File: Test2dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 6696ms, 84.47% of 7927ms total Dropped 594 nodes (cum <= 39.63ms) flat flat% sum% cum cum% 0 0% 0% 7890ms 99.53% __libc_start_call_main 0 0% 0% 7890ms 99.53% __libc_start_main_impl 0 0% 0% 7890ms 99.53% _start 0 0% 0% 7873ms 99.32% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 7873ms 99.32% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 7873ms 99.32% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 7873ms 99.32% main 0 0% 0% 7834ms 98.83% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 7834ms 98.83% CxxTest::TestRunner::runTest (inline) 0 0% 0% 7834ms 98.83% Test2DMonolayerRepresentativeSimulation::Test2DMonolayerRepresentativeSimulationForProfiling 1ms 0.013% 0.013% 7831ms 98.79% AbstractCellBasedSimulation::Solve 1ms 0.013% 0.025% 3382ms 42.66% AbstractCellBasedSimulation::UpdateCellPopulation 3ms 0.038% 0.063% 2920ms 36.84% AbstractCellPopulation::WriteResultsToFiles 0 0% 0.063% 2856ms 36.03% MeshBasedCellPopulation::Update 3ms 0.038% 0.1% 1517ms 19.14% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 0.1% 1425ms 17.98% MeshBasedCellPopulation::UpdateNodePairs 0 0% 0.1% 1372ms 17.31% MutableMesh::ReMesh 1ms 0.013% 0.11% 1364ms 17.21% ForwardEulerNumericalMethod::UpdateAllNodePositions 5ms 0.063% 0.18% 1306ms 16.48% AbstractNumericalMethod::ComputeForcesIncludingDamping 14ms 0.18% 0.35% 1227ms 15.48% MeshBasedCellPopulation::SpringIterator::operator++ 90ms 1.14% 1.49% 1005ms 12.68% TetrahedralMesh::EdgeIterator::operator++ 429ms 5.41% 6.90% 972ms 12.26% std::_Rb_tree::_M_lower_bound (inline) 6ms 0.076% 6.98% 919ms 11.59% CellPopulationElementWriter::Visit 3ms 0.038% 7.01% 911ms 11.49% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 9ms 0.11% 7.13% 902ms 11.38% CellPropertyCollection::GetPropertiesType (inline) 3ms 0.038% 7.17% 896ms 11.30% AbstractTwoBodyInteractionForce::AddForceContribution 237ms 2.99% 10.16% 860ms 10.85% __dynamic_cast 63ms 0.79% 10.95% 796ms 10.04% AbstractVariableSizeTwoBodyInteractionForce::CalculateForceBetweenNodes 1ms 0.013% 10.96% 766ms 9.66% MeshBasedCellPopulation::AcceptCellWriter 32ms 0.4% 11.37% 735ms 9.27% AbstractCellPopulation::GetCellUsingLocationIndex 4ms 0.05% 11.42% 715ms 9.02% TetrahedralMesh::ImportFromMesher 3ms 0.038% 11.45% 700ms 8.83% AbstractCellProperty::IsSubType (inline) 1ms 0.013% 11.47% 676ms 8.53% std::ostream::operator<< (inline) 84ms 1.06% 12.53% 675ms 8.52% std::ostream::_M_insert 40ms 0.5% 13.03% 586ms 7.39% std::map::operator[] (partial-inline) 6ms 0.076% 13.11% 547ms 6.90% Cell::GetCellProliferativeType 41ms 0.52% 13.62% 546ms 6.89% operator new 3ms 0.038% 13.66% 532ms 6.71% std::set::insert (inline) 14ms 0.18% 13.84% 529ms 