File: Test2dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 6710ms, 84.04% of 7984ms total Dropped 578 nodes (cum <= 39.92ms) flat flat% sum% cum cum% 0 0% 0% 7944ms 99.50% __libc_start_call_main 0 0% 0% 7944ms 99.50% __libc_start_main_impl 0 0% 0% 7944ms 99.50% _start 0 0% 0% 7927ms 99.29% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 7927ms 99.29% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 7927ms 99.29% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 7927ms 99.29% main 0 0% 0% 7892ms 98.85% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 7892ms 98.85% CxxTest::TestRunner::runTest (inline) 0 0% 0% 7892ms 98.85% Test2DMonolayerRepresentativeSimulation::Test2DMonolayerRepresentativeSimulationForProfiling 0 0% 0% 7889ms 98.81% AbstractCellBasedSimulation::Solve 0 0% 0% 3403ms 42.62% AbstractCellBasedSimulation::UpdateCellPopulation 1ms 0.013% 0.013% 2942ms 36.85% AbstractCellPopulation::WriteResultsToFiles 1ms 0.013% 0.025% 2899ms 36.31% MeshBasedCellPopulation::Update 1ms 0.013% 0.038% 1538ms 19.26% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 0.038% 1434ms 17.96% MeshBasedCellPopulation::UpdateNodePairs 2ms 0.025% 0.063% 1409ms 17.65% MutableMesh::ReMesh 1ms 0.013% 0.075% 1403ms 17.57% ForwardEulerNumericalMethod::UpdateAllNodePositions 5ms 0.063% 0.14% 1354ms 16.96% AbstractNumericalMethod::ComputeForcesIncludingDamping 19ms 0.24% 0.38% 1243ms 15.57% MeshBasedCellPopulation::SpringIterator::operator++ 116ms 1.45% 1.83% 1002ms 12.55% TetrahedralMesh::EdgeIterator::operator++ 442ms 5.54% 7.36% 959ms 12.01% std::_Rb_tree::_M_lower_bound (inline) 1ms 0.013% 7.38% 957ms 11.99% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 1ms 0.013% 7.39% 928ms 11.62% AbstractTwoBodyInteractionForce::AddForceContribution 15ms 0.19% 7.58% 919ms 11.51% CellPropertyCollection::GetPropertiesType (inline) 8ms 0.1% 7.68% 916ms 11.47% CellPopulationElementWriter::Visit 243ms 3.04% 10.72% 893ms 11.18% __dynamic_cast 48ms 0.6% 11.32% 834ms 10.45% AbstractVariableSizeTwoBodyInteractionForce::CalculateForceBetweenNodes 0 0% 11.32% 799ms 10.01% MeshBasedCellPopulation::AcceptCellWriter 32ms 0.4% 11.72% 779ms 9.76% AbstractCellPopulation::GetCellUsingLocationIndex 6ms 0.075% 11.80% 699ms 8.76% TetrahedralMesh::ImportFromMesher 5ms 0.063% 11.86% 698ms 8.74% AbstractCellProperty::IsSubType (inline) 1ms 0.013% 11.87% 633ms 7.93% std::ostream::operator<< (inline) 79ms 0.99% 12.86% 631ms 7.90% std::ostream::_M_insert 37ms 0.46% 13.33% 614ms 7.69% operator new 46ms 0.58% 13.90% 588ms 7.36% std::map::operator[] (partial-inline) 8ms 0.1% 14.00% 573ms 7.18% std::set::insert (inline) 192ms 2.40% 16.41% 566ms 7.09% __GI___libc_malloc 18ms 0.23% 