File: Test2dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 6723ms, 84.06% of 7998ms total Dropped 604 nodes (cum <= 39.99ms) flat flat% sum% cum cum% 0 0% 0% 7957ms 99.49% __libc_start_call_main 0 0% 0% 7957ms 99.49% __libc_start_main_impl 0 0% 0% 7957ms 99.49% _start 0 0% 0% 7938ms 99.25% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 7938ms 99.25% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 7938ms 99.25% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 7938ms 99.25% main 0 0% 0% 7894ms 98.70% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 7894ms 98.70% CxxTest::TestRunner::runTest (inline) 0 0% 0% 7894ms 98.70% Test2DMonolayerRepresentativeSimulation::Test2DMonolayerRepresentativeSimulationForProfiling 0 0% 0% 7889ms 98.64% AbstractCellBasedSimulation::Solve 0 0% 0% 3415ms 42.70% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 2967ms 37.10% MeshBasedCellPopulation::Update 1ms 0.013% 0.013% 2867ms 35.85% AbstractCellPopulation::WriteResultsToFiles 3ms 0.038% 0.05% 1600ms 20.01% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 0.05% 1460ms 18.25% MutableMesh::ReMesh 0 0% 0.05% 1458ms 18.23% MeshBasedCellPopulation::UpdateNodePairs 0 0% 0.05% 1457ms 18.22% ForwardEulerNumericalMethod::UpdateAllNodePositions 4ms 0.05% 0.1% 1401ms 17.52% AbstractNumericalMethod::ComputeForcesIncludingDamping 24ms 0.3% 0.4% 1261ms 15.77% MeshBasedCellPopulation::SpringIterator::operator++ 113ms 1.41% 1.81% 1023ms 12.79% TetrahedralMesh::EdgeIterator::operator++ 5ms 0.063% 1.88% 990ms 12.38% AbstractTwoBodyInteractionForce::AddForceContribution 271ms 3.39% 5.26% 920ms 11.50% __dynamic_cast 407ms 5.09% 10.35% 919ms 11.49% std::_Rb_tree::_M_lower_bound (inline) 3ms 0.038% 10.39% 910ms 11.38% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 52ms 0.65% 11.04% 897ms 11.22% AbstractVariableSizeTwoBodyInteractionForce::CalculateForceBetweenNodes 8ms 0.1% 11.14% 887ms 11.09% CellPopulationElementWriter::Visit 11ms 0.14% 11.28% 862ms 10.78% CellPropertyCollection::GetPropertiesType (inline) 5ms 0.063% 11.34% 776ms 9.70% MeshBasedCellPopulation::AcceptCellWriter 27ms 0.34% 11.68% 774ms 9.68% AbstractCellPopulation::GetCellUsingLocationIndex 12ms 0.15% 11.83% 710ms 8.88% TetrahedralMesh::ImportFromMesher 4ms 0.05% 11.88% 706ms 8.83% AbstractCellProperty::IsSubType (inline) 1ms 0.013% 11.89% 603ms 7.54% triangulate 35ms 0.44% 12.33% 588ms 7.35% operator new 1ms 0.013% 12.34% 566ms 7.08% std::ostream::operator<< (inline) 93ms 1.16% 13.50% 562ms 7.03% std::ostream::_M_insert 61ms 0.76% 14.27% 554ms 6.93% std::map::operator[] (partial-inline) 0 0% 14.27% 550ms 6.88% delaunay 5ms 0.063% 14.33% 548ms 6.85% divconqdelaunay 199ms 2.49% 16.82% 539ms 6.74% __GI___libc_malloc 518ms 6.48% 23.29% 