File: Test2dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 6573ms, 84.73% of 7758ms total Dropped 587 nodes (cum <= 38.79ms) flat flat% sum% cum cum% 0 0% 0% 7724ms 99.56% __libc_start_call_main 0 0% 0% 7724ms 99.56% __libc_start_main_impl 0 0% 0% 7724ms 99.56% _start 0 0% 0% 7709ms 99.37% main 0 0% 0% 7708ms 99.36% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 7708ms 99.36% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 7708ms 99.36% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 7674ms 98.92% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 7674ms 98.92% CxxTest::TestRunner::runTest (inline) 0 0% 0% 7674ms 98.92% Test2DMonolayerRepresentativeSimulation::Test2DMonolayerRepresentativeSimulationForProfiling 0 0% 0% 7671ms 98.88% AbstractCellBasedSimulation::Solve 0 0% 0% 3309ms 42.65% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 2862ms 36.89% AbstractCellPopulation::WriteResultsToFiles 0 0% 0% 2848ms 36.71% MeshBasedCellPopulation::Update 1ms 0.013% 0.013% 1491ms 19.22% OffLatticeSimulation::UpdateCellLocationsAndTopology 2ms 0.026% 0.039% 1422ms 18.33% MeshBasedCellPopulation::UpdateNodePairs 0 0% 0.039% 1367ms 17.62% MutableMesh::ReMesh 0 0% 0.039% 1319ms 17.00% ForwardEulerNumericalMethod::UpdateAllNodePositions 4ms 0.052% 0.09% 1264ms 16.29% AbstractNumericalMethod::ComputeForcesIncludingDamping 17ms 0.22% 0.31% 1230ms 15.85% MeshBasedCellPopulation::SpringIterator::operator++ 131ms 1.69% 2.00% 1011ms 13.03% TetrahedralMesh::EdgeIterator::operator++ 2ms 0.026% 2.02% 939ms 12.10% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 12ms 0.15% 2.18% 874ms 11.27% CellPropertyCollection::GetPropertiesType (inline) 6ms 0.077% 2.26% 857ms 11.05% AbstractTwoBodyInteractionForce::AddForceContribution 224ms 2.89% 5.14% 855ms 11.02% __dynamic_cast 6ms 0.077% 5.22% 849ms 10.94% CellPopulationElementWriter::Visit 401ms 5.17% 10.39% 846ms 10.90% std::_Rb_tree::_M_lower_bound (inline) 6ms 0.077% 10.47% 790ms 10.18% MeshBasedCellPopulation::AcceptCellWriter 26ms 0.34% 10.80% 761ms 9.81% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 15ms 0.19% 11.00% 698ms 9.00% TetrahedralMesh::ImportFromMesher 6ms 0.077% 11.07% 681ms 8.78% AbstractCellProperty::IsSubType (inline) 23ms 0.3% 11.37% 675ms 8.70% AbstractCellPopulation::GetCellUsingLocationIndex 2ms 0.026% 11.39% 648ms 8.35% std::ostream::operator<< (inline) 91ms 1.17% 12.57% 645ms 8.31% std::ostream::_M_insert 54ms 0.7% 13.26% 579ms 7.46% operator new 30ms 0.39% 13.65% 536ms 6.91% std::__new_allocator::allocate (inline) 0 0% 13.65% 530ms 6.83% std::allocator_traits::allocate (inline) 0 0% 13.65% 530ms 6.83% triangulate 524ms 6.75% 20.40% 524ms 6.75% __strcmp_avx2 52ms 0.67% 21.08% 514ms 6.63% std::map::operator[] (partial-inline) 4ms 0.052% 