File: Test2dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 6705ms, 85.10% of 7879ms total Dropped 581 nodes (cum <= 39.40ms) flat flat% sum% cum cum% 0 0% 0% 7844ms 99.56% __libc_start_call_main 0 0% 0% 7844ms 99.56% __libc_start_main_impl 0 0% 0% 7844ms 99.56% _start 0 0% 0% 7829ms 99.37% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 7829ms 99.37% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 7829ms 99.37% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 7829ms 99.37% main 0 0% 0% 7790ms 98.87% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 7790ms 98.87% CxxTest::TestRunner::runTest (inline) 0 0% 0% 7790ms 98.87% Test2DMonolayerRepresentativeSimulation::Test2DMonolayerRepresentativeSimulationForProfiling 1ms 0.013% 0.013% 7786ms 98.82% AbstractCellBasedSimulation::Solve 0 0% 0.013% 3398ms 43.13% AbstractCellBasedSimulation::UpdateCellPopulation 1ms 0.013% 0.025% 2843ms 36.08% MeshBasedCellPopulation::Update 2ms 0.025% 0.051% 2819ms 35.78% AbstractCellPopulation::WriteResultsToFiles 2ms 0.025% 0.076% 1561ms 19.81% OffLatticeSimulation::UpdateCellLocationsAndTopology 1ms 0.013% 0.089% 1409ms 17.88% MeshBasedCellPopulation::UpdateNodePairs 1ms 0.013% 0.1% 1397ms 17.73% ForwardEulerNumericalMethod::UpdateAllNodePositions 0 0% 0.1% 1392ms 17.67% MutableMesh::ReMesh 3ms 0.038% 0.14% 1348ms 17.11% AbstractNumericalMethod::ComputeForcesIncludingDamping 9ms 0.11% 0.25% 1217ms 15.45% MeshBasedCellPopulation::SpringIterator::operator++ 122ms 1.55% 1.80% 1006ms 12.77% TetrahedralMesh::EdgeIterator::operator++ 4ms 0.051% 1.85% 987ms 12.53% AbstractTwoBodyInteractionForce::AddForceContribution 459ms 5.83% 7.68% 984ms 12.49% std::_Rb_tree::_M_lower_bound (inline) 4ms 0.051% 7.73% 904ms 11.47% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 247ms 3.13% 10.86% 892ms 11.32% __dynamic_cast 7ms 0.089% 10.95% 875ms 11.11% CellPopulationElementWriter::Visit 24ms 0.3% 11.26% 865ms 10.98% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 11ms 0.14% 11.40% 829ms 10.52% CellPropertyCollection::GetPropertiesType (inline) 6ms 0.076% 11.47% 747ms 9.48% MeshBasedCellPopulation::AcceptCellWriter 27ms 0.34% 11.82% 743ms 9.43% AbstractCellPopulation::GetCellUsingLocationIndex 9ms 0.11% 11.93% 710ms 9.01% TetrahedralMesh::ImportFromMesher 3ms 0.038% 11.97% 653ms 8.29% AbstractCellProperty::IsSubType (inline) 50ms 0.63% 12.60% 585ms 7.42% std::map::operator[] (partial-inline) 0 0% 12.60% 582ms 7.39% std::ostream::operator<< (inline) 92ms 1.17% 13.77% 580ms 7.36% std::ostream::_M_insert 22ms 0.28% 14.05% 545ms 6.92% std::_Rb_tree::find (inline) 4ms 0.051% 14.10% 536ms 6.80% AbstractCellBasedSimulation::DoCellBirth 35ms 0.44% 14.54% 535ms 6.79% operator new 5ms 0.063% 14.61% 522ms 6.63% Cell::GetCellProliferativeType 0 0% 14.61% 518ms 6.57% triangulate 6ms 0.076% 14.68% 510ms 