File: Test2dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 6576ms, 83.83% of 7844ms total Dropped 580 nodes (cum <= 39.22ms) flat flat% sum% cum cum% 0 0% 0% 7806ms 99.52% __libc_start_call_main 0 0% 0% 7806ms 99.52% __libc_start_main_impl 0 0% 0% 7806ms 99.52% _start 0 0% 0% 7790ms 99.31% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 7790ms 99.31% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 7790ms 99.31% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 7790ms 99.31% main 0 0% 0% 7753ms 98.84% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 7753ms 98.84% CxxTest::TestRunner::runTest (inline) 0 0% 0% 7753ms 98.84% Test2DMonolayerRepresentativeSimulation::Test2DMonolayerRepresentativeSimulationForProfiling 0 0% 0% 7751ms 98.81% AbstractCellBasedSimulation::Solve 0 0% 0% 3351ms 42.72% AbstractCellBasedSimulation::UpdateCellPopulation 1ms 0.013% 0.013% 2888ms 36.82% MeshBasedCellPopulation::Update 2ms 0.025% 0.038% 2865ms 36.52% AbstractCellPopulation::WriteResultsToFiles 2ms 0.025% 0.064% 1525ms 19.44% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 0.064% 1433ms 18.27% MutableMesh::ReMesh 0 0% 0.064% 1408ms 17.95% MeshBasedCellPopulation::UpdateNodePairs 0 0% 0.064% 1373ms 17.50% ForwardEulerNumericalMethod::UpdateAllNodePositions 8ms 0.1% 0.17% 1317ms 16.79% AbstractNumericalMethod::ComputeForcesIncludingDamping 20ms 0.25% 0.42% 1210ms 15.43% MeshBasedCellPopulation::SpringIterator::operator++ 106ms 1.35% 1.77% 964ms 12.29% TetrahedralMesh::EdgeIterator::operator++ 436ms 5.56% 7.33% 922ms 11.75% std::_Rb_tree::_M_lower_bound (inline) 4ms 0.051% 7.38% 911ms 11.61% AbstractTwoBodyInteractionForce::AddForceContribution 10ms 0.13% 7.51% 908ms 11.58% CellPopulationElementWriter::Visit 1ms 0.013% 7.52% 880ms 11.22% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 14ms 0.18% 7.70% 873ms 11.13% CellPropertyCollection::GetPropertiesType (inline) 235ms 3.00% 10.70% 857ms 10.93% __dynamic_cast 63ms 0.8% 11.50% 819ms 10.44% AbstractVariableSizeTwoBodyInteractionForce::CalculateForceBetweenNodes 38ms 0.48% 11.98% 742ms 9.46% AbstractCellPopulation::GetCellUsingLocationIndex 3ms 0.038% 12.02% 736ms 9.38% MeshBasedCellPopulation::AcceptCellWriter 10ms 0.13% 12.15% 718ms 9.15% TetrahedralMesh::ImportFromMesher 4ms 0.051% 12.20% 670ms 8.54% AbstractCellProperty::IsSubType (inline) 1ms 0.013% 12.21% 601ms 7.66% std::ostream::operator<< (inline) 79ms 1.01% 13.22% 597ms 7.61% std::ostream::_M_insert 45ms 0.57% 13.79% 591ms 7.53% std::map::operator[] (partial-inline) 33ms 0.42% 14.21% 550ms 7.01% operator new 1ms 0.013% 14.23% 547ms 6.97% triangulate 7ms 0.089% 14.32% 538ms 6.86% std::set::insert (inline) 6ms 0.076% 14.39% 531ms 