File: Test2dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 6698ms, 85.42% of 7841ms total Dropped 570 nodes (cum <= 39.20ms) flat flat% sum% cum cum% 0 0% 0% 7805ms 99.54% __libc_start_call_main 0 0% 0% 7805ms 99.54% __libc_start_main_impl 0 0% 0% 7805ms 99.54% _start 0 0% 0% 7791ms 99.36% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 7791ms 99.36% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 7791ms 99.36% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 7791ms 99.36% main 0 0% 0% 7756ms 98.92% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 7756ms 98.92% CxxTest::TestRunner::runTest (inline) 0 0% 0% 7756ms 98.92% Test2DMonolayerRepresentativeSimulation::Test2DMonolayerRepresentativeSimulationForProfiling 0 0% 0% 7752ms 98.86% AbstractCellBasedSimulation::Solve 0 0% 0% 3336ms 42.55% AbstractCellBasedSimulation::UpdateCellPopulation 2ms 0.026% 0.026% 2867ms 36.56% MeshBasedCellPopulation::Update 1ms 0.013% 0.038% 2843ms 36.26% AbstractCellPopulation::WriteResultsToFiles 1ms 0.013% 0.051% 1569ms 20.01% OffLatticeSimulation::UpdateCellLocationsAndTopology 2ms 0.026% 0.077% 1425ms 18.17% ForwardEulerNumericalMethod::UpdateAllNodePositions 0 0% 0.077% 1406ms 17.93% MeshBasedCellPopulation::UpdateNodePairs 0 0% 0.077% 1401ms 17.87% MutableMesh::ReMesh 7ms 0.089% 0.17% 1365ms 17.41% AbstractNumericalMethod::ComputeForcesIncludingDamping 22ms 0.28% 0.45% 1215ms 15.50% MeshBasedCellPopulation::SpringIterator::operator++ 93ms 1.19% 1.63% 1000ms 12.75% TetrahedralMesh::EdgeIterator::operator++ 3ms 0.038% 1.67% 964ms 12.29% AbstractTwoBodyInteractionForce::AddForceContribution 437ms 5.57% 7.24% 958ms 12.22% std::_Rb_tree::_M_lower_bound (inline) 2ms 0.026% 7.27% 913ms 11.64% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 8ms 0.1% 7.37% 879ms 11.21% CellPopulationElementWriter::Visit 46ms 0.59% 7.96% 849ms 10.83% GeneralisedLinearSpringForce::CalculateForceBetweenNodes (partial-inline) 15ms 0.19% 8.15% 846ms 10.79% CellPropertyCollection::GetPropertiesType (inline) 221ms 2.82% 10.97% 835ms 10.65% __dynamic_cast 26ms 0.33% 11.30% 763ms 9.73% AbstractCellPopulation::GetCellUsingLocationIndex 2ms 0.026% 11.33% 760ms 9.69% MeshBasedCellPopulation::AcceptCellWriter 8ms 0.1% 11.43% 718ms 9.16% TetrahedralMesh::ImportFromMesher 3ms 0.038% 11.47% 631ms 8.05% AbstractCellProperty::IsSubType (inline) 4ms 0.051% 11.52% 621ms 7.92% std::ostream::operator<< (inline) 85ms 1.08% 12.60% 616ms 7.86% std::ostream::_M_insert 64ms 0.82% 13.42% 608ms 7.75% std::map::operator[] (partial-inline) 36ms 0.46% 13.88% 550ms 7.01% operator new 8ms 0.1% 13.98% 522ms 6.66% std::set::insert (inline) 2ms 0.026% 14.00% 518ms 6.61% triangulate 12ms 0.15% 14.16% 514ms 6.56% std::_Rb_tree::_M_insert_unique 8ms 0.1% 14.26% 