File: Test2dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 6799ms, 84.55% of 8041ms total Dropped 603 nodes (cum <= 40.20ms) flat flat% sum% cum cum% 0 0% 0% 8002ms 99.51% __libc_start_call_main 0 0% 0% 8002ms 99.51% __libc_start_main_impl 0 0% 0% 8002ms 99.51% _start 0 0% 0% 7986ms 99.32% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 7986ms 99.32% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 7986ms 99.32% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 7986ms 99.32% main 0 0% 0% 7946ms 98.82% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 7946ms 98.82% CxxTest::TestRunner::runTest (inline) 0 0% 0% 7946ms 98.82% Test2DMonolayerRepresentativeSimulation::Test2DMonolayerRepresentativeSimulationForProfiling 0 0% 0% 7943ms 98.78% AbstractCellBasedSimulation::Solve 0 0% 0% 3399ms 42.27% AbstractCellBasedSimulation::UpdateCellPopulation 1ms 0.012% 0.012% 3012ms 37.46% AbstractCellPopulation::WriteResultsToFiles 1ms 0.012% 0.025% 2931ms 36.45% MeshBasedCellPopulation::Update 1ms 0.012% 0.037% 1522ms 18.93% OffLatticeSimulation::UpdateCellLocationsAndTopology 1ms 0.012% 0.05% 1445ms 17.97% MeshBasedCellPopulation::UpdateNodePairs 2ms 0.025% 0.075% 1429ms 17.77% MutableMesh::ReMesh 4ms 0.05% 0.12% 1373ms 17.07% ForwardEulerNumericalMethod::UpdateAllNodePositions 4ms 0.05% 0.17% 1314ms 16.34% AbstractNumericalMethod::ComputeForcesIncludingDamping 24ms 0.3% 0.47% 1265ms 15.73% MeshBasedCellPopulation::SpringIterator::operator++ 109ms 1.36% 1.83% 1024ms 12.73% TetrahedralMesh::EdgeIterator::operator++ 2ms 0.025% 1.85% 994ms 12.36% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 464ms 5.77% 7.62% 980ms 12.19% std::_Rb_tree::_M_lower_bound (inline) 13ms 0.16% 7.79% 938ms 11.67% CellPropertyCollection::GetPropertiesType (inline) 20ms 0.25% 8.03% 899ms 11.18% CellPopulationElementWriter::Visit 4ms 0.05% 8.08% 882ms 10.97% AbstractTwoBodyInteractionForce::AddForceContribution 239ms 2.97% 11.06% 869ms 10.81% __dynamic_cast 5ms 0.062% 11.12% 844ms 10.50% MeshBasedCellPopulation::AcceptCellWriter 54ms 0.67% 11.79% 786ms 9.77% AbstractVariableSizeTwoBodyInteractionForce::CalculateForceBetweenNodes 25ms 0.31% 12.10% 737ms 9.17% AbstractCellPopulation::GetCellUsingLocationIndex 8ms 0.099% 12.20% 715ms 8.89% TetrahedralMesh::ImportFromMesher 5ms 0.062% 12.26% 708ms 8.80% AbstractCellProperty::IsSubType (inline) 3ms 0.037% 12.30% 609ms 7.57% std::ostream::operator<< (inline) 90ms 1.12% 13.42% 606ms 7.54% std::ostream::_M_insert 56ms 0.7% 14.12% 602ms 7.49% std::map::operator[] (partial-inline) 5ms 0.062% 14.18% 560ms 6.96% LegacyCellProliferativeTypesWriter::VisitCell 40ms 0.5% 14.67% 559ms 6.95% operator new 7ms 0.087% 14.76% 540ms 6.72% Cell::GetCellProliferativeType 