518ms 6.48% __strcmp_avx2 3ms 0.038% 23.33% 517ms 6.46% LegacyCellProliferativeTypesWriter::VisitCell 20ms 0.25% 23.58% 515ms 6.44% std::_Rb_tree::find (inline) 28ms 0.35% 23.93% 515ms 6.44% std::__new_allocator::allocate (inline) 5ms 0.063% 23.99% 512ms 6.40% std::set::insert (inline) 0 0% 23.99% 509ms 6.36% std::allocator_traits::allocate (inline) 6ms 0.075% 24.07% 508ms 6.35% std::_Rb_tree::_M_insert_unique 3ms 0.038% 24.11% 481ms 6.01% Cell::GetCellProliferativeType 0 0% 24.11% 466ms 5.83% std::set::count (inline) 212ms 2.65% 26.76% 454ms 5.68% __cxxabiv1::__si_class_type_info::__do_dyncast 0 0% 26.76% 453ms 5.66% std::_Rb_tree::lower_bound (inline) 0 0% 26.76% 453ms 5.66% std::map::lower_bound (inline) 0 0% 26.76% 452ms 5.65% std::_Rb_tree::_M_create_node (inline) 3ms 0.038% 26.79% 443ms 5.54% AbstractCellBasedSimulation::DoCellBirth 0 0% 26.79% 434ms 5.43% std::_Rb_tree::_Alloc_node::operator() (inline) 30ms 0.38% 27.17% 423ms 5.29% std::_Rb_tree::~_Rb_tree (inline) 0 0% 27.17% 416ms 5.20% std::_Rb_tree::_M_get_node (inline) 0 0% 27.17% 397ms 4.96% std::set::~set (inline) 23ms 0.29% 27.46% 392ms 4.90% std::_Rb_tree::_Rb_tree (partial-inline) 80ms 1.00% 28.46% 391ms 4.89% std::_Rb_tree::_M_erase 2ms 0.025% 28.48% 370ms 4.63% Cell::GetMutationState 6ms 0.075% 28.56% 358ms 4.48% std::set::set (inline) 11ms 0.14% 28.69% 349ms 4.36% std::less::operator() (inline) 338ms 4.23% 32.92% 339ms 4.24% std::operator< (inline) 30ms 0.38% 33.30% 336ms 4.20% std::_Rb_tree::_M_copy (inline) 0 0% 33.30% 331ms 4.14% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 0 0% 33.30% 330ms 4.13% AbstractCellBasedWriter::OpenOutputFileForAppend 1ms 0.013% 33.31% 327ms 4.09% OutputFileHandler::OpenOutputFile 1ms 0.013% 33.32% 324ms 4.05% NodeLocationWriter::Visit 323ms 4.04% 37.36% 323ms 4.04% std::_Rb_tree::_S_right (inline) 18ms 0.23% 37.58% 319ms 3.99% std::_Rb_tree::_M_insert_ (inline) 4ms 0.05% 37.63% 314ms 3.93% MeshBasedCellPopulation::GetDampingConstant 5ms 0.063% 37.70% 309ms 3.86% AbstractCentreBasedCellPopulation::GetDampingConstant 7ms 0.088% 37.78% 301ms 3.76% AbstractCellPopulation::IsCellAttachedToLocationIndex 86ms 1.08% 38.86% 299ms 3.74% std::_Rb_tree::_M_clone_node (inline) 94ms 1.18% 40.04% 295ms 3.69% __GI___libc_free 11ms 0.14% 40.17% 293ms 3.66% divconqrecurse 5ms 0.063% 40.24% 292ms 3.65% Cell::ReadyToDivide 0 0% 40.24% 284ms 3.55% std::_Rb_tree::_M_drop_node (inline) 25ms 0.31% 40.55% 280ms 3.50% std::num_put::_M_insert_float 5ms 0.063% 40.61% 278ms 3.48% Element::Element 82ms 1.03% 41.64% 276ms 3.45% mergehulls 7ms 0.088% 41.72% 274ms 3.43% std::__new_allocator::deallocate (inline) 0 0% 41.72% 271ms 3.39% std::allocator_traits::deallocate (inline) 159ms 1.99% 43.71% 249ms 3.11% _int_malloc 