6.47% std::set::insert (inline) 5ms 0.063% 14.75% 504ms 6.40% std::_Rb_tree::_M_insert_unique 0 0% 14.75% 503ms 6.38% std::set::count (inline) 497ms 6.31% 21.06% 497ms 6.31% __strcmp_avx2 171ms 2.17% 23.23% 494ms 6.27% __GI___libc_malloc 0 0% 23.23% 493ms 6.26% std::_Rb_tree::lower_bound (inline) 0 0% 23.23% 493ms 6.26% std::map::lower_bound (inline) 219ms 2.78% 26.01% 489ms 6.21% __cxxabiv1::__si_class_type_info::__do_dyncast 35ms 0.44% 26.45% 484ms 6.14% std::__new_allocator::allocate (inline) 0 0% 26.45% 482ms 6.12% std::allocator_traits::allocate (inline) 8ms 0.1% 26.55% 474ms 6.02% LegacyCellProliferativeTypesWriter::VisitCell 0 0% 26.55% 451ms 5.72% delaunay 2ms 0.025% 26.58% 451ms 5.72% divconqdelaunay 0 0% 26.58% 425ms 5.39% std::_Rb_tree::_M_create_node (inline) 34ms 0.43% 27.01% 409ms 5.19% std::_Rb_tree::~_Rb_tree (inline) 0 0% 27.01% 408ms 5.18% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 27.01% 382ms 4.85% std::_Rb_tree::_M_get_node (inline) 0 0% 27.01% 378ms 4.80% std::set::~set (inline) 17ms 0.22% 27.22% 372ms 4.72% std::less::operator() (inline) 85ms 1.08% 28.30% 370ms 4.70% std::_Rb_tree::_M_erase 3ms 0.038% 28.34% 368ms 4.67% NodeLocationWriter::Visit 4ms 0.051% 28.39% 364ms 4.62% Cell::ReadyToDivide 24ms 0.3% 28.70% 359ms 4.56% std::_Rb_tree::_Rb_tree (partial-inline) 355ms 4.51% 33.20% 355ms 4.51% std::operator< (inline) 6ms 0.076% 33.28% 332ms 4.21% Element::Element 0 0% 33.28% 330ms 4.19% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 0 0% 33.28% 329ms 4.18% AbstractCellBasedWriter::OpenOutputFileForAppend 2ms 0.025% 33.30% 328ms 4.16% Cell::GetMutationState 0 0% 33.30% 328ms 4.16% OutputFileHandler::OpenOutputFile 17ms 0.22% 33.52% 324ms 4.11% std::_Rb_tree::_M_insert_ (inline) 1ms 0.013% 33.53% 313ms 3.97% std::set::set (inline) 34ms 0.43% 33.96% 310ms 3.93% std::_Rb_tree::_M_copy (inline) 28ms 0.36% 34.32% 308ms 3.91% std::num_put::_M_insert_float 301ms 3.82% 38.14% 301ms 3.82% std::_Rb_tree::_S_right (inline) 7ms 0.089% 38.23% 296ms 3.76% AbstractCellPopulation::IsCellAttachedToLocationIndex 98ms 1.24% 39.47% 288ms 3.66% __GI___libc_free 2ms 0.025% 39.50% 273ms 3.46% AbstractCentreBasedCellPopulation::GetDampingConstant 0 0% 39.50% 273ms 3.46% MeshBasedCellPopulation::GetDampingConstant 177ms 2.25% 41.74% 273ms 3.46% _int_malloc 80ms 1.02% 42.76% 273ms 3.46% std::_Rb_tree::_M_clone_node (inline) 0 0% 42.76% 267ms 3.39% std::_Rb_tree::_M_drop_node (inline) 9ms 0.11% 42.87% 262ms 3.33% divconqrecurse 17ms 0.22% 43.09% 259ms 3.29% std::__new_allocator::deallocate (inline) 8ms 0.1% 43.19% 254ms 3.22% CellPropertyCollection::HasProperty 0 0% 43.19% 254ms 3.22% std::allocator_traits::deallocate (inline) 0 0% 43.19% 252ms 3.20% Cell::HasCellProperty (inline) 75ms 0.95% 44.14% 246ms 3.12% mergehulls 5ms 0.063% 44.21% 244ms 3.10% AbstractCellProperty::IsType (inline) 5ms 0.063% 44.27% 244ms 3.10% AbstractPhaseBasedCellCycleModel::ReadyToDivide 18ms 0.23% 44.50% 236ms 3.00% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 8ms 0.1% 44.60% 234ms 2.97% std::__cxx11::collate::do_transform 3ms 0.038% 44.64% 227ms 2.88% CellProliferativeTypesWriter::VisitCell 3ms 0.038% 44.68% 221ms 2.80% ___vsnprintf 0 0% 44.68% 218ms 2.77% __vsnprintf_internal (inline) 18ms 0.23% 44.90% 214ms 2.72% __printf_buffer 4ms 0.051% 44.95% 211ms 2.68% Element::RegisterWithNodes (inline) 0 0% 44.95% 205ms 2.60% std::_Rb_tree::_M_put_node (inline) 1ms 0.013% 44.97% 203ms 2.58% Node::AddElement 14ms 0.18% 45.15% 195ms 2.47% TetrahedralMesh::Clear 5ms 0.063% 45.21% 190ms 2.41% MeshBasedCellPopulation::SpringsEnd (inline) 161ms 2.04% 47.25% 190ms 2.41% _int_free 50ms 0.63% 47.89% 185ms 2.35% AbstractCellProperty::IsSame 12ms 0.15% 48.04% 176ms 2.23% __printf_fp_l_buffer 0 0% 48.04% 176ms 2.23% __printf_fp_spec (inline) 56ms 0.71% 48.75% 175ms 2.22% std::_Rb_tree::_M_get_insert_unique_pos (inline) 55ms 0.7% 49.45% 165ms 2.09% TetrahedralMesh::EdgesEnd (partial-inline) 86ms 1.09% 50.54% 155ms 1.97% __printf_fp_buffer_1 62ms 0.79% 51.33% 155ms 1.97% std::__ostream_insert 14ms 0.18% 51.50% 154ms 1.95% AbstractTetrahedralElement::CalculateJacobian 0 0% 51.50% 151ms 1.92% FilesystemPermissions::SetFilePermissions (inline) 151ms 1.92% 53.42% 151ms 1.92% __GI_fchmodat 0 0% 53.42% 151ms 1.92% std::filesystem::permissions 0 0% 53.42% 148ms 1.88% std::basic_ofstream::basic_ofstream (inline) 1ms 0.013% 53.43% 145ms 1.84% std::basic_filebuf::open 0 0% 53.43% 145ms 1.84% std::basic_ofstream::open (inline) 1ms 0.013% 53.45% 141ms 1.79% OutputFileHandler::OutputFileHandler 16ms 0.2% 53.65% 141ms 1.79% boost::detail::shared_count::~shared_count (inline) 0 0% 53.65% 141ms 1.79% boost::shared_ptr::~shared_ptr (inline) 1ms 0.013% 53.66% 140ms 1.78% OutputFileHandler::CommonConstructor 1ms 0.013% 53.67% 137ms 1.74% TetrahedralMesh::RefreshJacobianCachedData 0 0% 53.67% 135ms 1.71% OutputFileHandler::MakeFoldersAndReturnFullPath 2ms 0.025% 53.70% 135ms 1.71% boost::numeric::ublas::vector_assign (inline) 38ms 0.48% 54.18% 135ms 1.71% std::type_info::operator== (inline) 30ms 0.38% 54.56% 133ms 1.69% std::num_put::_M_insert_int 0 0% 54.56% 132ms 1.68% AbstractCellPopulation::Iterator::operator++ (inline) 33ms 0.42% 54.98% 131ms 1.66% AbstractCellPopulation::Iterator::IsRealCell (inline) 6ms 0.076% 55.06% 128ms 1.62% AbstractTetrahedralElement::CalculateInverseJacobian 0 0% 55.06% 127ms 1.61% AbstractCellPopulation::CloseRoundRobinWritersFiles 2ms 0.025% 55.08% 126ms 1.60% AbstractCellBasedWriter::CloseFile 7ms 0.089% 55.17% 126ms 1.60% boost::numeric::ublas::c_vector::c_vector (inline) 13ms 0.16% 55.34% 125ms 1.59% Node::~Node 1ms 0.013% 55.35% 124ms 1.57% std::basic_filebuf::close 