File: Test2dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 6534ms, 83.13% of 7860ms total Dropped 596 nodes (cum <= 39.30ms) flat flat% sum% cum cum% 0 0% 0% 7824ms 99.54% __libc_start_call_main 0 0% 0% 7824ms 99.54% __libc_start_main_impl 0 0% 0% 7824ms 99.54% _start 0 0% 0% 7809ms 99.35% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 7809ms 99.35% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 7809ms 99.35% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 7809ms 99.35% main 0 0% 0% 7773ms 98.89% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 7773ms 98.89% CxxTest::TestRunner::runTest (inline) 0 0% 0% 7773ms 98.89% Test2DMonolayerRepresentativeSimulation::Test2DMonolayerRepresentativeSimulationForProfiling 0 0% 0% 7769ms 98.84% AbstractCellBasedSimulation::Solve 0 0% 0% 3342ms 42.52% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 2890ms 36.77% MeshBasedCellPopulation::Update 1ms 0.013% 0.013% 2860ms 36.39% AbstractCellPopulation::WriteResultsToFiles 0 0% 0.013% 1554ms 19.77% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 0.013% 1419ms 18.05% MeshBasedCellPopulation::UpdateNodePairs 0 0% 0.013% 1415ms 18.00% MutableMesh::ReMesh 1ms 0.013% 0.025% 1402ms 17.84% ForwardEulerNumericalMethod::UpdateAllNodePositions 10ms 0.13% 0.15% 1351ms 17.19% AbstractNumericalMethod::ComputeForcesIncludingDamping 9ms 0.11% 0.27% 1254ms 15.95% MeshBasedCellPopulation::SpringIterator::operator++ 110ms 1.40% 1.67% 1020ms 12.98% TetrahedralMesh::EdgeIterator::operator++ 433ms 5.51% 7.18% 989ms 12.58% std::_Rb_tree::_M_lower_bound (inline) 11ms 0.14% 7.32% 936ms 11.91% CellPopulationElementWriter::Visit 7ms 0.089% 7.40% 926ms 11.78% AbstractTwoBodyInteractionForce::AddForceContribution 15ms 0.19% 7.60% 894ms 11.37% CellPropertyCollection::GetPropertiesType (inline) 2ms 0.025% 7.62% 885ms 11.26% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 273ms 3.47% 11.09% 863ms 10.98% __dynamic_cast 49ms 0.62% 11.72% 812ms 10.33% GeneralisedLinearSpringForce::CalculateForceBetweenNodes (partial-inline) 6ms 0.076% 11.79% 762ms 9.69% MeshBasedCellPopulation::AcceptCellWriter 39ms 0.5% 12.29% 745ms 9.48% AbstractCellPopulation::GetCellUsingLocationIndex 9ms 0.11% 12.40% 716ms 9.11% TetrahedralMesh::ImportFromMesher 7ms 0.089% 12.49% 698ms 8.88% AbstractCellProperty::IsSubType (inline) 1ms 0.013% 12.51% 618ms 7.86% std::ostream::operator<< (inline) 103ms 1.31% 13.82% 616ms 7.84% std::ostream::_M_insert 35ms 0.45% 14.26% 609ms 7.75% std::map::operator[] (partial-inline) 2ms 0.025% 14.29% 552ms 7.02% triangulate 24ms 0.31% 14.59% 534ms 6.79% std::_Rb_tree::find (inline) 7ms 0.089% 14.68% 527ms 6.70% std::set::insert (inline) 34ms 0.43% 15.11% 520ms 6.62% operator new 18ms 0.23% 