21.13% 514ms 6.63% std::set::insert (inline) 186ms 2.40% 23.52% 513ms 6.61% __GI___libc_malloc 11ms 0.14% 23.67% 510ms 6.57% std::_Rb_tree::_M_insert_unique 4ms 0.052% 23.72% 505ms 6.51% Cell::GetCellProliferativeType 2ms 0.026% 23.74% 505ms 6.51% LegacyCellProliferativeTypesWriter::VisitCell 16ms 0.21% 23.95% 486ms 6.26% std::_Rb_tree::find (inline) 0 0% 23.95% 469ms 6.05% delaunay 1ms 0.013% 23.96% 468ms 6.03% divconqdelaunay 0 0% 23.96% 450ms 5.80% std::_Rb_tree::_M_create_node (inline) 4ms 0.052% 24.01% 447ms 5.76% AbstractCellBasedSimulation::DoCellBirth 201ms 2.59% 26.60% 447ms 5.76% __cxxabiv1::__si_class_type_info::__do_dyncast 0 0% 26.60% 446ms 5.75% std::set::count (inline) 0 0% 26.60% 424ms 5.47% std::_Rb_tree::_M_get_node (inline) 0 0% 26.60% 421ms 5.43% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 26.60% 405ms 5.22% std::_Rb_tree::lower_bound (inline) 0 0% 26.60% 405ms 5.22% std::map::lower_bound (inline) 23ms 0.3% 26.90% 402ms 5.18% std::_Rb_tree::_Rb_tree (partial-inline) 4ms 0.052% 26.95% 391ms 5.04% NodeLocationWriter::Visit 25ms 0.32% 27.28% 384ms 4.95% std::_Rb_tree::~_Rb_tree (inline) 5ms 0.064% 27.34% 370ms 4.77% Cell::GetMutationState 4ms 0.052% 27.39% 369ms 4.76% std::set::set (inline) 0 0% 27.39% 357ms 4.60% std::set::~set (inline) 75ms 0.97% 28.36% 356ms 4.59% std::_Rb_tree::_M_erase 29ms 0.37% 28.73% 349ms 4.50% std::num_put::_M_insert_float 10ms 0.13% 28.86% 341ms 4.40% std::less::operator() (inline) 331ms 4.27% 33.13% 331ms 4.27% std::operator< (inline) 40ms 0.52% 33.64% 330ms 4.25% std::_Rb_tree::_M_copy (inline) 1ms 0.013% 33.66% 325ms 4.19% AbstractCellBasedWriter::OpenOutputFileForAppend 0 0% 33.66% 325ms 4.19% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 17ms 0.22% 33.87% 325ms 4.19% std::_Rb_tree::_M_insert_ (inline) 0 0% 33.87% 322ms 4.15% OutputFileHandler::OpenOutputFile 1ms 0.013% 33.89% 314ms 4.05% MeshBasedCellPopulation::GetDampingConstant 3ms 0.039% 33.93% 313ms 4.03% AbstractCentreBasedCellPopulation::GetDampingConstant 3ms 0.039% 33.96% 310ms 4.00% Cell::ReadyToDivide 127ms 1.64% 35.60% 304ms 3.92% __GI___libc_free 76ms 0.98% 36.58% 287ms 3.70% std::_Rb_tree::_M_clone_node (inline) 4ms 0.052% 36.63% 283ms 3.65% Element::Element 6ms 0.077% 36.71% 280ms 3.61% AbstractCellPopulation::IsCellAttachedToLocationIndex 4ms 0.052% 36.76% 279ms 3.60% std::__cxx11::collate::do_transform 8ms 0.1% 36.87% 275ms 3.54% divconqrecurse 3ms 0.039% 36.90% 269ms 3.47% std::__new_allocator::deallocate (inline) 1ms 0.013% 36.92% 268ms 3.45% ___vsnprintf 0 0% 36.92% 267ms 3.44% __vsnprintf_internal (inline) 43ms 0.55% 37.47% 263ms 3.39% __printf_buffer 0 0% 37.47% 261ms 3.36% std::allocator_traits::deallocate (inline) 0 0% 37.47% 259ms 3.34% std::_Rb_tree::_M_drop_node (inline) 90ms 