6.67% std::_Rb_tree::_M_insert_unique 26ms 0.33% 14.17% 529ms 6.67% std::_Rb_tree::find (inline) 521ms 6.57% 20.74% 521ms 6.57% __strcmp_avx2 43ms 0.54% 21.28% 517ms 6.52% std::__new_allocator::allocate (inline) 0 0% 21.28% 513ms 6.47% std::allocator_traits::allocate (inline) 2ms 0.025% 21.31% 502ms 6.33% AbstractCellBasedSimulation::DoCellBirth 0 0% 21.31% 502ms 6.33% triangulate 175ms 2.21% 23.51% 500ms 6.31% __GI___libc_malloc 0 0% 23.51% 499ms 6.29% std::_Rb_tree::lower_bound (inline) 0 0% 23.51% 499ms 6.29% std::map::lower_bound (inline) 4ms 0.05% 23.57% 477ms 6.02% LegacyCellProliferativeTypesWriter::VisitCell 0 0% 23.57% 471ms 5.94% std::set::count (inline) 0 0% 23.57% 444ms 5.60% delaunay 2ms 0.025% 23.59% 443ms 5.59% divconqdelaunay 40ms 0.5% 24.09% 443ms 5.59% std::_Rb_tree::~_Rb_tree (inline) 207ms 2.61% 26.71% 437ms 5.51% __cxxabiv1::__si_class_type_info::__do_dyncast 0 0% 26.71% 437ms 5.51% std::_Rb_tree::_M_create_node (inline) 0 0% 26.71% 427ms 5.39% NodeLocationWriter::Visit 0 0% 26.71% 418ms 5.27% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 26.71% 411ms 5.18% std::set::~set (inline) 71ms 0.9% 27.60% 399ms 5.03% std::_Rb_tree::_M_erase 0 0% 27.60% 394ms 4.97% std::_Rb_tree::_M_get_node (inline) 10ms 0.13% 27.73% 372ms 4.69% std::less::operator() (inline) 39ms 0.49% 28.22% 368ms 4.64% std::num_put::_M_insert_float 362ms 4.57% 32.79% 362ms 4.57% std::operator< (inline) 0 0% 32.79% 355ms 4.48% Cell::GetMutationState 10ms 0.13% 32.91% 345ms 4.35% std::_Rb_tree::_Rb_tree (partial-inline) 340ms 4.29% 37.20% 340ms 4.29% std::_Rb_tree::_S_right (inline) 7ms 0.088% 37.29% 337ms 4.25% Cell::ReadyToDivide 113ms 1.43% 38.72% 333ms 4.20% __GI___libc_free 1ms 0.013% 38.73% 321ms 4.05% MeshBasedCellPopulation::GetDampingConstant 9ms 0.11% 38.84% 319ms 4.02% AbstractCellPopulation::IsCellAttachedToLocationIndex 2ms 0.025% 38.87% 319ms 4.02% AbstractCentreBasedCellPopulation::GetDampingConstant 13ms 0.16% 39.03% 317ms 4.00% std::_Rb_tree::_M_insert_ (inline) 3ms 0.038% 39.07% 317ms 4.00% std::set::set (inline) 0 0% 39.07% 312ms 3.94% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 0 0% 39.07% 310ms 3.91% AbstractCellBasedWriter::OpenOutputFileForAppend 1ms 0.013% 39.08% 307ms 3.87% OutputFileHandler::OpenOutputFile 23ms 0.29% 39.37% 301ms 3.80% std::_Rb_tree::_M_copy (inline) 12ms 0.15% 39.52% 301ms 3.80% std::__new_allocator::deallocate (inline) 0 0% 39.52% 298ms 3.76% std::_Rb_tree::_M_drop_node (inline) 0 0% 39.52% 295ms 3.72% std::allocator_traits::deallocate (inline) 5ms 0.063% 39.59% 286ms 3.61% Element::Element 72ms 0.91% 40.49% 277ms 3.49% std::_Rb_tree::_M_clone_node (inline) 5ms 0.063% 40.56% 271ms 3.42% CellProliferativeTypesWriter::VisitCell 7ms 0.088% 40.65% 