File: Test2dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 6591ms, 83.99% of 7847ms total Dropped 591 nodes (cum <= 39.23ms) flat flat% sum% cum cum% 0 0% 0% 7813ms 99.57% __libc_start_call_main 0 0% 0% 7813ms 99.57% __libc_start_main_impl 0 0% 0% 7813ms 99.57% _start 0 0% 0% 7799ms 99.39% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 7799ms 99.39% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 7799ms 99.39% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 7799ms 99.39% main 0 0% 0% 7761ms 98.90% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 7761ms 98.90% CxxTest::TestRunner::runTest (inline) 0 0% 0% 7761ms 98.90% Test2DMonolayerRepresentativeSimulation::Test2DMonolayerRepresentativeSimulationForProfiling 0 0% 0% 7758ms 98.87% AbstractCellBasedSimulation::Solve 1ms 0.013% 0.013% 3340ms 42.56% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0.013% 2876ms 36.65% AbstractCellPopulation::WriteResultsToFiles 2ms 0.025% 0.038% 2873ms 36.61% MeshBasedCellPopulation::Update 1ms 0.013% 0.051% 1532ms 19.52% OffLatticeSimulation::UpdateCellLocationsAndTopology 1ms 0.013% 0.064% 1425ms 18.16% MutableMesh::ReMesh 0 0% 0.064% 1394ms 17.76% ForwardEulerNumericalMethod::UpdateAllNodePositions 3ms 0.038% 0.1% 1391ms 17.73% MeshBasedCellPopulation::UpdateNodePairs 8ms 0.1% 0.2% 1346ms 17.15% AbstractNumericalMethod::ComputeForcesIncludingDamping 15ms 0.19% 0.4% 1217ms 15.51% MeshBasedCellPopulation::SpringIterator::operator++ 101ms 1.29% 1.68% 998ms 12.72% TetrahedralMesh::EdgeIterator::operator++ 432ms 5.51% 7.19% 962ms 12.26% std::_Rb_tree::_M_lower_bound (inline) 4ms 0.051% 7.24% 920ms 11.72% AbstractTwoBodyInteractionForce::AddForceContribution 1ms 0.013% 7.25% 919ms 11.71% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 16ms 0.2% 7.46% 897ms 11.43% CellPropertyCollection::GetPropertiesType (inline) 6ms 0.076% 7.53% 873ms 11.13% CellPopulationElementWriter::Visit 243ms 3.10% 10.63% 857ms 10.92% __dynamic_cast 31ms 0.4% 11.02% 822ms 10.48% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 4ms 0.051% 11.07% 792ms 10.09% MeshBasedCellPopulation::AcceptCellWriter 26ms 0.33% 11.41% 760ms 9.69% AbstractCellPopulation::GetCellUsingLocationIndex 9ms 0.11% 11.52% 717ms 9.14% TetrahedralMesh::ImportFromMesher 5ms 0.064% 11.58% 678ms 8.64% AbstractCellProperty::IsSubType (inline) 82ms 1.04% 12.63% 611ms 7.79% std::ostream::_M_insert 0 0% 12.63% 611ms 7.79% std::ostream::operator<< (inline) 43ms 0.55% 13.18% 587ms 7.48% operator new 49ms 0.62% 13.80% 583ms 7.43% std::map::operator[] (partial-inline) 8ms 0.1% 13.90% 546ms 6.96% Cell::GetCellProliferativeType 181ms 2.31% 16.21% 540ms 6.88% __GI___libc_malloc 24ms 0.31% 16.52% 536ms 6.83% std::_Rb_tree::find (inline) 3ms 