File: Test2dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 6573ms, 83.98% of 7827ms total Dropped 582 nodes (cum <= 39.13ms) flat flat% sum% cum cum% 0 0% 0% 7791ms 99.54% __libc_start_call_main 0 0% 0% 7791ms 99.54% __libc_start_main_impl 0 0% 0% 7791ms 99.54% _start 0 0% 0% 7776ms 99.35% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 7776ms 99.35% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 7776ms 99.35% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 7776ms 99.35% main 0 0% 0% 7738ms 98.86% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 7738ms 98.86% CxxTest::TestRunner::runTest (inline) 0 0% 0% 7738ms 98.86% Test2DMonolayerRepresentativeSimulation::Test2DMonolayerRepresentativeSimulationForProfiling 1ms 0.013% 0.013% 7735ms 98.82% AbstractCellBasedSimulation::Solve 0 0% 0.013% 3360ms 42.93% AbstractCellBasedSimulation::UpdateCellPopulation 1ms 0.013% 0.026% 2892ms 36.95% MeshBasedCellPopulation::Update 1ms 0.013% 0.038% 2870ms 36.67% AbstractCellPopulation::WriteResultsToFiles 1ms 0.013% 0.051% 1493ms 19.07% OffLatticeSimulation::UpdateCellLocationsAndTopology 1ms 0.013% 0.064% 1420ms 18.14% MeshBasedCellPopulation::UpdateNodePairs 1ms 0.013% 0.077% 1415ms 18.08% MutableMesh::ReMesh 0 0% 0.077% 1340ms 17.12% ForwardEulerNumericalMethod::UpdateAllNodePositions 6ms 0.077% 0.15% 1295ms 16.55% AbstractNumericalMethod::ComputeForcesIncludingDamping 25ms 0.32% 0.47% 1238ms 15.82% MeshBasedCellPopulation::SpringIterator::operator++ 118ms 1.51% 1.98% 1017ms 12.99% TetrahedralMesh::EdgeIterator::operator++ 463ms 5.92% 7.90% 964ms 12.32% std::_Rb_tree::_M_lower_bound (inline) 6ms 0.077% 7.97% 931ms 11.89% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 5ms 0.064% 8.04% 906ms 11.58% AbstractTwoBodyInteractionForce::AddForceContribution 3ms 0.038% 8.07% 899ms 11.49% CellPopulationElementWriter::Visit 9ms 0.11% 8.19% 855ms 10.92% CellPropertyCollection::GetPropertiesType (inline) 46ms 0.59% 8.78% 823ms 10.51% AbstractVariableSizeTwoBodyInteractionForce::CalculateForceBetweenNodes 254ms 3.25% 12.02% 812ms 10.37% __dynamic_cast 4ms 0.051% 12.07% 786ms 10.04% MeshBasedCellPopulation::AcceptCellWriter 43ms 0.55% 12.62% 773ms 9.88% AbstractCellPopulation::GetCellUsingLocationIndex 10ms 0.13% 12.75% 710ms 9.07% TetrahedralMesh::ImportFromMesher 5ms 0.064% 12.81% 643ms 8.22% AbstractCellProperty::IsSubType (inline) 2ms 0.026% 12.84% 626ms 8.00% std::ostream::operator<< (inline) 92ms 1.18% 14.02% 623ms 7.96% std::ostream::_M_insert 50ms 0.64% 14.65% 593ms 7.58% std::map::operator[] (partial-inline) 0 0% 14.65% 550ms 7.03% triangulate 36ms 0.46% 15.11% 549ms 7.01% operator new 9ms 0.11% 15.23% 532ms 