File: Test2dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 6879ms, 85.72% of 8025ms total Dropped 591 nodes (cum <= 40.12ms) flat flat% sum% cum cum% 0 0% 0% 7989ms 99.55% __libc_start_call_main 0 0% 0% 7989ms 99.55% __libc_start_main_impl 0 0% 0% 7989ms 99.55% _start 0 0% 0% 7971ms 99.33% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 7971ms 99.33% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 7971ms 99.33% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 7971ms 99.33% main 0 0% 0% 7931ms 98.83% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 7931ms 98.83% CxxTest::TestRunner::runTest (inline) 0 0% 0% 7931ms 98.83% Test2DMonolayerRepresentativeSimulation::Test2DMonolayerRepresentativeSimulationForProfiling 0 0% 0% 7928ms 98.79% AbstractCellBasedSimulation::Solve 1ms 0.012% 0.012% 3389ms 42.23% AbstractCellBasedSimulation::UpdateCellPopulation 3ms 0.037% 0.05% 2948ms 36.74% MeshBasedCellPopulation::Update 1ms 0.012% 0.062% 2947ms 36.72% AbstractCellPopulation::WriteResultsToFiles 0 0% 0.062% 1583ms 19.73% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 0.062% 1468ms 18.29% MutableMesh::ReMesh 2ms 0.025% 0.087% 1427ms 17.78% MeshBasedCellPopulation::UpdateNodePairs 0 0% 0.087% 1411ms 17.58% ForwardEulerNumericalMethod::UpdateAllNodePositions 5ms 0.062% 0.15% 1359ms 16.93% AbstractNumericalMethod::ComputeForcesIncludingDamping 19ms 0.24% 0.39% 1202ms 14.98% MeshBasedCellPopulation::SpringIterator::operator++ 1ms 0.012% 0.4% 973ms 12.12% AbstractTwoBodyInteractionForce::AddForceContribution 108ms 1.35% 1.74% 955ms 11.90% TetrahedralMesh::EdgeIterator::operator++ 2ms 0.025% 1.77% 951ms 11.85% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 266ms 3.31% 5.08% 946ms 11.79% __dynamic_cast 437ms 5.45% 10.53% 937ms 11.68% std::_Rb_tree::_M_lower_bound (inline) 11ms 0.14% 10.67% 915ms 11.40% CellPopulationElementWriter::Visit 10ms 0.12% 10.79% 888ms 11.07% CellPropertyCollection::GetPropertiesType (inline) 47ms 0.59% 11.38% 862ms 10.74% GeneralisedLinearSpringForce::CalculateForceBetweenNodes (partial-inline) 10ms 0.12% 11.50% 801ms 9.98% MeshBasedCellPopulation::AcceptCellWriter 35ms 0.44% 11.94% 758ms 9.45% AbstractCellPopulation::GetCellUsingLocationIndex 11ms 0.14% 12.07% 727ms 9.06% TetrahedralMesh::ImportFromMesher 3ms 0.037% 12.11% 702ms 8.75% AbstractCellProperty::IsSubType (inline) 69ms 0.86% 12.97% 608ms 7.58% std::map::operator[] (partial-inline) 2ms 0.025% 13.00% 582ms 7.25% std::ostream::operator<< (inline) 77ms 0.96% 13.96% 574ms 7.15% std::ostream::_M_insert 3ms 0.037% 13.99% 560ms 6.98% triangulate 28ms 0.35% 14.34% 556ms 6.93% operator new 538ms 6.70% 21.05% 538ms 6.70% __strcmp_avx2 6ms 0.075% 21.12% 528ms 6.58% LegacyCellProliferativeTypesWriter::VisitCell 2ms 0.025% 21.15% 519ms 6.47% std::set::insert (inline) 12ms 0.15% 21.30% 