File: Test2dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 6667ms, 84.81% of 7861ms total Dropped 597 nodes (cum <= 39.30ms) flat flat% sum% cum cum% 0 0% 0% 7825ms 99.54% __libc_start_call_main 0 0% 0% 7825ms 99.54% __libc_start_main_impl 0 0% 0% 7825ms 99.54% _start 0 0% 0% 7810ms 99.35% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 7810ms 99.35% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 7810ms 99.35% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 7810ms 99.35% main 0 0% 0% 7769ms 98.83% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 7769ms 98.83% CxxTest::TestRunner::runTest (inline) 0 0% 0% 7769ms 98.83% Test2DMonolayerRepresentativeSimulation::Test2DMonolayerRepresentativeSimulationForProfiling 0 0% 0% 7764ms 98.77% AbstractCellBasedSimulation::Solve 1ms 0.013% 0.013% 3349ms 42.60% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0.013% 2887ms 36.73% MeshBasedCellPopulation::Update 0 0% 0.013% 2825ms 35.94% AbstractCellPopulation::WriteResultsToFiles 1ms 0.013% 0.025% 1579ms 20.09% OffLatticeSimulation::UpdateCellLocationsAndTopology 1ms 0.013% 0.038% 1430ms 18.19% MeshBasedCellPopulation::UpdateNodePairs 2ms 0.025% 0.064% 1423ms 18.10% ForwardEulerNumericalMethod::UpdateAllNodePositions 0 0% 0.064% 1401ms 17.82% MutableMesh::ReMesh 7ms 0.089% 0.15% 1366ms 17.38% AbstractNumericalMethod::ComputeForcesIncludingDamping 19ms 0.24% 0.39% 1255ms 15.96% MeshBasedCellPopulation::SpringIterator::operator++ 109ms 1.39% 1.78% 1029ms 13.09% TetrahedralMesh::EdgeIterator::operator++ 420ms 5.34% 7.12% 948ms 12.06% std::_Rb_tree::_M_lower_bound (inline) 2ms 0.025% 7.15% 946ms 12.03% AbstractTwoBodyInteractionForce::AddForceContribution 3ms 0.038% 7.19% 912ms 11.60% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 10ms 0.13% 7.31% 900ms 11.45% CellPropertyCollection::GetPropertiesType (inline) 7ms 0.089% 7.40% 888ms 11.30% CellPopulationElementWriter::Visit 244ms 3.10% 10.51% 887ms 11.28% __dynamic_cast 46ms 0.59% 11.09% 833ms 10.60% GeneralisedLinearSpringForce::CalculateForceBetweenNodes (partial-inline) 4ms 0.051% 11.14% 775ms 9.86% MeshBasedCellPopulation::AcceptCellWriter 31ms 0.39% 11.54% 742ms 9.44% AbstractCellPopulation::GetCellUsingLocationIndex 4ms 0.051% 11.59% 692ms 8.80% AbstractCellProperty::IsSubType (inline) 10ms 0.13% 11.72% 685ms 8.71% TetrahedralMesh::ImportFromMesher 1ms 0.013% 11.73% 592ms 7.53% std::ostream::operator<< (inline) 93ms 1.18% 12.91% 591ms 7.52% std::ostream::_M_insert 53ms 0.67% 13.59% 583ms 7.42% std::map::operator[] (partial-inline) 36ms 0.46% 14.04% 566ms 7.20% operator new 1ms 0.013% 14.06% 559ms 7.11% triangulate 187ms 2.38% 16.44% 532ms 6.77% __GI___libc_malloc 26ms 0.33% 16.77% 528ms 6.72% std::_Rb_tree::find (inline) 7ms 0.089% 16.86% 524ms 6.67% Cell::GetCellProliferativeType 