File: Test2dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 6293ms, 84.66% of 7433ms total Dropped 541 nodes (cum <= 37.16ms) flat flat% sum% cum cum% 0 0% 0% 7401ms 99.57% __libc_start_call_main 0 0% 0% 7401ms 99.57% __libc_start_main_impl 0 0% 0% 7401ms 99.57% _start 0 0% 0% 7387ms 99.38% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 7387ms 99.38% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 7387ms 99.38% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 7387ms 99.38% main 0 0% 0% 7354ms 98.94% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 7354ms 98.94% CxxTest::TestRunner::runTest (inline) 0 0% 0% 7354ms 98.94% Test2DMonolayerRepresentativeSimulation::Test2DMonolayerRepresentativeSimulationForProfiling 0 0% 0% 7353ms 98.92% AbstractCellBasedSimulation::Solve 0 0% 0% 3289ms 44.25% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 2862ms 38.50% MeshBasedCellPopulation::Update 2ms 0.027% 0.027% 2543ms 34.21% AbstractCellPopulation::WriteResultsToFiles 0 0% 0.027% 1510ms 20.31% OffLatticeSimulation::UpdateCellLocationsAndTopology 2ms 0.027% 0.054% 1411ms 18.98% MeshBasedCellPopulation::UpdateNodePairs 1ms 0.013% 0.067% 1401ms 18.85% MutableMesh::ReMesh 2ms 0.027% 0.094% 1354ms 18.22% ForwardEulerNumericalMethod::UpdateAllNodePositions 1ms 0.013% 0.11% 1306ms 17.57% AbstractNumericalMethod::ComputeForcesIncludingDamping 15ms 0.2% 0.31% 1231ms 16.56% MeshBasedCellPopulation::SpringIterator::operator++ 109ms 1.47% 1.78% 1019ms 13.71% TetrahedralMesh::EdgeIterator::operator++ 7ms 0.094% 1.87% 951ms 12.79% AbstractTwoBodyInteractionForce::AddForceContribution 9ms 0.12% 1.99% 941ms 12.66% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 7ms 0.094% 2.09% 880ms 11.84% CellPopulationElementWriter::Visit 250ms 3.36% 5.45% 877ms 11.80% __dynamic_cast 35ms 0.47% 5.92% 835ms 11.23% GeneralisedLinearSpringForce::CalculateForceBetweenNodes (partial-inline) 355ms 4.78% 10.70% 830ms 11.17% std::_Rb_tree::_M_lower_bound (inline) 0 0% 10.70% 814ms 10.95% CellPropertyCollection::GetPropertiesType (inline) 9ms 0.12% 10.82% 773ms 10.40% MeshBasedCellPopulation::AcceptCellWriter 20ms 0.27% 11.09% 762ms 10.25% AbstractCellPopulation::GetCellUsingLocationIndex 12ms 0.16% 11.25% 733ms 9.86% TetrahedralMesh::ImportFromMesher 33ms 0.44% 11.69% 700ms 9.42% operator new 6ms 0.081% 11.77% 684ms 9.20% AbstractCellProperty::IsSubType (inline) 251ms 3.38% 15.15% 645ms 8.68% __GI___libc_malloc 18ms 0.24% 15.39% 610ms 8.21% std::__new_allocator::allocate (inline) 0 0% 15.39% 608ms 8.18% std::allocator_traits::allocate (inline) 9ms 0.12% 15.51% 579ms 7.79% std::set::insert (inline) 12ms 0.16% 15.67% 570ms 7.67% std::_Rb_tree::_M_insert_unique 3ms 0.04% 15.71% 517ms 6.96% LegacyCellProliferativeTypesWriter::VisitCell 2ms 0.027% 15.74% 514ms 6.92% std::ostream::operator<< (inline) 2ms 0.027% 15.77% 514ms 6.92% triangulate 20ms 0.27% 16.04% 511ms 6.87% std::_Rb_tree::find (inline) 84ms 1.13% 17.17% 508ms 6.83% std::ostream::_M_insert 71ms 0.96% 18.12% 497ms 6.69% std::_Rb_tree::~_Rb_tree (inline) 0 0% 18.12% 489ms 6.58% std::_Rb_tree::_M_create_node (inline) 1ms 0.013% 18.14% 488ms 6.57% Cell::GetCellProliferativeType 72ms 0.97% 19.10% 477ms 6.42% std::map::operator[] (partial-inline) 0 0% 19.10% 476ms 6.40% std::set::count (inline) 