513ms 6.54% Cell::GetCellProliferativeType 157ms 2.00% 16.26% 511ms 6.52% __GI___libc_malloc 0 0% 16.26% 505ms 6.44% std::_Rb_tree::lower_bound (inline) 0 0% 16.26% 505ms 6.44% std::map::lower_bound (inline) 23ms 0.29% 16.55% 502ms 6.40% std::_Rb_tree::find (inline) 31ms 0.4% 16.95% 498ms 6.35% std::__new_allocator::allocate (inline) 0 0% 16.95% 496ms 6.33% std::allocator_traits::allocate (inline) 493ms 6.29% 23.24% 493ms 6.29% __strcmp_avx2 0 0% 23.24% 459ms 5.85% std::set::count (inline) 4ms 0.051% 23.29% 457ms 5.83% LegacyCellProliferativeTypesWriter::VisitCell 2ms 0.026% 23.31% 453ms 5.78% AbstractCellBasedSimulation::DoCellBirth 0 0% 23.31% 451ms 5.75% delaunay 0 0% 23.31% 451ms 5.75% divconqdelaunay 198ms 2.53% 25.84% 432ms 5.51% __cxxabiv1::__si_class_type_info::__do_dyncast 33ms 0.42% 26.26% 418ms 5.33% std::_Rb_tree::~_Rb_tree (inline) 0 0% 26.26% 417ms 5.32% std::_Rb_tree::_M_create_node (inline) 0 0% 26.26% 395ms 5.04% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 26.26% 390ms 4.97% std::_Rb_tree::_M_get_node (inline) 0 0% 26.26% 390ms 4.97% std::set::~set (inline) 86ms 1.10% 27.36% 379ms 4.83% std::_Rb_tree::_M_erase 1ms 0.013% 27.37% 378ms 4.82% NodeLocationWriter::Visit 3ms 0.038% 27.41% 353ms 4.50% Cell::GetMutationState 22ms 0.28% 27.69% 349ms 4.45% std::_Rb_tree::_Rb_tree (partial-inline) 19ms 0.24% 27.93% 347ms 4.43% std::less::operator() (inline) 24ms 0.31% 28.24% 338ms 4.31% std::num_put::_M_insert_float 20ms 0.26% 28.49% 334ms 4.26% std::_Rb_tree::_M_insert_ (inline) 328ms 4.18% 32.67% 328ms 4.18% std::operator< (inline) 3ms 0.038% 32.71% 325ms 4.14% std::set::set (inline) 321ms 4.09% 36.81% 321ms 4.09% std::_Rb_tree::_S_right (inline) 1ms 0.013% 36.82% 315ms 4.02% AbstractCentreBasedCellPopulation::GetDampingConstant 0 0% 36.82% 315ms 4.02% MeshBasedCellPopulation::GetDampingConstant 5ms 0.064% 36.88% 307ms 3.92% Cell::ReadyToDivide 1ms 0.013% 36.90% 303ms 3.86% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 0 0% 36.90% 301ms 3.84% AbstractCellBasedWriter::OpenOutputFileForAppend 0 0% 36.90% 299ms 3.81% OutputFileHandler::OpenOutputFile 2ms 0.026% 36.92% 296ms 3.78% AbstractCellPopulation::IsCellAttachedToLocationIndex 37ms 0.47% 37.39% 293ms 3.74% std::_Rb_tree::_M_copy (inline) 5ms 0.064% 37.46% 291ms 3.71% Element::Element 92ms 1.17% 38.63% 285ms 3.63% __GI___libc_free 7ms 0.089% 38.72% 274ms 3.49% std::__cxx11::collate::do_transform 189ms 2.41% 41.13% 273ms 3.48% _int_malloc 8ms 0.1% 41.23% 273ms 3.48% divconqrecurse 0 0% 41.23% 269ms 3.43% std::_Rb_tree::_M_drop_node (inline) 3ms 0.038% 41.27% 268ms 3.42% CellProliferativeTypesWriter::VisitCell 2ms 0.026% 41.30% 262ms 3.34% ___vsnprintf 0 0% 41.30% 260ms 3.32% __vsnprintf_internal (inline) 31ms 0.4% 41.69% 253ms 