File: Test2dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 6801ms, 85.03% of 7998ms total Dropped 584 nodes (cum <= 39.99ms) flat flat% sum% cum cum% 0 0% 0% 7963ms 99.56% __libc_start_call_main 0 0% 0% 7963ms 99.56% __libc_start_main_impl 0 0% 0% 7963ms 99.56% _start 0 0% 0% 7949ms 99.39% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 7949ms 99.39% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 7949ms 99.39% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 7949ms 99.39% main 0 0% 0% 7913ms 98.94% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 7913ms 98.94% CxxTest::TestRunner::runTest (inline) 0 0% 0% 7913ms 98.94% Test2DMonolayerRepresentativeSimulation::Test2DMonolayerRepresentativeSimulationForProfiling 0 0% 0% 7908ms 98.87% AbstractCellBasedSimulation::Solve 0 0% 0% 3325ms 41.57% AbstractCellBasedSimulation::UpdateCellPopulation 1ms 0.013% 0.013% 3018ms 37.73% AbstractCellPopulation::WriteResultsToFiles 1ms 0.013% 0.025% 2868ms 35.86% MeshBasedCellPopulation::Update 3ms 0.038% 0.063% 1557ms 19.47% OffLatticeSimulation::UpdateCellLocationsAndTopology 2ms 0.025% 0.088% 1455ms 18.19% MeshBasedCellPopulation::UpdateNodePairs 0 0% 0.088% 1412ms 17.65% ForwardEulerNumericalMethod::UpdateAllNodePositions 6ms 0.075% 0.16% 1364ms 17.05% AbstractNumericalMethod::ComputeForcesIncludingDamping 1ms 0.013% 0.18% 1362ms 17.03% MutableMesh::ReMesh 16ms 0.2% 0.38% 1273ms 15.92% MeshBasedCellPopulation::SpringIterator::operator++ 138ms 1.73% 2.10% 1055ms 13.19% TetrahedralMesh::EdgeIterator::operator++ 8ms 0.1% 2.20% 1028ms 12.85% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 446ms 5.58% 7.78% 989ms 12.37% std::_Rb_tree::_M_lower_bound (inline) 4ms 0.05% 7.83% 961ms 12.02% AbstractTwoBodyInteractionForce::AddForceContribution 14ms 0.18% 8.00% 961ms 12.02% CellPropertyCollection::GetPropertiesType (inline) 264ms 3.30% 11.30% 942ms 11.78% __dynamic_cast 6ms 0.075% 11.38% 871ms 10.89% CellPopulationElementWriter::Visit 3ms 0.038% 11.42% 866ms 10.83% MeshBasedCellPopulation::AcceptCellWriter 34ms 0.43% 11.84% 847ms 10.59% GeneralisedLinearSpringForce::CalculateForceBetweenNodes (partial-inline) 4ms 0.05% 11.89% 759ms 9.49% AbstractCellProperty::IsSubType (inline) 31ms 0.39% 12.28% 740ms 9.25% AbstractCellPopulation::GetCellUsingLocationIndex 7ms 0.088% 12.37% 706ms 8.83% TetrahedralMesh::ImportFromMesher 0 0% 12.37% 646ms 8.08% std::ostream::operator<< (inline) 90ms 1.13% 13.49% 645ms 8.06% std::ostream::_M_insert 53ms 0.66% 14.15% 615ms 7.69% std::map::operator[] (partial-inline) 578ms 7.23% 21.38% 578ms 7.23% __strcmp_avx2 36ms 0.45% 21.83% 578ms 7.23% operator new 4ms 0.05% 21.88% 563ms 7.04% LegacyCellProliferativeTypesWriter::VisitCell 5ms 0.063% 21.94% 556ms 6.95% Cell::GetCellProliferativeType 182ms 