0 0% 19.10% 473ms 6.36% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 19.10% 473ms 6.36% std::set::~set (inline) 0 0% 19.10% 470ms 6.32% std::_Rb_tree::_M_get_node (inline) 215ms 2.89% 22.00% 461ms 6.20% __cxxabiv1::__si_class_type_info::__do_dyncast 0 0% 22.00% 450ms 6.05% delaunay 3ms 0.04% 22.04% 448ms 6.03% divconqdelaunay 436ms 5.87% 27.90% 436ms 5.87% __strcmp_evex 46ms 0.62% 28.52% 419ms 5.64% std::_Rb_tree::_M_erase 1ms 0.013% 28.53% 412ms 5.54% AbstractCellBasedSimulation::DoCellBirth 9ms 0.12% 28.66% 407ms 5.48% std::_Rb_tree::_Rb_tree (partial-inline) 35ms 0.47% 29.13% 377ms 5.07% std::_Rb_tree::_M_copy (inline) 24ms 0.32% 29.45% 372ms 5.00% std::_Rb_tree::_M_insert_ (inline) 5ms 0.067% 29.52% 369ms 4.96% std::set::set (inline) 3ms 0.04% 29.56% 368ms 4.95% Cell::GetMutationState 0 0% 29.56% 367ms 4.94% std::_Rb_tree::_M_drop_node (inline) 0 0% 29.56% 361ms 4.86% std::_Rb_tree::lower_bound (inline) 0 0% 29.56% 361ms 4.86% std::map::lower_bound (inline) 75ms 1.01% 30.57% 350ms 4.71% __GI___libc_free 127ms 1.71% 32.27% 335ms 4.51% std::_Rb_tree::_M_clone_node (inline) 14ms 0.19% 32.46% 308ms 4.14% std::less::operator() (inline) 223ms 3.00% 35.46% 305ms 4.10% _int_malloc 5ms 0.067% 35.53% 304ms 4.09% Element::Element 9ms 0.12% 35.65% 303ms 4.08% std::__new_allocator::deallocate (inline) 0 0% 35.65% 298ms 4.01% NodeLocationWriter::Visit 0 0% 35.65% 297ms 4.00% std::allocator_traits::deallocate (inline) 294ms 3.96% 39.61% 294ms 3.96% std::operator< (inline) 8ms 0.11% 39.71% 290ms 3.90% AbstractCellPopulation::IsCellAttachedToLocationIndex 6ms 0.081% 39.80% 277ms 3.73% Cell::ReadyToDivide 2ms 0.027% 39.82% 274ms 3.69% MeshBasedCellPopulation::GetDampingConstant 15ms 0.2% 40.02% 272ms 3.66% boost::detail::shared_count::~shared_count (inline) 0 0% 40.02% 272ms 3.66% boost::shared_ptr::~shared_ptr (inline) 5ms 0.067% 40.09% 270ms 3.63% AbstractCentreBasedCellPopulation::GetDampingConstant 230ms 3.09% 43.19% 264ms 3.55% _int_free 12ms 0.16% 43.35% 264ms 3.55% std::num_put::_M_insert_float 245ms 3.30% 46.64% 245ms 3.30% [libchaste_cell_based.so] 243ms 3.27% 49.91% 243ms 3.27% boost::detail::sp_counted_base::release 7ms 0.094% 50.01% 241ms 3.24% divconqrecurse 0 0% 50.01% 239ms 3.22% std::_Rb_tree::_M_put_node (inline) 65ms 0.87% 50.88% 228ms 3.07% mergehulls 7ms 0.094% 50.98% 223ms 3.00% Element::RegisterWithNodes (inline) 2ms 0.027% 51.00% 221ms 2.97% std::__cxx11::collate::do_transform 3ms 0.04% 51.04% 214ms 2.88% Node::AddElement 214ms 2.88% 53.92% 214ms 2.88% std::_Rb_tree::_S_right (inline) 2ms 0.027% 53.95% 212ms 2.85% ___vsnprintf 0 0% 53.95% 210ms 2.83% __vsnprintf_internal (inline) 1ms 0.013% 53.96% 209ms 2.81% CellProliferativeTypesWriter::VisitCell 29ms 0.39% 54.35% 209ms 2.81% __printf_buffer 4ms 0.054% 54.41% 208ms 2.80% AbstractPhaseBasedCellCycleModel::ReadyToDivide 6ms 0.081% 54.49% 199ms 2.68% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 14ms 0.19% 54.68% 190ms 2.56% AbstractCellProperty::IsType (inline) 62ms 0.83% 55.51% 187ms 2.52% std::_Rb_tree::_M_get_insert_unique_pos (inline) 1ms 0.013% 55.52% 186ms 2.50% Cell::HasCellProperty (inline) 3ms 0.04% 55.56% 185ms 2.49% CellPropertyCollection::HasProperty 5ms 0.067% 55.63% 177ms 2.38% MeshBasedCellPopulation::SpringsEnd (inline) 0 0% 55.63% 176ms 