26ms 0.32% 15.09% 538ms 6.69% std::_Rb_tree::find (inline) 9ms 0.11% 15.20% 538ms 6.69% std::set::insert (inline) 1ms 0.012% 15.21% 534ms 6.64% triangulate 9ms 0.11% 15.32% 529ms 6.58% std::_Rb_tree::_M_insert_unique 159ms 1.98% 17.30% 513ms 6.38% __GI___libc_malloc 0 0% 17.30% 507ms 6.31% std::_Rb_tree::lower_bound (inline) 0 0% 17.30% 507ms 6.31% std::map::lower_bound (inline) 506ms 6.29% 23.59% 506ms 6.29% __strcmp_avx2 0 0% 23.59% 502ms 6.24% std::set::count (inline) 27ms 0.34% 23.93% 490ms 6.09% std::__new_allocator::allocate (inline) 0 0% 23.93% 484ms 6.02% std::allocator_traits::allocate (inline) 0 0% 23.93% 471ms 5.86% delaunay 1ms 0.012% 23.94% 469ms 5.83% divconqdelaunay 215ms 2.67% 26.61% 463ms 5.76% __cxxabiv1::__si_class_type_info::__do_dyncast 3ms 0.037% 26.65% 452ms 5.62% AbstractCellBasedSimulation::DoCellBirth 0 0% 26.65% 410ms 5.10% std::_Rb_tree::_M_create_node (inline) 6ms 0.075% 26.73% 403ms 5.01% Cell::GetMutationState 33ms 0.41% 27.14% 392ms 4.88% std::_Rb_tree::~_Rb_tree (inline) 0 0% 27.14% 391ms 4.86% std::_Rb_tree::_Alloc_node::operator() (inline) 8ms 0.099% 27.24% 382ms 4.75% std::less::operator() (inline) 374ms 4.65% 31.89% 374ms 4.65% std::operator< (inline) 0 0% 31.89% 372ms 4.63% std::_Rb_tree::_M_get_node (inline) 2ms 0.025% 31.91% 367ms 4.56% NodeLocationWriter::Visit 29ms 0.36% 32.27% 364ms 4.53% std::_Rb_tree::_Rb_tree (partial-inline) 0 0% 32.27% 364ms 4.53% std::set::~set (inline) 81ms 1.01% 33.28% 355ms 4.41% std::_Rb_tree::_M_erase 27ms 0.34% 33.62% 342ms 4.25% std::_Rb_tree::_M_insert_ (inline) 0 0% 33.62% 335ms 4.17% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 1ms 0.012% 33.63% 334ms 4.15% std::set::set (inline) 0 0% 33.63% 333ms 4.14% AbstractCellBasedWriter::OpenOutputFileForAppend 1ms 0.012% 33.64% 330ms 4.10% OutputFileHandler::OpenOutputFile 1ms 0.012% 33.65% 328ms 4.08% MeshBasedCellPopulation::GetDampingConstant 1ms 0.012% 33.66% 327ms 4.07% AbstractCentreBasedCellPopulation::GetDampingConstant 25ms 0.31% 33.98% 321ms 3.99% std::num_put::_M_insert_float 9ms 0.11% 34.09% 310ms 3.86% Cell::ReadyToDivide 109ms 1.36% 35.44% 304ms 3.78% __GI___libc_free 41ms 0.51% 35.95% 302ms 3.76% std::_Rb_tree::_M_copy (inline) 3ms 0.037% 35.99% 294ms 3.66% AbstractCellPopulation::IsCellAttachedToLocationIndex 293ms 3.64% 39.63% 293ms 3.64% std::_Rb_tree::_S_right (inline) 4ms 0.05% 39.68% 280ms 3.48% Element::Element 176ms 2.19% 41.87% 271ms 3.37% _int_malloc 10ms 0.12% 42.00% 268ms 3.33% std::__new_allocator::deallocate (inline) 12ms 0.15% 42.15% 264ms 3.28% divconqrecurse 0 0% 42.15% 259ms 3.22% std::allocator_traits::deallocate (inline) 84ms 1.04% 43.19% 258ms 3.21% std::_Rb_tree::_M_clone_node (inline) 0 0% 43.19% 255ms 