2.28% 24.22% 539ms 6.74% __GI___libc_malloc 0 0% 24.22% 522ms 6.53% std::_Rb_tree::lower_bound (inline) 0 0% 24.22% 522ms 6.53% std::map::lower_bound (inline) 7ms 0.088% 24.31% 521ms 6.51% std::set::insert (inline) 34ms 0.43% 24.73% 520ms 6.50% std::__new_allocator::allocate (inline) 0 0% 24.73% 515ms 6.44% std::allocator_traits::allocate (inline) 8ms 0.1% 24.83% 514ms 6.43% std::_Rb_tree::_M_insert_unique 17ms 0.21% 25.04% 504ms 6.30% std::_Rb_tree::find (inline) 1ms 0.013% 25.06% 499ms 6.24% triangulate 0 0% 25.06% 468ms 5.85% std::set::count (inline) 4ms 0.05% 25.11% 445ms 5.56% AbstractCellBasedSimulation::DoCellBirth 0 0% 25.11% 444ms 5.55% std::_Rb_tree::_M_create_node (inline) 189ms 2.36% 27.47% 439ms 5.49% __cxxabiv1::__si_class_type_info::__do_dyncast 0 0% 27.47% 433ms 5.41% delaunay 3ms 0.038% 27.51% 432ms 5.40% divconqdelaunay 0 0% 27.51% 418ms 5.23% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 27.51% 412ms 5.15% NodeLocationWriter::Visit 0 0% 27.51% 404ms 5.05% std::_Rb_tree::_M_get_node (inline) 1ms 0.013% 27.52% 400ms 5.00% Cell::GetMutationState 23ms 0.29% 27.81% 398ms 4.98% std::_Rb_tree::~_Rb_tree (inline) 72ms 0.9% 28.71% 370ms 4.63% std::_Rb_tree::_M_erase 25ms 0.31% 29.02% 370ms 4.63% std::_Rb_tree::_Rb_tree (partial-inline) 0 0% 29.02% 367ms 4.59% std::set::~set (inline) 30ms 0.38% 29.39% 363ms 4.54% std::num_put::_M_insert_float 10ms 0.13% 29.52% 358ms 4.48% std::less::operator() (inline) 348ms 4.35% 33.87% 348ms 4.35% std::operator< (inline) 24ms 0.3% 34.17% 342ms 4.28% std::_Rb_tree::_M_insert_ (inline) 3ms 0.038% 34.21% 336ms 4.20% std::set::set (inline) 7ms 0.088% 34.30% 328ms 4.10% AbstractCellPopulation::IsCellAttachedToLocationIndex 1ms 0.013% 34.31% 328ms 4.10% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 0 0% 34.31% 326ms 4.08% AbstractCellBasedWriter::OpenOutputFileForAppend 0 0% 34.31% 326ms 4.08% MeshBasedCellPopulation::GetDampingConstant 1ms 0.013% 34.32% 325ms 4.06% AbstractCentreBasedCellPopulation::GetDampingConstant 0 0% 34.32% 324ms 4.05% OutputFileHandler::OpenOutputFile 320ms 4.00% 38.32% 320ms 4.00% std::_Rb_tree::_S_right (inline) 27ms 0.34% 38.66% 307ms 3.84% std::_Rb_tree::_M_copy (inline) 7ms 0.088% 38.75% 304ms 3.80% Cell::ReadyToDivide 101ms 1.26% 40.01% 299ms 3.74% __GI___libc_free 2ms 0.025% 40.04% 288ms 3.60% Element::Element 73ms 0.91% 40.95% 278ms 3.48% std::_Rb_tree::_M_clone_node (inline) 0 0% 40.95% 277ms 3.46% std::_Rb_tree::_M_drop_node (inline) 169ms 2.11% 43.06% 269ms 3.36% _int_malloc 8ms 0.1% 43.16% 265ms 3.31% std::__cxx11::collate::do_transform 5ms 0.063% 43.22% 264ms 3.30% CellProliferativeTypesWriter::VisitCell 11ms 0.14% 43.36% 257ms 3.21% std::__new_allocator::deallocate (inline) 0 0% 43.36% 256ms 3.20% std::allocator_traits::deallocate (inline) 