0.038% 16.55% 530ms 6.75% std::set::insert (inline) 4ms 0.051% 16.61% 530ms 6.75% triangulate 35ms 0.45% 17.05% 528ms 6.73% std::__new_allocator::allocate (inline) 8ms 0.1% 17.15% 527ms 6.72% std::_Rb_tree::_M_insert_unique 0 0% 17.15% 525ms 6.69% std::allocator_traits::allocate (inline) 504ms 6.42% 23.58% 504ms 6.42% __strcmp_avx2 0 0% 23.58% 498ms 6.35% std::set::count (inline) 4ms 0.051% 23.63% 481ms 6.13% LegacyCellProliferativeTypesWriter::VisitCell 0 0% 23.63% 480ms 6.12% std::_Rb_tree::lower_bound (inline) 0 0% 23.63% 480ms 6.12% std::map::lower_bound (inline) 0 0% 23.63% 457ms 5.82% delaunay 1ms 0.013% 23.64% 457ms 5.82% divconqdelaunay 0 0% 23.64% 452ms 5.76% std::_Rb_tree::_M_create_node (inline) 5ms 0.064% 23.70% 451ms 5.75% AbstractCellBasedSimulation::DoCellBirth 196ms 2.50% 26.20% 447ms 5.70% __cxxabiv1::__si_class_type_info::__do_dyncast 0 0% 26.20% 432ms 5.51% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 26.20% 420ms 5.35% std::_Rb_tree::_M_get_node (inline) 28ms 0.36% 26.56% 388ms 4.94% std::_Rb_tree::_Rb_tree (partial-inline) 34ms 0.43% 26.99% 382ms 4.87% std::_Rb_tree::~_Rb_tree (inline) 2ms 0.025% 27.02% 374ms 4.77% NodeLocationWriter::Visit 0 0% 27.02% 370ms 4.72% std::set::~set (inline) 5ms 0.064% 27.08% 355ms 4.52% Cell::GetMutationState 16ms 0.2% 27.28% 354ms 4.51% std::less::operator() (inline) 16ms 0.2% 27.49% 352ms 4.49% std::_Rb_tree::_M_insert_ (inline) 77ms 0.98% 28.47% 346ms 4.41% std::_Rb_tree::_M_erase 3ms 0.038% 28.51% 344ms 4.38% std::set::set (inline) 0 0% 28.51% 341ms 4.35% AbstractCellBasedWriter::OpenOutputFileForAppend 0 0% 28.51% 341ms 4.35% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 18ms 0.23% 28.74% 340ms 4.33% std::num_put::_M_insert_float 338ms 4.31% 33.04% 338ms 4.31% std::operator< (inline) 0 0% 33.04% 336ms 4.28% OutputFileHandler::OpenOutputFile 3ms 0.038% 33.08% 328ms 4.18% MeshBasedCellPopulation::GetDampingConstant 3ms 0.038% 33.12% 325ms 4.14% AbstractCentreBasedCellPopulation::GetDampingConstant 33ms 0.42% 33.54% 316ms 4.03% std::_Rb_tree::_M_copy (inline) 316ms 4.03% 37.57% 316ms 4.03% std::_Rb_tree::_S_right (inline) 3ms 0.038% 37.61% 314ms 4.00% Cell::ReadyToDivide 9ms 0.11% 37.72% 305ms 3.89% Element::Element 99ms 1.26% 38.98% 295ms 3.76% __GI___libc_free 7ms 0.089% 39.07% 294ms 3.75% AbstractCellPopulation::IsCellAttachedToLocationIndex 191ms 2.43% 41.51% 284ms 3.62% _int_malloc 5ms 0.064% 41.57% 279ms 3.56% std::__cxx11::collate::do_transform 80ms 1.02% 42.59% 274ms 3.49% std::_Rb_tree::_M_clone_node (inline) 1ms 0.013% 42.60% 271ms 3.45% CellProliferativeTypesWriter::VisitCell 11ms 0.14% 42.74% 271ms 3.45% divconqrecurse 1ms 0.013% 42.76% 268ms 3.42% ___vsnprintf 0 0% 42.76% 267ms 3.40% __vsnprintf_internal (inline) 34ms 0.43% 43.19% 261ms 3.33% __printf_buffer 81ms 1.03% 44.22% 251ms 3.20% mergehulls 4ms 0.051% 44.27% 244ms 3.11% AbstractCellProperty::IsType (inline) 7ms 0.089% 44.36% 241ms 3.07% std::__new_allocator::deallocate (inline) 0 0% 44.36% 238ms 3.03% std::_Rb_tree::_M_drop_node (inline) 0 0% 44.36% 230ms 2.93% std::allocator_traits::deallocate (inline) 0 0% 44.36% 226ms 2.88% Cell::HasCellProperty (inline) 4ms 0.051% 44.41% 225ms 2.87% CellPropertyCollection::HasProperty 5ms 0.064% 44.48% 212ms 2.70% AbstractPhaseBasedCellCycleModel::ReadyToDivide 6ms 0.076% 44.55% 210ms 2.68% __printf_fp_l_buffer 0 0% 44.55% 210ms 2.68% __printf_fp_spec (inline) 7ms 0.089% 44.64% 203ms 2.59% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 5ms 0.064% 44.70% 201ms 2.56% Element::RegisterWithNodes (inline) 15ms 0.19% 44.90% 199ms 2.54% TetrahedralMesh::Clear 103ms 1.31% 46.21% 196ms 2.50% __printf_fp_buffer_1 172ms 2.19% 48.40% 196ms 2.50% _int_free 1ms 0.013% 48.41% 195ms 2.49% Node::AddElement 5ms 0.064% 48.48% 191ms 2.43% MeshBasedCellPopulation::SpringsEnd (inline) 0 0% 48.48% 185ms 2.36% std::_Rb_tree::_M_put_node (inline) 14ms 0.18% 48.66% 167ms 2.13% AbstractTetrahedralElement::CalculateJacobian 58ms 0.74% 49.39% 167ms 2.13% std::_Rb_tree::_M_get_insert_unique_pos (inline) 38ms 0.48% 49.88% 163ms 2.08% AbstractCellProperty::IsSame 0 0% 49.88% 162ms 2.06% std::basic_ofstream::basic_ofstream (inline) 1ms 0.013% 49.89% 160ms 2.04% TetrahedralMesh::RefreshJacobianCachedData 1ms 0.013% 49.90% 155ms 1.98% std::basic_filebuf::open 0 0% 49.90% 155ms 1.98% std::basic_ofstream::open (inline) 42ms 0.54% 50.44% 149ms 1.90% TetrahedralMesh::EdgesEnd (partial-inline) 4ms 0.051% 50.49% 148ms 1.89% AbstractTetrahedralElement::CalculateInverseJacobian 0 0% 50.49% 148ms 1.89% OutputFileHandler::CommonConstructor 0 0% 50.49% 148ms 1.89% OutputFileHandler::OutputFileHandler 0 0% 50.49% 147ms 1.87% FilesystemPermissions::SetFilePermissions (inline) 1ms 0.013% 50.50% 147ms 1.87% std::filesystem::permissions 146ms 1.86% 52.36% 146ms 1.86% __GI_fchmodat 0 0% 52.36% 141ms 1.80% std::basic_filebuf::close 0 0% 52.36% 140ms 1.78% AbstractCellBasedWriter::CloseFile 0 0% 52.36% 140ms 1.78% AbstractCellPopulation::CloseRoundRobinWritersFiles 0 0% 52.36% 140ms 1.78% OutputFileHandler::MakeFoldersAndReturnFullPath 0 0% 52.36% 140ms 1.78% std::basic_ofstream::close (inline) 41ms 0.52% 52.89% 138ms 1.76% std::num_put::_M_insert_int 1ms 0.013% 52.90% 134ms 1.71% boost::numeric::ublas::vector_assign (inline) 59ms 0.75% 53.65% 134ms 1.71% std::__ostream_insert 4ms 0.051% 53.70% 125ms 1.59% boost::numeric::ublas::c_vector::c_vector (inline) 20ms 0.25% 53.96% 125ms 1.59% std::type_info::operator== (inline) 13ms 0.17% 54.12% 