6.80% std::set::insert (inline) 17ms 0.22% 15.45% 523ms 6.68% std::_Rb_tree::_M_insert_unique 22ms 0.28% 15.73% 516ms 6.59% std::_Rb_tree::find (inline) 169ms 2.16% 17.89% 506ms 6.46% __GI___libc_malloc 0 0% 17.89% 491ms 6.27% delaunay 0 0% 17.89% 491ms 6.27% std::_Rb_tree::lower_bound (inline) 0 0% 17.89% 491ms 6.27% std::map::lower_bound (inline) 2ms 0.026% 17.91% 490ms 6.26% divconqdelaunay 7ms 0.089% 18.00% 489ms 6.25% LegacyCellProliferativeTypesWriter::VisitCell 30ms 0.38% 18.39% 486ms 6.21% std::__new_allocator::allocate (inline) 5ms 0.064% 18.45% 484ms 6.18% Cell::GetCellProliferativeType 0 0% 18.45% 482ms 6.16% std::allocator_traits::allocate (inline) 467ms 5.97% 24.42% 467ms 5.97% __strcmp_avx2 0 0% 24.42% 463ms 5.92% std::set::count (inline) 1ms 0.013% 24.43% 459ms 5.86% AbstractCellBasedSimulation::DoCellBirth 48ms 0.61% 25.04% 444ms 5.67% std::_Rb_tree::~_Rb_tree (inline) 0 0% 25.04% 421ms 5.38% std::set::~set (inline) 189ms 2.41% 27.46% 412ms 5.26% __cxxabiv1::__si_class_type_info::__do_dyncast 0 0% 27.46% 408ms 5.21% std::_Rb_tree::_M_create_node (inline) 1ms 0.013% 27.47% 400ms 5.11% NodeLocationWriter::Visit 92ms 1.18% 28.64% 392ms 5.01% std::_Rb_tree::_M_erase 0 0% 28.64% 381ms 4.87% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 28.64% 378ms 4.83% std::_Rb_tree::_M_get_node (inline) 5ms 0.064% 28.71% 366ms 4.68% Cell::GetMutationState 11ms 0.14% 28.85% 342ms 4.37% std::less::operator() (inline) 31ms 0.4% 29.24% 340ms 4.34% std::num_put::_M_insert_float 23ms 0.29% 29.54% 334ms 4.27% std::_Rb_tree::_M_insert_ (inline) 331ms 4.23% 33.77% 331ms 4.23% std::operator< (inline) 19ms 0.24% 34.01% 322ms 4.11% std::_Rb_tree::_Rb_tree (partial-inline) 107ms 1.37% 35.38% 319ms 4.08% __GI___libc_free 2ms 0.026% 35.40% 312ms 3.99% AbstractCentreBasedCellPopulation::GetDampingConstant 0 0% 35.40% 312ms 3.99% MeshBasedCellPopulation::GetDampingConstant 9ms 0.11% 35.52% 298ms 3.81% Cell::ReadyToDivide 2ms 0.026% 35.54% 297ms 3.79% std::set::set (inline) 8ms 0.1% 35.65% 292ms 3.73% divconqrecurse 0 0% 35.65% 289ms 3.69% AbstractCellBasedWriter::OpenOutputFileForAppend 0 0% 35.65% 289ms 3.69% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 10ms 0.13% 35.77% 288ms 3.68% AbstractCellPopulation::IsCellAttachedToLocationIndex 1ms 0.013% 35.79% 287ms 3.67% OutputFileHandler::OpenOutputFile 282ms 3.60% 39.39% 282ms 3.60% std::_Rb_tree::_S_right (inline) 0 0% 39.39% 279ms 3.56% std::_Rb_tree::_M_drop_node (inline) 27ms 0.34% 39.73% 278ms 3.55% std::_Rb_tree::_M_copy (inline) 6ms 0.077% 39.81% 277ms 3.54% std::__new_allocator::deallocate (inline) 74ms 0.95% 40.76% 276ms 3.53% mergehulls 4ms 0.051% 40.81% 274ms 3.50% Element::Element 