File: Test2dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 6550ms, 85.03% of 7703ms total Dropped 563 nodes (cum <= 38.52ms) flat flat% sum% cum cum% 0 0% 0% 7666ms 99.52% __libc_start_call_main 0 0% 0% 7666ms 99.52% __libc_start_main_impl 0 0% 0% 7666ms 99.52% _start 0 0% 0% 7650ms 99.31% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 7650ms 99.31% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 7650ms 99.31% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 7650ms 99.31% main 0 0% 0% 7607ms 98.75% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 7607ms 98.75% CxxTest::TestRunner::runTest (inline) 0 0% 0% 7607ms 98.75% Test2DMonolayerRepresentativeSimulation::Test2DMonolayerRepresentativeSimulationForProfiling 0 0% 0% 7604ms 98.71% AbstractCellBasedSimulation::Solve 0 0% 0% 3396ms 44.09% AbstractCellBasedSimulation::UpdateCellPopulation 3ms 0.039% 0.039% 2957ms 38.39% MeshBasedCellPopulation::Update 0 0% 0.039% 2673ms 34.70% AbstractCellPopulation::WriteResultsToFiles 2ms 0.026% 0.065% 1530ms 19.86% OffLatticeSimulation::UpdateCellLocationsAndTopology 1ms 0.013% 0.078% 1482ms 19.24% MutableMesh::ReMesh 1ms 0.013% 0.091% 1422ms 18.46% MeshBasedCellPopulation::UpdateNodePairs 0 0% 0.091% 1375ms 17.85% ForwardEulerNumericalMethod::UpdateAllNodePositions 7ms 0.091% 0.18% 1307ms 16.97% AbstractNumericalMethod::ComputeForcesIncludingDamping 14ms 0.18% 0.36% 1243ms 16.14% MeshBasedCellPopulation::SpringIterator::operator++ 106ms 1.38% 1.74% 1009ms 13.10% TetrahedralMesh::EdgeIterator::operator++ 399ms 5.18% 6.92% 926ms 12.02% std::_Rb_tree::_M_lower_bound (inline) 250ms 3.25% 10.16% 921ms 11.96% __dynamic_cast 6ms 0.078% 10.24% 901ms 11.70% CellPopulationElementWriter::Visit 7ms 0.091% 10.33% 896ms 11.63% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 2ms 0.026% 10.36% 892ms 11.58% AbstractTwoBodyInteractionForce::AddForceContribution 12ms 0.16% 10.52% 878ms 11.40% CellPropertyCollection::GetPropertiesType (inline) 43ms 0.56% 11.07% 807ms 10.48% GeneralisedLinearSpringForce::CalculateForceBetweenNodes (partial-inline) 7ms 0.091% 11.16% 761ms 9.88% MeshBasedCellPopulation::AcceptCellWriter 22ms 0.29% 11.45% 747ms 9.70% AbstractCellPopulation::GetCellUsingLocationIndex 13ms 0.17% 11.62% 735ms 9.54% TetrahedralMesh::ImportFromMesher 3ms 0.039% 11.66% 722ms 9.37% AbstractCellProperty::IsSubType (inline) 0 0% 11.66% 601ms 7.80% std::ostream::operator<< (inline) 110ms 1.43% 13.09% 598ms 7.76% std::ostream::_M_insert 2ms 0.026% 13.11% 584ms 7.58% triangulate 42ms 0.55% 13.66% 564ms 7.32% operator new 43ms 0.56% 14.22% 553ms 7.18% std::map::operator[] (partial-inline) 5ms 0.065% 14.28% 546ms 7.09% std::set::insert (inline) 3ms 0.039% 14.32% 541ms 7.02% std::_Rb_tree::_M_insert_unique 538ms 6.98% 21.30% 538ms 6.98% __strcmp_avx2 0 0% 21.30% 519ms 