517ms 6.44% std::_Rb_tree::_M_insert_unique 39ms 0.49% 21.78% 515ms 6.42% std::__new_allocator::allocate (inline) 6ms 0.075% 21.86% 514ms 6.40% Cell::GetCellProliferativeType 148ms 1.84% 23.70% 514ms 6.40% __GI___libc_malloc 0 0% 23.70% 512ms 6.38% std::allocator_traits::allocate (inline) 217ms 2.70% 26.40% 500ms 6.23% __cxxabiv1::__si_class_type_info::__do_dyncast 0 0% 26.40% 495ms 6.17% delaunay 1ms 0.012% 26.42% 491ms 6.12% divconqdelaunay 0 0% 26.42% 488ms 6.08% std::_Rb_tree::lower_bound (inline) 0 0% 26.42% 488ms 6.08% std::map::lower_bound (inline) 16ms 0.2% 26.62% 483ms 6.02% std::_Rb_tree::find (inline) 0 0% 26.62% 444ms 5.53% std::set::count (inline) 40ms 0.5% 27.12% 443ms 5.52% std::_Rb_tree::~_Rb_tree (inline) 5ms 0.062% 27.18% 427ms 5.32% AbstractCellBasedSimulation::DoCellBirth 0 0% 27.18% 419ms 5.22% std::_Rb_tree::_M_create_node (inline) 0 0% 27.18% 411ms 5.12% std::set::~set (inline) 0 0% 27.18% 399ms 4.97% std::_Rb_tree::_Alloc_node::operator() (inline) 97ms 1.21% 28.39% 398ms 4.96% std::_Rb_tree::_M_erase 0 0% 28.39% 389ms 4.85% std::_Rb_tree::_M_get_node (inline) 0 0% 28.39% 373ms 4.65% NodeLocationWriter::Visit 4ms 0.05% 28.44% 372ms 4.64% Cell::GetMutationState 34ms 0.42% 28.86% 344ms 4.29% std::_Rb_tree::_Rb_tree (partial-inline) 1ms 0.012% 28.87% 335ms 4.17% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 0 0% 28.87% 334ms 4.16% AbstractCellBasedWriter::OpenOutputFileForAppend 1ms 0.012% 28.88% 330ms 4.11% OutputFileHandler::OpenOutputFile 6ms 0.075% 28.96% 323ms 4.02% std::less::operator() (inline) 6ms 0.075% 29.03% 317ms 3.95% Element::Element 18ms 0.22% 29.26% 317ms 3.95% std::_Rb_tree::_M_insert_ (inline) 317ms 3.95% 33.21% 317ms 3.95% std::operator< (inline) 24ms 0.3% 33.51% 314ms 3.91% std::num_put::_M_insert_float 310ms 3.86% 37.37% 310ms 3.86% std::_Rb_tree::_S_right (inline) 3ms 0.037% 37.41% 306ms 3.81% std::set::set (inline) 2ms 0.025% 37.43% 301ms 3.75% MeshBasedCellPopulation::GetDampingConstant 10ms 0.12% 37.56% 298ms 3.71% AbstractCellPopulation::IsCellAttachedToLocationIndex 0 0% 37.56% 297ms 3.70% AbstractCentreBasedCellPopulation::GetDampingConstant 188ms 2.34% 39.90% 285ms 3.55% _int_malloc 4ms 0.05% 39.95% 283ms 3.53% Cell::ReadyToDivide 32ms 0.4% 40.35% 279ms 3.48% std::_Rb_tree::_M_copy (inline) 0 0% 40.35% 278ms 3.46% std::_Rb_tree::_M_drop_node (inline) 78ms 0.97% 41.32% 275ms 3.43% __GI___libc_free 10ms 0.12% 41.45% 266ms 3.31% divconqrecurse 9ms 0.11% 41.56% 261ms 3.25% std::__new_allocator::deallocate (inline) 0 0% 41.56% 258ms 3.21% std::allocator_traits::deallocate (inline) 3ms 0.037% 41.60% 257ms 3.20% std::__cxx11::collate::do_transform 3ms 0.037% 41.63% 245ms 3.05% ___vsnprintf 69ms 0.86% 42.49% 245ms 3.05% mergehulls 4ms 0.05% 42.54% 242ms 3.02% AbstractCellProperty::IsType (inline) 0 0% 42.54% 242ms 3.02% __vsnprintf_internal (inline) 68ms 0.85% 43.39% 237ms 2.95% std::_Rb_tree::_M_clone_node (inline) 21ms 0.26% 43.65% 236ms 2.94% __printf_buffer 5ms 0.062% 43.71% 234ms 2.92% CellPropertyCollection::HasProperty 0 0% 43.71% 232ms 2.89% Cell::HasCellProperty (inline) 3ms 0.037% 43.75% 229ms 2.85% CellProliferativeTypesWriter::VisitCell 0 0% 43.75% 221ms 2.75% std::_Rb_tree::_M_put_node (inline) 6ms 0.075% 43.83% 208ms 2.59% AbstractPhaseBasedCellCycleModel::ReadyToDivide 10ms 0.12% 43.95% 207ms 2.58% MeshBasedCellPopulation::SpringsEnd (inline) 47ms 0.59% 44.54% 206ms 2.57% TetrahedralMesh::EdgesEnd (partial-inline) 6ms 0.075% 44.61% 204ms 2.54% __printf_fp_l_buffer 0 0% 44.61% 204ms 2.54% __printf_fp_spec (inline) 6ms 0.075% 44.69% 199ms 2.48% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 159ms 1.98% 46.67% 197ms 2.45% _int_free 4ms 0.05% 46.72% 196ms 2.44% Element::RegisterWithNodes (inline) 101ms 1.26% 47.98% 195ms 2.43% __printf_fp_buffer_1 11ms 0.14% 48.11% 194ms 2.42% TetrahedralMesh::Clear 3ms 0.037% 48.15% 191ms 2.38% Node::AddElement 56ms 0.7% 48.85% 188ms 2.34% std::_Rb_tree::_M_get_insert_unique_pos (inline) 13ms 0.16% 49.01% 169ms 2.11% AbstractTetrahedralElement::CalculateJacobian 40ms 0.5% 49.51% 167ms 2.08% AbstractCellProperty::IsSame 0 0% 49.51% 167ms 2.08% std::basic_ofstream::basic_ofstream (inline) 48ms 0.6% 50.11% 165ms 2.06% std::__ostream_insert 1ms 0.012% 50.12% 161ms 2.01% std::basic_filebuf::open 0 0% 50.12% 161ms 2.01% std::basic_ofstream::open (inline) 2ms 0.025% 50.14% 157ms 1.96% TetrahedralMesh::RefreshJacobianCachedData 0 0% 50.14% 150ms 1.87% AbstractCellPopulation::CloseRoundRobinWritersFiles 0 0% 50.14% 150ms 1.87% std::basic_filebuf::close 0 0% 50.14% 149ms 1.86% AbstractCellBasedWriter::CloseFile 0 0% 50.14% 149ms 1.86% OutputFileHandler::CommonConstructor 0 0% 50.14% 149ms 1.86% OutputFileHandler::OutputFileHandler 0 0% 50.14% 149ms 1.86% std::basic_ofstream::close (inline) 0 0% 50.14% 145ms 1.81% OutputFileHandler::MakeFoldersAndReturnFullPath 98ms 1.22% 51.36% 144ms 1.79% TetrahedralMesh::EdgeIterator::EdgeIterator (partial-inline) 1ms 0.012% 51.38% 144ms 1.79% std::operator<< (inline) 10ms 0.12% 51.50% 140ms 1.74% AbstractTetrahedralElement::CalculateInverseJacobian 4ms 0.05% 51.55% 138ms 1.72% alternateaxes 119ms 1.48% 53.03% 137ms 1.71% std::basic_filebuf::xsputn 29ms 0.36% 53.40% 137ms 1.71% std::num_put::_M_insert_int 0 0% 53.40% 134ms 1.67% FilesystemPermissions::SetFilePermissions (inline) 134ms 1.67% 55.07% 134ms 1.67% __GI_fchmodat 0 0% 55.07% 134ms 1.67% std::filesystem::permissions 10ms 0.12% 55.19% 133ms 1.66% boost::detail::shared_count::~shared_count (inline) 0 0% 55.19% 133ms 1.66% boost::shared_ptr::~shared_ptr (inline) 15ms 0.19% 55.38% 132ms 1.64% MeshBasedCellPopulation::SpringIterator::SpringIterator 0 0% 55.38% 132ms 