271ms 3.42% std::__cxx11::collate::do_transform 4ms 0.05% 40.70% 260ms 3.28% AbstractCellProperty::IsType (inline) 8ms 0.1% 40.80% 258ms 3.25% divconqrecurse 8ms 0.1% 40.90% 256ms 3.23% CellPropertyCollection::HasProperty 2ms 0.025% 40.92% 255ms 3.22% ___vsnprintf 0 0% 40.92% 253ms 3.19% Cell::HasCellProperty (inline) 0 0% 40.92% 253ms 3.19% __vsnprintf_internal (inline) 151ms 1.90% 42.83% 248ms 3.13% _int_malloc 32ms 0.4% 43.23% 246ms 3.10% __printf_buffer 0 0% 43.23% 244ms 3.08% std::_Rb_tree::_M_put_node (inline) 72ms 0.91% 44.14% 239ms 3.02% mergehulls 3ms 0.038% 44.18% 217ms 2.74% AbstractPhaseBasedCellCycleModel::ReadyToDivide 184ms 2.32% 46.50% 217ms 2.74% _int_free 5ms 0.063% 46.56% 212ms 2.67% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 19ms 0.24% 46.80% 208ms 2.62% TetrahedralMesh::Clear 11ms 0.14% 46.94% 204ms 2.57% MeshBasedCellPopulation::SpringsEnd (inline) 14ms 0.18% 47.12% 201ms 2.54% __printf_fp_l_buffer 0 0% 47.12% 201ms 2.54% __printf_fp_spec (inline) 69ms 0.87% 47.99% 198ms 2.50% std::_Rb_tree::_M_get_insert_unique_pos (inline) 48ms 0.61% 48.59% 196ms 2.47% AbstractCellProperty::IsSame 7ms 0.088% 48.68% 185ms 2.33% Element::RegisterWithNodes (inline) 94ms 1.19% 49.87% 182ms 2.30% __printf_fp_buffer_1 2ms 0.025% 49.89% 177ms 2.23% Node::AddElement 0 0% 49.89% 159ms 2.01% std::basic_ofstream::basic_ofstream (inline) 0 0% 49.89% 156ms 1.97% std::basic_ofstream::open (inline) 2ms 0.025% 49.92% 155ms 1.96% std::basic_filebuf::open 42ms 0.53% 50.45% 153ms 1.93% TetrahedralMesh::EdgesEnd (partial-inline) 14ms 0.18% 50.62% 151ms 1.90% AbstractTetrahedralElement::CalculateJacobian 35ms 0.44% 51.07% 151ms 1.90% std::num_put::_M_insert_int 0 0% 51.07% 148ms 1.87% OutputFileHandler::OutputFileHandler 23ms 0.29% 51.36% 148ms 1.87% std::type_info::operator== (inline) 0 0% 51.36% 147ms 1.85% OutputFileHandler::CommonConstructor 22ms 0.28% 51.63% 145ms 1.83% AbstractCellPopulation::Iterator::IsRealCell (inline) 0 0% 51.63% 144ms 1.82% AbstractCellPopulation::Iterator::operator++ (inline) 0 0% 51.63% 139ms 1.75% OutputFileHandler::MakeFoldersAndReturnFullPath 4ms 0.05% 51.68% 130ms 1.64% boost::numeric::ublas::c_vector::c_vector (inline) 3ms 0.038% 51.72% 127ms 1.60% boost::numeric::ublas::vector_assign (inline) 1ms 0.013% 51.73% 126ms 1.59% TetrahedralMesh::RefreshJacobianCachedData 0 0% 51.73% 125ms 1.58% _IO_new_fopen 0 0% 51.73% 125ms 1.58% __fopen_internal (inline) 0 0% 51.73% 125ms 1.58% std::__basic_file::open 0 0% 51.73% 120ms 1.51% AbstractCellPopulation::CloseRoundRobinWritersFiles 0 0% 51.73% 120ms 1.51% FilesystemPermissions::SetFilePermissions (inline) 120ms 1.51% 53.25% 120ms 1.51% __GI_fchmodat 0 0% 53.25% 120ms 1.51% std::filesystem::permissions 0 0% 53.25% 