File: Test2dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 6666ms, 84.44% of 7894ms total Dropped 557 nodes (cum <= 39.47ms) flat flat% sum% cum cum% 0 0% 0% 7857ms 99.53% __libc_start_call_main 0 0% 0% 7857ms 99.53% __libc_start_main_impl 0 0% 0% 7857ms 99.53% _start 0 0% 0% 7840ms 99.32% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 7840ms 99.32% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 7840ms 99.32% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 7840ms 99.32% main 0 0% 0% 7799ms 98.80% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 7799ms 98.80% CxxTest::TestRunner::runTest (inline) 0 0% 0% 7799ms 98.80% Test2DMonolayerRepresentativeSimulation::Test2DMonolayerRepresentativeSimulationForProfiling 1ms 0.013% 0.013% 7796ms 98.76% AbstractCellBasedSimulation::Solve 1ms 0.013% 0.025% 3325ms 42.12% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0.025% 2920ms 36.99% AbstractCellPopulation::WriteResultsToFiles 1ms 0.013% 0.038% 2838ms 35.95% MeshBasedCellPopulation::Update 1ms 0.013% 0.051% 1537ms 19.47% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 0.051% 1392ms 17.63% MutableMesh::ReMesh 2ms 0.025% 0.076% 1391ms 17.62% ForwardEulerNumericalMethod::UpdateAllNodePositions 2ms 0.025% 0.1% 1377ms 17.44% MeshBasedCellPopulation::UpdateNodePairs 6ms 0.076% 0.18% 1330ms 16.85% AbstractNumericalMethod::ComputeForcesIncludingDamping 13ms 0.16% 0.34% 1209ms 15.32% MeshBasedCellPopulation::SpringIterator::operator++ 101ms 1.28% 1.62% 1009ms 12.78% TetrahedralMesh::EdgeIterator::operator++ 6ms 0.076% 1.70% 988ms 12.52% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 426ms 5.40% 7.09% 940ms 11.91% std::_Rb_tree::_M_lower_bound (inline) 5ms 0.063% 7.16% 923ms 11.69% CellPopulationElementWriter::Visit 7ms 0.089% 7.25% 920ms 11.65% AbstractTwoBodyInteractionForce::AddForceContribution 16ms 0.2% 7.45% 911ms 11.54% CellPropertyCollection::GetPropertiesType (inline) 269ms 3.41% 10.86% 882ms 11.17% __dynamic_cast 1ms 0.013% 10.87% 843ms 10.68% MeshBasedCellPopulation::AcceptCellWriter 31ms 0.39% 11.26% 806ms 10.21% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 17ms 0.22% 11.48% 734ms 9.30% AbstractCellPopulation::GetCellUsingLocationIndex 5ms 0.063% 11.54% 689ms 8.73% TetrahedralMesh::ImportFromMesher 3ms 0.038% 11.58% 688ms 8.72% AbstractCellProperty::IsSubType (inline) 4ms 0.051% 11.63% 637ms 8.07% std::ostream::operator<< (inline) 103ms 1.30% 12.93% 632ms 8.01% std::ostream::_M_insert 46ms 0.58% 13.52% 553ms 7.01% operator new 46ms 0.58% 14.10% 552ms 6.99% std::map::operator[] (partial-inline) 2ms 0.025% 14.12% 538ms 6.82% triangulate 27ms 0.34% 14.47% 530ms 6.71% std::_Rb_tree::find (inline) 2ms 0.025% 14.49% 525ms 6.65% LegacyCellProliferativeTypesWriter::VisitCell 44ms 0.56% 15.05% 516ms 6.54% std::__new_allocator::allocate (inline) 5ms 0.063% 15.11% 