File: Test2dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 6722ms, 83.76% of 8025ms total Dropped 607 nodes (cum <= 40.12ms) flat flat% sum% cum cum% 0 0% 0% 7986ms 99.51% __libc_start_call_main 0 0% 0% 7986ms 99.51% __libc_start_main_impl 0 0% 0% 7986ms 99.51% _start 0 0% 0% 7968ms 99.29% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 7968ms 99.29% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 7968ms 99.29% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 7968ms 99.29% main 0 0% 0% 7928ms 98.79% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 7928ms 98.79% CxxTest::TestRunner::runTest (inline) 0 0% 0% 7928ms 98.79% Test2DMonolayerRepresentativeSimulation::Test2DMonolayerRepresentativeSimulationForProfiling 0 0% 0% 7924ms 98.74% AbstractCellBasedSimulation::Solve 0 0% 0% 3467ms 43.20% AbstractCellBasedSimulation::UpdateCellPopulation 1ms 0.012% 0.012% 2920ms 36.39% MeshBasedCellPopulation::Update 0 0% 0.012% 2842ms 35.41% AbstractCellPopulation::WriteResultsToFiles 0 0% 0.012% 1607ms 20.02% OffLatticeSimulation::UpdateCellLocationsAndTopology 1ms 0.012% 0.025% 1457ms 18.16% ForwardEulerNumericalMethod::UpdateAllNodePositions 0 0% 0.025% 1449ms 18.06% MutableMesh::ReMesh 1ms 0.012% 0.037% 1410ms 17.57% MeshBasedCellPopulation::UpdateNodePairs 8ms 0.1% 0.14% 1406ms 17.52% AbstractNumericalMethod::ComputeForcesIncludingDamping 20ms 0.25% 0.39% 1207ms 15.04% MeshBasedCellPopulation::SpringIterator::operator++ 2ms 0.025% 0.41% 1000ms 12.46% AbstractTwoBodyInteractionForce::AddForceContribution 127ms 1.58% 1.99% 957ms 11.93% TetrahedralMesh::EdgeIterator::operator++ 282ms 3.51% 5.51% 933ms 11.63% __dynamic_cast 410ms 5.11% 10.62% 924ms 11.51% std::_Rb_tree::_M_lower_bound (inline) 5ms 0.062% 10.68% 913ms 11.38% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 8ms 0.1% 10.78% 901ms 11.23% CellPropertyCollection::GetPropertiesType (inline) 57ms 0.71% 11.49% 892ms 11.12% AbstractVariableSizeTwoBodyInteractionForce::CalculateForceBetweenNodes 9ms 0.11% 11.60% 857ms 10.68% CellPopulationElementWriter::Visit 7ms 0.087% 11.69% 761ms 9.48% MeshBasedCellPopulation::AcceptCellWriter 28ms 0.35% 12.04% 751ms 9.36% AbstractCellPopulation::GetCellUsingLocationIndex 1ms 0.012% 12.05% 724ms 9.02% AbstractCellProperty::IsSubType (inline) 10ms 0.12% 12.17% 697ms 8.69% TetrahedralMesh::ImportFromMesher 56ms 0.7% 12.87% 600ms 7.48% std::map::operator[] (partial-inline) 2ms 0.025% 12.90% 576ms 7.18% triangulate 0 0% 12.90% 568ms 7.08% std::ostream::operator<< (inline) 87ms 1.08% 13.98% 566ms 7.05% std::ostream::_M_insert 537ms 6.69% 20.67% 537ms 6.69% __strcmp_avx2 3ms 0.037% 20.71% 532ms 6.63% AbstractCellBasedSimulation::DoCellBirth 27ms 