1.16% 38.63% 256ms 3.30% mergehulls 4ms 0.052% 38.68% 249ms 3.21% CellProliferativeTypesWriter::VisitCell 170ms 2.19% 40.87% 247ms 3.18% _int_malloc 3ms 0.039% 40.91% 245ms 3.16% AbstractCellProperty::IsType (inline) 0 0% 40.91% 243ms 3.13% Cell::HasCellProperty (inline) 5ms 0.064% 40.98% 243ms 3.13% CellPropertyCollection::HasProperty 230ms 2.96% 43.94% 230ms 2.96% std::_Rb_tree::_S_right (inline) 2ms 0.026% 43.97% 209ms 2.69% AbstractPhaseBasedCellCycleModel::ReadyToDivide 0 0% 43.97% 209ms 2.69% std::_Rb_tree::_M_put_node (inline) 11ms 0.14% 44.11% 205ms 2.64% __printf_fp_l_buffer 0 0% 44.11% 205ms 2.64% __printf_fp_spec (inline) 16ms 0.21% 44.32% 203ms 2.62% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 4ms 0.052% 44.37% 202ms 2.60% MeshBasedCellPopulation::SpringsEnd (inline) 91ms 1.17% 45.54% 184ms 2.37% __printf_fp_buffer_1 39ms 0.5% 46.04% 181ms 2.33% AbstractCellProperty::IsSame 23ms 0.3% 46.34% 181ms 2.33% TetrahedralMesh::Clear 149ms 1.92% 48.26% 177ms 2.28% _int_free 5ms 0.064% 48.32% 176ms 2.27% Element::RegisterWithNodes (inline) 64ms 0.82% 49.15% 174ms 2.24% std::_Rb_tree::_M_get_insert_unique_pos (inline) 5ms 0.064% 49.21% 165ms 2.13% Node::AddElement 0 0% 49.21% 163ms 2.10% std::basic_ofstream::basic_ofstream (inline) 0 0% 49.21% 158ms 2.04% std::basic_ofstream::open (inline) 2ms 0.026% 49.24% 157ms 2.02% std::basic_filebuf::open 14ms 0.18% 49.42% 156ms 2.01% AbstractTetrahedralElement::CalculateJacobian 43ms 0.55% 49.97% 154ms 1.99% TetrahedralMesh::EdgesEnd (partial-inline) 35ms 0.45% 50.43% 153ms 1.97% std::num_put::_M_insert_int 3ms 0.039% 50.46% 151ms 1.95% boost::numeric::ublas::vector_assign (inline) 0 0% 50.46% 145ms 1.87% OutputFileHandler::OutputFileHandler 2ms 0.026% 50.49% 145ms 1.87% boost::numeric::ublas::c_vector::c_vector (inline) 2ms 0.026% 50.52% 144ms 1.86% OutputFileHandler::CommonConstructor 34ms 0.44% 50.95% 142ms 1.83% std::type_info::operator== (inline) 0 0% 50.95% 140ms 1.80% OutputFileHandler::MakeFoldersAndReturnFullPath 23ms 0.3% 51.25% 138ms 1.78% MeshBasedCellPopulation::SpringIterator::SpringIterator 0 0% 51.25% 136ms 1.75% AbstractCellPopulation::CloseRoundRobinWritersFiles 2ms 0.026% 51.28% 135ms 1.74% AbstractCellBasedWriter::CloseFile 0 0% 51.28% 133ms 1.71% std::basic_filebuf::close 0 0% 51.28% 133ms 1.71% std::basic_ofstream::close (inline) 0 0% 51.28% 131ms 1.69% _IO_new_fopen 0 0% 51.28% 131ms 1.69% __fopen_internal (inline) 0 0% 51.28% 131ms 1.69% std::__basic_file::open 2ms 0.026% 51.30% 130ms 1.68% _IO_new_file_fopen 62ms 0.8% 52.10% 128ms 1.65% std::__ostream_insert 1ms 0.013% 52.11% 127ms 1.64% __GI__IO_file_open 3ms 0.039% 52.15% 125ms 1.61% alternateaxes 0 0% 52.15% 123ms 1.59% FilesystemPermissions::SetFilePermissions (inline) 3ms 0.039% 52.19% 123ms 