1ms 0.013% 43.72% 247ms 3.09% AbstractCellProperty::IsType (inline) 0 0% 43.72% 234ms 2.93% std::_Rb_tree::_M_put_node (inline) 0 0% 43.72% 233ms 2.91% Cell::HasCellProperty (inline) 9ms 0.11% 43.84% 233ms 2.91% CellPropertyCollection::HasProperty 4ms 0.05% 43.89% 231ms 2.89% std::__cxx11::collate::do_transform 0 0% 43.89% 224ms 2.80% ___vsnprintf 1ms 0.013% 43.90% 224ms 2.80% __vsnprintf_internal (inline) 38ms 0.48% 44.37% 223ms 2.79% __printf_buffer 3ms 0.038% 44.41% 217ms 2.71% CellProliferativeTypesWriter::VisitCell 10ms 0.13% 44.54% 216ms 2.70% TetrahedralMesh::Clear 173ms 2.16% 46.70% 201ms 2.51% _int_free 3ms 0.038% 46.74% 196ms 2.45% AbstractPhaseBasedCellCycleModel::ReadyToDivide 9ms 0.11% 46.85% 196ms 2.45% MeshBasedCellPopulation::SpringsEnd (inline) 4ms 0.05% 46.90% 193ms 2.41% Element::RegisterWithNodes (inline) 9ms 0.11% 47.01% 189ms 2.36% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 5ms 0.063% 47.07% 184ms 2.30% Node::AddElement 57ms 0.71% 47.79% 183ms 2.29% std::_Rb_tree::_M_get_insert_unique_pos (inline) 38ms 0.48% 48.26% 178ms 2.23% AbstractCellProperty::IsSame 38ms 0.48% 48.74% 178ms 2.23% TetrahedralMesh::EdgesEnd (partial-inline) 2ms 0.025% 48.76% 169ms 2.11% __printf_fp_l_buffer 0 0% 48.76% 169ms 2.11% __printf_fp_spec (inline) 0 0% 48.76% 168ms 2.10% std::basic_ofstream::basic_ofstream (inline) 1ms 0.013% 48.77% 165ms 2.06% std::basic_ofstream::open (inline) 1ms 0.013% 48.79% 164ms 2.05% std::basic_filebuf::open 96ms 1.20% 49.99% 163ms 2.04% __printf_fp_buffer_1 5ms 0.063% 50.05% 159ms 1.99% alternateaxes 0 0% 50.05% 158ms 1.98% AbstractCellPopulation::CloseRoundRobinWritersFiles 0 0% 50.05% 157ms 1.96% AbstractCellBasedWriter::CloseFile 1ms 0.013% 50.06% 157ms 1.96% std::basic_filebuf::close 0 0% 50.06% 157ms 1.96% std::basic_ofstream::close (inline) 141ms 1.76% 51.83% 154ms 1.93% vertexmedian 1ms 0.013% 51.84% 153ms 1.91% OutputFileHandler::CommonConstructor 0 0% 51.84% 153ms 1.91% OutputFileHandler::OutputFileHandler 1ms 0.013% 51.85% 150ms 1.88% OutputFileHandler::MakeFoldersAndReturnFullPath 30ms 0.38% 52.23% 140ms 1.75% std::type_info::operator== (inline) 7ms 0.088% 52.31% 137ms 1.71% Node::~Node 5ms 0.063% 52.38% 133ms 1.66% AbstractTetrahedralElement::CalculateJacobian 47ms 0.59% 52.96% 132ms 1.65% std::__ostream_insert 19ms 0.24% 53.20% 131ms 1.64% boost::detail::shared_count::~shared_count (inline) 0 0% 53.20% 131ms 1.64% boost::shared_ptr::~shared_ptr (inline) 34ms 0.43% 53.63% 130ms 1.63% std::num_put::_M_insert_int 1ms 0.013% 53.64% 128ms 1.60% _IO_new_fopen 128ms 1.60% 55.24% 128ms 1.60% incircle 0 0% 55.24% 128ms 1.60% std::__basic_file::open 91ms 1.14% 56.38% 127ms 1.59% TetrahedralMesh::EdgeIterator::EdgeIterator (partial-inline) 2ms 0.025% 