512ms 6.49% std::set::insert (inline) 0 0% 15.11% 511ms 6.47% std::allocator_traits::allocate (inline) 8ms 0.1% 15.21% 507ms 6.42% std::_Rb_tree::_M_insert_unique 1ms 0.013% 15.23% 505ms 6.40% Cell::GetCellProliferativeType 156ms 1.98% 17.20% 495ms 6.27% __GI___libc_malloc 0 0% 17.20% 490ms 6.21% std::set::count (inline) 484ms 6.13% 23.33% 484ms 6.13% __strcmp_avx2 7ms 0.089% 23.42% 470ms 5.95% AbstractCellBasedSimulation::DoCellBirth 227ms 2.88% 26.30% 466ms 5.90% __cxxabiv1::__si_class_type_info::__do_dyncast 0 0% 26.30% 463ms 5.87% std::_Rb_tree::lower_bound (inline) 0 0% 26.30% 463ms 5.87% std::map::lower_bound (inline) 0 0% 26.30% 459ms 5.81% delaunay 2ms 0.025% 26.32% 456ms 5.78% divconqdelaunay 0 0% 26.32% 434ms 5.50% std::_Rb_tree::_M_create_node (inline) 30ms 0.38% 26.70% 423ms 5.36% std::_Rb_tree::~_Rb_tree (inline) 0 0% 26.70% 421ms 5.33% std::_Rb_tree::_Alloc_node::operator() (inline) 5ms 0.063% 26.77% 417ms 5.28% Cell::GetMutationState 34ms 0.43% 27.20% 403ms 5.11% std::_Rb_tree::_Rb_tree (partial-inline) 0 0% 27.20% 395ms 5.00% std::set::~set (inline) 93ms 1.18% 28.38% 393ms 4.98% std::_Rb_tree::_M_erase 0 0% 28.38% 386ms 4.89% std::_Rb_tree::_M_get_node (inline) 9ms 0.11% 28.49% 372ms 4.71% std::less::operator() (inline) 363ms 4.60% 33.09% 363ms 4.60% std::operator< (inline) 3ms 0.038% 33.13% 363ms 4.60% std::set::set (inline) 2ms 0.025% 33.15% 362ms 4.59% NodeLocationWriter::Visit 3ms 0.038% 33.19% 343ms 4.35% AbstractCentreBasedCellPopulation::GetDampingConstant 0 0% 33.19% 343ms 4.35% MeshBasedCellPopulation::GetDampingConstant 30ms 0.38% 33.57% 333ms 4.22% std::_Rb_tree::_M_copy (inline) 115ms 1.46% 35.03% 327ms 4.14% __GI___libc_free 17ms 0.22% 35.24% 321ms 4.07% std::num_put::_M_insert_float 6ms 0.076% 35.32% 320ms 4.05% AbstractCellPopulation::IsCellAttachedToLocationIndex 18ms 0.23% 35.55% 307ms 3.89% std::_Rb_tree::_M_insert_ (inline) 6ms 0.076% 35.62% 306ms 3.88% Cell::ReadyToDivide 301ms 3.81% 39.44% 301ms 3.81% std::_Rb_tree::_S_right (inline) 80ms 1.01% 40.45% 300ms 3.80% std::_Rb_tree::_M_clone_node (inline) 0 0% 40.45% 298ms 3.78% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 0 0% 40.45% 296ms 3.75% AbstractCellBasedWriter::OpenOutputFileForAppend 0 0% 40.45% 289ms 3.66% OutputFileHandler::OpenOutputFile 0 0% 40.45% 277ms 3.51% std::_Rb_tree::_M_drop_node (inline) 4ms 0.051% 40.50% 271ms 3.43% CellProliferativeTypesWriter::VisitCell 12ms 0.15% 40.65% 270ms 3.42% std::__new_allocator::deallocate (inline) 4ms 0.051% 40.70% 269ms 3.41% Element::Element 0 0% 40.70% 262ms 3.32% std::allocator_traits::deallocate (inline) 168ms 2.13% 42.83% 258ms 3.27% _int_malloc 5ms 0.063% 42.89% 258ms 3.27% std::__cxx11::collate::do_transform 12ms 0.15% 43.05% 257ms 3.26% divconqrecurse 4ms 0.051% 43.10% 246ms 3.12% ___vsnprintf 3ms 0.038% 43.13% 245ms 3.10% AbstractCellProperty::IsType (inline) 0 0% 43.13% 242ms 3.07% __vsnprintf_internal (inline) 5ms 0.063% 43.20% 241ms 3.05% CellPropertyCollection::HasProperty 0 0% 43.20% 240ms 3.04% Cell::HasCellProperty (inline) 71ms 0.9% 44.10% 236ms 2.99% mergehulls 25ms 0.32% 44.41% 235ms 2.98% __printf_buffer 0 0% 44.41% 229ms 2.90% std::_Rb_tree::_M_put_node (inline) 25ms 0.32% 44.73% 217ms 2.75% TetrahedralMesh::Clear 179ms 2.27% 47.00% 212ms 2.69% _int_free 4ms 0.051% 47.05% 205ms 2.60% AbstractPhaseBasedCellCycleModel::ReadyToDivide 13ms 0.16% 47.21% 198ms 2.51% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 59ms 0.75% 47.96% 193ms 2.44% std::_Rb_tree::_M_get_insert_unique_pos (inline) 1ms 0.013% 47.97% 187ms 2.37% __printf_fp_spec (inline) 11ms 0.14% 48.11% 186ms 2.36% __printf_fp_l_buffer 40ms 0.51% 48.62% 180ms 2.28% AbstractCellProperty::IsSame 5ms 0.063% 48.68% 179ms 2.27% Element::RegisterWithNodes (inline) 2ms 0.025% 48.71% 174ms 2.20% Node::AddElement 102ms 1.29% 50.00% 171ms 2.17% __printf_fp_buffer_1 9ms 0.11% 50.11% 161ms 2.04% MeshBasedCellPopulation::SpringsEnd (inline) 2ms 0.025% 50.14% 147ms 1.86% TetrahedralMesh::RefreshJacobianCachedData 59ms 0.75% 50.89% 145ms 1.84% std::__ostream_insert 41ms 0.52% 51.41% 144ms 1.82% std::num_put::_M_insert_int 3ms 0.038% 51.44% 143ms 1.81% boost::numeric::ublas::vector_assign (inline) 33ms 0.42% 51.86% 141ms 1.79% TetrahedralMesh::EdgesEnd (partial-inline) 14ms 0.18% 52.04% 140ms 1.77% AbstractTetrahedralElement::CalculateJacobian 34ms 0.43% 52.47% 140ms 1.77% std::type_info::operator== (inline) 4ms 0.051% 52.52% 136ms 1.72% boost::numeric::ublas::c_vector::c_vector (inline) 8ms 0.1% 52.62% 135ms 1.71% AbstractTetrahedralElement::CalculateInverseJacobian 0 0% 52.62% 131ms 1.66% std::basic_ofstream::basic_ofstream (inline) 1ms 0.013% 52.63% 129ms 1.63% OutputFileHandler::OutputFileHandler 0 0% 52.63% 128ms 1.62% OutputFileHandler::CommonConstructor 12ms 0.15% 52.79% 127ms 1.61% AbstractCellPopulation::Iterator::IsRealCell (inline) 9ms 0.11% 52.90% 127ms 1.61% std::_Rb_tree_const_iterator::operator++ (inline) 126ms 1.60% 54.50% 126ms 1.60% std::_Rb_tree_increment 1ms 0.013% 54.51% 126ms 1.60% std::basic_filebuf::open 0 0% 54.51% 126ms 1.60% std::basic_ofstream::open (inline) 0 0% 54.51% 125ms 1.58% std::_Vector_base::_M_allocate (inline) 0 0% 54.51% 124ms 1.57% AbstractCellPopulation::Iterator::operator++ (inline) 4ms 0.051% 54.56% 123ms 1.56% alternateaxes 59ms 0.75% 55.31% 123ms 1.56% boost::shared_ptr::shared_ptr (inline) 0 0% 55.31% 122ms 1.55% AbstractCellPopulation::CloseRoundRobinWritersFiles 0 0% 55.31% 121ms 1.53% AbstractCellBasedWriter::CloseFile 0 0% 55.31% 121ms 1.53% FilesystemPermissions::SetFilePermissions (inline) 1ms 0.013% 55.32% 121ms 1.53% OutputFileHandler::MakeFoldersAndReturnFullPath 2ms 0.025% 55.35% 121ms 1.53% std::basic_filebuf::close 0 0% 