38ms 0.48% 17.34% 520ms 6.61% std::__new_allocator::allocate (inline) 513ms 6.53% 23.86% 513ms 6.53% __strcmp_avx2 0 0% 23.86% 513ms 6.53% std::allocator_traits::allocate (inline) 13ms 0.17% 24.03% 511ms 6.50% std::set::insert (inline) 5ms 0.064% 24.09% 498ms 6.34% std::_Rb_tree::_M_insert_unique 0 0% 24.09% 495ms 6.30% delaunay 2ms 0.025% 24.12% 494ms 6.28% divconqdelaunay 208ms 2.65% 26.77% 486ms 6.18% __cxxabiv1::__si_class_type_info::__do_dyncast 9ms 0.11% 26.88% 479ms 6.09% LegacyCellProliferativeTypesWriter::VisitCell 0 0% 26.88% 479ms 6.09% std::_Rb_tree::lower_bound (inline) 0 0% 26.88% 479ms 6.09% std::map::lower_bound (inline) 0 0% 26.88% 472ms 6.00% std::set::count (inline) 3ms 0.038% 26.92% 443ms 5.64% AbstractCellBasedSimulation::DoCellBirth 0 0% 26.92% 435ms 5.53% std::_Rb_tree::_M_create_node (inline) 0 0% 26.92% 407ms 5.18% std::_Rb_tree::_Alloc_node::operator() (inline) 38ms 0.48% 27.40% 398ms 5.06% std::_Rb_tree::~_Rb_tree (inline) 0 0% 27.40% 396ms 5.04% std::_Rb_tree::_M_get_node (inline) 2ms 0.025% 27.43% 377ms 4.80% Cell::GetMutationState 2ms 0.025% 27.45% 364ms 4.63% NodeLocationWriter::Visit 0 0% 27.45% 362ms 4.61% std::set::~set (inline) 85ms 1.08% 28.53% 359ms 4.57% std::_Rb_tree::_M_erase 11ms 0.14% 28.67% 357ms 4.54% std::less::operator() (inline) 20ms 0.25% 28.93% 349ms 4.44% std::_Rb_tree::_Rb_tree (partial-inline) 346ms 4.40% 33.33% 346ms 4.40% std::operator< (inline) 1ms 0.013% 33.34% 328ms 4.17% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 0 0% 33.34% 324ms 4.12% AbstractCellBasedWriter::OpenOutputFileForAppend 1ms 0.013% 33.35% 324ms 4.12% MeshBasedCellPopulation::GetDampingConstant 2ms 0.025% 33.38% 323ms 4.11% AbstractCentreBasedCellPopulation::GetDampingConstant 22ms 0.28% 33.66% 322ms 4.10% std::_Rb_tree::_M_insert_ (inline) 5ms 0.064% 33.72% 321ms 4.08% Cell::ReadyToDivide 25ms 0.32% 34.04% 321ms 4.08% std::num_put::_M_insert_float 0 0% 34.04% 319ms 4.06% OutputFileHandler::OpenOutputFile 318ms 4.05% 38.09% 318ms 4.05% std::_Rb_tree::_S_right (inline) 0 0% 38.09% 311ms 3.96% std::set::set (inline) 34ms 0.43% 38.52% 305ms 3.88% std::_Rb_tree::_M_copy (inline) 7ms 0.089% 38.61% 296ms 3.77% AbstractCellPopulation::IsCellAttachedToLocationIndex 10ms 0.13% 38.74% 291ms 3.70% divconqrecurse 111ms 1.41% 40.15% 288ms 3.66% __GI___libc_free 4ms 0.051% 40.20% 273ms 3.47% Element::Element 169ms 2.15% 42.35% 268ms 3.41% _int_malloc 96ms 1.22% 43.57% 268ms 3.41% mergehulls 66ms 0.84% 44.41% 267ms 3.40% std::_Rb_tree::_M_clone_node (inline) 7ms 0.089% 44.50% 260ms 3.31% std::__cxx11::collate::do_transform 3ms 0.038% 44.54% 259ms 3.29% CellProliferativeTypesWriter::VisitCell 11ms 0.14% 44.68% 254ms 3.23% std::__new_allocator::deallocate (inline) 0 0% 44.68% 251ms 3.19% std::allocator_traits::deallocate (inline) 0 0% 44.68% 245ms 3.12% std::_Rb_tree::_M_drop_node (inline) 2ms 0.025% 44.70% 243ms 3.09% ___vsnprintf 0 0% 44.70% 241ms 3.07% __vsnprintf_internal (inline) 29ms 0.37% 45.07% 234ms 2.98% __printf_buffer 2ms 0.025% 45.10% 231ms 2.94% AbstractCellProperty::IsType (inline) 9ms 0.11% 45.21% 227ms 2.89% CellPropertyCollection::HasProperty 0 0% 45.21% 223ms 2.84% Cell::HasCellProperty (inline) 3ms 0.038% 45.25% 222ms 2.82% AbstractPhaseBasedCellCycleModel::ReadyToDivide 12ms 0.15% 45.40% 217ms 2.76% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 0 0% 45.40% 200ms 2.54% std::_Rb_tree::_M_put_node (inline) 5ms 0.064% 45.46% 194ms 2.47% MeshBasedCellPopulation::SpringsEnd (inline) 2ms 0.025% 45.49% 194ms 2.47% __printf_fp_spec (inline) 9ms 0.11% 45.60% 192ms 2.44% __printf_fp_l_buffer 15ms 0.19% 45.80% 180ms 2.29% TetrahedralMesh::Clear 158ms 2.01% 47.81% 176ms 2.24% _int_free 100ms 1.27% 49.08% 174ms 2.21% __printf_fp_buffer_1 67ms 0.85% 49.93% 171ms 2.18% std::_Rb_tree::_M_get_insert_unique_pos (inline) 42ms 0.53% 50.46% 170ms 2.16% AbstractCellProperty::IsSame 7ms 0.089% 50.55% 167ms 2.12% Element::RegisterWithNodes (inline) 2ms 0.025% 50.58% 160ms 2.04% Node::AddElement 51ms 0.65% 51.23% 159ms 2.02% TetrahedralMesh::EdgesEnd (partial-inline) 0 0% 51.23% 155ms 1.97% std::basic_ofstream::basic_ofstream (inline) 20ms 0.25% 51.48% 153ms 1.95% AbstractTetrahedralElement::CalculateJacobian 0 0% 51.48% 149ms 1.90% std::basic_ofstream::open (inline) 3ms 0.038% 51.52% 148ms 1.88% std::basic_filebuf::open 5ms 0.064% 51.58% 144ms 1.83% boost::numeric::ublas::vector_assign (inline) 3ms 0.038% 51.62% 143ms 1.82% boost::numeric::ublas::c_vector::c_vector (inline) 2ms 0.025% 51.65% 140ms 1.78% TetrahedralMesh::RefreshJacobianCachedData 0 0% 51.65% 135ms 1.72% FilesystemPermissions::SetFilePermissions (inline) 1ms 0.013% 51.66% 135ms 1.72% std::filesystem::permissions 134ms 1.70% 53.36% 134ms 1.70% __GI_fchmodat 4ms 0.051% 53.42% 133ms 1.69% alternateaxes 1ms 0.013% 53.43% 131ms 1.67% OutputFileHandler::CommonConstructor 0 0% 53.43% 131ms 1.67% OutputFileHandler::OutputFileHandler 5ms 0.064% 53.49% 129ms 1.64% AbstractTetrahedralElement::CalculateInverseJacobian 118ms 1.50% 54.99% 129ms 1.64% vertexmedian 28ms 0.36% 55.35% 128ms 1.63% std::type_info::operator== (inline) 13ms 0.17% 55.51% 127ms 1.62% MeshBasedCellPopulation::SpringIterator::SpringIterator 0 0% 55.51% 125ms 1.59% OutputFileHandler::MakeFoldersAndReturnFullPath 54ms 0.69% 56.20% 125ms 1.59% std::__ostream_insert 124ms 1.58% 57.78% 124ms 1.58% std::_Rb_tree_increment 11ms 0.14% 57.92% 122ms 1.55% std::_Rb_tree_const_iterator::operator++ (inline) 28ms 0.36% 58.28% 122ms 1.55% std::num_put::_M_insert_int 10ms 0.13% 58.40% 121ms 1.54% std::vector::push_back (inline) 