6.77% std::_Rb_tree::_M_insert_unique 36ms 0.46% 14.85% 511ms 6.51% std::__new_allocator::allocate (inline) 173ms 2.21% 17.06% 508ms 6.48% __GI___libc_malloc 0 0% 17.06% 505ms 6.44% std::allocator_traits::allocate (inline) 0 0% 17.06% 503ms 6.41% std::_Rb_tree::lower_bound (inline) 0 0% 17.06% 503ms 6.41% std::map::lower_bound (inline) 500ms 6.37% 23.43% 500ms 6.37% __strcmp_avx2 2ms 0.025% 23.46% 480ms 6.12% Cell::GetCellProliferativeType 2ms 0.025% 23.48% 477ms 6.08% LegacyCellProliferativeTypesWriter::VisitCell 22ms 0.28% 23.76% 470ms 5.99% std::_Rb_tree::find (inline) 0 0% 23.76% 464ms 5.92% delaunay 1ms 0.013% 23.78% 462ms 5.89% divconqdelaunay 1ms 0.013% 23.79% 445ms 5.67% AbstractCellBasedSimulation::DoCellBirth 213ms 2.72% 26.50% 444ms 5.66% __cxxabiv1::__si_class_type_info::__do_dyncast 0 0% 26.50% 434ms 5.53% std::set::count (inline) 2ms 0.025% 26.53% 402ms 5.12% NodeLocationWriter::Visit 0 0% 26.53% 402ms 5.12% std::_Rb_tree::_M_create_node (inline) 38ms 0.48% 27.01% 396ms 5.05% std::_Rb_tree::~_Rb_tree (inline) 2ms 0.025% 27.04% 392ms 5.00% Cell::GetMutationState 0 0% 27.04% 383ms 4.88% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 27.04% 374ms 4.77% std::_Rb_tree::_M_get_node (inline) 0 0% 27.04% 368ms 4.69% std::set::~set (inline) 30ms 0.38% 27.42% 366ms 4.67% std::_Rb_tree::_Rb_tree (partial-inline) 88ms 1.12% 28.54% 356ms 4.54% std::_Rb_tree::_M_erase 22ms 0.28% 28.82% 345ms 4.40% std::_Rb_tree::_M_insert_ (inline) 27ms 0.34% 29.17% 342ms 4.36% std::num_put::_M_insert_float 4ms 0.051% 29.22% 332ms 4.23% std::set::set (inline) 17ms 0.22% 29.44% 322ms 4.11% std::less::operator() (inline) 2ms 0.025% 29.46% 313ms 3.99% Cell::ReadyToDivide 310ms 3.95% 33.41% 310ms 3.95% std::_Rb_tree::_S_right (inline) 0 0% 33.41% 308ms 3.93% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 5ms 0.064% 33.48% 307ms 3.91% AbstractCellPopulation::IsCellAttachedToLocationIndex 0 0% 33.48% 306ms 3.90% AbstractCellBasedWriter::OpenOutputFileForAppend 305ms 3.89% 37.37% 305ms 3.89% std::operator< (inline) 3ms 0.038% 37.40% 301ms 3.84% MeshBasedCellPopulation::GetDampingConstant 1ms 0.013% 37.42% 301ms 3.84% OutputFileHandler::OpenOutputFile 1ms 0.013% 37.43% 297ms 3.79% AbstractCentreBasedCellPopulation::GetDampingConstant 42ms 0.54% 37.97% 296ms 3.77% std::_Rb_tree::_M_copy (inline) 109ms 1.39% 39.35% 287ms 3.66% __GI___libc_free 2ms 0.025% 39.38% 277ms 3.53% Element::Element 176ms 2.24% 41.62% 270ms 3.44% _int_malloc 8ms 0.1% 41.73% 259ms 3.30% std::__cxx11::collate::do_transform 19ms 0.24% 41.97% 255ms 3.25% std::__new_allocator::deallocate (inline) 2ms 0.025% 41.99% 248ms 3.16% AbstractCellProperty::IsType (inline) 0 0% 41.99% 248ms 3.16% std::allocator_traits::deallocate (inline) 78ms 0.99% 42.99% 246ms 3.14% std::_Rb_tree::_M_clone_node (inline) 1ms 0.013% 43.00% 244ms 3.11% ___vsnprintf 0 0% 43.00% 243ms 3.10% __vsnprintf_internal (inline) 6ms 0.076% 43.08% 242ms 3.09% divconqrecurse 0 0% 43.08% 242ms 3.09% std::_Rb_tree::_M_drop_node (inline) 31ms 0.4% 43.47% 237ms 3.02% __printf_buffer 1ms 0.013% 43.49% 230ms 2.93% CellProliferativeTypesWriter::VisitCell 7ms 0.089% 43.57% 228ms 2.91% CellPropertyCollection::HasProperty 0 0% 43.57% 226ms 2.88% Cell::HasCellProperty (inline) 57ms 0.73% 44.30% 222ms 2.83% mergehulls 13ms 0.17% 44.47% 221ms 2.82% MeshBasedCellPopulation::SpringsEnd (inline) 5ms 0.064% 44.53% 213ms 2.72% AbstractPhaseBasedCellCycleModel::ReadyToDivide 12ms 0.15% 44.68% 206ms 2.63% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 22ms 0.28% 44.96% 203ms 2.59% TetrahedralMesh::Clear 2ms 0.025% 44.99% 200ms 2.55% Element::RegisterWithNodes (inline) 62ms 0.79% 45.78% 198ms 2.52% AbstractCellProperty::IsSame 3ms 0.038% 45.82% 195ms 2.49% Node::AddElement 0 0% 45.82% 195ms 2.49% std::_Rb_tree::_M_put_node (inline) 1ms 0.013% 45.83% 187ms 2.38% __printf_fp_spec (inline) 5ms 0.064% 45.89% 186ms 2.37% __printf_fp_l_buffer 55ms 0.7% 46.60% 184ms 2.35% TetrahedralMesh::EdgesEnd (partial-inline) 65ms 0.83% 47.42% 181ms 2.31% std::_Rb_tree::_M_get_insert_unique_pos (inline) 97ms 1.24% 48.66% 177ms 2.26% __printf_fp_buffer_1 150ms 1.91% 50.57% 177ms 2.26% _int_free 0 0% 50.57% 152ms 1.94% std::basic_ofstream::basic_ofstream (inline) 0 0% 50.57% 149ms 1.90% TetrahedralMesh::RefreshJacobianCachedData 0 0% 50.57% 147ms 1.87% std::basic_ofstream::open (inline) 0 0% 50.57% 146ms 1.86% std::basic_filebuf::open 51ms 0.65% 51.22% 144ms 1.84% std::__ostream_insert 13ms 0.17% 51.39% 142ms 1.81% AbstractTetrahedralElement::CalculateJacobian 0 0% 51.39% 138ms 1.76% AbstractCellPopulation::CloseRoundRobinWritersFiles 0 0% 51.39% 138ms 1.76% OutputFileHandler::CommonConstructor 0 0% 51.39% 138ms 1.76% OutputFileHandler::OutputFileHandler 0 0% 51.39% 137ms 1.75% AbstractCellBasedWriter::CloseFile 1ms 0.013% 51.40% 137ms 1.75% AbstractTetrahedralElement::CalculateInverseJacobian 2ms 0.025% 51.43% 137ms 1.75% std::basic_filebuf::close 2ms 0.025% 51.45% 137ms 1.75% std::basic_ofstream::close (inline) 2ms 0.025% 51.48% 137ms 1.75% std::vector::push_back (inline) 26ms 0.33% 51.81% 136ms 1.73% std::type_info::operator== (inline) 4ms 0.051% 51.86% 135ms 1.72% std::_Vector_base::_M_allocate (inline) 24ms 0.31% 52.17% 134ms 1.71% MeshBasedCellPopulation::SpringIterator::SpringIterator 0 0% 52.17% 133ms 1.70% OutputFileHandler::MakeFoldersAndReturnFullPath 5ms 0.064% 52.23% 133ms 1.70% alternateaxes 13ms 0.17% 52.40% 130ms 