0 0% 40.81% 274ms 3.50% std::allocator_traits::deallocate (inline) 172ms 2.20% 43.00% 265ms 3.39% _int_malloc 6ms 0.077% 43.08% 265ms 3.39% std::__cxx11::collate::do_transform 6ms 0.077% 43.16% 260ms 3.32% AbstractCellProperty::IsType (inline) 6ms 0.077% 43.23% 259ms 3.31% CellPropertyCollection::HasProperty 5ms 0.064% 43.30% 256ms 3.27% CellProliferativeTypesWriter::VisitCell 0 0% 43.30% 255ms 3.26% Cell::HasCellProperty (inline) 3ms 0.038% 43.34% 251ms 3.21% ___vsnprintf 28ms 0.36% 43.69% 248ms 3.17% __printf_buffer 0 0% 43.69% 248ms 3.17% __vsnprintf_internal (inline) 78ms 1% 44.69% 246ms 3.14% std::_Rb_tree::_M_clone_node (inline) 0 0% 44.69% 225ms 2.87% std::_Rb_tree::_M_put_node (inline) 180ms 2.30% 46.99% 212ms 2.71% _int_free 10ms 0.13% 47.12% 209ms 2.67% TetrahedralMesh::Clear 57ms 0.73% 47.85% 196ms 2.50% AbstractCellProperty::IsSame 7ms 0.089% 47.94% 191ms 2.44% __printf_fp_l_buffer 0 0% 47.94% 191ms 2.44% __printf_fp_spec (inline) 8ms 0.1% 48.04% 189ms 2.41% MeshBasedCellPopulation::SpringsEnd (inline) 94ms 1.20% 49.24% 175ms 2.24% __printf_fp_buffer_1 66ms 0.84% 50.08% 172ms 2.20% std::_Rb_tree::_M_get_insert_unique_pos (inline) 7ms 0.089% 50.17% 168ms 2.15% Element::RegisterWithNodes (inline) 4ms 0.051% 50.22% 166ms 2.12% AbstractPhaseBasedCellCycleModel::ReadyToDivide 8ms 0.1% 50.33% 165ms 2.11% AbstractTetrahedralElement::CalculateJacobian 1ms 0.013% 50.34% 160ms 2.04% Node::AddElement 4ms 0.051% 50.39% 158ms 2.02% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 44ms 0.56% 50.95% 156ms 1.99% TetrahedralMesh::EdgesEnd (partial-inline) 0 0% 50.95% 140ms 1.79% std::basic_ofstream::basic_ofstream (inline) 26ms 0.33% 51.28% 139ms 1.78% AbstractCellPopulation::Iterator::IsRealCell (inline) 23ms 0.29% 51.58% 139ms 1.78% std::type_info::operator== (inline) 0 0% 51.58% 137ms 1.75% std::basic_filebuf::open 0 0% 51.58% 136ms 1.74% AbstractCellPopulation::Iterator::operator++ (inline) 48ms 0.61% 52.19% 136ms 1.74% std::__ostream_insert 0 0% 52.19% 136ms 1.74% std::basic_ofstream::open (inline) 0 0% 52.19% 135ms 1.72% AbstractCellPopulation::CloseRoundRobinWritersFiles 2ms 0.026% 52.22% 135ms 1.72% TetrahedralMesh::RefreshJacobianCachedData 1ms 0.013% 52.23% 134ms 1.71% OutputFileHandler::CommonConstructor 0 0% 52.23% 134ms 1.71% OutputFileHandler::OutputFileHandler 1ms 0.013% 52.24% 133ms 1.70% AbstractCellBasedWriter::CloseFile 0 0% 52.24% 132ms 1.69% std::basic_filebuf::close 0 0% 52.24% 132ms 1.69% std::basic_ofstream::close (inline) 6ms 0.077% 52.32% 131ms 1.67% Node::~Node 0 0% 52.32% 129ms 1.65% OutputFileHandler::MakeFoldersAndReturnFullPath 2ms 0.026% 52.34% 126ms 1.61% AbstractTetrahedralElement::CalculateInverseJacobian 