File: Test2dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 6560ms, 84.16% of 7795ms total Dropped 544 nodes (cum <= 38.98ms) flat flat% sum% cum cum% 0 0% 0% 7760ms 99.55% __libc_start_call_main 0 0% 0% 7760ms 99.55% __libc_start_main_impl 0 0% 0% 7760ms 99.55% _start 0 0% 0% 7744ms 99.35% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 7744ms 99.35% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 7744ms 99.35% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 7744ms 99.35% main 0 0% 0% 7710ms 98.91% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 7710ms 98.91% CxxTest::TestRunner::runTest (inline) 0 0% 0% 7710ms 98.91% Test2DMonolayerRepresentativeSimulation::Test2DMonolayerRepresentativeSimulationForProfiling 0 0% 0% 7708ms 98.88% AbstractCellBasedSimulation::Solve 0 0% 0% 3337ms 42.81% AbstractCellBasedSimulation::UpdateCellPopulation 1ms 0.013% 0.013% 2850ms 36.56% AbstractCellPopulation::WriteResultsToFiles 1ms 0.013% 0.026% 2843ms 36.47% MeshBasedCellPopulation::Update 1ms 0.013% 0.038% 1513ms 19.41% OffLatticeSimulation::UpdateCellLocationsAndTopology 1ms 0.013% 0.051% 1419ms 18.20% MeshBasedCellPopulation::UpdateNodePairs 0 0% 0.051% 1385ms 17.77% MutableMesh::ReMesh 0 0% 0.051% 1363ms 17.49% ForwardEulerNumericalMethod::UpdateAllNodePositions 5ms 0.064% 0.12% 1301ms 16.69% AbstractNumericalMethod::ComputeForcesIncludingDamping 14ms 0.18% 0.3% 1251ms 16.05% MeshBasedCellPopulation::SpringIterator::operator++ 159ms 2.04% 2.33% 1026ms 13.16% TetrahedralMesh::EdgeIterator::operator++ 418ms 5.36% 7.70% 949ms 12.17% std::_Rb_tree::_M_lower_bound (inline) 1ms 0.013% 7.71% 923ms 11.84% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 0 0% 7.71% 904ms 11.60% AbstractTwoBodyInteractionForce::AddForceContribution 6ms 0.077% 7.79% 904ms 11.60% CellPopulationElementWriter::Visit 10ms 0.13% 7.92% 891ms 11.43% CellPropertyCollection::GetPropertiesType (inline) 261ms 3.35% 11.26% 848ms 10.88% __dynamic_cast 54ms 0.69% 11.96% 799ms 10.25% AbstractVariableSizeTwoBodyInteractionForce::CalculateForceBetweenNodes 28ms 0.36% 12.32% 789ms 10.12% AbstractCellPopulation::GetCellUsingLocationIndex 5ms 0.064% 12.38% 774ms 9.93% MeshBasedCellPopulation::AcceptCellWriter 12ms 0.15% 12.53% 693ms 8.89% TetrahedralMesh::ImportFromMesher 5ms 0.064% 12.60% 685ms 8.79% AbstractCellProperty::IsSubType (inline) 2ms 0.026% 12.62% 608ms 7.80% std::ostream::operator<< (inline) 70ms 0.9% 13.52% 606ms 7.77% std::ostream::_M_insert 46ms 0.59% 14.11% 598ms 7.67% std::map::operator[] (partial-inline) 50ms 0.64% 14.75% 593ms 7.61% operator new 1ms 0.013% 14.77% 543ms 6.97% triangulate 167ms 2.14% 16.91% 540ms 6.93% __GI___libc_malloc 24ms 0.31% 17.22% 537ms 6.89% std::__new_allocator::allocate (inline) 8ms 0.1% 17.32% 535ms 6.86% Cell::GetCellProliferativeType 