119ms 1.50% AbstractCellBasedWriter::CloseFile 0 0% 53.25% 119ms 1.50% std::_Vector_base::_M_allocate (inline) 1ms 0.013% 53.26% 119ms 1.50% std::basic_filebuf::close 0 0% 53.26% 119ms 1.50% std::basic_ofstream::close (inline) 16ms 0.2% 53.46% 118ms 1.49% MeshBasedCellPopulation::SpringIterator::SpringIterator 6ms 0.076% 53.54% 118ms 1.49% Node::~Node 2ms 0.025% 53.56% 118ms 1.49% _IO_new_file_fopen 14ms 0.18% 53.74% 117ms 1.48% boost::detail::shared_count::~shared_count (inline) 0 0% 53.74% 117ms 1.48% boost::shared_ptr::~shared_ptr (inline) 12ms 0.15% 53.89% 116ms 1.46% std::vector::push_back (inline) 2ms 0.025% 53.92% 115ms 1.45% __GI__IO_file_open 49ms 0.62% 54.54% 115ms 1.45% std::__ostream_insert 3ms 0.038% 54.57% 114ms 1.44% AbstractTetrahedralElement::CalculateInverseJacobian 12ms 0.15% 54.72% 114ms 1.44% AbstractTetrahedralElement::RefreshJacobian 14ms 0.18% 54.90% 112ms 1.41% std::_Rb_tree_const_iterator::operator++ (inline) 1ms 0.013% 54.91% 109ms 1.38% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (partial-inline) 109ms 1.38% 56.29% 109ms 1.38% incircle 109ms 1.38% 57.66% 109ms 1.38% std::_Rb_tree_increment 2ms 0.025% 57.69% 107ms 1.35% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 107ms 1.35% 59.04% 107ms 1.35% __libc_open64 3ms 0.038% 59.08% 105ms 1.32% AbstractTetrahedralElement::AbstractTetrahedralElement 60ms 0.76% 59.83% 104ms 1.31% TetrahedralMesh::EdgeIterator::EdgeIterator (partial-inline) 1ms 0.013% 59.85% 104ms 1.31% alternateaxes 94ms 1.19% 61.03% 102ms 1.29% vertexmedian 99ms 1.25% 62.28% 101ms 1.27% boost::detail::sp_counted_base::release 101ms 1.27% 63.55% 101ms 1.27% std::_Rb_tree_insert_and_rebalance 1ms 0.013% 63.57% 101ms 1.27% std::basic_filebuf::overflow 1ms 0.013% 63.58% 101ms 1.27% std::operator<< (inline) 1ms 0.013% 63.59% 100ms 1.26% std::basic_filebuf::_M_convert_to_external 0 0% 63.59% 100ms 1.26% std::basic_filebuf::_M_terminate_output 6ms 0.076% 63.67% 100ms 1.26% std::vector::_M_realloc_insert 97ms 1.22% 64.89% 98ms 1.24% __GI___libc_write 1ms 0.013% 64.90% 98ms 1.24% std::__basic_file::xsputn 43ms 0.54% 65.45% 97ms 1.22% boost::shared_ptr::shared_ptr (inline) 3ms 0.038% 65.49% 92ms 1.16% AbstractCellPopulation::GetLocationIndexUsingCell 43ms 0.54% 66.03% 92ms 1.16% AbstractElement::GetNodeLocation 62ms 0.78% 66.81% 92ms 1.16% std::basic_streambuf::xsputn 90ms 1.14% 67.94% 90ms 1.14% [libchaste_cell_based.so] 30ms 0.38% 68.32% 90ms 1.14% boost::numeric::ublas::indexing_vector_assign 89ms 1.12% 69.45% 89ms 1.12% TetrahedralMesh::EdgeIterator::operator!