6.74% delaunay 167ms 2.17% 23.47% 518ms 6.72% __GI___libc_malloc 1ms 0.013% 23.48% 518ms 6.72% divconqdelaunay 29ms 0.38% 23.86% 518ms 6.72% std::__new_allocator::allocate (inline) 0 0% 23.86% 514ms 6.67% std::allocator_traits::allocate (inline) 17ms 0.22% 24.08% 513ms 6.66% std::_Rb_tree::find (inline) 3ms 0.039% 24.12% 512ms 6.65% Cell::GetCellProliferativeType 1ms 0.013% 24.13% 487ms 6.32% LegacyCellProliferativeTypesWriter::VisitCell 218ms 2.83% 26.96% 480ms 6.23% __cxxabiv1::__si_class_type_info::__do_dyncast 0 0% 26.96% 461ms 5.98% std::_Rb_tree::lower_bound (inline) 0 0% 26.96% 461ms 5.98% std::map::lower_bound (inline) 0 0% 26.96% 461ms 5.98% std::set::count (inline) 37ms 0.48% 27.44% 446ms 5.79% std::_Rb_tree::~_Rb_tree (inline) 4ms 0.052% 27.50% 430ms 5.58% AbstractCellBasedSimulation::DoCellBirth 0 0% 27.50% 417ms 5.41% std::_Rb_tree::_M_create_node (inline) 0 0% 27.50% 416ms 5.40% std::set::~set (inline) 104ms 1.35% 28.85% 406ms 5.27% std::_Rb_tree::_M_erase 0 0% 28.85% 393ms 5.10% std::_Rb_tree::_M_get_node (inline) 0 0% 28.85% 392ms 5.09% std::_Rb_tree::_Alloc_node::operator() (inline) 2ms 0.026% 28.87% 374ms 4.86% Cell::GetMutationState 9ms 0.12% 28.99% 373ms 4.84% std::less::operator() (inline) 364ms 4.73% 33.71% 364ms 4.73% std::operator< (inline) 3ms 0.039% 33.75% 361ms 4.69% NodeLocationWriter::Visit 19ms 0.25% 34.00% 355ms 4.61% std::_Rb_tree::_Rb_tree (partial-inline) 321ms 4.17% 38.17% 321ms 4.17% std::_Rb_tree::_S_right (inline) 2ms 0.026% 38.19% 318ms 4.13% MeshBasedCellPopulation::GetDampingConstant 5ms 0.065% 38.26% 318ms 4.13% std::set::set (inline) 1ms 0.013% 38.27% 316ms 4.10% AbstractCentreBasedCellPopulation::GetDampingConstant 4ms 0.052% 38.32% 315ms 4.09% Element::Element 30ms 0.39% 38.71% 313ms 4.06% std::num_put::_M_insert_float 22ms 0.29% 39.00% 310ms 4.02% std::_Rb_tree::_M_insert_ (inline) 92ms 1.19% 40.19% 302ms 3.92% __GI___libc_free 33ms 0.43% 40.62% 299ms 3.88% std::_Rb_tree::_M_copy (inline) 3ms 0.039% 40.66% 289ms 3.75% Cell::ReadyToDivide 0 0% 40.66% 289ms 3.75% std::_Rb_tree::_M_drop_node (inline) 11ms 0.14% 40.80% 286ms 3.71% divconqrecurse 6ms 0.078% 40.88% 282ms 3.66% AbstractCellPopulation::IsCellAttachedToLocationIndex 62ms 0.8% 41.69% 268ms 3.48% mergehulls 6ms 0.078% 41.76% 267ms 3.47% std::__new_allocator::deallocate (inline) 67ms 0.87% 42.63% 265ms 3.44% std::_Rb_tree::_M_clone_node (inline) 168ms 2.18% 44.81% 264ms 3.43% _int_malloc 0 0% 44.81% 262ms 3.40% std::allocator_traits::deallocate (inline) 5ms 0.065% 44.88% 245ms 3.18% std::__cxx11::collate::do_transform 4ms 0.052% 44.93% 234ms 3.04% CellProliferativeTypesWriter::VisitCell 2ms 0.026% 44.96% 233ms 3.02% ___vsnprintf 1ms 0.013% 44.97% 231ms 3.00% __vsnprintf_internal (inline) 69ms 0.9% 45.87% 228ms 2.96% std::_Rb_tree::_M_get_insert_unique_pos (inline) 22ms 0.29% 