0.34% 21.05% 532ms 6.63% operator new 3ms 0.037% 21.08% 521ms 6.49% Cell::GetCellProliferativeType 1ms 0.012% 21.10% 520ms 6.48% delaunay 1ms 0.012% 21.11% 515ms 6.42% divconqdelaunay 6ms 0.075% 21.18% 515ms 6.42% std::set::insert (inline) 14ms 0.17% 21.36% 509ms 6.34% std::_Rb_tree::_M_insert_unique 170ms 2.12% 23.48% 504ms 6.28% __GI___libc_malloc 27ms 0.34% 23.81% 490ms 6.11% std::__new_allocator::allocate (inline) 0 0% 23.81% 487ms 6.07% std::allocator_traits::allocate (inline) 1ms 0.012% 23.83% 486ms 6.06% LegacyCellProliferativeTypesWriter::VisitCell 22ms 0.27% 24.10% 485ms 6.04% std::_Rb_tree::find (inline) 0 0% 24.10% 483ms 6.02% std::_Rb_tree::lower_bound (inline) 0 0% 24.10% 483ms 6.02% std::map::lower_bound (inline) 41ms 0.51% 24.61% 457ms 5.69% std::_Rb_tree::~_Rb_tree (inline) 214ms 2.67% 27.28% 453ms 5.64% __cxxabiv1::__si_class_type_info::__do_dyncast 0 0% 27.28% 433ms 5.40% std::set::~set (inline) 0 0% 27.28% 427ms 5.32% std::set::count (inline) 84ms 1.05% 28.32% 410ms 5.11% std::_Rb_tree::_M_erase 0 0% 28.32% 396ms 4.93% std::_Rb_tree::_M_create_node (inline) 4ms 0.05% 28.37% 377ms 4.70% Cell::GetMutationState 0 0% 28.37% 371ms 4.62% std::_Rb_tree::_Alloc_node::operator() (inline) 13ms 0.16% 28.54% 367ms 4.57% std::less::operator() (inline) 0 0% 28.54% 362ms 4.51% std::_Rb_tree::_M_get_node (inline) 20ms 0.25% 28.79% 359ms 4.47% std::_Rb_tree::_Rb_tree (partial-inline) 4ms 0.05% 28.83% 357ms 4.45% Cell::ReadyToDivide 354ms 4.41% 33.25% 354ms 4.41% std::operator< (inline) 1ms 0.012% 33.26% 350ms 4.36% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 0 0% 33.26% 348ms 4.34% AbstractCellBasedWriter::OpenOutputFileForAppend 0 0% 33.26% 343ms 4.27% OutputFileHandler::OpenOutputFile 0 0% 33.26% 340ms 4.24% NodeLocationWriter::Visit 1ms 0.012% 33.27% 330ms 4.11% MeshBasedCellPopulation::GetDampingConstant 3ms 0.037% 33.31% 330ms 4.11% std::set::set (inline) 4ms 0.05% 33.36% 329ms 4.10% AbstractCentreBasedCellPopulation::GetDampingConstant 13ms 0.16% 33.52% 323ms 4.02% AbstractCellPopulation::IsCellAttachedToLocationIndex 96ms 1.20% 34.72% 317ms 3.95% __GI___libc_free 308ms 3.84% 38.55% 308ms 3.84% std::_Rb_tree::_S_right (inline) 0 0% 38.55% 303ms 3.78% std::_Rb_tree::_M_drop_node (inline) 19ms 0.24% 38.79% 297ms 3.70% std::_Rb_tree::_M_insert_ (inline) 34ms 0.42% 39.21% 296ms 3.69% std::_Rb_tree::_M_copy (inline) 4ms 0.05% 39.26% 295ms 3.68% Element::Element 9ms 0.11% 39.38% 295ms 3.68% std::__new_allocator::deallocate (inline) 28ms 0.35% 39.73% 293ms 3.65% std::num_put::_M_insert_float 0 0% 39.73% 292ms 3.64% std::allocator_traits::deallocate (inline) 9ms 0.11% 39.84% 288ms 3.59% divconqrecurse 7ms 0.087% 39.93% 277ms 