0 0% 17.32% 531ms 6.81% std::allocator_traits::allocate (inline) 3ms 0.038% 17.36% 516ms 6.62% std::set::insert (inline) 17ms 0.22% 17.58% 513ms 6.58% std::_Rb_tree::_M_insert_unique 0 0% 17.58% 503ms 6.45% std::_Rb_tree::lower_bound (inline) 0 0% 17.58% 503ms 6.45% std::map::lower_bound (inline) 30ms 0.38% 17.96% 499ms 6.40% std::_Rb_tree::find (inline) 486ms 6.23% 24.19% 486ms 6.23% __strcmp_avx2 1ms 0.013% 24.21% 481ms 6.17% delaunay 1ms 0.013% 24.22% 480ms 6.16% divconqdelaunay 3ms 0.038% 24.26% 477ms 6.12% AbstractCellBasedSimulation::DoCellBirth 6ms 0.077% 24.34% 457ms 5.86% LegacyCellProliferativeTypesWriter::VisitCell 0 0% 24.34% 453ms 5.81% std::set::count (inline) 0 0% 24.34% 433ms 5.55% std::_Rb_tree::_M_create_node (inline) 202ms 2.59% 26.93% 426ms 5.47% __cxxabiv1::__si_class_type_info::__do_dyncast 0 0% 26.93% 411ms 5.27% std::_Rb_tree::_M_get_node (inline) 0 0% 26.93% 407ms 5.22% std::_Rb_tree::_Alloc_node::operator() (inline) 34ms 0.44% 27.36% 396ms 5.08% std::_Rb_tree::~_Rb_tree (inline) 2ms 0.026% 27.39% 394ms 5.05% NodeLocationWriter::Visit 21ms 0.27% 27.66% 369ms 4.73% std::_Rb_tree::_Rb_tree (partial-inline) 0 0% 27.66% 361ms 4.63% std::set::~set (inline) 3ms 0.038% 27.70% 359ms 4.61% Cell::GetMutationState 83ms 1.06% 28.76% 356ms 4.57% std::_Rb_tree::_M_erase 2ms 0.026% 28.79% 355ms 4.55% std::set::set (inline) 31ms 0.4% 29.19% 354ms 4.54% std::num_put::_M_insert_float 12ms 0.15% 29.34% 352ms 4.52% std::less::operator() (inline) 2ms 0.026% 29.36% 349ms 4.48% Cell::ReadyToDivide 340ms 4.36% 33.73% 340ms 4.36% std::operator< (inline) 325ms 4.17% 37.90% 325ms 4.17% std::_Rb_tree::_S_right (inline) 19ms 0.24% 38.14% 315ms 4.04% std::_Rb_tree::_M_insert_ (inline) 0 0% 38.14% 312ms 4.00% AbstractCentreBasedCellPopulation::GetDampingConstant 0 0% 38.14% 312ms 4.00% MeshBasedCellPopulation::GetDampingConstant 30ms 0.38% 38.52% 311ms 3.99% std::_Rb_tree::_M_copy (inline) 11ms 0.14% 38.67% 308ms 3.95% AbstractCellPopulation::IsCellAttachedToLocationIndex 0 0% 38.67% 303ms 3.89% AbstractCellBasedWriter::OpenOutputFileForAppend 0 0% 38.67% 303ms 3.89% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 0 0% 38.67% 298ms 3.82% OutputFileHandler::OpenOutputFile 3ms 0.038% 38.70% 295ms 3.78% Element::Element 110ms 1.41% 40.12% 294ms 3.77% __GI___libc_free 5ms 0.064% 40.18% 287ms 3.68% CellProliferativeTypesWriter::VisitCell 9ms 0.12% 40.30% 280ms 3.59% std::__cxx11::collate::do_transform 8ms 0.1% 40.40% 279ms 3.58% divconqrecurse 88ms 1.13% 41.53% 276ms 3.54% std::_Rb_tree::_M_clone_node (inline) 189ms 2.42% 43.95% 274ms 3.52% _int_malloc 10ms 0.13% 44.08% 265ms 3.40% CellPropertyCollection::HasProperty 12ms 0.15% 44.23% 264ms 3.39% ___vsnprintf 7ms 0.09% 44.32% 264ms 3.39% std::__new_allocator::deallocate (inline) 0 0% 