File: Test2dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 6764ms, 84.31% of 8023ms total Dropped 559 nodes (cum <= 40.12ms) flat flat% sum% cum cum% 0 0% 0% 7982ms 99.49% __libc_start_call_main 0 0% 0% 7982ms 99.49% __libc_start_main_impl 0 0% 0% 7982ms 99.49% _start 0 0% 0% 7964ms 99.26% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 7964ms 99.26% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 7964ms 99.26% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 7964ms 99.26% main 0 0% 0% 7924ms 98.77% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 7924ms 98.77% CxxTest::TestRunner::runTest (inline) 0 0% 0% 7924ms 98.77% Test2DMonolayerRepresentativeSimulation::Test2DMonolayerRepresentativeSimulationForProfiling 0 0% 0% 7921ms 98.73% AbstractCellBasedSimulation::Solve 0 0% 0% 3463ms 43.16% AbstractCellBasedSimulation::UpdateCellPopulation 2ms 0.025% 0.025% 2992ms 37.29% MeshBasedCellPopulation::Update 0 0% 0.025% 2940ms 36.64% AbstractCellPopulation::WriteResultsToFiles 0 0% 0.025% 1512ms 18.85% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 0.025% 1489ms 18.56% MutableMesh::ReMesh 1ms 0.012% 0.037% 1441ms 17.96% MeshBasedCellPopulation::UpdateNodePairs 0 0% 0.037% 1388ms 17.30% ForwardEulerNumericalMethod::UpdateAllNodePositions 2ms 0.025% 0.062% 1332ms 16.60% AbstractNumericalMethod::ComputeForcesIncludingDamping 20ms 0.25% 0.31% 1253ms 15.62% MeshBasedCellPopulation::SpringIterator::operator++ 116ms 1.45% 1.76% 992ms 12.36% TetrahedralMesh::EdgeIterator::operator++ 6ms 0.075% 1.83% 963ms 12.00% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 10ms 0.12% 1.96% 935ms 11.65% CellPopulationElementWriter::Visit 427ms 5.32% 7.28% 922ms 11.49% std::_Rb_tree::_M_lower_bound (inline) 7ms 0.087% 7.37% 921ms 11.48% CellPropertyCollection::GetPropertiesType (inline) 3ms 0.037% 7.40% 905ms 11.28% AbstractTwoBodyInteractionForce::AddForceContribution 272ms 3.39% 10.79% 894ms 11.14% __dynamic_cast 4ms 0.05% 10.84% 807ms 10.06% MeshBasedCellPopulation::AcceptCellWriter 45ms 0.56% 11.40% 782ms 9.75% AbstractVariableSizeTwoBodyInteractionForce::CalculateForceBetweenNodes 35ms 0.44% 11.84% 747ms 9.31% AbstractCellPopulation::GetCellUsingLocationIndex 3ms 0.037% 11.88% 715ms 8.91% AbstractCellProperty::IsSubType (inline) 13ms 0.16% 12.04% 710ms 8.85% TetrahedralMesh::ImportFromMesher 2ms 0.025% 12.07% 604ms 7.53% std::ostream::operator<< (inline) 101ms 1.26% 13.32% 600ms 7.48% std::ostream::_M_insert 1ms 0.012% 13.34% 585ms 7.29% triangulate 56ms 0.7% 14.03% 561ms 6.99% std::map::operator[] (partial-inline) 28ms 0.35% 14.38% 548ms 6.83% operator new 8ms 0.1% 14.48% 538ms 6.71% std::set::insert (inline) 7ms 0.087% 14.57% 530ms 6.61% std::_Rb_tree::_M_insert_unique 0 0% 14.57% 520ms 