3.17% std::_Rb_tree::_M_drop_node (inline) 6ms 0.075% 43.27% 251ms 3.12% std::__cxx11::collate::do_transform 64ms 0.8% 44.06% 247ms 3.07% mergehulls 5ms 0.062% 44.12% 236ms 2.93% CellProliferativeTypesWriter::VisitCell 6ms 0.075% 44.20% 236ms 2.93% CellPropertyCollection::HasProperty 0 0% 44.20% 235ms 2.92% Cell::HasCellProperty (inline) 4ms 0.05% 44.25% 230ms 2.86% ___vsnprintf 2ms 0.025% 44.27% 228ms 2.84% AbstractCellProperty::IsType (inline) 0 0% 44.27% 226ms 2.81% __vsnprintf_internal (inline) 31ms 0.39% 44.66% 222ms 2.76% __printf_buffer 3ms 0.037% 44.70% 213ms 2.65% AbstractPhaseBasedCellCycleModel::ReadyToDivide 9ms 0.11% 44.81% 206ms 2.56% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 26ms 0.32% 45.13% 202ms 2.51% TetrahedralMesh::Clear 0 0% 45.13% 200ms 2.49% std::_Rb_tree::_M_put_node (inline) 167ms 2.08% 47.21% 195ms 2.43% _int_free 10ms 0.12% 47.33% 194ms 2.41% MeshBasedCellPopulation::SpringsEnd (inline) 6ms 0.075% 47.41% 182ms 2.26% Element::RegisterWithNodes (inline) 1ms 0.012% 47.42% 178ms 2.21% __printf_fp_spec (inline) 50ms 0.62% 48.04% 178ms 2.21% std::_Rb_tree::_M_get_insert_unique_pos (inline) 7ms 0.087% 48.13% 177ms 2.20% __printf_fp_l_buffer 2ms 0.025% 48.15% 175ms 2.18% Node::AddElement 11ms 0.14% 48.29% 174ms 2.16% AbstractTetrahedralElement::CalculateJacobian 45ms 0.56% 48.85% 173ms 2.15% AbstractCellProperty::IsSame 85ms 1.06% 49.91% 167ms 2.08% __printf_fp_buffer_1 0 0% 49.91% 162ms 2.01% std::basic_ofstream::basic_ofstream (inline) 2ms 0.025% 49.93% 160ms 1.99% TetrahedralMesh::RefreshJacobianCachedData 0 0% 49.93% 158ms 1.96% std::basic_filebuf::open 0 0% 49.93% 158ms 1.96% std::basic_ofstream::open (inline) 40ms 0.5% 50.43% 154ms 1.92% TetrahedralMesh::EdgesEnd (partial-inline) 1ms 0.012% 50.44% 152ms 1.89% AbstractCellPopulation::CloseRoundRobinWritersFiles 0 0% 50.44% 152ms 1.89% OutputFileHandler::CommonConstructor 0 0% 50.44% 152ms 1.89% OutputFileHandler::OutputFileHandler 0 0% 50.44% 150ms 1.87% AbstractCellBasedWriter::CloseFile 1ms 0.012% 50.45% 150ms 1.87% std::basic_filebuf::close 0 0% 50.45% 150ms 1.87% std::basic_ofstream::close (inline) 0 0% 50.45% 148ms 1.84% OutputFileHandler::MakeFoldersAndReturnFullPath 2ms 0.025% 50.48% 145ms 1.80% AbstractTetrahedralElement::CalculateInverseJacobian 1ms 0.012% 50.49% 142ms 1.77% boost::numeric::ublas::vector_assign (inline) 58ms 0.72% 51.21% 142ms 1.77% std::__ostream_insert 39ms 0.49% 51.70% 141ms 1.75% std::num_put::_M_insert_int 4ms 0.05% 51.75% 140ms 1.74% boost::numeric::ublas::c_vector::c_vector (inline) 9ms 0.11% 51.86% 133ms 1.65% std::_Rb_tree_const_iterator::operator++ (inline) 0 0% 51.86% 132ms 1.64% FilesystemPermissions::SetFilePermissions (inline) 13ms 0.16% 52.02% 131ms 