3.45% AbstractCellProperty::IsType (inline) 73ms 0.91% 40.83% 267ms 3.33% mergehulls 173ms 2.16% 42.99% 258ms 3.21% _int_malloc 85ms 1.06% 44.05% 258ms 3.21% std::_Rb_tree::_M_clone_node (inline) 0 0% 44.05% 256ms 3.19% Cell::HasCellProperty (inline) 2ms 0.025% 44.07% 255ms 3.18% CellPropertyCollection::HasProperty 0 0% 44.07% 248ms 3.09% std::_Rb_tree::_M_put_node (inline) 3ms 0.037% 44.11% 241ms 3.00% AbstractPhaseBasedCellCycleModel::ReadyToDivide 3ms 0.037% 44.15% 239ms 2.98% CellProliferativeTypesWriter::VisitCell 6ms 0.075% 44.22% 235ms 2.93% std::__cxx11::collate::do_transform 3ms 0.037% 44.26% 233ms 2.90% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 194ms 2.42% 46.68% 220ms 2.74% _int_free 60ms 0.75% 47.43% 217ms 2.70% AbstractCellProperty::IsSame 3ms 0.037% 47.46% 215ms 2.68% ___vsnprintf 0 0% 47.46% 212ms 2.64% __vsnprintf_internal (inline) 25ms 0.31% 47.78% 210ms 2.62% __printf_buffer 10ms 0.12% 47.90% 203ms 2.53% MeshBasedCellPopulation::SpringsEnd (inline) 66ms 0.82% 48.72% 198ms 2.47% std::_Rb_tree::_M_get_insert_unique_pos (inline) 16ms 0.2% 48.92% 195ms 2.43% TetrahedralMesh::Clear 6ms 0.075% 49.00% 187ms 2.33% Element::RegisterWithNodes (inline) 5ms 0.062% 49.06% 178ms 2.22% Node::AddElement 10ms 0.12% 49.18% 177ms 2.21% __printf_fp_l_buffer 0 0% 49.18% 177ms 2.21% __printf_fp_spec (inline) 17ms 0.21% 49.40% 176ms 2.19% AbstractTetrahedralElement::CalculateJacobian 38ms 0.47% 49.87% 167ms 2.08% TetrahedralMesh::EdgesEnd (partial-inline) 0 0% 49.87% 158ms 1.97% std::basic_ofstream::basic_ofstream (inline) 32ms 0.4% 50.27% 157ms 1.96% std::type_info::operator== (inline) 1ms 0.012% 50.28% 155ms 1.93% std::basic_filebuf::open 0 0% 50.28% 155ms 1.93% std::basic_ofstream::open (inline) 0 0% 50.28% 153ms 1.91% FilesystemPermissions::SetFilePermissions (inline) 0 0% 50.28% 153ms 1.91% std::filesystem::permissions 0 0% 50.28% 152ms 1.89% OutputFileHandler::CommonConstructor 0 0% 50.28% 152ms 1.89% OutputFileHandler::OutputFileHandler 151ms 1.88% 52.16% 151ms 1.88% __GI_fchmodat 0 0% 52.16% 150ms 1.87% TetrahedralMesh::RefreshJacobianCachedData 84ms 1.05% 53.21% 150ms 1.87% __printf_fp_buffer_1 0 0% 53.21% 145ms 1.81% OutputFileHandler::MakeFoldersAndReturnFullPath 8ms 0.1% 53.31% 144ms 1.79% AbstractTetrahedralElement::CalculateInverseJacobian 0 0% 53.31% 143ms 1.78% AbstractCellBasedWriter::CloseFile 0 0% 53.31% 143ms 1.78% AbstractCellPopulation::CloseRoundRobinWritersFiles 2ms 0.025% 53.33% 143ms 1.78% std::basic_filebuf::close 0 0% 53.33% 143ms 1.78% std::basic_ofstream::close (inline) 16ms 0.2% 53.53% 140ms 1.74% AbstractCellPopulation::Iterator::IsRealCell (inline) 0 0% 53.53% 139ms 1.73% AbstractCellPopulation::Iterator::operator++ (inline) 