16.63% 565ms 7.08% std::_Rb_tree::_M_insert_unique 1ms 0.013% 16.65% 555ms 6.95% triangulate 30ms 0.38% 17.02% 538ms 6.74% std::__new_allocator::allocate (inline) 0 0% 17.02% 534ms 6.69% std::allocator_traits::allocate (inline) 4ms 0.05% 17.07% 516ms 6.46% Cell::GetCellProliferativeType 515ms 6.45% 23.52% 515ms 6.45% __strcmp_avx2 4ms 0.05% 23.57% 510ms 6.39% LegacyCellProliferativeTypesWriter::VisitCell 0 0% 23.57% 500ms 6.26% std::_Rb_tree::lower_bound (inline) 0 0% 23.57% 500ms 6.26% std::map::lower_bound (inline) 20ms 0.25% 23.82% 499ms 6.25% std::_Rb_tree::find (inline) 5ms 0.063% 23.89% 494ms 6.19% AbstractCellBasedSimulation::DoCellBirth 1ms 0.013% 23.90% 488ms 6.11% delaunay 0 0% 23.90% 487ms 6.10% divconqdelaunay 0 0% 23.90% 479ms 6.00% std::_Rb_tree::_M_create_node (inline) 229ms 2.87% 26.77% 474ms 5.94% __cxxabiv1::__si_class_type_info::__do_dyncast 0 0% 26.77% 459ms 5.75% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 26.77% 454ms 5.69% std::set::count (inline) 0 0% 26.77% 441ms 5.52% std::_Rb_tree::_M_get_node (inline) 34ms 0.43% 27.19% 406ms 5.09% std::_Rb_tree::_Rb_tree (partial-inline) 0 0% 27.19% 382ms 4.78% Cell::GetMutationState 2ms 0.025% 27.22% 378ms 4.73% std::set::set (inline) 29ms 0.36% 27.58% 374ms 4.68% std::_Rb_tree::~_Rb_tree (inline) 0 0% 27.58% 368ms 4.61% NodeLocationWriter::Visit 13ms 0.16% 27.74% 355ms 4.45% std::less::operator() (inline) 23ms 0.29% 28.03% 353ms 4.42% std::_Rb_tree::_M_insert_ (inline) 0 0% 28.03% 349ms 4.37% std::set::~set (inline) 342ms 4.28% 32.31% 342ms 4.28% std::operator< (inline) 73ms 0.91% 33.23% 340ms 4.26% std::_Rb_tree::_M_erase 26ms 0.33% 33.55% 331ms 4.15% std::_Rb_tree::_M_copy (inline) 5ms 0.063% 33.62% 330ms 4.13% Cell::ReadyToDivide 0 0% 33.62% 326ms 4.08% AbstractCentreBasedCellPopulation::GetDampingConstant 0 0% 33.62% 326ms 4.08% MeshBasedCellPopulation::GetDampingConstant 3ms 0.038% 33.65% 323ms 4.05% Element::Element 21ms 0.26% 33.92% 321ms 4.02% std::num_put::_M_insert_float 0 0% 33.92% 313ms 3.92% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 1ms 0.013% 33.93% 312ms 3.91% AbstractCellBasedWriter::OpenOutputFileForAppend 0 0% 33.93% 310ms 3.88% OutputFileHandler::OpenOutputFile 309ms 3.87% 37.80% 309ms 3.87% std::_Rb_tree::_S_right (inline) 13ms 0.16% 37.96% 307ms 3.85% AbstractCellPopulation::IsCellAttachedToLocationIndex 87ms 1.09% 39.05% 299ms 3.74% std::_Rb_tree::_M_clone_node (inline) 208ms 2.61% 41.66% 290ms 3.63% _int_malloc 91ms 1.14% 42.80% 273ms 3.42% __GI___libc_free 7ms 0.088% 42.89% 266ms 3.33% divconqrecurse 2ms 0.025% 42.91% 265ms 3.32% AbstractCellProperty::IsType (inline) 7ms 0.088% 43.00% 264ms 3.31% std::__cxx11::collate::do_transform 4ms 0.05% 