0 0% 55.35% 124ms 1.57% std::basic_ofstream::close (inline) 1ms 0.013% 55.36% 124ms 1.57% std::operator<< (inline) 18ms 0.23% 55.59% 123ms 1.56% MeshBasedCellPopulation::SpringIterator::SpringIterator 2ms 0.025% 55.62% 121ms 1.54% AbstractTetrahedralElement::AbstractTetrahedralElement 14ms 0.18% 55.79% 118ms 1.50% AbstractTetrahedralElement::RefreshJacobian 116ms 1.47% 57.27% 118ms 1.50% boost::detail::sp_counted_base::release 9ms 0.11% 57.38% 115ms 1.46% std::_Rb_tree_const_iterator::operator++ (inline) 114ms 1.45% 58.83% 114ms 1.45% std::_Rb_tree_increment 112ms 1.42% 60.25% 112ms 1.42% incircle 1ms 0.013% 60.26% 106ms 1.35% _IO_new_fopen 0 0% 60.26% 105ms 1.33% __fopen_internal (inline) 27ms 0.34% 60.60% 105ms 1.33% boost::numeric::ublas::indexing_vector_assign 0 0% 60.60% 105ms 1.33% std::__basic_file::open 0 0% 60.60% 102ms 1.29% _IO_new_file_fopen 0 0% 60.60% 102ms 1.29% __GI__IO_file_open 3ms 0.038% 60.64% 102ms 1.29% alternateaxes 102ms 1.29% 61.94% 102ms 1.29% std::_Rb_tree_insert_and_rebalance 32ms 0.41% 62.34% 101ms 1.28% boost::shared_ptr::shared_ptr (inline) 1ms 0.013% 62.36% 101ms 1.28% std::_Vector_base::_M_allocate (inline) 92ms 1.17% 63.52% 99ms 1.26% vertexmedian 95ms 1.21% 64.73% 96ms 1.22% __libc_open64 93ms 1.18% 65.91% 93ms 1.18% [libchaste_cell_based.so] 64ms 0.81% 66.72% 93ms 1.18% std::basic_streambuf::xsputn 5ms 0.063% 66.79% 93ms 1.18% std::vector::push_back (inline) 46ms 0.58% 67.37% 92ms 1.17% AbstractElement::GetNodeLocation 60ms 0.76% 68.13% 90ms 1.14% TetrahedralMesh::EdgeIterator::EdgeIterator (partial-inline) 2ms 0.025% 68.16% 89ms 1.13% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 4ms 0.051% 68.21% 84ms 1.07% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (partial-inline) 5ms 0.063% 68.27% 83ms 1.05% std::vector::_M_realloc_insert 52ms 0.66% 68.93% 82ms 1.04% std::basic_filebuf::xsputn 81ms 1.03% 69.96% 81ms 1.03% TetrahedralMesh::EdgeIterator::operator!= (partial-inline) 53ms 0.67% 70.63% 79ms 1.00% malloc_consolidate 0 0% 70.63% 78ms 0.99% std::basic_filebuf::_M_terminate_output 1ms 0.013% 70.64% 77ms 0.98% std::basic_filebuf::overflow 76ms 0.96% 71.61% 76ms 0.96% __GI___libc_write 76ms 0.96% 72.57% 76ms 0.96% __memcpy_avx_unaligned_erms 0 0% 72.57% 76ms 0.96% std::__basic_file::xsputn 0 0% 72.57% 76ms 0.96% std::basic_filebuf::_M_convert_to_external 66ms 0.84% 73.41% 73ms 0.93% vertexsort 72ms 0.91% 74.32% 72ms 0.91% Node::GetIndex 0 0% 74.32% 69ms 0.88% FilesystemPermissions::CreateDirectoryWithPermissions (inline) 69ms 0.88% 75.20% 69ms 0.88% __GI___fstatat64 68ms 0.86% 76.06% 69ms 0.88% boost::detail::shared_count::shared_count (inline) 1ms 0.013% 76.08% 69ms 0.88% std::filesystem::create_directory 0 0% 76.08% 69ms 0.88% std::filesystem::status 2ms 0.025% 76.10% 65ms 0.82% AbstractCellPopulation::GetLocationIndexUsingCell 0 0% 