6.48% delaunay 4ms 0.05% 14.62% 520ms 6.48% divconqdelaunay 3ms 0.037% 14.66% 519ms 6.47% Cell::GetCellProliferativeType 43ms 0.54% 15.19% 517ms 6.44% std::__new_allocator::allocate (inline) 166ms 2.07% 17.26% 512ms 6.38% __GI___libc_malloc 0 0% 17.26% 512ms 6.38% std::allocator_traits::allocate (inline) 509ms 6.34% 23.61% 509ms 6.34% __strcmp_avx2 16ms 0.2% 23.81% 493ms 6.14% std::_Rb_tree::find (inline) 6ms 0.075% 23.88% 487ms 6.07% LegacyCellProliferativeTypesWriter::VisitCell 0 0% 23.88% 467ms 5.82% std::_Rb_tree::lower_bound (inline) 0 0% 23.88% 467ms 5.82% std::map::lower_bound (inline) 4ms 0.05% 23.93% 462ms 5.76% AbstractCellBasedSimulation::DoCellBirth 209ms 2.61% 26.54% 441ms 5.50% __cxxabiv1::__si_class_type_info::__do_dyncast 0 0% 26.54% 435ms 5.42% std::set::count (inline) 35ms 0.44% 26.97% 425ms 5.30% std::_Rb_tree::~_Rb_tree (inline) 0 0% 26.97% 414ms 5.16% std::_Rb_tree::_M_create_node (inline) 0 0% 26.97% 401ms 5.00% std::set::~set (inline) 0 0% 26.97% 395ms 4.92% std::_Rb_tree::_Alloc_node::operator() (inline) 100ms 1.25% 28.22% 387ms 4.82% std::_Rb_tree::_M_erase 2ms 0.025% 28.24% 380ms 4.74% Cell::GetMutationState 0 0% 28.24% 378ms 4.71% std::_Rb_tree::_M_get_node (inline) 26ms 0.32% 28.57% 368ms 4.59% std::_Rb_tree::_Rb_tree (partial-inline) 0 0% 28.57% 344ms 4.29% NodeLocationWriter::Visit 1ms 0.012% 28.58% 336ms 4.19% MeshBasedCellPopulation::GetDampingConstant 3ms 0.037% 28.62% 336ms 4.19% std::set::set (inline) 0 0% 28.62% 335ms 4.18% AbstractCentreBasedCellPopulation::GetDampingConstant 28ms 0.35% 28.97% 334ms 4.16% std::_Rb_tree::_M_insert_ (inline) 8ms 0.1% 29.07% 334ms 4.16% std::less::operator() (inline) 1ms 0.012% 29.08% 332ms 4.14% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 0 0% 29.08% 331ms 4.13% AbstractCellBasedWriter::OpenOutputFileForAppend 7ms 0.087% 29.17% 328ms 4.09% AbstractCellPopulation::IsCellAttachedToLocationIndex 0 0% 29.17% 326ms 4.06% OutputFileHandler::OpenOutputFile 326ms 4.06% 33.23% 326ms 4.06% std::operator< (inline) 40ms 0.5% 33.73% 309ms 3.85% std::_Rb_tree::_M_copy (inline) 8ms 0.1% 33.83% 306ms 3.81% Element::Element 16ms 0.2% 34.03% 303ms 3.78% std::num_put::_M_insert_float 8ms 0.1% 34.13% 301ms 3.75% Cell::ReadyToDivide 295ms 3.68% 37.80% 295ms 3.68% std::_Rb_tree::_S_right (inline) 11ms 0.14% 37.94% 292ms 3.64% divconqrecurse 77ms 0.96% 38.90% 289ms 3.60% __GI___libc_free 65ms 0.81% 39.71% 272ms 3.39% mergehulls 0 0% 39.71% 270ms 3.37% std::_Rb_tree::_M_drop_node (inline) 170ms 2.12% 41.83% 268ms 3.34% _int_malloc 0 0% 41.83% 267ms 3.33% CellProliferativeTypesWriter::VisitCell 67ms 0.84% 42.66% 262ms 3.27% std::_Rb_tree::_M_clone_node (inline) 4ms 0.05% 42.71% 258ms 3.22% CellPropertyCollection::HasProperty 0 0% 42.71% 256ms 