3.23% __printf_buffer 83ms 1.06% 42.75% 252ms 3.21% std::_Rb_tree::_M_clone_node (inline) 8ms 0.1% 42.85% 252ms 3.21% std::__new_allocator::deallocate (inline) 77ms 0.98% 43.83% 250ms 3.19% mergehulls 0 0% 43.83% 250ms 3.19% std::allocator_traits::deallocate (inline) 5ms 0.064% 43.90% 224ms 2.86% CellPropertyCollection::HasProperty 0 0% 43.90% 222ms 2.83% Cell::HasCellProperty (inline) 2ms 0.026% 43.92% 221ms 2.82% AbstractCellProperty::IsType (inline) 5ms 0.064% 43.99% 217ms 2.77% AbstractPhaseBasedCellCycleModel::ReadyToDivide 0 0% 43.99% 208ms 2.65% std::_Rb_tree::_M_put_node (inline) 12ms 0.15% 44.14% 207ms 2.64% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 1ms 0.013% 44.15% 200ms 2.55% __printf_fp_spec (inline) 14ms 0.18% 44.33% 199ms 2.54% __printf_fp_l_buffer 18ms 0.23% 44.56% 193ms 2.46% TetrahedralMesh::Clear 168ms 2.14% 46.70% 193ms 2.46% _int_free 9ms 0.11% 46.82% 190ms 2.42% Element::RegisterWithNodes (inline) 1ms 0.013% 46.83% 178ms 2.27% Node::AddElement 98ms 1.25% 48.08% 177ms 2.26% __printf_fp_buffer_1 6ms 0.077% 48.16% 169ms 2.16% MeshBasedCellPopulation::SpringsEnd (inline) 54ms 0.69% 48.85% 169ms 2.16% std::_Rb_tree::_M_get_insert_unique_pos (inline) 46ms 0.59% 49.43% 165ms 2.10% TetrahedralMesh::EdgesEnd (partial-inline) 40ms 0.51% 49.94% 162ms 2.07% AbstractCellProperty::IsSame 14ms 0.18% 50.12% 161ms 2.05% AbstractTetrahedralElement::CalculateJacobian 0 0% 50.12% 151ms 1.93% OutputFileHandler::CommonConstructor 0 0% 50.12% 151ms 1.93% OutputFileHandler::OutputFileHandler 0 0% 50.12% 148ms 1.89% TetrahedralMesh::RefreshJacobianCachedData 0 0% 50.12% 146ms 1.86% OutputFileHandler::MakeFoldersAndReturnFullPath 6ms 0.077% 50.20% 146ms 1.86% boost::numeric::ublas::c_vector::c_vector (inline) 6ms 0.077% 50.27% 144ms 1.84% boost::numeric::ublas::vector_assign (inline) 8ms 0.1% 50.38% 142ms 1.81% std::_Rb_tree_const_iterator::operator++ (inline) 140ms 1.79% 52.16% 140ms 1.79% std::_Rb_tree_increment 7ms 0.089% 52.25% 138ms 1.76% AbstractTetrahedralElement::CalculateInverseJacobian 2ms 0.026% 52.28% 136ms 1.73% AbstractCellBasedWriter::CloseFile 0 0% 52.28% 136ms 1.73% AbstractCellPopulation::CloseRoundRobinWritersFiles 0 0% 52.28% 135ms 1.72% std::basic_ofstream::basic_ofstream (inline) 1ms 0.013% 52.29% 134ms 1.71% std::basic_ofstream::close (inline) 0 0% 52.29% 134ms 1.71% std::basic_ofstream::open (inline) 2ms 0.026% 52.31% 133ms 1.70% std::basic_filebuf::close 1ms 0.013% 52.33% 133ms 1.70% std::basic_filebuf::open 1ms 0.013% 52.34% 132ms 1.68% FilesystemPermissions::SetFilePermissions (inline) 132ms 1.68% 54.02% 132ms 1.68% __GI_fchmodat 0 0% 54.02% 132ms 1.68% std::filesystem::permissions 9ms 0.11% 54.14% 130ms 1.66% boost::detail::shared_count::~shared_count (inline) 0 0% 54.14% 130ms 