= (partial-inline) 0 0% 69.45% 86ms 1.08% FilesystemPermissions::CreateDirectoryWithPermissions (inline) 58ms 0.73% 70.18% 86ms 1.08% std::basic_filebuf::xsputn 1ms 0.013% 70.19% 86ms 1.08% std::filesystem::create_directory 81ms 1.02% 71.21% 81ms 1.02% Node::GetIndex 79ms 1% 72.21% 79ms 1% __memcpy_avx_unaligned_erms 56ms 0.71% 72.92% 79ms 1% malloc_consolidate 10ms 0.13% 73.04% 75ms 0.95% CellPropertyCollection::AddProperty 66ms 0.83% 73.87% 74ms 0.93% AbstractElement::GetNodeGlobalIndex 74ms 0.93% 74.81% 74ms 0.93% std::vector::size (inline) 2ms 0.025% 74.83% 73ms 0.92% Cell::GetCellId 66ms 0.83% 75.67% 72ms 0.91% vertexsort 0 0% 75.67% 71ms 0.9% tcache_get (inline) 71ms 0.9% 76.56% 71ms 0.9% tcache_get_n (inline) 70ms 0.88% 77.44% 70ms 0.88% __GI___fstatat64 0 0% 77.44% 70ms 0.88% std::filesystem::status 8ms 0.1% 77.55% 67ms 0.85% TetrahedralMesh::EdgeIterator::GetNodeA 54ms 0.68% 78.23% 67ms 0.85% std::num_put::do_put 31ms 0.39% 78.62% 61ms 0.77% AbstractTetrahedralMesh::GetElement 60ms 0.76% 79.37% 60ms 0.76% [libchaste_mesh.so] 60ms 0.76% 80.13% 60ms 0.76% counterclockwise 5ms 0.063% 80.19% 57ms 0.72% Node::ConstructNodeAttributes (inline) 6ms 0.076% 80.27% 56ms 0.71% std::_Vector_base::_M_deallocate (inline) 1ms 0.013% 80.28% 55ms 0.69% Node::ClearAppliedForce 2ms 0.025% 80.31% 55ms 0.69% TetrahedralMesh::EdgeIterator::GetNodeB 0 0% 80.31% 54ms 0.68% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 53ms 0.67% 80.98% 54ms 0.68% boost::detail::shared_count::shared_count (inline) 0 0% 80.98% 54ms 0.68% std::_Rb_tree::_M_destroy_node (inline) 0 0% 80.98% 54ms 0.68% std::__new_allocator::destroy (inline) 0 0% 80.98% 54ms 0.68% std::allocator_traits::destroy (inline) 32ms 0.4% 81.38% 51ms 0.64% hack_digit 0 0% 81.38% 51ms 0.64% std::map::find (inline) 0 0% 81.38% 49ms 0.62% std::vector::vector (inline) 0 0% 81.38% 48ms 0.61% MeshBasedCellPopulation::SpringIterator::~SpringIterator (inline) 4ms 0.05% 81.43% 48ms 0.61% std::__new_allocator::construct (inline) 0 0% 81.43% 48ms 0.61% std::allocator_traits::construct (inline) 47ms 0.59% 82.02% 47ms 0.59% Node::IsDeleted 2ms 0.025% 82.05% 47ms 0.59% std::_Rb_tree::_M_emplace_hint_unique 14ms 0.18% 82.23% 46ms 0.58% AbstractTetrahedralMesh::GetNumAllElements 46ms 0.58% 82.81% 46ms 0.58% boost::shared_ptr::operator-> (inline) 0 0% 82.81% 45ms 0.57% BoundaryNodeWriter::Visit 0 0% 82.81% 44ms 0.56% std::_Vector_base::_Vector_base (inline) 44ms 0.56% 83.36% 44ms 0.56% std::ostream::sentry::sentry 0 0% 83.36% 43ms 0.54% AbstractCentreBasedCellPopulation::CreateCellPair 0 0% 83.36% 43ms 0.54% std::_Rb_tree::_M_construct_node (inline) 0 0% 83.36% 42ms 0.53% CellPropertyCollection::~CellPropertyCollection (inline) 42ms 0.53% 83.89% 42ms 0.53% [libstdc++.so.6.0.33] 42ms 0.53% 84.42% 42ms 0.53% __GI___mkdir 0 0% 84.42% 41ms 0.52% std::_Vector_base::_M_create_storage (inline) 4ms 0.05% 84.47% 40ms 0.5% Element::~Element