10ms 0.13% 43.49% 254ms 3.18% AbstractCellProperty::IsType (inline) 6ms 0.075% 43.56% 253ms 3.16% CellPropertyCollection::HasProperty 0 0% 43.56% 252ms 3.15% Cell::HasCellProperty (inline) 4ms 0.05% 43.61% 251ms 3.14% ___vsnprintf 11ms 0.14% 43.75% 250ms 3.13% divconqrecurse 0 0% 43.75% 247ms 3.09% __vsnprintf_internal (inline) 40ms 0.5% 44.25% 245ms 3.06% __printf_buffer 75ms 0.94% 45.19% 233ms 2.91% mergehulls 0 0% 45.19% 215ms 2.69% std::_Rb_tree::_M_put_node (inline) 3ms 0.038% 45.22% 199ms 2.49% AbstractPhaseBasedCellCycleModel::ReadyToDivide 23ms 0.29% 45.51% 199ms 2.49% TetrahedralMesh::Clear 163ms 2.04% 47.55% 197ms 2.46% _int_free 2ms 0.025% 47.57% 193ms 2.41% __printf_fp_spec (inline) 9ms 0.11% 47.69% 192ms 2.40% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 5ms 0.063% 47.75% 191ms 2.39% __printf_fp_l_buffer 6ms 0.075% 47.82% 187ms 2.34% Element::RegisterWithNodes (inline) 3ms 0.038% 47.86% 181ms 2.26% Node::AddElement 104ms 1.30% 49.16% 181ms 2.26% __printf_fp_buffer_1 45ms 0.56% 49.72% 175ms 2.19% AbstractCellProperty::IsSame 5ms 0.063% 49.79% 170ms 2.13% MeshBasedCellPopulation::SpringsEnd (inline) 0 0% 49.79% 165ms 2.06% std::basic_ofstream::basic_ofstream (inline) 54ms 0.68% 50.46% 164ms 2.05% std::_Rb_tree::_M_get_insert_unique_pos (inline) 44ms 0.55% 51.01% 159ms 1.99% TetrahedralMesh::EdgesEnd (partial-inline) 0 0% 51.01% 158ms 1.98% std::basic_ofstream::open (inline) 0 0% 51.01% 156ms 1.95% std::basic_filebuf::open 14ms 0.18% 51.19% 151ms 1.89% AbstractTetrahedralElement::CalculateJacobian 0 0% 51.19% 150ms 1.88% OutputFileHandler::CommonConstructor 0 0% 51.19% 150ms 1.88% OutputFileHandler::OutputFileHandler 0 0% 51.19% 144ms 1.80% OutputFileHandler::MakeFoldersAndReturnFullPath 0 0% 51.19% 138ms 1.73% AbstractCellPopulation::CloseRoundRobinWritersFiles 69ms 0.86% 52.05% 138ms 1.73% std::__ostream_insert 0 0% 52.05% 137ms 1.71% AbstractCellBasedWriter::CloseFile 0 0% 52.05% 137ms 1.71% std::basic_filebuf::close 0 0% 52.05% 137ms 1.71% std::basic_ofstream::close (inline) 35ms 0.44% 52.49% 136ms 1.70% std::num_put::_M_insert_int 0 0% 52.49% 133ms 1.66% boost::numeric::ublas::vector_assign (inline) 1ms 0.013% 52.50% 132ms 1.65% TetrahedralMesh::RefreshJacobianCachedData 26ms 0.33% 52.83% 130ms 1.63% std::type_info::operator== (inline) 0 0% 52.83% 128ms 1.60% FilesystemPermissions::SetFilePermissions (inline) 128ms 1.60% 54.43% 128ms 1.60% __GI_fchmodat 0 0% 54.43% 128ms 1.60% std::filesystem::permissions 10ms 0.13% 54.55% 127ms 1.59% boost::detail::shared_count::~shared_count (inline) 0 0% 54.55% 127ms 1.59% boost::shared_ptr::~shared_ptr (inline) 7ms 0.088% 54.64% 126ms 1.58% boost::numeric::ublas::c_vector::c_vector (inline) 16ms 0.2% 54.84% 119ms 1.49% AbstractCellPopulation::Iterator::IsRealCell (inline) 6ms 0.075% 54.91% 119ms 1.49% Node::~Node 1ms 0.013% 54.93% 119ms 1.49% std::__basic_file::open 0 0% 54.93% 117ms 1.46% AbstractCellPopulation::Iterator::operator++ (inline) 5ms 0.063% 54.99% 117ms 1.46% AbstractTetrahedralElement::CalculateInverseJacobian 0 0% 54.99% 117ms 1.46% _IO_new_fopen 2ms 0.025% 55.01% 117ms 1.46% __fopen_internal (inline) 20ms 0.25% 55.26% 116ms 1.45% MeshBasedCellPopulation::SpringIterator::SpringIterator 0 0% 55.26% 113ms 1.41% _IO_new_file_fopen 7ms 0.088% 55.35% 113ms 1.41% std::operator<< (inline) 0 0% 55.35% 112ms 1.40% __GI__IO_file_open 0 0% 55.35% 111ms 1.39% std::_Vector_base::_M_allocate (inline) 13ms 0.16% 55.51% 110ms 1.38% AbstractTetrahedralElement::RefreshJacobian 0 0% 55.51% 110ms 1.38% alternateaxes 108ms 1.35% 56.86% 110ms 1.38% boost::detail::sp_counted_base::release 110ms 1.38% 58.24% 110ms 1.38% std::_Rb_tree_increment 104ms 1.30% 59.54% 110ms 1.38% vertexmedian 8ms 0.1% 59.64% 108ms 1.35% std::_Rb_tree_const_iterator::operator++ (inline) 107ms 1.34% 60.98% 107ms 1.34% std::_Rb_tree_insert_and_rebalance 4ms 0.05% 61.03% 107ms 1.34% std::vector::push_back (inline) 2ms 0.025% 61.05% 104ms 1.30% AbstractTetrahedralElement::AbstractTetrahedralElement 64ms 0.8% 61.85% 104ms 1.30% TetrahedralMesh::EdgeIterator::EdgeIterator (partial-inline) 32ms 0.4% 62.25% 103ms 1.29% boost::numeric::ublas::indexing_vector_assign 1ms 0.013% 62.27% 101ms 1.26% std::basic_filebuf::_M_terminate_output 100ms 1.25% 63.52% 100ms 1.25% __GI___libc_write 0 0% 63.52% 100ms 1.25% std::__basic_file::xsputn 0 0% 63.52% 100ms 1.25% std::basic_filebuf::_M_convert_to_external 0 0% 63.52% 100ms 1.25% std::basic_filebuf::overflow 98ms 1.23% 64.74% 98ms 1.23% __libc_open64 55ms 0.69% 65.43% 97ms 1.21% boost::shared_ptr::shared_ptr (inline) 10ms 0.13% 65.55% 97ms 1.21% std::vector::_M_realloc_insert 94ms 1.18% 66.73% 94ms 1.18% [libchaste_cell_based.so] 0 0% 66.73% 90ms 1.13% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 90ms 1.13% 67.85% 90ms 1.13% incircle 0 0% 67.85% 89ms 1.11% FilesystemPermissions::CreateDirectoryWithPermissions (inline) 1ms 0.013% 67.87% 89ms 1.11% std::filesystem::create_directory 37ms 0.46% 68.33% 87ms 1.09% AbstractElement::GetNodeLocation 3ms 0.038% 68.37% 86ms 1.08% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (partial-inline) 47ms 0.59% 68.95% 85ms 1.06% std::basic_filebuf::xsputn 52ms 0.65% 69.60% 84ms 1.05% malloc_consolidate 0 0% 69.60% 84ms 1.05% tcache_get (inline) 84ms 1.05% 70.66% 84ms 1.05% tcache_get_n (inline) 1ms 0.013% 70.67% 79ms 0.99% std::filesystem::status 78ms 0.98% 71.64% 78ms 0.98% __GI___fstatat64 54ms 0.68% 72.32% 75ms 0.94% std::basic_streambuf::xsputn 58ms 0.73% 73.04% 74ms 0.93% AbstractElement::GetNodeGlobalIndex 7ms 0.088% 73.13% 74ms 0.93% CellPropertyCollection::AddProperty 71ms 0.89% 74.02% 71ms 0.89% TetrahedralMesh::EdgeIterator::operator!