44.32% 262ms 3.36% std::allocator_traits::deallocate (inline) 0 0% 44.32% 261ms 3.35% Cell::HasCellProperty (inline) 79ms 1.01% 45.34% 260ms 3.34% mergehulls 3ms 0.038% 45.38% 259ms 3.32% AbstractCellProperty::IsType (inline) 0 0% 45.38% 252ms 3.23% __vsnprintf_internal (inline) 0 0% 45.38% 251ms 3.22% std::_Rb_tree::_M_drop_node (inline) 25ms 0.32% 45.70% 249ms 3.19% __printf_buffer 6ms 0.077% 45.77% 213ms 2.73% AbstractPhaseBasedCellCycleModel::ReadyToDivide 8ms 0.1% 45.88% 203ms 2.60% __printf_fp_l_buffer 0 0% 45.88% 203ms 2.60% __printf_fp_spec (inline) 0 0% 45.88% 203ms 2.60% std::_Rb_tree::_M_put_node (inline) 15ms 0.19% 46.07% 202ms 2.59% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 56ms 0.72% 46.79% 201ms 2.58% AbstractCellProperty::IsSame 16ms 0.21% 46.99% 187ms 2.40% MeshBasedCellPopulation::SpringsEnd (inline) 160ms 2.05% 49.04% 184ms 2.36% _int_free 100ms 1.28% 50.33% 183ms 2.35% __printf_fp_buffer_1 10ms 0.13% 50.46% 182ms 2.33% Element::RegisterWithNodes (inline) 55ms 0.71% 51.16% 182ms 2.33% std::_Rb_tree::_M_get_insert_unique_pos (inline) 6ms 0.077% 51.24% 169ms 2.17% Node::AddElement 12ms 0.15% 51.39% 165ms 2.12% TetrahedralMesh::Clear 44ms 0.56% 51.96% 152ms 1.95% TetrahedralMesh::EdgesEnd (partial-inline) 13ms 0.17% 52.12% 149ms 1.91% AbstractTetrahedralElement::CalculateJacobian 0 0% 52.12% 147ms 1.89% std::basic_ofstream::basic_ofstream (inline) 27ms 0.35% 52.47% 145ms 1.86% std::type_info::operator== (inline) 1ms 0.013% 52.48% 144ms 1.85% std::basic_ofstream::open (inline) 2ms 0.026% 52.51% 143ms 1.83% std::basic_filebuf::open 3ms 0.038% 52.55% 138ms 1.77% boost::numeric::ublas::vector_assign (inline) 1ms 0.013% 52.56% 132ms 1.69% TetrahedralMesh::RefreshJacobianCachedData 2ms 0.026% 52.58% 127ms 1.63% boost::numeric::ublas::c_vector::c_vector (inline) 31ms 0.4% 52.98% 125ms 1.60% std::num_put::_M_insert_int 53ms 0.68% 53.66% 123ms 1.58% std::__ostream_insert 0 0% 53.66% 122ms 1.57% OutputFileHandler::CommonConstructor 0 0% 53.66% 122ms 1.57% OutputFileHandler::OutputFileHandler 2ms 0.026% 53.69% 122ms 1.57% std::_Vector_base::_M_allocate (inline) 0 0% 53.69% 121ms 1.55% alternateaxes 4ms 0.051% 53.74% 120ms 1.54% AbstractTetrahedralElement::AbstractTetrahedralElement 111ms 1.42% 55.16% 120ms 1.54% vertexmedian 6ms 0.077% 55.24% 119ms 1.53% AbstractTetrahedralElement::CalculateInverseJacobian 0 0% 55.24% 119ms 1.53% OutputFileHandler::MakeFoldersAndReturnFullPath 15ms 0.19% 55.43% 116ms 1.49% AbstractCellPopulation::Iterator::IsRealCell (inline) 0 0% 55.43% 115ms 1.48% AbstractCellPopulation::CloseRoundRobinWritersFiles 0 0% 55.43% 115ms 1.48% FilesystemPermissions::SetFilePermissions (inline) 115ms 1.48% 56.91% 115ms 1.48% __GI_fchmodat 115ms 1.48% 58.38% 115ms 1.48% std::_Rb_tree_increment 0 0% 58.38% 115ms 