3.19% Cell::HasCellProperty (inline) 3ms 0.037% 42.75% 254ms 3.17% AbstractCellProperty::IsType (inline) 11ms 0.14% 42.89% 253ms 3.15% std::__new_allocator::deallocate (inline) 5ms 0.062% 42.95% 248ms 3.09% std::__cxx11::collate::do_transform 0 0% 42.95% 248ms 3.09% std::allocator_traits::deallocate (inline) 0 0% 42.95% 241ms 3.00% ___vsnprintf 0 0% 42.95% 241ms 3.00% __vsnprintf_internal (inline) 38ms 0.47% 43.43% 238ms 2.97% __printf_buffer 0 0% 43.43% 213ms 2.65% std::_Rb_tree::_M_put_node (inline) 173ms 2.16% 45.58% 212ms 2.64% _int_free 9ms 0.11% 45.69% 208ms 2.59% MeshBasedCellPopulation::SpringsEnd (inline) 54ms 0.67% 46.37% 205ms 2.56% AbstractCellProperty::IsSame 8ms 0.1% 46.47% 190ms 2.37% Element::RegisterWithNodes (inline) 61ms 0.76% 47.23% 189ms 2.36% std::_Rb_tree::_M_get_insert_unique_pos (inline) 9ms 0.11% 47.34% 188ms 2.34% TetrahedralMesh::Clear 6ms 0.075% 47.41% 188ms 2.34% __printf_fp_l_buffer 0 0% 47.41% 188ms 2.34% __printf_fp_spec (inline) 2ms 0.025% 47.44% 183ms 2.28% AbstractPhaseBasedCellCycleModel::ReadyToDivide 15ms 0.19% 47.63% 182ms 2.27% AbstractTetrahedralElement::CalculateJacobian 31ms 0.39% 48.01% 182ms 2.27% TetrahedralMesh::EdgesEnd (partial-inline) 7ms 0.087% 48.10% 179ms 2.23% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 5ms 0.062% 48.16% 179ms 2.23% Node::AddElement 0 0% 48.16% 174ms 2.17% TetrahedralMesh::RefreshJacobianCachedData 94ms 1.17% 49.33% 174ms 2.17% __printf_fp_buffer_1 7ms 0.087% 49.42% 160ms 1.99% AbstractTetrahedralElement::CalculateInverseJacobian 38ms 0.47% 49.89% 151ms 1.88% std::type_info::operator== (inline) 0 0% 49.89% 150ms 1.87% AbstractCellPopulation::CloseRoundRobinWritersFiles 2ms 0.025% 49.92% 150ms 1.87% std::basic_filebuf::close 0 0% 49.92% 149ms 1.86% AbstractCellBasedWriter::CloseFile 0 0% 49.92% 149ms 1.86% std::basic_ofstream::close (inline) 0 0% 49.92% 148ms 1.84% std::basic_ofstream::basic_ofstream (inline) 98ms 1.22% 51.14% 146ms 1.82% TetrahedralMesh::EdgeIterator::EdgeIterator (partial-inline) 63ms 0.79% 51.93% 146ms 1.82% std::__ostream_insert 2ms 0.025% 51.95% 145ms 1.81% alternateaxes 0 0% 51.95% 141ms 1.76% FilesystemPermissions::SetFilePermissions (inline) 2ms 0.025% 51.98% 141ms 1.76% std::basic_ofstream::open (inline) 1ms 0.012% 51.99% 141ms 1.76% std::filesystem::permissions 133ms 1.66% 53.65% 141ms 1.76% vertexmedian 140ms 1.74% 55.39% 140ms 1.74% __GI_fchmodat 12ms 0.15% 55.54% 140ms 1.74% boost::detail::shared_count::~shared_count (inline) 0 0% 55.54% 140ms 1.74% boost::shared_ptr::~shared_ptr (inline) 2ms 0.025% 55.57% 139ms 1.73% std::basic_filebuf::open 4ms 0.05% 55.62% 137ms 1.71% boost::numeric::ublas::vector_assign (inline) 136ms 1.70% 57.31% 136ms 1.70% incircle 0 0% 57.31% 135ms 