2.37% AbstractCellBasedWriter::OpenOutputFileForAppend 0 0% 55.63% 176ms 2.37% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 2ms 0.027% 55.66% 173ms 2.33% TetrahedralMesh::Clear 1ms 0.013% 55.67% 172ms 2.31% OutputFileHandler::OpenOutputFile 59ms 0.79% 56.46% 165ms 2.22% std::__ostream_insert 11ms 0.15% 56.61% 164ms 2.21% __printf_fp_l_buffer 0 0% 56.61% 164ms 2.21% __printf_fp_spec (inline) 3ms 0.04% 56.65% 151ms 2.03% boost::numeric::ublas::vector_assign (inline) 82ms 1.10% 57.76% 147ms 1.98% __printf_fp_buffer_1 11ms 0.15% 57.90% 146ms 1.96% std::vector::push_back (inline) 24ms 0.32% 58.23% 144ms 1.94% TetrahedralMesh::EdgesEnd (partial-inline) 5ms 0.067% 58.29% 141ms 1.90% boost::numeric::ublas::c_vector::c_vector (inline) 140ms 1.88% 60.18% 140ms 1.88% [libchaste_mesh.so] 0 0% 60.18% 140ms 1.88% std::operator<< (inline) 0 0% 60.18% 138ms 1.86% std::_Vector_base::_M_allocate (inline) 0 0% 60.18% 137ms 1.84% TetrahedralMesh::RefreshJacobianCachedData 2ms 0.027% 60.20% 130ms 1.75% std::vector::_M_realloc_insert 6ms 0.081% 60.29% 129ms 1.74% alternateaxes 0 0% 60.29% 128ms 1.72% std::_Rb_tree::_M_destroy_node (inline) 0 0% 60.29% 128ms 1.72% std::__new_allocator::destroy (inline) 0 0% 60.29% 128ms 1.72% std::allocator_traits::destroy (inline) 7ms 0.094% 60.38% 126ms 1.70% AbstractTetrahedralElement::CalculateJacobian 6ms 0.081% 60.46% 122ms 1.64% AbstractTetrahedralElement::CalculateInverseJacobian 111ms 1.49% 61.95% 122ms 1.64% vertexmedian 30ms 0.4% 62.36% 119ms 1.60% std::num_put::_M_insert_int 19ms 0.26% 62.61% 118ms 1.59% MeshBasedCellPopulation::SpringIterator::SpringIterator 10ms 0.13% 62.75% 115ms 1.55% AbstractCellPopulation::Iterator::IsRealCell (inline) 24ms 0.32% 63.07% 114ms 1.53% AbstractCellProperty::IsSame 113ms 1.52% 64.59% 113ms 1.52% [libstdc++.so.6.0.33] 1ms 0.013% 64.60% 112ms 1.51% AbstractCellPopulation::Iterator::operator++ (inline) 36ms 0.48% 65.09% 111ms 1.49% boost::numeric::ublas::indexing_vector_assign 105ms 1.41% 66.50% 105ms 1.41% incircle 0 0% 66.50% 97ms 1.30% std::basic_ofstream::basic_ofstream (inline) 19ms 0.26% 66.76% 96ms 1.29% AbstractTetrahedralElement::RefreshJacobian 9ms 0.12% 66.88% 95ms 1.28% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (partial-inline) 1ms 0.013% 66.89% 94ms 1.26% std::basic_ofstream::open (inline) 93ms 1.25% 68.14% 93ms 1.25% std::_Rb_tree_insert_and_rebalance 1ms 0.013% 68.16% 93ms 1.25% std::basic_filebuf::open 79ms 1.06% 69.22% 92ms 1.24% TetrahedralMesh::EdgeIterator::EdgeIterator (partial-inline) 17ms 0.23% 69.45% 90ms 1.21% std::type_info::operator== (inline) 2ms 0.027% 69.47% 88ms 1.18% std::basic_filebuf::close 0 0% 69.47% 87ms 1.17% AbstractCellPopulation::CloseRoundRobinWritersFiles 1ms 0.013% 69.49% 87ms 1.17% Node::~Node 0 0% 69.49% 86ms 1.16% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 86ms 1.16% 70.64% 86ms 1.16% std::_Rb_tree::_S_left (inline) 0 0% 70.64% 86ms 1.16% std::basic_ofstream::close (inline) 0 0% 70.64% 85ms 1.14% AbstractCellBasedWriter::CloseFile 3ms 0.04% 70.68% 85ms 1.14% AbstractTetrahedralElement::AbstractTetrahedralElement 0 0% 70.68% 83ms 1.12% OutputFileHandler::CommonConstructor 0 0% 70.68% 83ms 1.12% OutputFileHandler::OutputFileHandler 60ms 0.81% 71.49% 83ms 1.12% std::basic_filebuf::xsputn 7ms 0.094% 