1.48% std::filesystem::permissions 0 0% 58.38% 114ms 1.46% AbstractCellBasedWriter::CloseFile 0 0% 58.38% 114ms 1.46% AbstractCellPopulation::Iterator::operator++ (inline) 10ms 0.13% 58.51% 114ms 1.46% std::_Rb_tree_const_iterator::operator++ (inline) 0 0% 58.51% 114ms 1.46% std::basic_filebuf::close 0 0% 58.51% 114ms 1.46% std::basic_ofstream::close (inline) 4ms 0.051% 58.56% 114ms 1.46% std::vector::push_back (inline) 21ms 0.27% 58.83% 113ms 1.45% AbstractTetrahedralElement::RefreshJacobian 112ms 1.44% 60.27% 112ms 1.44% incircle 12ms 0.15% 60.42% 111ms 1.42% MeshBasedCellPopulation::SpringIterator::SpringIterator 2ms 0.026% 60.45% 111ms 1.42% std::__basic_file::open 0 0% 60.45% 109ms 1.40% _IO_new_file_fopen 0 0% 60.45% 109ms 1.40% _IO_new_fopen 0 0% 60.45% 109ms 1.40% __fopen_internal (inline) 1ms 0.013% 60.46% 106ms 1.36% __GI__IO_file_open 4ms 0.051% 60.51% 106ms 1.36% std::operator<< (inline) 14ms 0.18% 60.69% 106ms 1.36% std::vector::_M_realloc_insert 64ms 0.82% 61.51% 100ms 1.28% TetrahedralMesh::EdgeIterator::EdgeIterator (partial-inline) 26ms 0.33% 61.85% 99ms 1.27% boost::numeric::ublas::indexing_vector_assign 5ms 0.064% 61.91% 98ms 1.26% Node::~Node 97ms 1.24% 63.16% 97ms 1.24% __libc_open64 49ms 0.63% 63.78% 97ms 1.24% boost::shared_ptr::shared_ptr (inline) 0 0% 63.78% 88ms 1.13% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 88ms 1.13% 64.91% 88ms 1.13% [libchaste_cell_based.so] 0 0% 64.91% 88ms 1.13% tcache_get (inline) 88ms 1.13% 66.04% 88ms 1.13% tcache_get_n (inline) 7ms 0.09% 66.13% 87ms 1.12% boost::detail::shared_count::~shared_count (inline) 0 0% 66.13% 87ms 1.12% boost::shared_ptr::~shared_ptr (inline) 86ms 1.10% 67.24% 86ms 1.10% std::_Rb_tree_insert_and_rebalance 3ms 0.038% 67.27% 85ms 1.09% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (partial-inline) 0 0% 67.27% 85ms 1.09% std::basic_filebuf::_M_terminate_output 1ms 0.013% 67.29% 85ms 1.09% std::basic_filebuf::overflow 1ms 0.013% 67.30% 84ms 1.08% std::basic_filebuf::_M_convert_to_external 83ms 1.06% 68.36% 83ms 1.06% __GI___libc_write 0 0% 68.36% 82ms 1.05% std::__basic_file::xsputn 79ms 1.01% 69.38% 79ms 1.01% TetrahedralMesh::EdgeIterator::operator!= (partial-inline) 78ms 1.00% 70.38% 79ms 1.01% boost::detail::sp_counted_base::release 32ms 0.41% 70.79% 78ms 1.00% AbstractElement::GetNodeLocation 0 0% 70.79% 77ms 0.99% Cell::GetCellId 9ms 0.12% 70.90% 77ms 0.99% CellPropertyCollection::AddProperty 50ms 0.64% 71.55% 76ms 0.97% std::basic_filebuf::xsputn 52ms 0.67% 72.21% 73ms 0.94% malloc_consolidate 55ms 0.71% 72.92% 73ms 0.94% std::basic_streambuf::xsputn 0 0% 72.92% 72ms 0.92% AbstractCellPopulation::GetLocationIndexUsingCell 72ms 0.92% 73.84% 72ms 0.92% __memcpy_avx_unaligned_erms 71ms 0.91% 74.75% 71ms 0.91% Node::GetIndex 71ms 0.91% 75.66% 71ms 