121ms 1.54% MeshBasedCellPopulation::SpringIterator::SpringIterator 1ms 0.013% 54.14% 121ms 1.54% _IO_new_fopen 0 0% 54.14% 120ms 1.53% __fopen_internal (inline) 0 0% 54.14% 120ms 1.53% std::__basic_file::open 15ms 0.19% 54.33% 119ms 1.52% AbstractTetrahedralElement::RefreshJacobian 6ms 0.076% 54.40% 119ms 1.52% Node::~Node 0 0% 54.40% 119ms 1.52% _IO_new_file_fopen 1ms 0.013% 54.42% 118ms 1.50% __GI__IO_file_open 7ms 0.089% 54.50% 112ms 1.43% std::vector::push_back (inline) 1ms 0.013% 54.52% 111ms 1.41% alternateaxes 111ms 1.41% 55.93% 111ms 1.41% std::_Rb_tree_insert_and_rebalance 9ms 0.11% 56.05% 110ms 1.40% std::_Rb_tree_const_iterator::operator++ (inline) 103ms 1.31% 57.36% 110ms 1.40% vertexmedian 107ms 1.36% 58.72% 107ms 1.36% incircle 1ms 0.013% 58.74% 105ms 1.34% AbstractTetrahedralElement::AbstractTetrahedralElement 103ms 1.31% 60.05% 105ms 1.34% __libc_open64 105ms 1.34% 61.39% 105ms 1.34% std::_Rb_tree_increment 0 0% 61.39% 105ms 1.34% std::_Vector_base::_M_allocate (inline) 8ms 0.1% 61.49% 104ms 1.33% boost::detail::shared_count::~shared_count (inline) 0 0% 61.49% 104ms 1.33% boost::shared_ptr::~shared_ptr (inline) 20ms 0.25% 61.74% 103ms 1.31% AbstractCellPopulation::Iterator::IsRealCell (inline) 0 0% 61.74% 103ms 1.31% AbstractCellPopulation::Iterator::operator++ (inline) 4ms 0.051% 61.79% 103ms 1.31% std::operator<< (inline) 9ms 0.11% 61.91% 103ms 1.31% std::vector::_M_realloc_insert 102ms 1.30% 63.21% 102ms 1.30% [libchaste_cell_based.so] 2ms 0.025% 63.23% 101ms 1.29% std::basic_filebuf::_M_terminate_output 65ms 0.83% 64.06% 100ms 1.27% TetrahedralMesh::EdgeIterator::EdgeIterator (partial-inline) 1ms 0.013% 64.08% 99ms 1.26% std::__basic_file::xsputn 0 0% 64.08% 99ms 1.26% std::basic_filebuf::_M_convert_to_external 0 0% 64.08% 99ms 1.26% std::basic_filebuf::overflow 97ms 1.24% 65.31% 98ms 1.25% __GI___libc_write 94ms 1.20% 66.51% 95ms 1.21% boost::detail::sp_counted_base::release 23ms 0.29% 66.80% 92ms 1.17% boost::numeric::ublas::indexing_vector_assign 34ms 0.43% 67.24% 92ms 1.17% boost::shared_ptr::shared_ptr (inline) 89ms 1.13% 68.37% 89ms 1.13% TetrahedralMesh::EdgeIterator::operator!= (partial-inline) 39ms 0.5% 68.87% 88ms 1.12% AbstractElement::GetNodeLocation 7ms 0.089% 68.96% 85ms 1.08% CellPropertyCollection::AddProperty 53ms 0.68% 69.63% 82ms 1.04% std::basic_filebuf::xsputn 0 0% 69.63% 80ms 1.02% FilesystemPermissions::CreateDirectoryWithPermissions (inline) 2ms 0.025% 69.66% 80ms 1.02% std::filesystem::create_directory 0 0% 69.66% 76ms 0.97% Cell::GetCellId 76ms 0.97% 70.63% 76ms 0.97% Node::GetIndex 76ms 0.97% 71.59% 76ms 0.97% [libchaste_mesh.so] 3ms 0.038% 71.63% 73ms 0.93% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (partial-inline) 2ms 0.025% 