18ms 0.22% 53.76% 133ms 1.66% MeshBasedCellPopulation::SpringIterator::SpringIterator 1ms 0.012% 53.77% 132ms 1.64% alternateaxes 47ms 0.59% 54.36% 130ms 1.62% std::__ostream_insert 119ms 1.48% 55.84% 130ms 1.62% vertexmedian 23ms 0.29% 56.12% 129ms 1.61% AbstractTetrahedralElement::RefreshJacobian 0 0% 56.12% 127ms 1.58% _IO_new_fopen 0 0% 56.12% 127ms 1.58% __fopen_internal (inline) 1ms 0.012% 56.14% 126ms 1.57% std::_Vector_base::_M_allocate (inline) 0 0% 56.14% 126ms 1.57% std::__basic_file::open 4ms 0.05% 56.19% 125ms 1.56% boost::numeric::ublas::vector_assign (inline) 23ms 0.29% 56.47% 123ms 1.53% std::num_put::_M_insert_int 1ms 0.012% 56.49% 122ms 1.52% _IO_new_file_fopen 7ms 0.087% 56.57% 122ms 1.52% boost::numeric::ublas::c_vector::c_vector (inline) 17ms 0.21% 56.79% 121ms 1.51% boost::detail::shared_count::~shared_count (inline) 0 0% 56.79% 121ms 1.51% boost::shared_ptr::~shared_ptr (inline) 0 0% 56.79% 120ms 1.50% __GI__IO_file_open 8ms 0.1% 56.88% 119ms 1.48% Node::~Node 119ms 1.48% 58.37% 119ms 1.48% incircle 80ms 1% 59.36% 116ms 1.45% TetrahedralMesh::EdgeIterator::EdgeIterator (partial-inline) 2ms 0.025% 59.39% 114ms 1.42% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (partial-inline) 57ms 0.71% 60.10% 114ms 1.42% boost::shared_ptr::shared_ptr (inline) 2ms 0.025% 60.12% 112ms 1.40% AbstractTetrahedralElement::AbstractTetrahedralElement 111ms 1.38% 61.51% 111ms 1.38% __libc_open64 5ms 0.062% 61.57% 110ms 1.37% std::vector::push_back (inline) 1ms 0.012% 61.58% 109ms 1.36% std::operator<< (inline) 105ms 1.31% 62.89% 105ms 1.31% [libchaste_cell_based.so] 1ms 0.012% 62.90% 103ms 1.28% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 61ms 0.76% 63.66% 101ms 1.26% std::basic_filebuf::xsputn 1ms 0.012% 63.68% 100ms 1.25% std::basic_filebuf::_M_convert_to_external 0 0% 63.68% 100ms 1.25% std::basic_filebuf::_M_terminate_output 0 0% 63.68% 100ms 1.25% std::basic_filebuf::overflow 1ms 0.012% 63.69% 99ms 1.23% std::__basic_file::xsputn 11ms 0.14% 63.83% 99ms 1.23% std::vector::_M_realloc_insert 97ms 1.21% 65.03% 97ms 1.21% __GI___libc_write 89ms 1.11% 66.14% 96ms 1.20% boost::detail::sp_counted_base::release 7ms 0.087% 66.23% 95ms 1.18% std::_Rb_tree_const_iterator::operator++ (inline) 1ms 0.012% 66.24% 93ms 1.16% AbstractCellPopulation::GetLocationIndexUsingCell 93ms 1.16% 67.40% 93ms 1.16% std::_Rb_tree_increment 33ms 0.41% 67.81% 91ms 1.13% AbstractElement::GetNodeLocation 26ms 0.32% 68.14% 90ms 1.12% boost::numeric::ublas::indexing_vector_assign 88ms 1.10% 69.23% 88ms 1.10% TetrahedralMesh::EdgeIterator::operator!