 420ms 5.42% AbstractCellBasedSimulation::DoCellBirth 0 0% 28.95% 409ms 5.28% std::_Rb_tree::lower_bound (inline) 0 0% 28.95% 409ms 5.28% std::map::lower_bound (inline) 42ms 0.54% 29.49% 407ms 5.25% std::_Rb_tree::_M_insert_ (inline) 18ms 0.23% 29.72% 401ms 5.17% std::_Rb_tree::_Rb_tree (partial-inline) 5ms 0.065% 29.78% 376ms 4.85% boost::detail::shared_count::~shared_count (inline) 0 0% 29.78% 376ms 4.85% boost::shared_ptr::~shared_ptr (inline) 6ms 0.077% 29.86% 367ms 4.74% Element::Element 2ms 0.026% 29.89% 365ms 4.71% std::set::set (inline) 355ms 4.58% 34.47% 355ms 4.58% boost::detail::sp_counted_base::release 2ms 0.026% 34.49% 352ms 4.54% NodeLocationWriter::Visit 1ms 0.013% 34.51% 351ms 4.53% Cell::GetMutationState 43ms 0.55% 35.06% 351ms 4.53% std::_Rb_tree::_M_copy (inline) 70ms 0.9% 35.97% 327ms 4.22% __GI___libc_free 222ms 2.86% 38.83% 327ms 4.22% _int_malloc 2ms 0.026% 38.86% 303ms 3.91% AbstractCellPopulation::IsCellAttachedToLocationIndex 25ms 0.32% 39.18% 301ms 3.88% std::num_put::_M_insert_float 106ms 1.37% 40.55% 292ms 3.77% std::_Rb_tree::_M_clone_node (inline) 9ms 0.12% 40.66% 289ms 3.73% std::__new_allocator::deallocate (inline) 288ms 3.72% 44.38% 288ms 3.72% std::_Rb_tree::_S_right (inline) 0 0% 44.38% 284ms 3.66% std::allocator_traits::deallocate (inline) 0 0% 44.38% 274ms 3.54% AbstractCentreBasedCellPopulation::GetDampingConstant 0 0% 44.38% 274ms 3.54% MeshBasedCellPopulation::GetDampingConstant 20ms 0.26% 44.64% 274ms 3.54% std::less::operator() (inline) 5ms 0.065% 44.70% 270ms 3.48% divconqrecurse 5ms 0.065% 44.77% 266ms 3.43% Cell::ReadyToDivide 2ms 0.026% 44.79% 255ms 3.29% Element::RegisterWithNodes (inline) 75ms 0.97% 45.76% 255ms 3.29% mergehulls 254ms 3.28% 49.04% 254ms 3.28% std::operator< (inline) 11ms 0.14% 49.18% 249ms 3.21% Node::AddElement 209ms 2.70% 51.88% 248ms 3.20% _int_free 246ms 3.17% 55.05% 246ms 3.17% [libchaste_cell_based.so] 11ms 0.14% 55.19% 242ms 3.12% std::__cxx11::collate::do_transform 0 0% 55.19% 238ms 3.07% std::_Rb_tree::_M_put_node (inline) 85ms 1.10% 56.29% 230ms 2.97% std::_Rb_tree::_M_get_insert_unique_pos (inline) 2ms 0.026% 56.32% 222ms 2.86% ___vsnprintf 25ms 0.32% 56.64% 220ms 2.84% __printf_buffer 0 0% 56.64% 220ms 2.84% __vsnprintf_internal (inline) 0 0% 56.64% 209ms 2.70% CellProliferativeTypesWriter::VisitCell 4ms 0.052% 56.69% 209ms 2.70% CellPropertyCollection::HasProperty 0 0% 56.69% 206ms 2.66% Cell::HasCellProperty (inline) 9ms 0.12% 56.81% 205ms 2.65% AbstractCellProperty::IsType (inline) 1ms 0.013% 56.82% 197ms 2.54% AbstractPhaseBasedCellCycleModel::ReadyToDivide 3ms 0.039% 56.86% 192ms 2.48% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 4ms 0.052% 56.91% 187ms 2.41% MeshBasedCellPopulation::SpringsEnd (inline) 15ms 0.19% 57.10% 186ms 2.40% AbstractTetrahedralElement::CalculateJacobian 0 0% 57.10% 185ms 2.39% std::_Rb_tree::_M_destroy_node (inline) 0 0% 57.10% 185ms 2.39% std::__new_allocator::destroy (inline) 0 0% 57.10% 185ms 2.39% std::allocator_traits::destroy (inline) 20ms 0.26% 57.36% 177ms 2.28% TetrahedralMesh::EdgesEnd (partial-inline) 2ms 0.026% 57.39% 177ms 2.28% __printf_fp_spec (inline) 3ms 0.039% 57.43% 175ms 2.26% __printf_fp_l_buffer 0 0% 57.43% 170ms 2.19% AbstractCellBasedWriter::OpenOutputFileForAppend 0 0% 57.43% 