76.10% 62ms 0.79% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 76.10% 62ms 0.79% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 0 0% 76.10% 62ms 0.79% std::_Rb_tree::_M_destroy_node (inline) 0 0% 76.10% 62ms 0.79% std::__new_allocator::destroy (inline) 0 0% 76.10% 62ms 0.79% std::allocator_traits::destroy (inline) 4ms 0.051% 76.15% 61ms 0.77% TetrahedralMesh::EdgeIterator::GetNodeB 2ms 0.025% 76.18% 60ms 0.76% Cell::GetCellId 10ms 0.13% 76.30% 60ms 0.76% CellPropertyCollection::AddProperty 59ms 0.75% 77.05% 59ms 0.75% [libchaste_mesh.so] 0 0% 77.05% 59ms 0.75% std::vector::vector (inline) 58ms 0.74% 77.79% 58ms 0.74% counterclockwise 47ms 0.6% 78.39% 56ms 0.71% AbstractElement::GetNodeGlobalIndex 7ms 0.089% 78.47% 56ms 0.71% std::_Vector_base::_M_deallocate (inline) 4ms 0.051% 78.53% 55ms 0.7% Node::ConstructNodeAttributes (inline) 0 0% 78.53% 53ms 0.67% Node::ClearAppliedForce 0 0% 78.53% 51ms 0.65% TetrahedralMesh::EdgeIterator::GetNodeA 0 0% 78.53% 51ms 0.65% std::_Vector_base::_Vector_base (inline) 0 0% 78.53% 50ms 0.63% std::map::map (inline) 49ms 0.62% 79.15% 49ms 0.62% Node::IsDeleted 0 0% 79.15% 48ms 0.61% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 48ms 0.61% 79.76% 48ms 0.61% [libstdc++.so.6.0.33] 0 0% 79.76% 48ms 0.61% boost::numeric::ublas::norm_2 (inline) 14ms 0.18% 79.93% 48ms 0.61% boost::numeric::ublas::vector_norm_2::apply (inline) 0 0% 79.93% 48ms 0.61% std::_Vector_base::_M_create_storage (inline) 0 0% 79.93% 47ms 0.6% MeshBasedCellPopulation::SpringIterator::~SpringIterator (inline) 28ms 0.36% 80.29% 47ms 0.6% boost::numeric::ublas::c_matrix::operator() 0 0% 80.29% 47ms 0.6% std::__new_allocator::construct (inline) 0 0% 80.29% 47ms 0.6% std::allocator_traits::construct (inline) 45ms 0.57% 80.86% 45ms 0.57% boost::numeric::ublas::c_vector::operator() 44ms 0.56% 81.42% 44ms 0.56% boost::shared_ptr::operator-> (inline) 27ms 0.34% 81.76% 44ms 0.56% hack_digit 1ms 0.013% 81.77% 44ms 0.56% std::__basic_file::close 36ms 0.46% 82.23% 44ms 0.56% std::num_put::do_put 44ms 0.56% 82.79% 44ms 0.56% std::vector::size (inline) 0 0% 82.79% 43ms 0.55% _IO_new_fclose 0 0% 82.79% 43ms 0.55% std::_Rb_tree::_M_construct_node (inline) 0 0% 82.79% 43ms 0.55% tcache_get (inline) 43ms 0.55% 83.34% 43ms 0.55% tcache_get_n (inline) 0 0% 83.34% 42ms 0.53% MeshBasedCellPopulation::SpringIterator::GetNodeB (inline) 1ms 0.013% 83.35% 42ms 0.53% _IO_new_file_close_it 0 0% 83.35% 42ms 0.53% std::_Rb_tree::_M_emplace_hint_unique 10ms 0.13% 83.48% 41ms 0.52% Inverse 41ms 0.52% 84.00% 41ms 0.52% __GI___close_nocancel 41ms 0.52% 84.52% 41ms 0.52% std::ostream::sentry::sentry 0 0% 84.52% 40ms 0.51% CellPropertyCollection::~CellPropertyCollection (inline) 6ms 0.076% 84.59% 40ms 0.51% NodeAttributes::NodeAttributes 40ms 0.51% 85.10% 40ms 0.51% boost::numeric::ublas::same_impl_ex