15.34% 520ms 6.62% std::_Rb_tree::_M_insert_unique 0 0% 15.34% 515ms 6.55% std::_Rb_tree::lower_bound (inline) 0 0% 15.34% 515ms 6.55% std::map::lower_bound (inline) 1ms 0.013% 15.36% 502ms 6.39% Cell::GetCellProliferativeType 0 0% 15.36% 494ms 6.28% std::set::count (inline) 150ms 1.91% 17.26% 486ms 6.18% __GI___libc_malloc 4ms 0.051% 17.32% 481ms 6.12% LegacyCellProliferativeTypesWriter::VisitCell 33ms 0.42% 17.74% 475ms 6.04% std::__new_allocator::allocate (inline) 0 0% 17.74% 469ms 5.97% delaunay 1ms 0.013% 17.75% 468ms 5.95% divconqdelaunay 0 0% 17.75% 467ms 5.94% std::allocator_traits::allocate (inline) 459ms 5.84% 23.59% 459ms 5.84% __strcmp_avx2 193ms 2.46% 26.04% 430ms 5.47% __cxxabiv1::__si_class_type_info::__do_dyncast 3ms 0.038% 26.08% 429ms 5.46% AbstractCellBasedSimulation::DoCellBirth 3ms 0.038% 26.12% 411ms 5.23% Cell::GetMutationState 29ms 0.37% 26.49% 406ms 5.17% std::_Rb_tree::~_Rb_tree (inline) 0 0% 26.49% 398ms 5.06% std::_Rb_tree::_M_create_node (inline) 0 0% 26.49% 378ms 4.81% std::set::~set (inline) 87ms 1.11% 27.60% 377ms 4.80% std::_Rb_tree::_M_erase 3ms 0.038% 27.63% 375ms 4.77% NodeLocationWriter::Visit 0 0% 27.63% 370ms 4.71% std::_Rb_tree::_Alloc_node::operator() (inline) 16ms 0.2% 27.84% 361ms 4.59% std::less::operator() (inline) 0 0% 27.84% 356ms 4.53% std::_Rb_tree::_M_get_node (inline) 352ms 4.48% 32.32% 352ms 4.48% std::_Rb_tree::_S_right (inline) 345ms 4.39% 36.70% 345ms 4.39% std::operator< (inline) 14ms 0.18% 36.88% 341ms 4.34% std::_Rb_tree::_Rb_tree (partial-inline) 1ms 0.013% 36.90% 330ms 4.20% AbstractCentreBasedCellPopulation::GetDampingConstant 0 0% 36.90% 330ms 4.20% MeshBasedCellPopulation::GetDampingConstant 29ms 0.37% 37.26% 314ms 3.99% std::num_put::_M_insert_float 3ms 0.038% 37.30% 314ms 3.99% std::set::set (inline) 5ms 0.064% 37.37% 311ms 3.96% AbstractCellPopulation::IsCellAttachedToLocationIndex 1ms 0.013% 37.38% 310ms 3.94% AbstractCellBasedWriter::OpenOutputFileForAppend 0 0% 37.38% 310ms 3.94% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 20ms 0.25% 37.63% 308ms 3.92% std::_Rb_tree::_M_insert_ (inline) 2ms 0.025% 37.66% 302ms 3.84% Element::Element 1ms 0.013% 37.67% 302ms 3.84% OutputFileHandler::OpenOutputFile 40ms 0.51% 38.18% 293ms 3.73% std::_Rb_tree::_M_copy (inline) 2ms 0.025% 38.21% 292ms 3.72% Cell::ReadyToDivide 105ms 1.34% 39.54% 292ms 3.72% __GI___libc_free 13ms 0.17% 39.71% 276ms 3.51% divconqrecurse 0 0% 39.71% 265ms 3.37% std::_Rb_tree::_M_drop_node (inline) 11ms 0.14% 39.85% 263ms 3.35% std::__new_allocator::deallocate (inline) 184ms 2.34% 42.19% 259ms 3.30% _int_malloc 0 0% 42.19% 258ms 3.28% std::allocator_traits::deallocate (inline) 71ms 0.9% 43.09% 257ms 3.27% mergehulls 71ms 0.9% 43.99% 250ms 