170ms 2.19% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 1ms 0.013% 57.44% 169ms 2.18% OutputFileHandler::OpenOutputFile 0 0% 57.44% 168ms 2.17% TetrahedralMesh::RefreshJacobianCachedData 81ms 1.05% 58.48% 164ms 2.12% __printf_fp_buffer_1 5ms 0.065% 58.55% 162ms 2.09% AbstractTetrahedralElement::CalculateInverseJacobian 2ms 0.026% 58.58% 152ms 1.96% TetrahedralMesh::Clear 105ms 1.36% 59.93% 144ms 1.86% TetrahedralMesh::EdgeIterator::EdgeIterator (partial-inline) 0 0% 59.93% 143ms 1.85% std::_Vector_base::_M_allocate (inline) 140ms 1.81% 61.74% 140ms 1.81% [libchaste_mesh.so] 17ms 0.22% 61.96% 136ms 1.76% AbstractCellProperty::IsSame 70ms 0.9% 62.86% 136ms 1.76% std::__ostream_insert 17ms 0.22% 63.08% 135ms 1.74% AbstractTetrahedralElement::RefreshJacobian 3ms 0.039% 63.12% 134ms 1.73% boost::numeric::ublas::c_vector::c_vector (inline) 19ms 0.25% 63.36% 131ms 1.69% MeshBasedCellPopulation::SpringIterator::SpringIterator 2ms 0.026% 63.39% 130ms 1.68% alternateaxes 2ms 0.026% 63.41% 128ms 1.65% boost::numeric::ublas::vector_assign (inline) 2ms 0.026% 63.44% 127ms 1.64% std::vector::push_back (inline) 108ms 1.39% 64.83% 127ms 1.64% vertexmedian 33ms 0.43% 65.26% 125ms 1.61% std::num_put::_M_insert_int 12ms 0.15% 65.41% 119ms 1.54% std::type_info::operator== (inline) 8ms 0.1% 65.52% 119ms 1.54% std::vector::_M_realloc_insert 10ms 0.13% 65.65% 118ms 1.52% AbstractCellPopulation::Iterator::IsRealCell (inline) 0 0% 65.65% 117ms 1.51% AbstractCellPopulation::Iterator::operator++ (inline) 0 0% 65.65% 117ms 1.51% std::operator<< (inline) 2ms 0.026% 65.67% 112ms 1.45% AbstractTetrahedralElement::AbstractTetrahedralElement 112ms 1.45% 67.12% 112ms 1.45% incircle 39ms 0.5% 67.62% 111ms 1.43% AbstractElement::GetNodeLocation 110ms 1.42% 69.04% 110ms 1.42% [libstdc++.so.6.0.33] 108ms 1.39% 70.43% 108ms 1.39% std::_Rb_tree_insert_and_rebalance 5ms 0.065% 70.50% 95ms 1.23% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (partial-inline) 0 0% 70.50% 92ms 1.19% std::basic_ofstream::basic_ofstream (inline) 91ms 1.17% 71.67% 91ms 1.17% std::vector::size (inline) 0 0% 71.67% 90ms 1.16% std::basic_filebuf::open 1ms 0.013% 71.69% 89ms 1.15% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 0 0% 71.69% 89ms 1.15% std::basic_ofstream::open (inline) 1ms 0.013% 71.70% 88ms 1.14% Cell::GetCellId 18ms 0.23% 71.93% 87ms 1.12% boost::numeric::ublas::indexing_vector_assign 7ms 0.09% 72.02% 84ms 1.08% TetrahedralMesh::EdgeIterator::GetNodeA 60ms 0.77% 72.80% 84ms 1.08% malloc_consolidate 0 0% 72.80% 84ms 1.08% tcache_get (inline) 84ms 1.08% 73.88% 84ms 1.08% tcache_get_n (inline) 0 0% 73.88% 82ms 1.06% Node::~Node 2ms 0.026% 73.91% 78ms 1.01% AbstractCellPopulation::GetLocationIndexUsingCell 76ms 0.98% 74.89% 76ms 0.98% TetrahedralMesh::EdgeIterator::operator!