1ms 0.013% 58.41% 118ms 1.50% std::_Vector_base::_M_allocate (inline) 2ms 0.025% 58.44% 116ms 1.48% std::basic_filebuf::close 0 0% 58.44% 115ms 1.46% AbstractCellBasedWriter::CloseFile 0 0% 58.44% 115ms 1.46% AbstractCellPopulation::CloseRoundRobinWritersFiles 0 0% 58.44% 115ms 1.46% std::basic_ofstream::close (inline) 5ms 0.064% 58.50% 113ms 1.44% AbstractTetrahedralElement::AbstractTetrahedralElement 0 0% 58.50% 111ms 1.41% _IO_new_fopen 0 0% 58.50% 111ms 1.41% __fopen_internal (inline) 0 0% 58.50% 110ms 1.40% std::__basic_file::open 33ms 0.42% 58.92% 107ms 1.36% boost::numeric::ublas::indexing_vector_assign 8ms 0.1% 59.03% 106ms 1.35% std::vector::_M_realloc_insert 5ms 0.064% 59.09% 104ms 1.32% Node::~Node 2ms 0.025% 59.11% 104ms 1.32% _IO_new_file_fopen 104ms 1.32% 60.44% 104ms 1.32% incircle 19ms 0.24% 60.68% 103ms 1.31% AbstractTetrahedralElement::RefreshJacobian 8ms 0.1% 60.78% 103ms 1.31% boost::detail::shared_count::~shared_count (inline) 0 0% 60.78% 103ms 1.31% boost::shared_ptr::~shared_ptr (inline) 9ms 0.11% 60.90% 102ms 1.30% AbstractCellPopulation::Iterator::IsRealCell (inline) 0 0% 60.90% 102ms 1.30% AbstractCellPopulation::Iterator::operator++ (inline) 0 0% 60.90% 101ms 1.28% __GI__IO_file_open 51ms 0.65% 61.54% 101ms 1.28% boost::shared_ptr::shared_ptr (inline) 2ms 0.025% 61.57% 99ms 1.26% std::operator<< (inline) 98ms 1.25% 62.82% 98ms 1.25% std::_Rb_tree_insert_and_rebalance 64ms 0.81% 63.63% 97ms 1.23% TetrahedralMesh::EdgeIterator::EdgeIterator (partial-inline) 96ms 1.22% 64.85% 96ms 1.22% [libchaste_cell_based.so] 94ms 1.20% 66.05% 94ms 1.20% __libc_open64 91ms 1.16% 67.21% 92ms 1.17% boost::detail::sp_counted_base::release 5ms 0.064% 67.27% 91ms 1.16% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (partial-inline) 89ms 1.13% 68.40% 89ms 1.13% Node::GetIndex 2ms 0.025% 68.43% 87ms 1.11% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 87ms 1.11% 69.53% 87ms 1.11% TetrahedralMesh::EdgeIterator::operator!= (partial-inline) 0 0% 69.53% 85ms 1.08% std::basic_filebuf::_M_terminate_output 2ms 0.025% 69.56% 85ms 1.08% std::basic_filebuf::overflow 1ms 0.013% 69.57% 83ms 1.06% std::__basic_file::xsputn 0 0% 69.57% 83ms 1.06% std::basic_filebuf::_M_convert_to_external 81ms 1.03% 70.60% 82ms 1.04% __GI___libc_write 0 0% 70.60% 77ms 0.98% AbstractCellPopulation::GetLocationIndexUsingCell 59ms 0.75% 71.35% 77ms 0.98% malloc_consolidate 48ms 0.61% 71.96% 76ms 0.97% std::basic_filebuf::xsputn 0 0% 71.96% 75ms 0.95% Cell::GetCellId 0 0% 71.96% 73ms 0.93% FilesystemPermissions::CreateDirectoryWithPermissions (inline) 2ms 0.025% 71.99% 73ms 0.93% std::filesystem::create_directory 58ms 0.74% 72.73% 72ms 0.92% AbstractElement::GetNodeGlobalIndex 37ms 0.47% 73.20% 72ms 0.92% AbstractElement::GetNodeLocation 5ms 0.064% 73.26% 