1.68% OutputFileHandler::CommonConstructor 0 0% 57.31% 135ms 1.68% OutputFileHandler::OutputFileHandler 1ms 0.012% 57.32% 135ms 1.68% std::_Vector_base::_M_allocate (inline) 34ms 0.42% 57.75% 135ms 1.68% std::num_put::_M_insert_int 19ms 0.24% 57.98% 133ms 1.66% AbstractTetrahedralElement::RefreshJacobian 1ms 0.012% 58.00% 132ms 1.65% OutputFileHandler::MakeFoldersAndReturnFullPath 4ms 0.05% 58.05% 131ms 1.63% boost::numeric::ublas::c_vector::c_vector (inline) 11ms 0.14% 58.18% 130ms 1.62% AbstractCellPopulation::Iterator::IsRealCell (inline) 1ms 0.012% 58.20% 128ms 1.60% AbstractCellPopulation::Iterator::operator++ (inline) 13ms 0.16% 58.36% 128ms 1.60% MeshBasedCellPopulation::SpringIterator::SpringIterator 49ms 0.61% 58.97% 125ms 1.56% boost::shared_ptr::shared_ptr (inline) 6ms 0.075% 59.04% 121ms 1.51% std::_Rb_tree_const_iterator::operator++ (inline) 2ms 0.025% 59.07% 120ms 1.50% Node::~Node 114ms 1.42% 60.49% 119ms 1.48% boost::detail::sp_counted_base::release 119ms 1.48% 61.97% 119ms 1.48% std::_Rb_tree_increment 2ms 0.025% 62.00% 117ms 1.46% AbstractTetrahedralElement::AbstractTetrahedralElement 13ms 0.16% 62.16% 113ms 1.41% std::vector::push_back (inline) 110ms 1.37% 63.53% 110ms 1.37% std::_Rb_tree_insert_and_rebalance 1ms 0.012% 63.54% 109ms 1.36% _IO_new_fopen 0 0% 63.54% 108ms 1.35% __fopen_internal (inline) 0 0% 63.54% 108ms 1.35% std::__basic_file::open 3ms 0.037% 63.58% 106ms 1.32% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (partial-inline) 1ms 0.012% 63.59% 106ms 1.32% std::operator<< (inline) 0 0% 63.59% 105ms 1.31% _IO_new_file_fopen 2ms 0.025% 63.62% 105ms 1.31% __GI__IO_file_open 3ms 0.037% 63.65% 103ms 1.28% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 0 0% 63.65% 103ms 1.28% std::basic_filebuf::_M_terminate_output 2ms 0.025% 63.68% 103ms 1.28% std::basic_filebuf::overflow 1ms 0.012% 63.69% 101ms 1.26% std::basic_filebuf::_M_convert_to_external 1ms 0.012% 63.70% 100ms 1.25% std::__basic_file::xsputn 99ms 1.23% 64.94% 99ms 1.23% __GI___libc_write 54ms 0.67% 65.61% 97ms 1.21% AbstractElement::GetNodeLocation 2ms 0.025% 65.64% 96ms 1.20% Cell::GetCellId 3ms 0.037% 65.67% 96ms 1.20% std::vector::_M_realloc_insert 57ms 0.71% 66.38% 95ms 1.18% std::basic_filebuf::xsputn 94ms 1.17% 67.56% 94ms 1.17% [libchaste_cell_based.so] 90ms 1.12% 68.68% 90ms 1.12% TetrahedralMesh::EdgeIterator::operator!