1.64% std::__basic_file::open 1ms 0.012% 55.39% 131ms 1.63% _IO_new_fopen 125ms 1.56% 56.95% 131ms 1.63% vertexmedian 2ms 0.025% 56.97% 130ms 1.62% __fopen_internal (inline) 5ms 0.062% 57.03% 129ms 1.61% boost::numeric::ublas::c_vector::c_vector (inline) 2ms 0.025% 57.06% 129ms 1.61% boost::numeric::ublas::vector_assign (inline) 127ms 1.58% 58.64% 127ms 1.58% [libchaste_cell_based.so] 38ms 0.47% 59.12% 127ms 1.58% std::type_info::operator== (inline) 7ms 0.087% 59.20% 126ms 1.57% Node::~Node 1ms 0.012% 59.21% 126ms 1.57% _IO_new_file_fopen 15ms 0.19% 59.40% 124ms 1.55% AbstractTetrahedralElement::RefreshJacobian 1ms 0.012% 59.41% 124ms 1.55% __GI__IO_file_open 1ms 0.012% 59.43% 124ms 1.55% std::_Vector_base::_M_allocate (inline) 4ms 0.05% 59.48% 123ms 1.53% AbstractTetrahedralElement::AbstractTetrahedralElement 108ms 1.35% 60.82% 114ms 1.42% boost::detail::sp_counted_base::release 110ms 1.37% 62.19% 110ms 1.37% __libc_open64 110ms 1.37% 63.56% 110ms 1.37% incircle 14ms 0.17% 63.74% 109ms 1.36% AbstractCellPopulation::Iterator::IsRealCell (inline) 1ms 0.012% 63.75% 107ms 1.33% std::basic_filebuf::_M_terminate_output 3ms 0.037% 63.79% 107ms 1.33% std::basic_filebuf::overflow 7ms 0.087% 63.88% 107ms 1.33% std::vector::push_back (inline) 51ms 0.64% 64.51% 106ms 1.32% boost::shared_ptr::shared_ptr (inline) 0 0% 64.51% 105ms 1.31% AbstractCellPopulation::Iterator::operator++ (inline) 1ms 0.012% 64.52% 104ms 1.30% std::basic_filebuf::_M_convert_to_external 99ms 1.23% 65.76% 101ms 1.26% __GI___libc_write 0 0% 65.76% 101ms 1.26% std::__basic_file::xsputn 36ms 0.45% 66.21% 99ms 1.23% AbstractElement::GetNodeLocation 13ms 0.16% 66.37% 95ms 1.18% std::vector::_M_realloc_insert 6ms 0.075% 66.44% 90ms 1.12% TetrahedralMesh::EdgeIterator::GetNodeB 30ms 0.37% 66.82% 90ms 1.12% boost::numeric::ublas::indexing_vector_assign 0 0% 66.82% 89ms 1.11% FilesystemPermissions::CreateDirectoryWithPermissions (inline) 0 0% 66.82% 89ms 1.11% std::filesystem::create_directory 88ms 1.10% 67.91% 88ms 1.10% TetrahedralMesh::EdgeIterator::operator!= (partial-inline) 8ms 0.1% 68.01% 85ms 1.06% std::_Rb_tree_const_iterator::operator++ (inline) 83ms 1.03% 69.05% 83ms 1.03% std::_Rb_tree_increment 74ms 0.92% 69.97% 79ms 0.98% vertexsort 1ms 0.012% 69.98% 77ms 0.96% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 45ms 0.56% 70.54% 77ms 0.96% malloc_consolidate 77ms 0.96% 71.50% 77ms 0.96% std::_Rb_tree_insert_and_rebalance 1ms 0.012% 71.51% 77ms 0.96% std::filesystem::status 5ms 0.062% 71.58% 75ms 0.93% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (partial-inline) 0 0% 71.58% 75ms 0.93% Cell::GetCellId 75ms 0.93% 72.51% 75ms 0.93% __GI___fstatat64 0 0% 72.51% 75ms 0.93% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 72.51% 75ms 0.93% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 0 0% 72.51% 75ms 