72ms 0.92% CellPropertyCollection::AddProperty 54ms 0.69% 73.95% 71ms 0.9% std::basic_streambuf::xsputn 68ms 0.87% 74.81% 68ms 0.87% counterclockwise 1ms 0.013% 74.83% 65ms 0.83% std::filesystem::status 0 0% 74.83% 65ms 0.83% tcache_get (inline) 65ms 0.83% 75.65% 65ms 0.83% tcache_get_n (inline) 63ms 0.8% 76.45% 63ms 0.8% __GI___fstatat64 57ms 0.73% 77.18% 63ms 0.8% vertexsort 0 0% 77.18% 62ms 0.79% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 77.18% 62ms 0.79% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 36ms 0.46% 77.64% 60ms 0.76% AbstractTetrahedralMesh::GetElement 60ms 0.76% 78.40% 60ms 0.76% __memcpy_avx_unaligned_erms 33ms 0.42% 78.82% 60ms 0.76% boost::numeric::ublas::c_matrix::operator() (partial-inline) 3ms 0.038% 78.86% 59ms 0.75% Node::ConstructNodeAttributes (inline) 0 0% 78.86% 56ms 0.71% Node::ClearAppliedForce 1ms 0.013% 78.87% 55ms 0.7% TetrahedralMesh::EdgeIterator::GetNodeA 4ms 0.051% 78.92% 55ms 0.7% TetrahedralMesh::EdgeIterator::GetNodeB 53ms 0.67% 79.60% 53ms 0.67% std::vector::size (inline) 4ms 0.051% 79.65% 52ms 0.66% std::_Vector_base::_M_deallocate (inline) 2ms 0.025% 79.67% 51ms 0.65% std::_Rb_tree::_M_emplace_hint_unique 0 0% 79.67% 51ms 0.65% std::map::find (inline) 50ms 0.64% 80.31% 50ms 0.64% Node::IsDeleted 50ms 0.64% 80.94% 50ms 0.64% boost::detail::shared_count::shared_count (inline) 49ms 0.62% 81.57% 49ms 0.62% [libchaste_mesh.so] 32ms 0.41% 81.97% 49ms 0.62% std::num_put::do_put 0 0% 81.97% 48ms 0.61% BoundaryNodeWriter::Visit 0 0% 81.97% 48ms 0.61% std::vector::vector (inline) 46ms 0.59% 82.56% 46ms 0.59% boost::shared_ptr::operator-> (inline) 0 0% 82.56% 46ms 0.59% std::_Vector_base::_M_create_storage (inline) 0 0% 82.56% 46ms 0.59% std::_Vector_base::_Vector_base (inline) 8ms 0.1% 82.66% 45ms 0.57% Inverse 0 0% 82.66% 45ms 0.57% MeshBasedCellPopulation::SpringIterator::~SpringIterator (inline) 0 0% 82.66% 45ms 0.57% std::_Rb_tree::_M_destroy_node (inline) 0 0% 82.66% 45ms 0.57% std::__new_allocator::destroy (inline) 0 0% 82.66% 45ms 0.57% std::allocator_traits::destroy (inline) 0 0% 82.66% 44ms 0.56% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 0 0% 82.66% 44ms 0.56% boost::numeric::ublas::norm_2 (inline) 14ms 0.18% 82.84% 44ms 0.56% boost::numeric::ublas::vector_norm_2::apply (inline) 23ms 0.29% 83.13% 43ms 0.55% AbstractCellCycleModel::GetAge 1ms 0.013% 83.14% 43ms 0.55% std::__new_allocator::construct (inline) 0 0% 83.14% 43ms 0.55% std::allocator_traits::construct (inline) 43ms 0.55% 83.69% 43ms 0.55% std::ostream::sentry::sentry 7ms 0.089% 83.78% 41ms 0.52% NodeAttributes::NodeAttributes 41ms 0.52% 84.30% 41ms 0.52% boost::numeric::ublas::same_impl_ex 0 0% 84.30% 40ms 0.51% AbstractCentreBasedCellPopulation::CreateCellPair 40ms 0.51% 84.81% 40ms 0.51% Node::rGetLocation