= (partial-inline) 80ms 1% 70.23% 88ms 1.10% vertexsort 0 0% 70.23% 85ms 1.06% FilesystemPermissions::CreateDirectoryWithPermissions (inline) 2ms 0.025% 70.26% 85ms 1.06% std::filesystem::create_directory 1ms 0.012% 70.27% 81ms 1.01% Cell::GetCellId 80ms 1% 71.26% 80ms 1% std::_Rb_tree_insert_and_rebalance 79ms 0.98% 72.25% 79ms 0.98% std::vector::size (inline) 2ms 0.025% 72.27% 78ms 0.97% std::filesystem::status 77ms 0.96% 73.23% 77ms 0.96% __GI___fstatat64 77ms 0.96% 74.19% 77ms 0.96% counterclockwise 6ms 0.075% 74.27% 72ms 0.9% TetrahedralMesh::EdgeIterator::GetNodeB 0 0% 74.27% 71ms 0.88% tcache_get (inline) 71ms 0.88% 75.15% 71ms 0.88% tcache_get_n (inline) 43ms 0.54% 75.69% 68ms 0.85% malloc_consolidate 0 0% 75.69% 66ms 0.82% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 2ms 0.025% 75.71% 65ms 0.81% TetrahedralMesh::EdgeIterator::GetNodeA 65ms 0.81% 76.52% 65ms 0.81% __memcpy_avx_unaligned_erms 7ms 0.087% 76.61% 64ms 0.8% CellPropertyCollection::AddProperty 0 0% 76.61% 63ms 0.79% MeshBasedCellPopulation::SpringIterator::~SpringIterator (inline) 61ms 0.76% 77.37% 61ms 0.76% Node::GetIndex 6ms 0.075% 77.45% 61ms 0.76% std::_Rb_tree::_M_emplace_hint_unique 60ms 0.75% 78.19% 60ms 0.75% [libstdc++.so.6.0.33] 50ms 0.62% 78.82% 60ms 0.75% std::num_put::do_put 56ms 0.7% 79.51% 57ms 0.71% boost::detail::shared_count::shared_count (inline) 24ms 0.3% 79.81% 55ms 0.69% AbstractTetrahedralMesh::GetElement 38ms 0.47% 80.29% 55ms 0.69% boost::numeric::ublas::c_matrix::operator() (partial-inline) 0 0% 80.29% 55ms 0.69% std::_Rb_tree::_M_destroy_node (inline) 0 0% 80.29% 55ms 0.69% std::__new_allocator::destroy (inline) 0 0% 80.29% 55ms 0.69% std::allocator_traits::destroy (inline) 0 0% 80.29% 53ms 0.66% std::vector::vector (inline) 0 0% 80.29% 51ms 0.64% std::_Vector_base::_Vector_base (inline) 35ms 0.44% 80.72% 51ms 0.64% std::basic_streambuf::xsputn 24ms 0.3% 81.02% 50ms 0.62% AbstractTetrahedralMesh::GetNumAllElements 0 0% 81.02% 50ms 0.62% std::map::find (inline) 1ms 0.012% 81.03% 49ms 0.61% AbstractCentreBasedCellPopulation::CreateCellPair 34ms 0.42% 81.46% 49ms 0.61% AbstractElement::GetNodeGlobalIndex 1ms 0.012% 81.47% 49ms 0.61% std::_Vector_base::_M_create_storage (inline) 0 0% 81.47% 48ms 0.6% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 81.47% 48ms 0.6% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 0 0% 81.47% 46ms 0.57% BoundaryNodeWriter::Visit 45ms 0.56% 82.03% 45ms 0.56% Node::rGetLocation 3ms 0.037% 82.07% 45ms 0.56% std::_Vector_base::_M_deallocate (inline) 23ms 0.29% 82.36% 43ms 0.54% AbstractCellCycleModel::GetAge 43ms 0.54% 82.89% 43ms 0.54% boost::shared_ptr::operator-> (inline) 43ms 0.54% 83.43% 43ms 0.54% std::ostream::sentry::sentry 24ms 0.3% 83.73% 42ms 0.52% hack_digit 3ms 0.037% 83.76% 41ms 0.51% std::__basic_file::close