3.18% std::_Rb_tree::_M_clone_node (inline) 1ms 0.013% 44.01% 244ms 3.10% CellProliferativeTypesWriter::VisitCell 6ms 0.076% 44.08% 244ms 3.10% std::__cxx11::collate::do_transform 1ms 0.013% 44.10% 231ms 2.94% ___vsnprintf 2ms 0.025% 44.12% 230ms 2.93% __vsnprintf_internal (inline) 30ms 0.38% 44.50% 226ms 2.88% __printf_buffer 6ms 0.076% 44.58% 223ms 2.84% MeshBasedCellPopulation::SpringsEnd (inline) 0 0% 44.58% 215ms 2.74% std::_Rb_tree::_M_put_node (inline) 2ms 0.025% 44.61% 214ms 2.72% AbstractCellProperty::IsType (inline) 3ms 0.038% 44.64% 209ms 2.66% AbstractPhaseBasedCellCycleModel::ReadyToDivide 5ms 0.064% 44.71% 204ms 2.60% Element::RegisterWithNodes (inline) 7ms 0.089% 44.80% 202ms 2.57% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 17ms 0.22% 45.01% 202ms 2.57% TetrahedralMesh::Clear 0 0% 45.01% 201ms 2.56% Cell::HasCellProperty (inline) 3ms 0.038% 45.05% 201ms 2.56% CellPropertyCollection::HasProperty 74ms 0.94% 45.99% 194ms 2.47% std::_Rb_tree::_M_get_insert_unique_pos (inline) 8ms 0.1% 46.09% 193ms 2.46% Node::AddElement 171ms 2.18% 48.27% 187ms 2.38% _int_free 1ms 0.013% 48.28% 173ms 2.20% __printf_fp_spec (inline) 5ms 0.064% 48.35% 172ms 2.19% __printf_fp_l_buffer 24ms 0.31% 48.65% 164ms 2.09% MeshBasedCellPopulation::SpringIterator::SpringIterator 86ms 1.09% 49.75% 160ms 2.04% __printf_fp_buffer_1 0 0% 49.75% 158ms 2.01% std::basic_ofstream::basic_ofstream (inline) 41ms 0.52% 50.27% 156ms 1.98% AbstractCellProperty::IsSame 21ms 0.27% 50.53% 151ms 1.92% TetrahedralMesh::EdgesEnd (partial-inline) 35ms 0.45% 50.98% 151ms 1.92% std::num_put::_M_insert_int 3ms 0.038% 51.02% 150ms 1.91% AbstractTetrahedralElement::CalculateJacobian 0 0% 51.02% 149ms 1.90% std::basic_ofstream::open (inline) 2ms 0.025% 51.04% 148ms 1.88% std::basic_filebuf::open 63ms 0.8% 51.84% 145ms 1.84% std::__ostream_insert 7ms 0.089% 51.93% 141ms 1.79% boost::numeric::ublas::vector_assign (inline) 7ms 0.089% 52.02% 140ms 1.78% boost::numeric::ublas::c_vector::c_vector (inline) 0 0% 52.02% 139ms 1.77% AbstractCellBasedWriter::CloseFile 0 0% 52.02% 139ms 1.77% AbstractCellPopulation::CloseRoundRobinWritersFiles 0 0% 52.02% 139ms 1.77% OutputFileHandler::CommonConstructor 0 0% 52.02% 139ms 1.77% OutputFileHandler::OutputFileHandler 110ms 1.40% 53.42% 139ms 1.77% TetrahedralMesh::EdgeIterator::EdgeIterator (partial-inline) 1ms 0.013% 53.44% 139ms 1.77% std::basic_ofstream::close (inline) 2ms 0.025% 53.46% 137ms 1.74% std::basic_filebuf::close 0 0% 53.46% 134ms 1.70% TetrahedralMesh::RefreshJacobianCachedData 0 0% 53.46% 131ms 1.67% OutputFileHandler::MakeFoldersAndReturnFullPath 6ms 0.076% 53.54% 124ms 1.58% AbstractTetrahedralElement::CalculateInverseJacobian 20ms 0.25% 53.79% 121ms 1.54% AbstractCellPopulation::Iterator::IsRealCell (inline) 12ms 0.15% 53.94% 121ms 1.54% AbstractTetrahedralElement::RefreshJacobian 2ms 0.025% 53.97% 121ms 1.54% std::operator<< (inline) 0 0% 53.97% 120ms 1.53% FilesystemPermissions::SetFilePermissions (inline) 120ms 1.53% 55.50% 120ms 1.53% __GI_fchmodat 0 0% 55.50% 120ms 1.53% std::filesystem::permissions 0 0% 55.50% 119ms 1.51% AbstractCellPopulation::Iterator::operator++ (inline) 3ms 0.038% 55.53% 119ms 1.51% alternateaxes 7ms 0.089% 55.62% 117ms 1.49% Node::~Node 25ms 0.32% 55.94% 115ms 1.46% std::type_info::operator== (inline) 106ms 1.35% 57.29% 115ms 1.46% vertexmedian 9ms 0.11% 57.40% 113ms 1.44% boost::detail::shared_count::~shared_count (inline) 0 0% 57.40% 113ms 1.44% boost::shared_ptr::~shared_ptr (inline) 0 0% 57.40% 112ms 1.42% _IO_new_fopen 1ms 0.013% 57.42% 112ms 1.42% __fopen_internal (inline) 1ms 0.013% 57.43% 112ms 1.42% std::__basic_file::open 111ms 1.41% 58.84% 111ms 1.41% incircle 0 0% 58.84% 111ms 1.41% std::_Vector_base::_M_allocate (inline) 3ms 0.038% 58.88% 109ms 1.39% _IO_new_file_fopen 105ms 1.34% 60.22% 105ms 1.34% [libchaste_cell_based.so] 38ms 0.48% 60.70% 105ms 1.34% boost::shared_ptr::shared_ptr (inline) 105ms 1.34% 62.04% 105ms 1.34% std::_Rb_tree_insert_and_rebalance 2ms 0.025% 62.06% 104ms 1.32% AbstractTetrahedralElement::AbstractTetrahedralElement 0 0% 62.06% 104ms 1.32% __GI__IO_file_open 1ms 0.013% 62.07% 104ms 1.32% std::vector::push_back (inline) 99ms 1.26% 63.33% 100ms 1.27% boost::detail::sp_counted_base::release 8ms 0.1% 63.44% 100ms 1.27% std::_Rb_tree_const_iterator::operator++ (inline) 100ms 1.27% 64.71% 100ms 1.27% std::_Rb_tree_increment 10ms 0.13% 64.83% 100ms 1.27% std::vector::_M_realloc_insert 0 0% 64.83% 98ms 1.25% std::basic_filebuf::_M_terminate_output 2ms 0.025% 64.86% 97ms 1.23% std::basic_filebuf::overflow 1ms 0.013% 64.87% 95ms 1.21% std::basic_filebuf::_M_convert_to_external 2ms 0.025% 64.90% 94ms 1.20% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (partial-inline) 23ms 0.29% 65.19% 94ms 1.20% boost::numeric::ublas::indexing_vector_assign 1ms 0.013% 65.20% 94ms 1.20% std::__basic_file::xsputn 45ms 0.57% 65.78% 93ms 1.18% AbstractElement::GetNodeLocation 92ms 1.17% 66.95% 93ms 1.18% __GI___libc_write 51ms 0.65% 67.60% 88ms 1.12% std::basic_filebuf::xsputn 0 0% 67.60% 87ms 1.11% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 85ms 1.08% 68.68% 85ms 1.08% __libc_open64 84ms 1.07% 69.75% 84ms 1.07% TetrahedralMesh::EdgeIterator::operator!