= (partial-inline) 1ms 0.013% 74.03% 70ms 0.88% TetrahedralMesh::EdgeIterator::GetNodeB 1ms 0.013% 74.04% 69ms 0.86% Cell::GetCellId 69ms 0.86% 74.91% 69ms 0.86% Node::GetIndex 2ms 0.025% 74.93% 68ms 0.85% AbstractCellPopulation::GetLocationIndexUsingCell 32ms 0.4% 75.33% 67ms 0.84% AbstractTetrahedralMesh::GetElement 67ms 0.84% 76.17% 67ms 0.84% __memcpy_avx_unaligned_erms 0 0% 76.17% 63ms 0.79% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 76.17% 63ms 0.79% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 3ms 0.038% 76.21% 62ms 0.78% TetrahedralMesh::EdgeIterator::GetNodeA 62ms 0.78% 76.98% 62ms 0.78% counterclockwise 0 0% 76.98% 62ms 0.78% std::_Rb_tree::_M_destroy_node (inline) 0 0% 76.98% 62ms 0.78% std::__new_allocator::destroy (inline) 0 0% 76.98% 62ms 0.78% std::allocator_traits::destroy (inline) 50ms 0.63% 77.61% 62ms 0.78% std::num_put::do_put 56ms 0.7% 78.31% 61ms 0.76% vertexsort 60ms 0.75% 79.06% 60ms 0.75% [libchaste_mesh.so] 56ms 0.7% 79.76% 56ms 0.7% std::vector::size (inline) 5ms 0.063% 79.82% 50ms 0.63% Node::ConstructNodeAttributes (inline) 1ms 0.013% 79.83% 47ms 0.59% Node::ClearAppliedForce 0 0% 79.83% 46ms 0.58% boost::numeric::ublas::norm_2 (inline) 17ms 0.21% 80.05% 46ms 0.58% boost::numeric::ublas::vector_norm_2::apply (inline) 0 0% 80.05% 45ms 0.56% AbstractCentreBasedCellPopulation::CreateCellPair 2ms 0.025% 80.07% 45ms 0.56% std::__new_allocator::construct (inline) 0 0% 80.07% 45ms 0.56% std::allocator_traits::construct (inline) 0 0% 80.07% 45ms 0.56% std::vector::vector (inline) 44ms 0.55% 80.62% 44ms 0.55% Node::rGetLocation 44ms 0.55% 81.17% 44ms 0.55% boost::numeric::ublas::c_vector::operator() (partial-inline) 5ms 0.063% 81.23% 44ms 0.55% std::_Vector_base::_M_deallocate (inline) 18ms 0.23% 81.46% 43ms 0.54% AbstractCellCycleModel::GetAge 0 0% 81.46% 43ms 0.54% MeshBasedCellPopulation::SpringIterator::~SpringIterator (inline) 0 0% 81.46% 43ms 0.54% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 43ms 0.54% 82.00% 43ms 0.54% boost::shared_ptr::operator-> (inline) 0 0% 82.00% 43ms 0.54% std::_Vector_base::_Vector_base (inline) 43ms 0.54% 82.53% 43ms 0.54% unlink_chunk 40ms 0.5% 83.03% 42ms 0.53% boost::detail::shared_count::shared_count (inline) 28ms 0.35% 83.38% 42ms 0.53% hack_digit 1ms 0.013% 83.40% 41ms 0.51% BoundaryNodeWriter::Visit 25ms 0.31% 83.71% 41ms 0.51% boost::numeric::ublas::c_matrix::operator() 25ms 0.31% 84.02% 40ms 0.5% AbstractMesh::GetNode 40ms 0.5% 84.52% 40ms 0.5% Node::IsDeleted 0 0% 84.52% 40ms 0.5% std::_Rb_tree::_M_construct_node (inline) 1ms 0.013% 84.53% 40ms 0.5% std::_Rb_tree::_M_emplace_hint_unique 40ms 0.5% 85.03% 40ms 0.5% std::ostream::sentry::sentry