= (partial-inline) 89ms 1.11% 69.79% 89ms 1.11% __libc_open64 27ms 0.34% 70.12% 88ms 1.10% boost::numeric::ublas::indexing_vector_assign 2ms 0.025% 70.15% 86ms 1.07% AbstractCellPopulation::GetLocationIndexUsingCell 7ms 0.087% 70.24% 82ms 1.02% TetrahedralMesh::EdgeIterator::GetNodeA 82ms 1.02% 71.26% 82ms 1.02% std::vector::size (inline) 54ms 0.67% 71.93% 79ms 0.98% malloc_consolidate 7ms 0.087% 72.02% 77ms 0.96% CellPropertyCollection::AddProperty 76ms 0.95% 72.97% 76ms 0.95% boost::detail::shared_count::shared_count (inline) 0 0% 72.97% 74ms 0.92% FilesystemPermissions::CreateDirectoryWithPermissions (inline) 1ms 0.012% 72.98% 74ms 0.92% std::filesystem::create_directory 72ms 0.9% 73.88% 72ms 0.9% counterclockwise 65ms 0.81% 74.69% 71ms 0.88% vertexsort 70ms 0.87% 75.56% 70ms 0.87% __memcpy_avx_unaligned_erms 0 0% 75.56% 70ms 0.87% tcache_get (inline) 70ms 0.87% 76.43% 70ms 0.87% tcache_get_n (inline) 68ms 0.85% 77.28% 68ms 0.85% Node::GetIndex 34ms 0.42% 77.70% 67ms 0.84% AbstractTetrahedralMesh::GetElement 48ms 0.6% 78.30% 64ms 0.8% AbstractElement::GetNodeGlobalIndex 1ms 0.012% 78.31% 64ms 0.8% TetrahedralMesh::EdgeIterator::GetNodeB 41ms 0.51% 78.82% 64ms 0.8% std::basic_streambuf::xsputn 3ms 0.037% 78.86% 63ms 0.79% Node::ConstructNodeAttributes (inline) 37ms 0.46% 79.32% 63ms 0.79% boost::numeric::ublas::c_matrix::operator() (partial-inline) 0 0% 79.32% 61ms 0.76% std::vector::vector (inline) 0 0% 79.32% 60ms 0.75% Node::ClearAppliedForce 59ms 0.74% 80.06% 59ms 0.74% [libchaste_mesh.so] 58ms 0.72% 80.78% 58ms 0.72% __GI___fstatat64 1ms 0.012% 80.79% 58ms 0.72% std::filesystem::status 0 0% 80.79% 57ms 0.71% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 0 0% 80.79% 57ms 0.71% std::_Rb_tree::_M_destroy_node (inline) 0 0% 80.79% 57ms 0.71% std::__new_allocator::destroy (inline) 0 0% 80.79% 57ms 0.71% std::allocator_traits::destroy (inline) 46ms 0.57% 81.37% 57ms 0.71% std::num_put::do_put 0 0% 81.37% 55ms 0.69% std::map::find (inline) 0 0% 81.37% 53ms 0.66% MeshBasedCellPopulation::SpringIterator::~SpringIterator (inline) 0 0% 81.37% 53ms 0.66% std::_Vector_base::_Vector_base (inline) 0 0% 81.37% 52ms 0.65% AbstractCentreBasedCellPopulation::CreateCellPair 0 0% 81.37% 51ms 0.64% std::_Vector_base::_M_create_storage (inline) 0 0% 81.37% 50ms 0.62% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 81.37% 50ms 0.62% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 0 0% 81.37% 46ms 0.57% NodeAttributes::NodeAttributes 0 0% 81.37% 45ms 0.56% AbstractCentreBasedCellPopulation::IsMarkedSpring 45ms 0.56% 81.93% 45ms 0.56% boost::shared_ptr::operator-> (inline) 28ms 0.35% 82.28% 45ms 0.56% hack_digit 16ms 0.2% 82.48% 44ms 0.55% AbstractTetrahedralMesh::GetNumAllElements 10ms 0.12% 82.60% 44ms 0.55% Determinant (inline) 0 0% 82.60% 44ms 0.55% _dl_init 0 0% 82.60% 44ms 0.55% call_init (inline) 43ms 0.54% 83.14% 43ms 0.54% boost::numeric::ublas::c_vector::operator() (inline) 0 0% 83.14% 42ms 0.52% BoundaryNodeWriter::Visit 42ms 0.52% 83.66% 42ms 0.52% boost::numeric::ublas::same_impl_ex 11ms 0.14% 83.80% 41ms 0.51% Inverse 41ms 0.51% 84.31% 41ms 0.51% [libstdc++.so.6.0.33]