1.59% std::filesystem::permissions 1ms 0.013% 52.20% 121ms 1.56% TetrahedralMesh::RefreshJacobianCachedData 110ms 1.42% 53.62% 121ms 1.56% vertexmedian 120ms 1.55% 55.17% 120ms 1.55% __GI_fchmodat 4ms 0.052% 55.22% 119ms 1.53% std::vector::push_back (inline) 18ms 0.23% 55.45% 118ms 1.52% AbstractCellPopulation::Iterator::IsRealCell (inline) 62ms 0.8% 56.25% 117ms 1.51% TetrahedralMesh::EdgeIterator::EdgeIterator (partial-inline) 12ms 0.15% 56.41% 116ms 1.50% boost::detail::shared_count::~shared_count (inline) 0 0% 56.41% 116ms 1.50% boost::shared_ptr::~shared_ptr (inline) 0 0% 56.41% 115ms 1.48% AbstractCellPopulation::Iterator::operator++ (inline) 7ms 0.09% 56.50% 113ms 1.46% std::_Rb_tree_const_iterator::operator++ (inline) 4ms 0.052% 56.55% 112ms 1.44% AbstractTetrahedralElement::CalculateInverseJacobian 18ms 0.23% 56.78% 112ms 1.44% AbstractTetrahedralElement::RefreshJacobian 112ms 1.44% 58.22% 112ms 1.44% std::_Rb_tree_increment 12ms 0.15% 58.38% 112ms 1.44% std::vector::_M_realloc_insert 24ms 0.31% 58.69% 110ms 1.42% boost::numeric::ublas::indexing_vector_assign 108ms 1.39% 60.08% 109ms 1.41% __libc_open64 1ms 0.013% 60.09% 107ms 1.38% AbstractTetrahedralElement::AbstractTetrahedralElement 1ms 0.013% 60.11% 107ms 1.38% std::_Vector_base::_M_allocate (inline) 2ms 0.026% 60.13% 106ms 1.37% std::operator<< (inline) 104ms 1.34% 61.47% 104ms 1.34% incircle 102ms 1.31% 62.79% 103ms 1.33% boost::detail::sp_counted_base::release 98ms 1.26% 64.05% 98ms 1.26% std::_Rb_tree_insert_and_rebalance 40ms 0.52% 64.57% 97ms 1.25% boost::shared_ptr::shared_ptr (inline) 6ms 0.077% 64.64% 95ms 1.22% Node::~Node 2ms 0.026% 64.67% 92ms 1.19% std::basic_filebuf::_M_terminate_output 3ms 0.039% 64.71% 91ms 1.17% std::basic_filebuf::overflow 1ms 0.013% 64.72% 90ms 1.16% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (partial-inline) 0 0% 64.72% 88ms 1.13% std::__basic_file::xsputn 0 0% 64.72% 88ms 1.13% std::basic_filebuf::_M_convert_to_external 87ms 1.12% 65.84% 87ms 1.12% __GI___libc_write 85ms 1.10% 66.94% 85ms 1.10% TetrahedralMesh::EdgeIterator::operator!= (partial-inline) 55ms 0.71% 67.65% 84ms 1.08% std::basic_filebuf::xsputn 37ms 0.48% 68.12% 81ms 1.04% AbstractElement::GetNodeLocation 1ms 0.013% 68.14% 80ms 1.03% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 79ms 1.02% 69.15% 79ms 1.02% [libchaste_cell_based.so] 79ms 1.02% 70.17% 79ms 1.02% __GI___fstatat64 0 0% 70.17% 78ms 1.01% std::filesystem::status 2ms 0.026% 70.20% 74ms 0.95% AbstractCellPopulation::GetLocationIndexUsingCell 0 0% 70.20% 74ms 0.95% FilesystemPermissions::CreateDirectoryWithPermissions (inline) 0 0% 70.20% 74ms 0.95% std::filesystem::create_directory 2ms 0.026% 70.22% 73ms 0.94% Cell::GetCellId 62ms 0.8% 71.02% 73ms 0.94% std::num_put::do_put 0 