0.91% std::vector::size (inline) 68ms 0.87% 76.54% 71ms 0.91% vertexsort 0 0% 76.54% 69ms 0.89% FilesystemPermissions::CreateDirectoryWithPermissions (inline) 0 0% 76.54% 69ms 0.89% std::filesystem::create_directory 8ms 0.1% 76.64% 64ms 0.82% std::_Vector_base::_M_deallocate (inline) 4ms 0.051% 76.69% 63ms 0.81% TetrahedralMesh::EdgeIterator::GetNodeA 0 0% 76.69% 62ms 0.8% std::vector::vector (inline) 49ms 0.63% 77.32% 61ms 0.78% AbstractElement::GetNodeGlobalIndex 4ms 0.051% 77.37% 61ms 0.78% TetrahedralMesh::EdgeIterator::GetNodeB 61ms 0.78% 78.15% 61ms 0.78% counterclockwise 60ms 0.77% 78.92% 60ms 0.77% __GI___fstatat64 0 0% 78.92% 60ms 0.77% std::filesystem::status 58ms 0.74% 79.67% 58ms 0.74% Node::IsDeleted 57ms 0.73% 80.40% 57ms 0.73% [libchaste_mesh.so] 27ms 0.35% 80.74% 53ms 0.68% AbstractTetrahedralMesh::GetElement 3ms 0.038% 80.78% 53ms 0.68% Node::ConstructNodeAttributes (inline) 0 0% 80.78% 53ms 0.68% std::_Vector_base::_M_create_storage (inline) 0 0% 80.78% 53ms 0.68% std::_Vector_base::_Vector_base (inline) 44ms 0.56% 81.35% 53ms 0.68% std::num_put::do_put 1ms 0.013% 81.36% 51ms 0.65% Node::ClearAppliedForce 31ms 0.4% 81.76% 50ms 0.64% hack_digit 1ms 0.013% 81.77% 49ms 0.63% std::_Rb_tree::_M_emplace_hint_unique 48ms 0.62% 82.39% 48ms 0.62% boost::detail::shared_count::shared_count (inline) 0 0% 82.39% 48ms 0.62% std::_Rb_tree::_M_destroy_node (inline) 0 0% 82.39% 48ms 0.62% std::__new_allocator::destroy (inline) 0 0% 82.39% 48ms 0.62% std::allocator_traits::destroy (inline) 0 0% 82.39% 46ms 0.59% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 82.39% 46ms 0.59% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 46ms 0.59% 82.98% 46ms 0.59% std::ostream::sentry::sentry 12ms 0.15% 83.13% 44ms 0.56% AbstractTetrahedralMesh::GetNumAllElements 24ms 0.31% 83.44% 44ms 0.56% boost::numeric::ublas::c_matrix::operator() (partial-inline) 0 0% 83.44% 43ms 0.55% AbstractCentreBasedCellPopulation::CreateCellPair 43ms 0.55% 83.99% 43ms 0.55% boost::numeric::ublas::c_vector::operator() (inline) 5ms 0.064% 84.05% 42ms 0.54% std::__copy_move::__copy_m (inline) 0 0% 84.05% 42ms 0.54% std::__copy_move_a (inline) 0 0% 84.05% 42ms 0.54% std::__copy_move_a1 (inline) 0 0% 84.05% 42ms 0.54% std::__copy_move_a2 (inline) 0 0% 84.05% 42ms 0.54% std::copy (inline) 0 0% 84.05% 41ms 0.53% CellPropertyCollection::~CellPropertyCollection (inline) 3ms 0.038% 84.09% 41ms 0.53% NodeAttributes::NodeAttributes 0 0% 84.09% 41ms 0.53% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 1ms 0.013% 84.11% 40ms 0.51% AbstractMesh::NodeIterator::operator++ (inline) 0 0% 84.11% 39ms 0.5% AbstractCentreBasedCellPopulation::IsMarkedSpring 4ms 0.051% 84.16% 39ms 0.5% AbstractMesh::NodeIterator::IsAllowedNode (inline) 0 0% 84.16% 39ms 0.5% std::map::find (inline)