1.66% boost::shared_ptr::~shared_ptr (inline) 27ms 0.34% 54.48% 126ms 1.61% std::num_put::_M_insert_int 29ms 0.37% 54.85% 122ms 1.56% std::type_info::operator== (inline) 49ms 0.62% 55.48% 121ms 1.54% std::__ostream_insert 21ms 0.27% 55.75% 120ms 1.53% AbstractCellPopulation::Iterator::IsRealCell (inline) 118ms 1.50% 57.25% 118ms 1.50% boost::detail::sp_counted_base::release 6ms 0.077% 57.33% 117ms 1.49% Node::~Node 0 0% 57.33% 116ms 1.48% AbstractCellPopulation::Iterator::operator++ (inline) 2ms 0.026% 57.35% 113ms 1.44% alternateaxes 3ms 0.038% 57.39% 113ms 1.44% std::vector::push_back (inline) 24ms 0.31% 57.70% 112ms 1.43% boost::numeric::ublas::indexing_vector_assign 12ms 0.15% 57.85% 111ms 1.42% MeshBasedCellPopulation::SpringIterator::SpringIterator 106ms 1.35% 59.20% 111ms 1.42% vertexmedian 46ms 0.59% 59.79% 110ms 1.40% TetrahedralMesh::EdgeIterator::EdgeIterator (partial-inline) 3ms 0.038% 59.83% 109ms 1.39% std::_Vector_base::_M_allocate (inline) 26ms 0.33% 60.16% 108ms 1.38% AbstractTetrahedralElement::RefreshJacobian 15ms 0.19% 60.35% 107ms 1.36% std::vector::_M_realloc_insert 1ms 0.013% 60.36% 105ms 1.34% std::__basic_file::open 0 0% 60.36% 103ms 1.31% _IO_new_file_fopen 0 0% 60.36% 103ms 1.31% _IO_new_fopen 0 0% 60.36% 103ms 1.31% __fopen_internal (inline) 4ms 0.051% 60.41% 102ms 1.30% AbstractTetrahedralElement::AbstractTetrahedralElement 2ms 0.026% 60.44% 102ms 1.30% __GI__IO_file_open 101ms 1.29% 61.73% 101ms 1.29% [libchaste_cell_based.so] 96ms 1.22% 62.95% 96ms 1.22% incircle 1ms 0.013% 62.96% 96ms 1.22% std::basic_filebuf::_M_terminate_output 2ms 0.026% 62.99% 96ms 1.22% std::basic_filebuf::overflow 39ms 0.5% 63.49% 95ms 1.21% boost::shared_ptr::shared_ptr (inline) 3ms 0.038% 63.53% 95ms 1.21% std::operator<< (inline) 1ms 0.013% 63.54% 94ms 1.20% std::basic_filebuf::_M_convert_to_external 93ms 1.19% 64.72% 93ms 1.19% std::_Rb_tree_insert_and_rebalance 1ms 0.013% 64.74% 93ms 1.19% std::__basic_file::xsputn 91ms 1.16% 65.90% 91ms 1.16% __GI___libc_write 89ms 1.14% 67.03% 91ms 1.16% __libc_open64 2ms 0.026% 67.06% 87ms 1.11% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 67ms 0.85% 67.91% 85ms 1.08% AbstractElement::GetNodeGlobalIndex 84ms 1.07% 68.98% 84ms 1.07% TetrahedralMesh::EdgeIterator::operator!= (partial-inline) 83ms 1.06% 70.04% 83ms 1.06% std::vector::size (inline) 4ms 0.051% 70.09% 82ms 1.05% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (partial-inline) 80ms 1.02% 71.11% 80ms 1.02% counterclockwise 4ms 0.051% 71.16% 78ms 0.99% TetrahedralMesh::EdgeIterator::GetNodeA 1ms 0.013% 71.18% 73ms 0.93% std::filesystem::status 72ms 0.92% 72.10% 72ms 0.92% __GI___fstatat64 43ms 0.55% 72.64% 72ms 0.92% std::basic_filebuf::xsputn 0 0% 72.64% 71ms 0.91% FilesystemPermissions::CreateDirectoryWithPermissions (inline) 55ms 0.7% 73.35% 71ms 0.91% std::num_put::do_put 1ms 0.013% 73.36% 70ms 0.89% Cell::GetCellId 1ms 0.013% 73.37% 70ms 0.89% std::filesystem::create_directory 28ms 0.36% 73.73% 68ms 0.87% AbstractElement::GetNodeLocation 68ms 0.87% 74.60% 68ms 0.87% boost::shared_ptr::operator-> (inline) 0 0% 74.60% 68ms 0.87% tcache_get (inline) 68ms 0.87% 75.46% 68ms 0.87% tcache_get_n (inline) 1ms 0.013% 75.48% 67ms 0.85% AbstractCellPopulation::GetLocationIndexUsingCell 21ms 0.27% 75.74% 65ms 0.83% AbstractTetrahedralMesh::GetNumAllElements 44ms 0.56% 76.30% 65ms 0.83% std::basic_streambuf::xsputn 62ms 0.79% 77.09% 62ms 0.79% __memcpy_avx_unaligned_erms 40ms 0.51% 77.60% 62ms 0.79% boost::numeric::ublas::c_matrix::operator() (partial-inline) 0 0% 77.60% 62ms 0.79% std::_Rb_tree::_M_destroy_node (inline) 0 0% 77.60% 62ms 0.79% std::__new_allocator::destroy (inline) 0 0% 77.60% 62ms 0.79% std::allocator_traits::destroy (inline) 60ms 0.77% 78.37% 60ms 0.77% Node::GetIndex 43ms 0.55% 78.92% 60ms 0.77% malloc_consolidate 8ms 0.1% 79.02% 58ms 0.74% CellPropertyCollection::AddProperty 55ms 0.7% 79.72% 56ms 0.71% boost::detail::shared_count::shared_count (inline) 53ms 0.68% 80.40% 56ms 0.71% vertexsort 18ms 0.23% 80.63% 54ms 0.69% Determinant (inline) 0 0% 80.63% 53ms 0.68% CellPropertyCollection::~CellPropertyCollection (inline) 4ms 0.051% 80.68% 53ms 0.68% TetrahedralMesh::EdgeIterator::GetNodeB 4ms 0.051% 80.73% 52ms 0.66% Node::ConstructNodeAttributes (inline) 0 0% 80.73% 51ms 0.65% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 80.73% 51ms 0.65% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 1ms 0.013% 80.74% 50ms 0.64% AbstractCentreBasedCellPopulation::CreateCellPair 1ms 0.013% 80.76% 50ms 0.64% Node::ClearAppliedForce 50ms 0.64% 81.39% 50ms 0.64% Node::IsDeleted 33ms 0.42% 81.81% 49ms 0.62% AbstractTetrahedralMesh::GetElement 0 0% 81.81% 47ms 0.6% MeshBasedCellPopulation::SpringIterator::GetNodeA (inline) 47ms 0.6% 82.41% 47ms 0.6% [libchaste_mesh.so] 47ms 0.6% 83.01% 47ms 0.6% std::ostream::sentry::sentry 0 0% 83.01% 45ms 0.57% BoundaryNodeWriter::Visit 3ms 0.038% 83.05% 45ms 0.57% std::_Vector_base::_M_deallocate (inline) 44ms 0.56% 83.61% 44ms 0.56% boost::numeric::ublas::c_vector::operator() 0 0% 83.61% 42ms 0.54% MeshBasedCellPopulation::SpringIterator::~SpringIterator (inline) 0 0% 83.61% 41ms 0.52% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 41ms 0.52% 84.13% 41ms 0.52% [libstdc++.so.6.0.33] 41ms 0.52% 84.66% 41ms 0.52% std::pair::operator= (inline) 18ms 0.23% 84.89% 40ms 0.51% AbstractCellCycleModel::GetAge 2ms 0.026% 84.91% 40ms 0.51% OutputFileHandler::GetChasteTestOutputDirectory[abi:cxx11] 40ms 0.51% 85.42% 40ms 0.51% boost::numeric::ublas::same_impl_ex