1.63% AbstractTetrahedralElement::RefreshJacobian 131ms 1.63% 53.65% 131ms 1.63% __GI_fchmodat 0 0% 53.65% 131ms 1.63% std::filesystem::permissions 129ms 1.60% 55.25% 129ms 1.60% std::_Rb_tree_increment 25ms 0.31% 55.57% 128ms 1.59% std::type_info::operator== (inline) 22ms 0.27% 55.84% 125ms 1.55% MeshBasedCellPopulation::SpringIterator::SpringIterator 3ms 0.037% 55.88% 124ms 1.54% std::__basic_file::open 6ms 0.075% 55.95% 124ms 1.54% std::vector::push_back (inline) 1ms 0.012% 55.96% 122ms 1.52% _IO_new_fopen 1ms 0.012% 55.98% 122ms 1.52% alternateaxes 0 0% 55.98% 121ms 1.50% __fopen_internal (inline) 111ms 1.38% 57.36% 119ms 1.48% vertexmedian 10ms 0.12% 57.48% 117ms 1.46% Node::~Node 0 0% 57.48% 117ms 1.46% _IO_new_file_fopen 24ms 0.3% 57.78% 116ms 1.44% AbstractCellPopulation::Iterator::IsRealCell (inline) 0 0% 57.78% 116ms 1.44% std::basic_filebuf::_M_terminate_output 2ms 0.025% 57.80% 116ms 1.44% std::basic_filebuf::overflow 0 0% 57.80% 115ms 1.43% AbstractCellPopulation::Iterator::operator++ (inline) 1ms 0.012% 57.82% 115ms 1.43% __GI__IO_file_open 7ms 0.087% 57.90% 115ms 1.43% std::vector::_M_realloc_insert 2ms 0.025% 57.93% 114ms 1.42% std::_Vector_base::_M_allocate (inline) 0 0% 57.93% 113ms 1.41% std::__basic_file::xsputn 0 0% 57.93% 113ms 1.41% std::basic_filebuf::_M_convert_to_external 2ms 0.025% 57.95% 113ms 1.41% std::operator<< (inline) 109ms 1.36% 59.31% 111ms 1.38% __GI___libc_write 108ms 1.34% 60.65% 108ms 1.34% incircle 1ms 0.012% 60.66% 105ms 1.31% AbstractTetrahedralElement::AbstractTetrahedralElement 12ms 0.15% 60.81% 104ms 1.29% boost::detail::shared_count::~shared_count (inline) 0 0% 60.81% 104ms 1.29% boost::shared_ptr::~shared_ptr (inline) 104ms 1.29% 62.11% 104ms 1.29% std::_Rb_tree_insert_and_rebalance 47ms 0.58% 62.69% 103ms 1.28% AbstractElement::GetNodeLocation 72ms 0.9% 63.59% 102ms 1.27% TetrahedralMesh::EdgeIterator::EdgeIterator (partial-inline) 32ms 0.4% 63.98% 97ms 1.21% boost::numeric::ublas::indexing_vector_assign 48ms 0.6% 64.58% 97ms 1.21% boost::shared_ptr::shared_ptr (inline) 96ms 1.19% 65.78% 96ms 1.19% __libc_open64 95ms 1.18% 66.96% 95ms 1.18% TetrahedralMesh::EdgeIterator::operator!= (partial-inline) 89ms 1.11% 68.06% 89ms 1.11% boost::detail::sp_counted_base::release 87ms 1.08% 69.15% 87ms 1.08% [libchaste_cell_based.so] 4ms 0.05% 69.20% 85ms 1.06% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (partial-inline) 13ms 0.16% 69.36% 85ms 1.06% CellPropertyCollection::AddProperty 2ms 0.025% 69.38% 84ms 1.04% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 58ms 0.72% 70.10% 84ms 1.04% std::basic_streambuf::xsputn 49ms 0.61% 70.71% 74ms 0.92% malloc_consolidate 47ms 0.58% 71.30% 74ms 0.92% std::basic_filebuf::xsputn 0 0% 71.30% 73ms 0.91% tcache_get (inline) 73ms 0.91% 72.20% 73ms 0.91% tcache_get_n (inline) 62ms 0.77% 72.98% 72ms 0.9% vertexsort 3ms 0.037% 73.01% 71ms 0.88% Node::ConstructNodeAttributes (inline) 6ms 0.075% 73.09% 71ms 0.88% TetrahedralMesh::EdgeIterator::GetNodeB 71ms 0.88% 73.97% 71ms 0.88% __GI___fstatat64 1ms 0.012% 73.98% 71ms 0.88% std::filesystem::status 0 0% 73.98% 69ms 0.86% AbstractCellPopulation::GetLocationIndexUsingCell 0 0% 73.98% 69ms 0.86% Cell::GetCellId 0 0% 73.98% 69ms 0.86% FilesystemPermissions::CreateDirectoryWithPermissions (inline) 0 0% 73.98% 69ms 0.86% Node::ClearAppliedForce 69ms 0.86% 74.84% 69ms 0.86% counterclockwise 1ms 0.012% 74.85% 69ms 0.86% std::filesystem::create_directory 51ms 0.63% 75.49% 69ms 0.86% std::num_put::do_put 7ms 0.087% 75.58% 66ms 0.82% std::_Vector_base::_M_deallocate (inline) 65ms 0.81% 76.38% 65ms 0.81% Node::GetIndex 36ms 0.45% 76.83% 64ms 0.8% boost::numeric::ublas::c_matrix::operator() (partial-inline) 8ms 0.099% 76.93% 63ms 0.78% TetrahedralMesh::EdgeIterator::GetNodeA 62ms 0.77% 77.70% 62ms 0.77% __memcpy_avx_unaligned_erms 46ms 0.57% 78.27% 59ms 0.73% AbstractElement::GetNodeGlobalIndex 1ms 0.012% 78.29% 57ms 0.71% BoundaryNodeWriter::Visit 0 0% 78.29% 55ms 0.68% std::_Rb_tree::_M_destroy_node (inline) 0 0% 78.29% 55ms 0.68% std::__new_allocator::destroy (inline) 0 0% 78.29% 55ms 0.68% std::allocator_traits::destroy (inline) 55ms 0.68% 78.97% 55ms 0.68% std::vector::size (inline) 53ms 0.66% 79.63% 53ms 0.66% [libstdc++.so.6.0.33] 53ms 0.66% 80.29% 53ms 0.66% boost::shared_ptr::operator-> (inline) 52ms 0.65% 80.94% 52ms 0.65% [libchaste_mesh.so] 10ms 0.12% 81.06% 49ms 0.61% NodeAttributes::NodeAttributes 47ms 0.58% 81.64% 49ms 0.61% boost::detail::shared_count::shared_count (inline) 0 0% 81.64% 49ms 0.61% std::vector::vector (inline) 26ms 0.32% 81.97% 48ms 0.6% AbstractTetrahedralMesh::GetElement 0 0% 81.97% 48ms 0.6% CellPropertyCollection::~CellPropertyCollection (inline) 2ms 0.025% 81.99% 48ms 0.6% MeshBasedCellPopulation::SpringIterator::GetNodeB (inline) 29ms 0.36% 82.35% 47ms 0.58% hack_digit 26ms 0.32% 82.68% 46ms 0.57% AbstractCellCycleModel::GetAge 14ms 0.17% 82.85% 46ms 0.57% Determinant (inline) 45ms 0.56% 83.41% 45ms 0.56% Node::rGetLocation 0 0% 83.41% 45ms 0.56% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 0 0% 83.41% 45ms 0.56% std::_Vector_base::_Vector_base (inline) 0 0% 83.41% 43ms 0.53% AbstractCentreBasedCellPopulation::IsMarkedSpring 43ms 0.53% 83.94% 43ms 0.53% Node::IsDeleted 0 0% 83.94% 42ms 0.52% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 83.94% 42ms 0.52% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 8ms 0.099% 84.04% 41ms 0.51% Inverse 41ms 0.51% 84.55% 41ms 0.51% boost::numeric::ublas::same_impl_ex