= (partial-inline) 56ms 0.71% 70.46% 84ms 1.07% std::basic_streambuf::xsputn 1ms 0.013% 70.47% 80ms 1.02% AbstractCellPopulation::GetLocationIndexUsingCell 58ms 0.74% 71.21% 74ms 0.94% AbstractElement::GetNodeGlobalIndex 0 0% 71.21% 73ms 0.93% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 71.21% 73ms 0.93% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 0 0% 71.21% 72ms 0.92% FilesystemPermissions::CreateDirectoryWithPermissions (inline) 3ms 0.038% 71.25% 72ms 0.92% std::filesystem::create_directory 71ms 0.9% 72.15% 71ms 0.9% counterclockwise 10ms 0.13% 72.28% 68ms 0.87% CellPropertyCollection::AddProperty 68ms 0.87% 73.14% 68ms 0.87% std::vector::size (inline) 0 0% 73.14% 68ms 0.87% tcache_get (inline) 68ms 0.87% 74.01% 68ms 0.87% tcache_get_n (inline) 66ms 0.84% 74.85% 67ms 0.85% boost::detail::shared_count::shared_count (inline) 63ms 0.8% 75.65% 67ms 0.85% vertexsort 66ms 0.84% 76.49% 66ms 0.84% __GI___fstatat64 2ms 0.025% 76.51% 66ms 0.84% std::filesystem::status 50ms 0.64% 77.15% 66ms 0.84% std::num_put::do_put 65ms 0.83% 77.98% 65ms 0.83% __memcpy_avx_unaligned_erms 40ms 0.51% 78.49% 62ms 0.79% malloc_consolidate 8ms 0.1% 78.59% 61ms 0.78% Node::ConstructNodeAttributes (inline) 1ms 0.013% 78.60% 59ms 0.75% Cell::GetCellId 2ms 0.025% 78.63% 59ms 0.75% std::_Rb_tree::_M_emplace_hint_unique 2ms 0.025% 78.65% 58ms 0.74% TetrahedralMesh::EdgeIterator::GetNodeA 0 0% 78.65% 58ms 0.74% boost::numeric::ublas::norm_2 (inline) 16ms 0.2% 78.85% 58ms 0.74% boost::numeric::ublas::vector_norm_2::apply (inline) 56ms 0.71% 79.57% 56ms 0.71% Node::GetIndex 0 0% 79.57% 54ms 0.69% Node::ClearAppliedForce 53ms 0.67% 80.24% 53ms 0.67% boost::shared_ptr::operator-> (inline) 20ms 0.25% 80.50% 51ms 0.65% AbstractTetrahedralMesh::GetElement 51ms 0.65% 81.15% 51ms 0.65% [libchaste_mesh.so] 24ms 0.31% 81.45% 50ms 0.64% boost::numeric::ublas::c_matrix::operator() (partial-inline) 0 0% 81.45% 50ms 0.64% std::_Rb_tree::_M_destroy_node (inline) 0 0% 81.45% 50ms 0.64% std::__new_allocator::destroy (inline) 0 0% 81.45% 50ms 0.64% std::allocator_traits::destroy (inline) 48ms 0.61% 82.06% 48ms 0.61% [libstdc++.so.6.0.33] 6ms 0.076% 82.14% 48ms 0.61% std::_Vector_base::_M_deallocate (inline) 0 0% 82.14% 46ms 0.59% TetrahedralMesh::EdgeIterator::GetNodeB 46ms 0.59% 82.72% 46ms 0.59% boost::numeric::ublas::c_vector::operator() (partial-inline) 27ms 0.34% 83.07% 45ms 0.57% hack_digit 2ms 0.025% 83.09% 45ms 0.57% std::__new_allocator::construct (inline) 0 0% 83.09% 45ms 0.57% std::allocator_traits::construct (inline) 0 0% 83.09% 43ms 0.55% std::vector::vector (inline) 2ms 0.025% 83.12% 42ms 0.53% NodeAttributes::NodeAttributes 0 0% 83.12% 42ms 0.53% std::_Rb_tree::_M_construct_node (inline) 1ms 0.013% 83.13% 41ms 0.52% BoundaryNodeWriter::Visit 0 0% 83.13% 40ms 0.51% MeshBasedCellPopulation::SpringIterator::~SpringIterator (inline) 0 0% 83.13% 40ms 0.51% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 0 0% 83.13% 40ms 0.51% std::_Vector_base::_Vector_base (inline)