43.05% 260ms 3.26% CellProliferativeTypesWriter::VisitCell 10ms 0.13% 43.17% 257ms 3.22% CellPropertyCollection::HasProperty 0 0% 43.17% 255ms 3.19% Cell::HasCellProperty (inline) 1ms 0.013% 43.19% 246ms 3.08% ___vsnprintf 73ms 0.91% 44.10% 246ms 3.08% mergehulls 0 0% 44.10% 245ms 3.07% __vsnprintf_internal (inline) 0 0% 44.10% 241ms 3.02% std::_Rb_tree::_M_drop_node (inline) 9ms 0.11% 44.21% 239ms 2.99% std::__new_allocator::deallocate (inline) 31ms 0.39% 44.60% 237ms 2.97% __printf_buffer 0 0% 44.60% 230ms 2.88% std::allocator_traits::deallocate (inline) 2ms 0.025% 44.63% 220ms 2.76% AbstractPhaseBasedCellCycleModel::ReadyToDivide 12ms 0.15% 44.78% 218ms 2.73% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 4ms 0.05% 44.83% 215ms 2.69% Element::RegisterWithNodes (inline) 6ms 0.075% 44.90% 210ms 2.63% Node::AddElement 49ms 0.61% 45.52% 196ms 2.45% AbstractCellProperty::IsSame 66ms 0.83% 46.34% 195ms 2.44% std::_Rb_tree::_M_get_insert_unique_pos (inline) 15ms 0.19% 46.53% 193ms 2.42% MeshBasedCellPopulation::SpringsEnd (inline) 0 0% 46.53% 191ms 2.39% std::_Rb_tree::_M_put_node (inline) 19ms 0.24% 46.77% 186ms 2.33% __printf_fp_l_buffer 0 0% 46.77% 186ms 2.33% __printf_fp_spec (inline) 17ms 0.21% 46.98% 185ms 2.32% TetrahedralMesh::Clear 41ms 0.51% 47.49% 182ms 2.28% std::num_put::_M_insert_int 154ms 1.93% 49.42% 181ms 2.27% _int_free 0 0% 49.42% 167ms 2.09% OutputFileHandler::OutputFileHandler 1ms 0.013% 49.44% 166ms 2.08% OutputFileHandler::CommonConstructor 45ms 0.56% 50.00% 166ms 2.08% TetrahedralMesh::EdgesEnd (partial-inline) 0 0% 50.00% 166ms 2.08% std::basic_ofstream::basic_ofstream (inline) 0 0% 50.00% 161ms 2.02% OutputFileHandler::MakeFoldersAndReturnFullPath 9ms 0.11% 50.11% 159ms 1.99% AbstractTetrahedralElement::CalculateJacobian 80ms 1.00% 51.11% 159ms 1.99% __printf_fp_buffer_1 3ms 0.038% 51.15% 159ms 1.99% std::basic_filebuf::open 0 0% 51.15% 158ms 1.98% std::basic_ofstream::open (inline) 36ms 0.45% 51.60% 147ms 1.84% std::type_info::operator== (inline) 0 0% 51.60% 143ms 1.79% AbstractCellPopulation::CloseRoundRobinWritersFiles 0 0% 51.60% 142ms 1.78% AbstractCellBasedWriter::CloseFile 1ms 0.013% 51.62% 142ms 1.78% std::basic_filebuf::close 0 0% 51.62% 142ms 1.78% std::basic_ofstream::close (inline) 3ms 0.038% 51.65% 140ms 1.75% alternateaxes 0 0% 51.65% 137ms 1.72% TetrahedralMesh::RefreshJacobianCachedData 5ms 0.063% 51.72% 136ms 1.70% boost::numeric::ublas::vector_assign (inline) 129ms 1.62% 53.33% 136ms 1.70% vertexmedian 54ms 0.68% 54.01% 135ms 1.69% std::__ostream_insert 20ms 0.25% 54.26% 134ms 1.68% AbstractCellPopulation::Iterator::IsRealCell (inline) 0 0% 54.26% 134ms 1.68% AbstractCellPopulation::Iterator::operator++ (inline) 2ms 0.025% 54.28% 129ms 1.62% boost::numeric::ublas::c_vector::c_vector (inline) 18ms 0.23% 54.51% 125ms 1.57% AbstractTetrahedralElement::RefreshJacobian 5ms 0.063% 54.57% 123ms 1.54% AbstractTetrahedralElement::CalculateInverseJacobian 1ms 0.013% 54.58% 123ms 1.54% std::__basic_file::open 0 0% 54.58% 122ms 1.53% _IO_new_fopen 1ms 0.013% 54.60% 122ms 1.53% __fopen_internal (inline) 2ms 0.025% 54.62% 118ms 1.48% _IO_new_file_fopen 1ms 0.013% 54.63% 116ms 1.45% __GI__IO_file_open 0 0% 54.63% 115ms 1.44% FilesystemPermissions::SetFilePermissions (inline) 2ms 0.025% 54.66% 115ms 1.44% std::filesystem::permissions 15ms 0.19% 54.85% 114ms 1.43% MeshBasedCellPopulation::SpringIterator::SpringIterator 112ms 1.40% 56.25% 112ms 1.40% __GI_fchmodat 10ms 0.13% 56.38% 111ms 1.39% std::_Rb_tree_const_iterator::operator++ (inline) 2ms 0.025% 56.40% 110ms 1.38% std::operator<< (inline) 4ms 0.05% 56.45% 109ms 1.37% AbstractTetrahedralElement::AbstractTetrahedralElement 8ms 0.1% 56.55% 109ms 1.37% Node::~Node 68ms 0.85% 57.40% 109ms 1.37% TetrahedralMesh::EdgeIterator::EdgeIterator (partial-inline) 108ms 1.35% 58.76% 108ms 1.35% incircle 106ms 1.33% 60.08% 106ms 1.33% std::_Rb_tree_increment 0 0% 60.08% 105ms 1.32% std::basic_filebuf::_M_terminate_output 2ms 0.025% 60.11% 105ms 1.32% std::basic_filebuf::overflow 102ms 1.28% 61.39% 104ms 1.30% __libc_open64 7ms 0.088% 61.47% 104ms 1.30% boost::detail::shared_count::~shared_count (inline) 0 0% 61.47% 104ms 1.30% boost::shared_ptr::~shared_ptr (inline) 1ms 0.013% 61.49% 103ms 1.29% std::basic_filebuf::_M_convert_to_external 1ms 0.013% 61.50% 102ms 1.28% std::__basic_file::xsputn 99ms 1.24% 62.74% 100ms 1.25% __GI___libc_write 68ms 0.85% 63.59% 99ms 1.24% std::basic_streambuf::xsputn 3ms 0.038% 63.63% 97ms 1.21% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 45ms 0.56% 64.19% 96ms 1.20% boost::shared_ptr::shared_ptr (inline) 93ms 1.16% 65.36% 94ms 1.18% boost::detail::sp_counted_base::release 94ms 1.18% 66.53% 94ms 1.18% std::_Rb_tree_insert_and_rebalance 0 0% 66.53% 93ms 1.16% std::_Vector_base::_M_allocate (inline) 5ms 0.063% 66.60% 91ms 1.14% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (partial-inline) 3ms 0.038% 66.63% 90ms 1.13% std::vector::push_back (inline) 48ms 0.6% 67.23% 88ms 1.10% AbstractElement::GetNodeLocation 87ms 1.09% 68.32% 87ms 1.09% [libchaste_cell_based.so] 27ms 0.34% 68.66% 87ms 1.09% boost::numeric::ublas::indexing_vector_assign 55ms 0.69% 69.35% 84ms 1.05% std::basic_filebuf::xsputn 14ms 0.18% 69.53% 83ms 1.04% CellPropertyCollection::AddProperty 9ms 0.11% 69.64% 83ms 1.04% std::vector::_M_realloc_insert 0 0% 69.64% 79ms 0.99% FilesystemPermissions::CreateDirectoryWithPermissions (inline) 79ms 0.99% 70.63% 79ms 0.99% TetrahedralMesh::EdgeIterator::operator!