0 0% 52.34% 126ms 1.61% alternateaxes 32ms 0.41% 52.75% 126ms 1.61% std::num_put::_M_insert_int 117ms 1.49% 54.25% 125ms 1.60% vertexmedian 120ms 1.53% 55.78% 120ms 1.53% incircle 7ms 0.089% 55.87% 119ms 1.52% std::_Rb_tree_const_iterator::operator++ (inline) 6ms 0.077% 55.95% 119ms 1.52% std::vector::push_back (inline) 0 0% 55.95% 118ms 1.51% FilesystemPermissions::SetFilePermissions (inline) 15ms 0.19% 56.14% 118ms 1.51% MeshBasedCellPopulation::SpringIterator::SpringIterator 118ms 1.51% 57.65% 118ms 1.51% std::_Rb_tree_increment 1ms 0.013% 57.66% 118ms 1.51% std::filesystem::permissions 24ms 0.31% 57.97% 116ms 1.48% AbstractTetrahedralElement::RefreshJacobian 116ms 1.48% 59.45% 116ms 1.48% __GI_fchmodat 3ms 0.038% 59.49% 111ms 1.42% std::operator<< (inline) 12ms 0.15% 59.64% 110ms 1.41% boost::detail::shared_count::~shared_count (inline) 0 0% 59.64% 110ms 1.41% boost::shared_ptr::~shared_ptr (inline) 3ms 0.038% 59.68% 108ms 1.38% AbstractTetrahedralElement::AbstractTetrahedralElement 44ms 0.56% 60.24% 108ms 1.38% boost::shared_ptr::shared_ptr (inline) 3ms 0.038% 60.28% 107ms 1.37% boost::numeric::ublas::vector_assign (inline) 7ms 0.089% 60.37% 107ms 1.37% std::vector::_M_realloc_insert 2ms 0.026% 60.39% 106ms 1.35% std::_Vector_base::_M_allocate (inline) 105ms 1.34% 61.74% 105ms 1.34% std::_Rb_tree_insert_and_rebalance 2ms 0.026% 61.76% 104ms 1.33% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (partial-inline) 2ms 0.026% 61.79% 104ms 1.33% boost::numeric::ublas::c_vector::c_vector (inline) 3ms 0.038% 61.82% 102ms 1.30% std::__basic_file::open 2ms 0.026% 61.85% 100ms 1.28% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 1ms 0.013% 61.86% 99ms 1.26% _IO_new_fopen 0 0% 61.86% 98ms 1.25% __fopen_internal (inline) 1ms 0.013% 61.88% 98ms 1.25% std::basic_filebuf::_M_terminate_output 2ms 0.026% 61.90% 97ms 1.24% std::__basic_file::xsputn 0 0% 61.90% 97ms 1.24% std::basic_filebuf::_M_convert_to_external 0 0% 61.90% 97ms 1.24% std::basic_filebuf::overflow 96ms 1.23% 63.13% 96ms 1.23% [libchaste_cell_based.so] 1ms 0.013% 63.14% 96ms 1.23% _IO_new_file_fopen 95ms 1.21% 64.35% 96ms 1.23% boost::detail::sp_counted_base::release 1ms 0.013% 64.37% 94ms 1.20% __GI__IO_file_open 93ms 1.19% 65.56% 94ms 1.20% __GI___libc_write 0 0% 65.56% 90ms 1.15% AbstractCellPopulation::GetLocationIndexUsingCell 69ms 0.88% 66.44% 89ms 1.14% TetrahedralMesh::EdgeIterator::EdgeIterator (partial-inline) 52ms 0.66% 67.10% 87ms 1.11% std::basic_filebuf::xsputn 15ms 0.19% 67.29% 84ms 1.07% CellPropertyCollection::AddProperty 82ms 1.05% 68.34% 82ms 1.05% counterclockwise 81ms 1.03% 69.38% 81ms 1.03% __libc_open64 35ms 0.45% 69.82% 80ms 1.02% AbstractElement::GetNodeLocation 0 0% 69.82% 77ms 0.98% Cell::GetCellId 53ms 0.68% 70.50% 76ms 0.97% std::basic_streambuf::xsputn 74ms 0.95% 71.44% 74ms 0.95% TetrahedralMesh::EdgeIterator::operator!