= (partial-inline) 4ms 0.052% 74.94% 75ms 0.97% CellPropertyCollection::AddProperty 0 0% 74.94% 74ms 0.95% CellPropertyCollection::~CellPropertyCollection (inline) 11ms 0.14% 75.08% 74ms 0.95% TetrahedralMesh::EdgeIterator::GetNodeB 28ms 0.36% 75.44% 72ms 0.93% AbstractElement::GetNodeGlobalIndex 1ms 0.013% 75.45% 69ms 0.89% OutputFileHandler::CommonConstructor 0 0% 75.45% 69ms 0.89% OutputFileHandler::OutputFileHandler 45ms 0.58% 76.04% 66ms 0.85% AbstractTetrahedralMesh::GetElement 1ms 0.013% 76.05% 65ms 0.84% Node::ClearAppliedForce 1ms 0.013% 76.06% 65ms 0.84% Node::ConstructNodeAttributes (inline) 58ms 0.75% 76.81% 65ms 0.84% vertexsort 0 0% 76.81% 63ms 0.81% OutputFileHandler::MakeFoldersAndReturnFullPath 5ms 0.065% 76.87% 63ms 0.81% std::_Rb_tree_const_iterator::operator++ (inline) 37ms 0.48% 77.35% 63ms 0.81% std::basic_streambuf::xsputn 62ms 0.8% 78.15% 62ms 0.8% counterclockwise 36ms 0.46% 78.62% 62ms 0.8% std::basic_filebuf::xsputn 0 0% 78.62% 61ms 0.79% std::vector::vector (inline) 0 0% 78.62% 59ms 0.76% std::_Vector_base::_Vector_base (inline) 0 0% 78.62% 58ms 0.75% AbstractCellPopulation::CloseRoundRobinWritersFiles 0 0% 78.62% 58ms 0.75% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 78.62% 58ms 0.75% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 0 0% 78.62% 57ms 0.74% AbstractCellBasedWriter::CloseFile 35ms 0.45% 79.07% 57ms 0.74% hack_digit 0 0% 79.07% 57ms 0.74% std::basic_filebuf::close 0 0% 79.07% 57ms 0.74% std::basic_ofstream::close (inline) 0 0% 79.07% 56ms 0.72% AbstractCentreBasedCellPopulation::CreateCellPair 56ms 0.72% 79.79% 56ms 0.72% std::_Rb_tree::_S_left (inline) 1ms 0.013% 79.80% 56ms 0.72% std::_Vector_base::_M_create_storage (inline) 0 0% 79.80% 55ms 0.71% MeshBasedCellPopulation::SpringIterator::GetNodeB (inline) 55ms 0.71% 80.51% 55ms 0.71% __memcpy_avx512_unaligned_erms 17ms 0.22% 80.73% 54ms 0.7% Determinant (inline) 37ms 0.48% 81.21% 53ms 0.68% boost::shared_ptr::shared_ptr (inline) 37ms 0.48% 81.69% 52ms 0.67% boost::numeric::ublas::c_matrix::operator() 0 0% 81.69% 51ms 0.66% MeshBasedCellPopulation::SpringIterator::GetNodeA (inline) 0 0% 81.69% 49ms 0.63% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 36ms 0.46% 82.15% 48ms 0.62% CellPropertyCollection::GetProperty 0 0% 82.15% 48ms 0.62% _IO_new_fopen 0 0% 82.15% 48ms 0.62% __fopen_internal (inline) 0 0% 82.15% 48ms 0.62% std::_Rb_tree::_M_emplace_hint_unique 0 0% 82.15% 48ms 0.62% std::__basic_file::open 0 0% 82.15% 47ms 0.61% FilesystemPermissions::SetFilePermissions (inline) 1ms 0.013% 82.17% 47ms 0.61% _IO_new_file_fopen 1ms 0.013% 82.18% 47ms 0.61% std::_Vector_base::_M_deallocate (inline) 1ms 0.013% 82.19% 47ms 0.61% std::filesystem::permissions 2ms 0.026% 82.22% 46ms 0.59% __GI__IO_file_open 46ms 0.59% 82.81% 46ms 0.59% __GI_fchmodat 0 0% 82.81% 46ms 0.59% std::map::map (inline) 0 0% 82.81% 45ms 0.58% BoundaryNodeWriter::Visit 44ms 0.57% 83.38% 44ms 0.57% std::_Rb_tree_increment 0 0% 83.38% 43ms 0.55% std::basic_filebuf::_M_terminate_output 1ms 0.013% 83.39% 43ms 0.55% std::basic_filebuf::overflow 34ms 0.44% 83.83% 43ms 0.55% writeedges 42ms 0.54% 84.37% 42ms 0.54% __GI___libc_write 0 0% 84.37% 42ms 0.54% std::__basic_file::xsputn 0 0% 84.37% 42ms 0.54% std::basic_filebuf::_M_convert_to_external 28ms 0.36% 84.73% 42ms 0.54% std::num_put::do_put 0 0% 84.73% 41ms 0.53% MeshBasedCellPopulation::SpringIterator::~SpringIterator (inline) 41ms 0.53% 85.26% 41ms 0.53% boost::numeric::ublas::same_impl_ex 0 0% 85.26% 41ms 0.53% std::basic_filebuf::_M_allocate_internal_buffer 0 0% 85.26% 40ms 0.52% AbstractCentreBasedCellPopulation::IsMarkedSpring 4ms 0.052% 85.31% 40ms 0.52% Inverse 2ms 0.026% 85.34% 39ms 0.5% NodeAttributes::NodeAttributes 0 0% 85.34% 39ms 0.5% std::map::~map (inline)