46.15% 227ms 2.95% __printf_buffer 3ms 0.039% 46.19% 222ms 2.88% AbstractCellProperty::IsType (inline) 7ms 0.091% 46.28% 221ms 2.87% Element::RegisterWithNodes (inline) 0 0% 46.28% 220ms 2.86% std::_Rb_tree::_M_put_node (inline) 3ms 0.039% 46.32% 216ms 2.80% AbstractPhaseBasedCellCycleModel::ReadyToDivide 5ms 0.065% 46.38% 216ms 2.80% CellPropertyCollection::HasProperty 0 0% 46.38% 214ms 2.78% Cell::HasCellProperty (inline) 5ms 0.065% 46.45% 209ms 2.71% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 175ms 2.27% 48.72% 209ms 2.71% _int_free 4ms 0.052% 48.77% 208ms 2.70% Node::AddElement 10ms 0.13% 48.90% 193ms 2.51% TetrahedralMesh::Clear 4ms 0.052% 48.95% 191ms 2.48% __printf_fp_l_buffer 0 0% 48.95% 191ms 2.48% __printf_fp_spec (inline) 14ms 0.18% 49.14% 187ms 2.43% MeshBasedCellPopulation::SpringsEnd (inline) 92ms 1.19% 50.33% 179ms 2.32% __printf_fp_buffer_1 36ms 0.47% 50.80% 170ms 2.21% AbstractCellProperty::IsSame 2ms 0.026% 50.82% 162ms 2.10% alternateaxes 0 0% 50.82% 157ms 2.04% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 147ms 1.91% 52.73% 156ms 2.03% vertexmedian 0 0% 52.73% 155ms 2.01% AbstractCellBasedWriter::OpenOutputFileForAppend 3ms 0.039% 52.77% 153ms 1.99% boost::numeric::ublas::c_vector::c_vector (inline) 26ms 0.34% 53.11% 151ms 1.96% TetrahedralMesh::EdgesEnd (partial-inline) 4ms 0.052% 53.16% 151ms 1.96% boost::numeric::ublas::vector_assign (inline) 16ms 0.21% 53.37% 150ms 1.95% AbstractTetrahedralElement::CalculateJacobian 0 0% 53.37% 150ms 1.95% OutputFileHandler::OpenOutputFile 58ms 0.75% 54.12% 149ms 1.93% std::__ostream_insert 2ms 0.026% 54.15% 147ms 1.91% std::basic_filebuf::close 0 0% 54.15% 147ms 1.91% std::basic_ofstream::basic_ofstream (inline) 0 0% 54.15% 145ms 1.88% AbstractCellBasedWriter::CloseFile 0 0% 54.15% 145ms 1.88% AbstractCellPopulation::CloseRoundRobinWritersFiles 1ms 0.013% 54.16% 145ms 1.88% std::basic_ofstream::close (inline) 0 0% 54.16% 145ms 1.88% std::basic_ofstream::open (inline) 0 0% 54.16% 144ms 1.87% std::basic_filebuf::open 0 0% 54.16% 139ms 1.80% TetrahedralMesh::RefreshJacobianCachedData 138ms 1.79% 55.95% 138ms 1.79% incircle 0 0% 55.95% 134ms 1.74% OutputFileHandler::CommonConstructor 0 0% 55.95% 134ms 1.74% OutputFileHandler::OutputFileHandler 30ms 0.39% 56.34% 134ms 1.74% std::type_info::operator== (inline) 10ms 0.13% 56.47% 129ms 1.67% AbstractTetrahedralElement::CalculateInverseJacobian 0 0% 56.47% 128ms 1.66% OutputFileHandler::MakeFoldersAndReturnFullPath 19ms 0.25% 56.72% 128ms 1.66% boost::detail::shared_count::~shared_count (inline) 0 0% 56.72% 128ms 1.66% boost::shared_ptr::~shared_ptr (inline) 8ms 0.1% 56.82% 128ms 1.66% std::vector::push_back (inline) 6ms 0.078% 56.90% 125ms 1.62% Node::~Node 23ms 0.3% 57.20% 123ms 1.60% std::num_put::_M_insert_int 0 0% 57.20% 122ms 1.58% std::operator<< (inline) 