71.66% 73ms 0.93% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 1ms 0.013% 71.67% 69ms 0.88% std::filesystem::status 68ms 0.87% 72.54% 68ms 0.87% __GI___fstatat64 61ms 0.78% 73.31% 68ms 0.87% vertexsort 55ms 0.7% 74.02% 67ms 0.85% std::basic_streambuf::xsputn 4ms 0.051% 74.07% 64ms 0.82% TetrahedralMesh::EdgeIterator::GetNodeB 64ms 0.82% 74.88% 64ms 0.82% __memcpy_avx_unaligned_erms 48ms 0.61% 75.49% 64ms 0.82% std::num_put::do_put 1ms 0.013% 75.51% 63ms 0.8% tcache_get (inline) 0 0% 75.51% 62ms 0.79% AbstractCellPopulation::GetLocationIndexUsingCell 41ms 0.52% 76.03% 62ms 0.79% malloc_consolidate 62ms 0.79% 76.82% 62ms 0.79% tcache_get_n (inline) 1ms 0.013% 76.83% 61ms 0.78% Node::ConstructNodeAttributes (inline) 51ms 0.65% 77.48% 60ms 0.76% AbstractElement::GetNodeGlobalIndex 0 0% 77.48% 60ms 0.76% Node::ClearAppliedForce 60ms 0.76% 78.25% 60ms 0.76% counterclockwise 56ms 0.71% 78.96% 58ms 0.74% boost::detail::shared_count::shared_count (inline) 0 0% 78.96% 56ms 0.71% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 78.96% 56ms 0.71% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 56ms 0.71% 79.67% 56ms 0.71% std::vector::size (inline) 0 0% 79.67% 54ms 0.69% std::_Rb_tree::_M_emplace_hint_unique 22ms 0.28% 79.95% 53ms 0.68% AbstractTetrahedralMesh::GetElement 38ms 0.48% 80.44% 53ms 0.68% boost::numeric::ublas::c_matrix::operator() 53ms 0.68% 81.11% 53ms 0.68% boost::numeric::ublas::c_vector::operator() (partial-inline) 0 0% 81.11% 53ms 0.68% std::_Rb_tree::_M_destroy_node (inline) 0 0% 81.11% 53ms 0.68% std::__new_allocator::destroy (inline) 0 0% 81.11% 53ms 0.68% std::allocator_traits::destroy (inline) 3ms 0.038% 81.15% 51ms 0.65% AbstractCentreBasedCellPopulation::CreateCellPair 20ms 0.25% 81.41% 51ms 0.65% Determinant (inline) 1ms 0.013% 81.42% 51ms 0.65% TetrahedralMesh::EdgeIterator::GetNodeA 29ms 0.37% 81.79% 50ms 0.64% AbstractCellCycleModel::GetAge 31ms 0.4% 82.18% 49ms 0.62% hack_digit 1ms 0.013% 82.20% 48ms 0.61% AbstractTetrahedralElement::~AbstractTetrahedralElement (inline) 48ms 0.61% 82.81% 48ms 0.61% Node::IsDeleted 0 0% 82.81% 48ms 0.61% std::map::map (inline) 4ms 0.051% 82.86% 47ms 0.6% NodeAttributes::NodeAttributes 4ms 0.051% 82.91% 46ms 0.59% Element::~Element 3ms 0.038% 82.95% 46ms 0.59% std::_Vector_base::_M_deallocate (inline) 0 0% 82.95% 44ms 0.56% std::vector::vector (inline) 0 0% 82.95% 43ms 0.55% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 1ms 0.013% 82.96% 42ms 0.54% BoundaryNodeWriter::Visit 41ms 0.52% 83.48% 41ms 0.52% [libstdc++.so.6.0.33] 0 0% 83.48% 40ms 0.51% MeshBasedCellPopulation::SpringIterator::~SpringIterator (inline) 0 0% 83.48% 40ms 0.51% std::_Vector_base::_Vector_base (inline) 40ms 0.51% 83.99% 40ms 0.51% unlink_chunk