= (partial-inline) 1ms 0.013% 70.64% 79ms 0.99% std::filesystem::create_directory 4ms 0.05% 70.69% 78ms 0.98% std::filesystem::status 0 0% 70.69% 77ms 0.96% Cell::GetCellId 0 0% 70.69% 77ms 0.96% tcache_get (inline) 77ms 0.96% 71.66% 77ms 0.96% tcache_get_n (inline) 74ms 0.93% 72.58% 74ms 0.93% __GI___fstatat64 58ms 0.73% 73.31% 74ms 0.93% std::num_put::do_put 1ms 0.013% 73.32% 73ms 0.91% AbstractCellPopulation::GetLocationIndexUsingCell 2ms 0.025% 73.35% 71ms 0.89% TetrahedralMesh::EdgeIterator::GetNodeA 71ms 0.89% 74.24% 71ms 0.89% __memcpy_avx_unaligned_erms 6ms 0.075% 74.31% 70ms 0.88% Node::ConstructNodeAttributes (inline) 70ms 0.88% 75.19% 70ms 0.88% std::vector::size (inline) 62ms 0.78% 75.96% 69ms 0.86% vertexsort 5ms 0.063% 76.03% 68ms 0.85% TetrahedralMesh::EdgeIterator::GetNodeB 68ms 0.85% 76.88% 68ms 0.85% [libchaste_mesh.so] 48ms 0.6% 77.48% 66ms 0.83% malloc_consolidate 1ms 0.013% 77.49% 65ms 0.81% Node::ClearAppliedForce 64ms 0.8% 78.29% 64ms 0.8% Node::GetIndex 64ms 0.8% 79.10% 64ms 0.8% counterclockwise 48ms 0.6% 79.70% 63ms 0.79% AbstractElement::GetNodeGlobalIndex 54ms 0.68% 80.37% 54ms 0.68% Node::IsDeleted 54ms 0.68% 81.05% 54ms 0.68% boost::shared_ptr::operator-> (inline) 50ms 0.63% 81.68% 51ms 0.64% boost::detail::shared_count::shared_count (inline) 0 0% 81.68% 50ms 0.63% std::_Rb_tree::_M_destroy_node (inline) 0 0% 81.68% 50ms 0.63% std::__new_allocator::destroy (inline) 0 0% 81.68% 50ms 0.63% std::allocator_traits::destroy (inline) 21ms 0.26% 81.94% 49ms 0.61% AbstractTetrahedralMesh::GetNumAllElements 0 0% 81.94% 49ms 0.61% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 49ms 0.61% 82.55% 49ms 0.61% [libstdc++.so.6.0.33] 0 0% 82.55% 48ms 0.6% AbstractCentreBasedCellPopulation::CreateCellPair 32ms 0.4% 82.95% 48ms 0.6% boost::numeric::ublas::c_matrix::operator() 11ms 0.14% 83.09% 46ms 0.58% AbstractTetrahedralMesh::GetElement 0 0% 83.09% 46ms 0.58% MeshBasedCellPopulation::SpringIterator::~SpringIterator (inline) 4ms 0.05% 83.14% 45ms 0.56% NodeAttributes::NodeAttributes 0 0% 83.14% 44ms 0.55% BoundaryNodeWriter::Visit 42ms 0.53% 83.67% 42ms 0.53% __GI___mkdir 28ms 0.35% 84.02% 42ms 0.53% hack_digit 0 0% 84.02% 42ms 0.53% std::_Rb_tree::_M_emplace_hint_unique 1ms 0.013% 84.03% 41ms 0.51% OutputFileHandler::GetChasteTestOutputDirectory[abi:cxx11] 1ms 0.013% 84.04% 41ms 0.51% std::__new_allocator::construct (inline) 0 0% 84.04% 41ms 0.51% std::allocator_traits::construct (inline) 0 0% 84.04% 40ms 0.5% _dl_init 0 0% 84.04% 40ms 0.5% _dl_start_user 0 0% 84.04% 40ms 0.5% call_init (inline) 0 0% 84.04% 40ms 0.5% std::vector::vector (inline)