71.59% 81ms 1.09% std::_Rb_tree_const_iterator::operator++ (inline) 53ms 0.71% 72.30% 79ms 1.06% std::basic_streambuf::xsputn 0 0% 72.30% 77ms 1.04% OutputFileHandler::MakeFoldersAndReturnFullPath 68ms 0.91% 73.21% 73ms 0.98% vertexsort 4ms 0.054% 73.27% 72ms 0.97% AbstractCellPopulation::GetLocationIndexUsingCell 57ms 0.77% 74.03% 72ms 0.97% malloc_consolidate 0 0% 74.03% 71ms 0.96% tcache_get (inline) 71ms 0.96% 74.99% 71ms 0.96% tcache_get_n (inline) 1ms 0.013% 75.00% 67ms 0.9% Cell::GetCellId 13ms 0.17% 75.18% 65ms 0.87% TetrahedralMesh::EdgeIterator::GetNodeB 1ms 0.013% 75.19% 64ms 0.86% Node::ClearAppliedForce 2ms 0.027% 75.22% 64ms 0.86% Node::ConstructNodeAttributes (inline) 1ms 0.013% 75.23% 64ms 0.86% std::basic_filebuf::overflow 35ms 0.47% 75.70% 63ms 0.85% AbstractElement::GetNodeLocation 1ms 0.013% 75.72% 63ms 0.85% std::basic_filebuf::_M_convert_to_external 0 0% 75.72% 63ms 0.85% std::basic_filebuf::_M_terminate_output 0 0% 75.72% 62ms 0.83% std::__basic_file::xsputn 61ms 0.82% 76.54% 61ms 0.82% __GI___libc_write 6ms 0.081% 76.62% 60ms 0.81% CellPropertyCollection::AddProperty 60ms 0.81% 77.42% 60ms 0.81% TetrahedralMesh::EdgeIterator::operator!= (partial-inline) 1ms 0.013% 77.44% 59ms 0.79% std::_Vector_base::_M_deallocate (inline) 58ms 0.78% 78.22% 58ms 0.78% std::_Rb_tree_increment 38ms 0.51% 78.73% 57ms 0.77% boost::shared_ptr::shared_ptr (inline) 0 0% 78.73% 55ms 0.74% std::__basic_file::open 0 0% 78.73% 54ms 0.73% _IO_new_fopen 0 0% 78.73% 54ms 0.73% __fopen_internal (inline) 54ms 0.73% 79.46% 54ms 0.73% counterclockwise 0 0% 79.46% 54ms 0.73% std::vector::vector (inline) 0 0% 79.46% 53ms 0.71% CellPropertyCollection::~CellPropertyCollection (inline) 4ms 0.054% 79.51% 52ms 0.7% MeshBasedCellPopulation::SpringIterator::GetNodeB (inline) 0 0% 79.51% 52ms 0.7% std::_Vector_base::_M_create_storage (inline) 0 0% 79.51% 52ms 0.7% std::_Vector_base::_Vector_base (inline) 0 0% 79.51% 50ms 0.67% _IO_new_file_fopen 0 0% 79.51% 48ms 0.65% __GI__IO_file_open 0 0% 79.51% 48ms 0.65% std::map::map (inline) 44ms 0.59% 80.10% 46ms 0.62% __libc_open64 4ms 0.054% 80.16% 45ms 0.61% TetrahedralMesh::EdgeIterator::GetNodeA 45ms 0.61% 80.76% 45ms 0.61% __memcpy_evex_unaligned_erms 0 0% 80.76% 45ms 0.61% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 80.76% 45ms 0.61% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 0 0% 80.76% 44ms 0.59% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 3ms 0.04% 80.80% 44ms 0.59% std::_Rb_tree::_M_emplace_hint_unique 31ms 0.42% 81.22% 43ms 0.58% CellPropertyCollection::GetProperty 9ms 0.12% 81.34% 43ms 0.58% Determinant (inline) 0 0% 81.34% 42ms 0.57% FilesystemPermissions::SetFilePermissions (inline) 42ms 0.57% 81.91% 42ms 0.57% __GI_fchmodat 26ms 0.35% 82.25% 42ms 0.57% hack_digit 0 0% 82.25% 42ms 0.57% std::filesystem::permissions 0 0% 82.25% 41ms 0.55% BoundaryNodeWriter::Visit 30ms 0.4% 82.66% 41ms 0.55% boost::numeric::ublas::c_matrix::operator() 9ms 0.12% 82.78% 40ms 0.54% Inverse 40ms 0.54% 83.32% 40ms 0.54% Node::GetIndex 24ms 0.32% 83.64% 39ms 0.52% AbstractMesh::GetNode 0 0% 83.64% 38ms 0.51% MeshBasedCellPopulation::SpringIterator::~SpringIterator (inline) 38ms 0.51% 84.15% 38ms 0.51% boost::numeric::ublas::same_impl_ex 38ms 0.51% 84.66% 38ms 0.51% std::vector::size (inline)