0.93% tcache_get (inline) 75ms 0.93% 73.45% 75ms 0.93% tcache_get_n (inline) 74ms 0.92% 74.37% 74ms 0.92% std::vector::size (inline) 71ms 0.88% 75.25% 71ms 0.88% __memcpy_avx_unaligned_erms 5ms 0.062% 75.31% 66ms 0.82% TetrahedralMesh::EdgeIterator::GetNodeA 66ms 0.82% 76.14% 66ms 0.82% counterclockwise 42ms 0.52% 76.66% 66ms 0.82% std::basic_streambuf::xsputn 0 0% 76.66% 65ms 0.81% std::vector::vector (inline) 1ms 0.012% 76.67% 64ms 0.8% AbstractCellPopulation::GetLocationIndexUsingCell 46ms 0.57% 77.25% 63ms 0.79% AbstractElement::GetNodeGlobalIndex 63ms 0.79% 78.03% 63ms 0.79% [libstdc++.so.6.0.33] 0 0% 78.03% 63ms 0.79% std::_Vector_base::_Vector_base (inline) 62ms 0.77% 78.80% 62ms 0.77% boost::shared_ptr::operator-> (inline) 1ms 0.012% 78.82% 61ms 0.76% std::_Vector_base::_M_create_storage (inline) 34ms 0.42% 79.24% 60ms 0.75% hack_digit 6ms 0.075% 79.31% 58ms 0.72% CellPropertyCollection::AddProperty 0 0% 79.31% 57ms 0.71% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 57ms 0.71% 80.02% 57ms 0.71% [libchaste_mesh.so] 0 0% 80.02% 57ms 0.71% std::_Rb_tree::_M_destroy_node (inline) 0 0% 80.02% 57ms 0.71% std::__new_allocator::destroy (inline) 0 0% 80.02% 57ms 0.71% std::allocator_traits::destroy (inline) 2ms 0.025% 80.05% 56ms 0.7% Node::ConstructNodeAttributes (inline) 0 0% 80.05% 55ms 0.69% MeshBasedCellPopulation::SpringIterator::~SpringIterator (inline) 55ms 0.69% 80.74% 55ms 0.69% boost::detail::shared_count::shared_count (inline) 0 0% 80.74% 55ms 0.69% boost::numeric::ublas::norm_2 (inline) 18ms 0.22% 80.96% 55ms 0.69% boost::numeric::ublas::vector_norm_2::apply (inline) 0 0% 80.96% 54ms 0.67% Node::ClearAppliedForce 0 0% 80.96% 51ms 0.64% MeshBasedCellPopulation::SpringIterator::GetNodeB (inline) 51ms 0.64% 81.60% 51ms 0.64% Node::GetIndex 2ms 0.025% 81.62% 51ms 0.64% std::_Rb_tree::_M_emplace_hint_unique 30ms 0.37% 81.99% 49ms 0.61% boost::numeric::ublas::c_matrix::operator() 0 0% 81.99% 48ms 0.6% AbstractCentreBasedCellPopulation::CreateCellPair 27ms 0.34% 82.33% 48ms 0.6% AbstractTetrahedralMesh::GetElement 47ms 0.59% 82.92% 47ms 0.59% __GI___mkdir 46ms 0.57% 83.49% 46ms 0.57% Node::rGetLocation 29ms 0.36% 83.85% 46ms 0.57% std::num_put::do_put 26ms 0.32% 84.17% 44ms 0.55% AbstractCellCycleModel::GetAge 16ms 0.2% 84.37% 43ms 0.54% AbstractTetrahedralMesh::GetNumAllElements 16ms 0.2% 84.57% 43ms 0.54% Determinant (inline) 43ms 0.54% 85.11% 43ms 0.54% Node::IsDeleted 43ms 0.54% 85.64% 43ms 0.54% unlink_chunk 0 0% 85.64% 42ms 0.52% std::map::map (inline) 1ms 0.012% 85.66% 41ms 0.51% NodeAttributes::NodeAttributes 5ms 0.062% 85.72% 41ms 0.51% std::__copy_move::__copy_m (inline) 0 0% 85.72% 41ms 0.51% std::__copy_move_a (inline) 0 0% 85.72% 41ms 0.51% std::__copy_move_a1 (inline) 0 0% 85.72% 41ms 0.51% std::__copy_move_a2 (inline) 0 0% 85.72% 41ms 0.51% std::copy (inline)