0% 71.02% 72ms 0.93% tcache_get (inline) 72ms 0.93% 71.95% 72ms 0.93% tcache_get_n (inline) 70ms 0.9% 72.85% 70ms 0.9% std::vector::size (inline) 12ms 0.15% 73.01% 67ms 0.86% CellPropertyCollection::AddProperty 32ms 0.41% 73.42% 66ms 0.85% AbstractTetrahedralMesh::GetElement 64ms 0.82% 74.25% 64ms 0.82% __memcpy_avx_unaligned_erms 45ms 0.58% 74.83% 63ms 0.81% malloc_consolidate 47ms 0.61% 75.43% 62ms 0.8% AbstractElement::GetNodeGlobalIndex 41ms 0.53% 75.96% 62ms 0.8% std::basic_streambuf::xsputn 0 0% 75.96% 61ms 0.79% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 75.96% 61ms 0.79% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 55ms 0.71% 76.67% 60ms 0.77% vertexsort 58ms 0.75% 77.42% 58ms 0.75% counterclockwise 55ms 0.71% 78.13% 57ms 0.73% boost::detail::shared_count::shared_count (inline) 56ms 0.72% 78.85% 56ms 0.72% Node::GetIndex 1ms 0.013% 78.86% 56ms 0.72% std::_Rb_tree::_M_emplace_hint_unique 4ms 0.052% 78.91% 54ms 0.7% Node::ConstructNodeAttributes (inline) 4ms 0.052% 78.96% 54ms 0.7% TetrahedralMesh::EdgeIterator::GetNodeA 3ms 0.039% 79.00% 54ms 0.7% TetrahedralMesh::EdgeIterator::GetNodeB 43ms 0.55% 79.56% 54ms 0.7% hack_digit 3ms 0.039% 79.60% 53ms 0.68% std::_Vector_base::_M_deallocate (inline) 52ms 0.67% 80.27% 52ms 0.67% [libchaste_mesh.so] 0 0% 80.27% 51ms 0.66% Node::ClearAppliedForce 51ms 0.66% 80.92% 51ms 0.66% boost::numeric::ublas::c_vector::operator() (partial-inline) 0 0% 80.92% 50ms 0.64% std::_Rb_tree::_M_destroy_node (inline) 0 0% 80.92% 50ms 0.64% std::__new_allocator::destroy (inline) 0 0% 80.92% 50ms 0.64% std::allocator_traits::destroy (inline) 0 0% 80.92% 49ms 0.63% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 2ms 0.026% 80.95% 48ms 0.62% AbstractCentreBasedCellPopulation::CreateCellPair 0 0% 80.95% 48ms 0.62% MeshBasedCellPopulation::SpringIterator::~SpringIterator (inline) 48ms 0.62% 81.57% 48ms 0.62% boost::shared_ptr::operator-> (inline) 0 0% 81.57% 46ms 0.59% std::_Rb_tree::_Rb_tree_impl::_Rb_tree_impl (inline) 6ms 0.077% 81.64% 46ms 0.59% std::_Rb_tree_header::_Rb_tree_header (inline) 45ms 0.58% 82.22% 45ms 0.58% [libstdc++.so.6.0.33] 16ms 0.21% 82.43% 44ms 0.57% Determinant (inline) 0 0% 82.43% 42ms 0.54% boost::numeric::ublas::norm_2 (inline) 21ms 0.27% 82.70% 42ms 0.54% boost::numeric::ublas::vector_norm_2::apply (inline) 0 0% 82.70% 42ms 0.54% std::vector::vector (inline) 26ms 0.34% 83.04% 40ms 0.52% AbstractCellCycleModel::GetAge 40ms 0.52% 83.55% 40ms 0.52% boost::numeric::ublas::same_impl_ex 40ms 0.52% 84.07% 40ms 0.52% std::_Rb_tree_header::_M_reset (inline) 21ms 0.27% 84.34% 39ms 0.5% AbstractTetrahedralMesh::GetNumAllElements 2ms 0.026% 84.36% 39ms 0.5% NodeAttributes::NodeAttributes 28ms 0.36% 84.73% 39ms 0.5% boost::numeric::ublas::c_matrix::operator()