1.66% std::vector::_M_realloc_insert 0 0% 52.40% 128ms 1.63% FilesystemPermissions::SetFilePermissions (inline) 80ms 1.02% 53.42% 128ms 1.63% TetrahedralMesh::EdgeIterator::EdgeIterator (partial-inline) 128ms 1.63% 55.05% 128ms 1.63% __GI_fchmodat 2ms 0.025% 55.07% 128ms 1.63% boost::numeric::ublas::vector_assign (inline) 0 0% 55.07% 128ms 1.63% std::filesystem::permissions 109ms 1.39% 56.46% 127ms 1.62% vertexmedian 3ms 0.038% 56.50% 124ms 1.58% std::operator<< (inline) 0 0% 56.50% 119ms 1.52% boost::numeric::ublas::c_vector::c_vector (inline) 2ms 0.025% 56.53% 119ms 1.52% std::__basic_file::open 0 0% 56.53% 116ms 1.48% _IO_new_fopen 0 0% 56.53% 116ms 1.48% __fopen_internal (inline) 1ms 0.013% 56.54% 115ms 1.47% _IO_new_file_fopen 115ms 1.47% 58.01% 115ms 1.47% std::_Rb_tree_insert_and_rebalance 31ms 0.4% 58.40% 115ms 1.47% std::num_put::_M_insert_int 11ms 0.14% 58.54% 114ms 1.45% AbstractCellPopulation::Iterator::IsRealCell (inline) 0 0% 58.54% 114ms 1.45% AbstractCellPopulation::Iterator::operator++ (inline) 12ms 0.15% 58.69% 113ms 1.44% std::_Rb_tree_const_iterator::operator++ (inline) 3ms 0.038% 58.73% 112ms 1.43% __GI__IO_file_open 112ms 1.43% 60.16% 112ms 1.43% std::_Rb_tree_increment 6ms 0.076% 60.24% 111ms 1.42% Node::~Node 109ms 1.39% 61.63% 109ms 1.39% incircle 13ms 0.17% 61.79% 105ms 1.34% boost::detail::shared_count::~shared_count (inline) 0 0% 61.79% 105ms 1.34% boost::shared_ptr::~shared_ptr (inline) 9ms 0.11% 61.91% 101ms 1.29% AbstractTetrahedralElement::RefreshJacobian 100ms 1.27% 63.18% 100ms 1.27% __libc_open64 67ms 0.85% 64.04% 94ms 1.20% std::basic_filebuf::xsputn 92ms 1.17% 65.21% 92ms 1.17% boost::detail::sp_counted_base::release 2ms 0.025% 65.23% 91ms 1.16% std::basic_filebuf::overflow 0 0% 65.23% 90ms 1.15% std::basic_filebuf::_M_terminate_output 87ms 1.11% 66.34% 89ms 1.13% __GI___libc_write 0 0% 66.34% 89ms 1.13% std::__basic_file::xsputn 0 0% 66.34% 89ms 1.13% std::basic_filebuf::_M_convert_to_external 39ms 0.5% 66.84% 88ms 1.12% boost::shared_ptr::shared_ptr (inline) 33ms 0.42% 67.26% 86ms 1.10% boost::numeric::ublas::indexing_vector_assign 2ms 0.025% 67.29% 82ms 1.05% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 3ms 0.038% 67.33% 81ms 1.03% AbstractTetrahedralElement::AbstractTetrahedralElement 81ms 1.03% 68.36% 81ms 1.03% TetrahedralMesh::EdgeIterator::operator!