= (partial-inline) 61ms 0.78% 72.22% 72ms 0.92% AbstractElement::GetNodeGlobalIndex 72ms 0.92% 73.14% 72ms 0.92% std::vector::size (inline) 0 0% 73.14% 69ms 0.88% FilesystemPermissions::CreateDirectoryWithPermissions (inline) 29ms 0.37% 73.51% 69ms 0.88% boost::numeric::ublas::indexing_vector_assign 1ms 0.013% 73.53% 69ms 0.88% std::filesystem::create_directory 67ms 0.86% 74.38% 67ms 0.86% Node::GetIndex 1ms 0.013% 74.40% 67ms 0.86% std::filesystem::status 46ms 0.59% 74.98% 66ms 0.84% malloc_consolidate 62ms 0.79% 75.78% 66ms 0.84% vertexsort 65ms 0.83% 76.61% 65ms 0.83% __GI___fstatat64 65ms 0.83% 77.44% 65ms 0.83% __memcpy_avx_unaligned_erms 59ms 0.75% 78.19% 64ms 0.82% boost::detail::shared_count::shared_count (inline) 0 0% 78.19% 62ms 0.79% tcache_get (inline) 62ms 0.79% 78.98% 62ms 0.79% tcache_get_n (inline) 26ms 0.33% 79.32% 60ms 0.77% AbstractCellCycleModel::GetAge 48ms 0.61% 79.93% 60ms 0.77% std::num_put::do_put 27ms 0.34% 80.27% 54ms 0.69% AbstractTetrahedralMesh::GetElement 54ms 0.69% 80.96% 54ms 0.69% [libchaste_mesh.so] 0 0% 80.96% 54ms 0.69% std::_Rb_tree::_M_destroy_node (inline) 0 0% 80.96% 54ms 0.69% std::__new_allocator::destroy (inline) 0 0% 80.96% 54ms 0.69% std::allocator_traits::destroy (inline) 40ms 0.51% 81.47% 53ms 0.68% boost::numeric::ublas::c_matrix::operator() (partial-inline) 5ms 0.064% 81.54% 52ms 0.66% std::_Rb_tree::_M_emplace_hint_unique 3ms 0.038% 81.58% 51ms 0.65% std::_Vector_base::_M_deallocate (inline) 0 0% 81.58% 50ms 0.64% AbstractCentreBasedCellPopulation::CreateCellPair 17ms 0.22% 81.79% 50ms 0.64% Determinant (inline) 3ms 0.038% 81.83% 50ms 0.64% TetrahedralMesh::EdgeIterator::GetNodeA 6ms 0.077% 81.91% 50ms 0.64% TetrahedralMesh::EdgeIterator::GetNodeB 0 0% 81.91% 49ms 0.63% Node::ClearAppliedForce 0 0% 81.91% 49ms 0.63% Node::ConstructNodeAttributes (inline) 0 0% 81.91% 49ms 0.63% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 0 0% 81.91% 48ms 0.61% std::map::find (inline) 0 0% 81.91% 47ms 0.6% MeshBasedCellPopulation::SpringIterator::~SpringIterator (inline) 46ms 0.59% 82.50% 46ms 0.59% [libstdc++.so.6.0.33] 0 0% 82.50% 46ms 0.59% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 82.50% 46ms 0.59% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 46ms 0.59% 83.08% 46ms 0.59% std::ostream::sentry::sentry 45ms 0.57% 83.66% 45ms 0.57% boost::shared_ptr::operator-> (inline) 25ms 0.32% 83.98% 43ms 0.55% hack_digit 0 0% 83.98% 43ms 0.55% std::vector::vector (inline)