56.40% 127ms 1.59% _IO_new_file_fopen 0 0% 56.40% 127ms 1.59% __fopen_internal (inline) 18ms 0.23% 56.63% 126ms 1.58% AbstractCellPopulation::Iterator::IsRealCell (inline) 0 0% 56.63% 126ms 1.58% FilesystemPermissions::SetFilePermissions (inline) 1ms 0.013% 56.64% 126ms 1.58% TetrahedralMesh::RefreshJacobianCachedData 2ms 0.025% 56.66% 126ms 1.58% std::filesystem::permissions 0 0% 56.66% 125ms 1.56% __GI__IO_file_open 123ms 1.54% 58.20% 123ms 1.54% __GI_fchmodat 0 0% 58.20% 122ms 1.53% AbstractCellPopulation::Iterator::operator++ (inline) 1ms 0.013% 58.21% 122ms 1.53% std::basic_filebuf::_M_convert_to_external 1ms 0.013% 58.23% 122ms 1.53% std::basic_filebuf::_M_terminate_output 0 0% 58.23% 122ms 1.53% std::basic_filebuf::overflow 13ms 0.16% 58.39% 121ms 1.51% MeshBasedCellPopulation::SpringIterator::SpringIterator 3ms 0.038% 58.43% 121ms 1.51% boost::numeric::ublas::vector_assign (inline) 1ms 0.013% 58.44% 121ms 1.51% std::__basic_file::xsputn 119ms 1.49% 59.93% 120ms 1.50% __GI___libc_write 3ms 0.038% 59.96% 119ms 1.49% boost::numeric::ublas::c_vector::c_vector (inline) 6ms 0.075% 60.04% 115ms 1.44% AbstractTetrahedralElement::CalculateInverseJacobian 60ms 0.75% 60.79% 115ms 1.44% boost::shared_ptr::shared_ptr (inline) 0 0% 60.79% 112ms 1.40% std::operator<< (inline) 105ms 1.31% 62.10% 106ms 1.33% __libc_open64 103ms 1.29% 63.39% 103ms 1.29% [libchaste_cell_based.so] 100ms 1.25% 64.64% 103ms 1.29% boost::detail::sp_counted_base::release 20ms 0.25% 64.89% 101ms 1.26% AbstractTetrahedralElement::RefreshJacobian 99ms 1.24% 66.13% 99ms 1.24% TetrahedralMesh::EdgeIterator::operator!= (partial-inline) 3ms 0.038% 66.17% 99ms 1.24% std::vector::push_back (inline) 4ms 0.05% 66.22% 96ms 1.20% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (partial-inline) 3ms 0.038% 66.25% 96ms 1.20% std::_Vector_base::_M_allocate (inline) 4ms 0.05% 66.30% 92ms 1.15% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 48ms 0.6% 66.90% 92ms 1.15% std::basic_filebuf::xsputn 9ms 0.11% 67.02% 91ms 1.14% std::vector::_M_realloc_insert 2ms 0.025% 67.04% 88ms 1.10% AbstractTetrahedralElement::AbstractTetrahedralElement 79ms 0.99% 68.03% 87ms 1.09% vertexsort 86ms 1.08% 69.10% 86ms 1.08% std::_Rb_tree_insert_and_rebalance 0 0% 69.10% 84ms 1.05% FilesystemPermissions::CreateDirectoryWithPermissions (inline) 3ms 0.038% 69.14% 84ms 1.05% std::filesystem::create_directory 2ms 0.025% 69.17% 83ms 1.04% Cell::GetCellId 28ms 0.35% 69.52% 82ms 1.03% boost::numeric::ublas::indexing_vector_assign 1ms 0.013% 69.53% 80ms 1.00% TetrahedralMesh::EdgeIterator::GetNodeB 0 0% 69.53% 80ms 1.00% tcache_get (inline) 80ms 1.00% 70.53% 80ms 1.00% tcache_get_n (inline) 79ms 0.99% 71.52% 79ms 0.99% std::_Rb_tree_increment 6ms 0.075% 71.59% 77ms 