= (partial-inline) 60ms 0.76% 69.12% 80ms 1.02% std::basic_streambuf::xsputn 2ms 0.025% 69.15% 77ms 0.98% TetrahedralMesh::EdgeIterator::GetNodeA 75ms 0.96% 70.10% 75ms 0.96% [libchaste_mesh.so] 1ms 0.013% 70.12% 75ms 0.96% std::filesystem::status 69ms 0.88% 71.00% 75ms 0.96% vertexsort 4ms 0.051% 71.05% 74ms 0.94% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (partial-inline) 73ms 0.93% 71.98% 73ms 0.93% [libchaste_cell_based.so] 73ms 0.93% 72.91% 73ms 0.93% __GI___fstatat64 38ms 0.48% 73.39% 71ms 0.91% AbstractElement::GetNodeLocation 0 0% 73.39% 70ms 0.89% Cell::GetCellId 59ms 0.75% 74.15% 68ms 0.87% AbstractElement::GetNodeGlobalIndex 1ms 0.013% 74.16% 68ms 0.87% FilesystemPermissions::CreateDirectoryWithPermissions (inline) 2ms 0.025% 74.18% 67ms 0.85% std::filesystem::create_directory 45ms 0.57% 74.76% 66ms 0.84% malloc_consolidate 0 0% 74.76% 64ms 0.82% tcache_get (inline) 64ms 0.82% 75.57% 64ms 0.82% tcache_get_n (inline) 9ms 0.11% 75.69% 63ms 0.8% CellPropertyCollection::AddProperty 61ms 0.78% 76.47% 61ms 0.78% __memcpy_avx_unaligned_erms 54ms 0.69% 77.15% 59ms 0.75% std::num_put::do_put 4ms 0.051% 77.21% 58ms 0.74% AbstractCellPopulation::GetLocationIndexUsingCell 58ms 0.74% 77.94% 58ms 0.74% Node::IsDeleted 0 0% 77.94% 57ms 0.73% Node::ClearAppliedForce 1ms 0.013% 77.96% 57ms 0.73% Node::ConstructNodeAttributes (inline) 57ms 0.73% 78.68% 57ms 0.73% Node::GetIndex 7ms 0.089% 78.77% 56ms 0.71% TetrahedralMesh::EdgeIterator::GetNodeB 56ms 0.71% 79.49% 56ms 0.71% [libstdc++.so.6.0.33] 56ms 0.71% 80.20% 56ms 0.71% counterclockwise 31ms 0.4% 80.60% 54ms 0.69% AbstractTetrahedralMesh::GetElement 1ms 0.013% 80.61% 52ms 0.66% std::_Vector_base::_M_deallocate (inline) 51ms 0.65% 81.26% 51ms 0.65% boost::shared_ptr::operator-> (inline) 29ms 0.37% 81.63% 50ms 0.64% boost::numeric::ublas::c_matrix::operator() (partial-inline) 48ms 0.61% 82.24% 49ms 0.62% boost::detail::shared_count::shared_count (inline) 1ms 0.013% 82.25% 48ms 0.61% BoundaryNodeWriter::Visit 48ms 0.61% 82.87% 48ms 0.61% std::vector::size (inline) 0 0% 82.87% 47ms 0.6% std::_Rb_tree::_M_destroy_node (inline) 0 0% 82.87% 47ms 0.6% std::__new_allocator::destroy (inline) 0 0% 82.87% 47ms 0.6% std::allocator_traits::destroy (inline) 0 0% 82.87% 46ms 0.59% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 0 0% 82.87% 45ms 0.57% std::vector::vector (inline) 19ms 0.24% 83.11% 44ms 0.56% Determinant (inline) 8ms 0.1% 83.21% 43ms 0.55% Inverse 0 0% 83.21% 43ms 0.55% MeshBasedCellPopulation::SpringIterator::GetNodeA (inline) 0 0% 83.21% 43ms 0.55% MeshBasedCellPopulation::SpringIterator::~SpringIterator (inline) 2ms 0.025% 83.24% 43ms 0.55% std::_Rb_tree::_M_emplace_hint_unique 0 0% 83.24% 42ms 0.54% AbstractCentreBasedCellPopulation::IsMarkedSpring 0 0% 83.24% 42ms 0.54% CellPropertyCollection::~CellPropertyCollection (inline) 2ms 0.025% 83.26% 42ms 0.54% NodeAttributes::NodeAttributes 3ms 0.038% 83.30% 41ms 0.52% Element::~Element 1ms 0.013% 83.31% 41ms 0.52% std::__basic_file::close 1ms 0.013% 83.32% 40ms 0.51% _IO_new_fclose 40ms 0.51% 83.83% 40ms 0.51% unlink_chunk