77ms 1% 58.20% 121ms 1.57% TetrahedralMesh::EdgeIterator::EdgeIterator (partial-inline) 0 0% 58.20% 121ms 1.57% std::_Vector_base::_M_allocate (inline) 15ms 0.19% 58.39% 120ms 1.56% MeshBasedCellPopulation::SpringIterator::SpringIterator 0 0% 58.39% 118ms 1.53% std::__basic_file::open 0 0% 58.39% 117ms 1.52% _IO_new_fopen 0 0% 58.39% 117ms 1.52% __fopen_internal (inline) 0 0% 58.39% 116ms 1.51% _IO_new_file_fopen 2ms 0.026% 58.42% 115ms 1.49% __GI__IO_file_open 5ms 0.065% 58.48% 113ms 1.47% std::vector::_M_realloc_insert 13ms 0.17% 58.65% 112ms 1.45% AbstractCellPopulation::Iterator::IsRealCell (inline) 0 0% 58.65% 110ms 1.43% AbstractCellPopulation::Iterator::operator++ (inline) 2ms 0.026% 58.68% 109ms 1.42% std::basic_filebuf::_M_terminate_output 2ms 0.026% 58.70% 108ms 1.40% std::basic_filebuf::overflow 20ms 0.26% 58.96% 107ms 1.39% AbstractTetrahedralElement::RefreshJacobian 1ms 0.013% 58.98% 106ms 1.38% std::basic_filebuf::_M_convert_to_external 104ms 1.35% 60.33% 105ms 1.36% __GI___libc_write 0 0% 60.33% 105ms 1.36% std::__basic_file::xsputn 33ms 0.43% 60.76% 104ms 1.35% boost::numeric::ublas::indexing_vector_assign 1ms 0.013% 60.77% 100ms 1.30% AbstractTetrahedralElement::AbstractTetrahedralElement 99ms 1.29% 62.05% 100ms 1.30% __libc_open64 86ms 1.12% 63.17% 97ms 1.26% boost::detail::sp_counted_base::release 96ms 1.25% 64.42% 96ms 1.25% [libchaste_cell_based.so] 38ms 0.49% 64.91% 94ms 1.22% boost::shared_ptr::shared_ptr (inline) 94ms 1.22% 66.13% 94ms 1.22% std::_Rb_tree_insert_and_rebalance 92ms 1.19% 67.32% 92ms 1.19% std::vector::size (inline) 0 0% 67.32% 89ms 1.16% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 67.32% 89ms 1.16% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 6ms 0.078% 67.40% 89ms 1.16% std::_Rb_tree_const_iterator::operator++ (inline) 88ms 1.14% 68.54% 88ms 1.14% TetrahedralMesh::EdgeIterator::operator!= (partial-inline) 52ms 0.68% 69.22% 87ms 1.13% std::basic_filebuf::xsputn 0 0% 69.22% 86ms 1.12% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (partial-inline) 86ms 1.12% 70.34% 86ms 1.12% std::_Rb_tree_increment 46ms 0.6% 70.93% 83ms 1.08% AbstractTetrahedralMesh::GetElement 5ms 0.065% 71.00% 83ms 1.08% TetrahedralMesh::EdgeIterator::GetNodeB 1ms 0.013% 71.01% 81ms 1.05% AbstractCellPopulation::GetLocationIndexUsingCell 2ms 0.026% 71.04% 80ms 1.04% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 0 0% 71.04% 79ms 1.03% tcache_get (inline) 79ms 1.03% 72.06% 79ms 1.03% tcache_get_n (inline) 1ms 0.013% 72.08% 78ms 1.01% Cell::GetCellId 30ms 0.39% 72.47% 75ms 0.97% AbstractElement::GetNodeLocation 56ms 0.73% 73.19% 69ms 0.9% malloc_consolidate 0 0% 73.19% 69ms 0.9% std::_Rb_tree::_M_destroy_node (inline) 0 0% 73.19% 69ms 0.9% std::__new_allocator::destroy (inline) 0 0% 73.19% 69ms 0.9% std::allocator_traits::destroy (inline) 44ms 0.57% 73.76% 69ms 0.9% std::basic_streambuf::xsputn 1ms 0.013% 73.78% 68ms 0.88% std::filesystem::create_directory 3ms 0.039% 73.82% 66ms 0.86% TetrahedralMesh::EdgeIterator::GetNodeA 0 0% 73.82% 66ms 0.86% boost::numeric::ublas::norm_2 (inline) 26ms 0.34% 74.15% 66ms 0.86% boost::numeric::ublas::vector_norm_2::apply (inline) 3ms 0.039% 74.19% 65ms 0.84% std::filesystem::status 64ms 0.83% 75.02% 64ms 0.83% __GI___fstatat64 63ms 0.82% 75.84% 63ms 0.82% counterclockwise 55ms 0.71% 76.55% 62ms 0.8% vertexsort 59ms 0.77% 77.32% 59ms 0.77% [libstdc++.so.6.0.33] 41ms 0.53% 77.85% 58ms 0.75% AbstractElement::GetNodeGlobalIndex 6ms 0.078% 77.93% 58ms 0.75% CellPropertyCollection::AddProperty 58ms 0.75% 78.68% 58ms 0.75% Node::GetIndex 18ms 0.23% 78.92% 57ms 0.74% AbstractTetrahedralMesh::GetNumAllElements 1ms 0.013% 78.93% 57ms 0.74% Node::ClearAppliedForce 1ms 0.013% 78.94% 57ms 0.74% Node::ConstructNodeAttributes (inline) 55ms 0.71% 79.66% 56ms 0.73% boost::detail::shared_count::shared_count (inline) 30ms 0.39% 80.05% 54ms 0.7% boost::numeric::ublas::c_matrix::operator() (partial-inline) 29ms 0.38% 80.42% 54ms 0.7% hack_digit 53ms 0.69% 81.11% 53ms 0.69% __memcpy_avx_unaligned_erms 48ms 0.62% 81.73% 52ms 0.68% std::num_put::do_put 0 0% 81.73% 50ms 0.65% std::vector::vector (inline) 4ms 0.052% 81.79% 49ms 0.64% std::_Rb_tree::_M_emplace_hint_unique 3ms 0.039% 81.83% 48ms 0.62% NodeAttributes::NodeAttributes 1ms 0.013% 81.84% 47ms 0.61% AbstractCentreBasedCellPopulation::CreateCellPair 0 0% 81.84% 47ms 0.61% std::map::find (inline) 0 0% 81.84% 46ms 0.6% std::_Vector_base::_Vector_base (inline) 0 0% 81.84% 44ms 0.57% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 44ms 0.57% 82.41% 44ms 0.57% [libchaste_mesh.so] 0 0% 82.41% 42ms 0.55% std::_Vector_base::_M_create_storage (inline) 0 0% 82.41% 42ms 0.55% std::map::map (inline) 27ms 0.35% 82.76% 41ms 0.53% CellPropertyCollection::GetProperty 1ms 0.013% 82.77% 41ms 0.53% std::_Vector_base::_M_deallocate (inline) 15ms 0.19% 82.97% 40ms 0.52% Determinant (inline) 0 0% 82.97% 40ms 0.52% MeshBasedCellPopulation::SpringIterator::GetNodeB (inline) 40ms 0.52% 83.49% 40ms 0.52% Node::rGetLocation 40ms 0.52% 84.01% 40ms 0.52% boost::numeric::ublas::c_vector::operator() 40ms 0.52% 84.53% 40ms 0.52% boost::numeric::ublas::same_impl_ex 0 0% 84.53% 39ms 0.51% CellPropertyCollection::~CellPropertyCollection (inline) 0 0% 84.53% 39ms 0.51% CxxTest::RealWorldDescription::setUp 0 0% 84.53% 39ms 0.51% MeshBasedCellPopulation::SpringIterator::~SpringIterator (inline) 0 0% 84.53% 39ms 0.51% PetscInitialize 0 0% 84.53% 39ms 0.51% PetscSetup::setUpWorld 0 0% 84.53% 39ms 0.51% PetscSetupUtils::CommonSetup 0 0% 84.53% 39ms 0.51% PetscSetupUtils::InitialisePetsc 39ms 0.51% 85.03% 39ms 0.51% boost::shared_ptr::operator-> (inline)