0.96% AbstractCellPopulation::GetLocationIndexUsingCell 3ms 0.038% 71.63% 77ms 0.96% std::_Rb_tree_const_iterator::operator++ (inline) 52ms 0.65% 72.28% 76ms 0.95% malloc_consolidate 75ms 0.94% 73.22% 75ms 0.94% __GI___fstatat64 0 0% 73.22% 75ms 0.94% std::filesystem::status 75ms 0.94% 74.16% 75ms 0.94% std::vector::size (inline) 3ms 0.038% 74.19% 70ms 0.88% TetrahedralMesh::EdgeIterator::GetNodeA 68ms 0.85% 75.04% 68ms 0.85% [libstdc++.so.6.0.33] 53ms 0.66% 75.71% 67ms 0.84% AbstractElement::GetNodeGlobalIndex 67ms 0.84% 76.54% 67ms 0.84% __memcpy_avx_unaligned_erms 29ms 0.36% 76.91% 65ms 0.81% AbstractElement::GetNodeLocation 64ms 0.8% 77.71% 64ms 0.8% counterclockwise 7ms 0.088% 77.79% 63ms 0.79% CellPropertyCollection::AddProperty 63ms 0.79% 78.58% 63ms 0.79% Node::GetIndex 29ms 0.36% 78.94% 61ms 0.76% AbstractTetrahedralMesh::GetElement 1ms 0.013% 78.96% 61ms 0.76% BoundaryNodeWriter::Visit 9ms 0.11% 79.07% 60ms 0.75% Node::ConstructNodeAttributes (inline) 54ms 0.68% 79.74% 55ms 0.69% boost::detail::shared_count::shared_count (inline) 41ms 0.51% 80.26% 55ms 0.69% std::num_put::do_put 0 0% 80.26% 53ms 0.66% Node::ClearAppliedForce 32ms 0.4% 80.66% 51ms 0.64% std::basic_streambuf::xsputn 1ms 0.013% 80.67% 50ms 0.63% AbstractCentreBasedCellPopulation::IsMarkedSpring 0 0% 80.67% 50ms 0.63% std::_Rb_tree::_M_destroy_node (inline) 0 0% 80.67% 50ms 0.63% std::__new_allocator::destroy (inline) 0 0% 80.67% 50ms 0.63% std::allocator_traits::destroy (inline) 20ms 0.25% 80.92% 49ms 0.61% AbstractTetrahedralMesh::GetNumAllElements 27ms 0.34% 81.26% 48ms 0.6% AbstractCellCycleModel::GetAge 47ms 0.59% 81.85% 47ms 0.59% [libchaste_mesh.so] 1ms 0.013% 81.86% 46ms 0.58% AbstractCentreBasedCellPopulation::CreateCellPair 32ms 0.4% 82.26% 45ms 0.56% boost::numeric::ublas::c_matrix::operator() (partial-inline) 44ms 0.55% 82.81% 44ms 0.55% boost::shared_ptr::operator-> (inline) 0 0% 82.81% 43ms 0.54% MeshBasedCellPopulation::SpringIterator::GetNodeB (inline) 42ms 0.53% 83.33% 42ms 0.53% __GI___mkdir 12ms 0.15% 83.48% 41ms 0.51% Determinant (inline) 0 0% 83.48% 41ms 0.51% MeshBasedCellPopulation::SpringIterator::GetNodeA (inline) 0 0% 83.48% 41ms 0.51% MeshBasedCellPopulation::SpringIterator::~SpringIterator (inline) 0 0% 83.48% 41ms 0.51% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 0 0% 83.48% 41ms 0.51% _dl_init 0 0% 83.48% 41ms 0.51% call_init (inline) 2ms 0.025% 83.51% 41ms 0.51% std::__new_allocator::construct (inline) 0 0% 83.51% 41ms 0.51% std::allocator_traits::construct (inline) 0 0% 83.51% 41ms 0.51% std::map::map (inline) 41ms 0.51% 84.02% 41ms 0.51% std::ostream::sentry::sentry 0 0% 84.02% 41ms 0.51% std::vector::vector (inline) 3ms 0.038% 84.06% 40ms 0.5% std::_Rb_tree::_M_emplace_hint_unique