55.35% 121ms 1.53% std::basic_ofstream::close (inline) 1ms 0.013% 55.36% 121ms 1.53% std::filesystem::permissions 9ms 0.11% 55.47% 120ms 1.52% Node::~Node 120ms 1.52% 56.99% 120ms 1.52% __GI_fchmodat 9ms 0.11% 57.11% 119ms 1.51% boost::detail::shared_count::~shared_count (inline) 0 0% 57.11% 119ms 1.51% boost::shared_ptr::~shared_ptr (inline) 109ms 1.38% 58.49% 119ms 1.51% vertexmedian 13ms 0.16% 58.65% 114ms 1.44% MeshBasedCellPopulation::SpringIterator::SpringIterator 81ms 1.03% 59.68% 111ms 1.41% TetrahedralMesh::EdgeIterator::EdgeIterator (partial-inline) 30ms 0.38% 60.06% 111ms 1.41% boost::numeric::ublas::indexing_vector_assign 109ms 1.38% 61.44% 109ms 1.38% incircle 2ms 0.025% 61.46% 108ms 1.37% std::operator<< (inline) 107ms 1.36% 62.82% 107ms 1.36% [libchaste_cell_based.so] 4ms 0.051% 62.87% 107ms 1.36% std::vector::push_back (inline) 104ms 1.32% 64.19% 105ms 1.33% boost::detail::sp_counted_base::release 16ms 0.2% 64.39% 103ms 1.30% AbstractTetrahedralElement::RefreshJacobian 8ms 0.1% 64.49% 102ms 1.29% std::vector::_M_realloc_insert 1ms 0.013% 64.50% 96ms 1.22% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 4ms 0.051% 64.56% 94ms 1.19% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (partial-inline) 94ms 1.19% 65.75% 94ms 1.19% std::_Rb_tree_insert_and_rebalance 3ms 0.038% 65.78% 92ms 1.17% AbstractTetrahedralElement::AbstractTetrahedralElement 2ms 0.025% 65.81% 91ms 1.15% std::__basic_file::open 0 0% 65.81% 87ms 1.10% _IO_new_fopen 0 0% 65.81% 87ms 1.10% __fopen_internal (inline) 2ms 0.025% 65.83% 87ms 1.10% std::basic_filebuf::overflow 0 0% 65.83% 86ms 1.09% _IO_new_file_fopen 0 0% 65.83% 86ms 1.09% __GI__IO_file_open 0 0% 65.83% 86ms 1.09% std::basic_filebuf::_M_terminate_output 1ms 0.013% 65.85% 85ms 1.08% std::__basic_file::xsputn 0 0% 65.85% 85ms 1.08% std::basic_filebuf::_M_convert_to_external 84ms 1.06% 66.91% 84ms 1.06% __GI___libc_write 53ms 0.67% 67.58% 82ms 1.04% std::basic_streambuf::xsputn 80ms 1.01% 68.60% 80ms 1.01% Node::GetIndex 79ms 1.00% 69.60% 79ms 1.00% __libc_open64 35ms 0.44% 70.04% 76ms 0.96% AbstractElement::GetNodeLocation 75ms 0.95% 70.99% 75ms 0.95% __memcpy_avx_unaligned_erms 56ms 0.71% 71.70% 75ms 0.95% malloc_consolidate 47ms 0.6% 72.30% 75ms 0.95% std::basic_filebuf::xsputn 74ms 0.94% 73.23% 74ms 0.94% TetrahedralMesh::EdgeIterator::operator!= (partial-inline) 0 0% 73.23% 74ms 0.94% tcache_get (inline) 74ms 0.94% 74.17% 74ms 0.94% tcache_get_n (inline) 62ms 0.79% 74.96% 73ms 0.92% AbstractElement::GetNodeGlobalIndex 60ms 0.76% 75.72% 71ms 0.9% std::num_put::do_put 3ms 0.038% 75.75% 70ms 0.89% AbstractCellPopulation::GetLocationIndexUsingCell 2ms 0.025% 75.78% 69ms 0.87% CellPropertyCollection::AddProperty 2ms 0.025% 75.80% 68ms 0.86% Cell::GetCellId 4ms 0.051% 75.86% 68ms 0.86% TetrahedralMesh::EdgeIterator::GetNodeB 62ms 0.79% 76.64% 63ms 0.8% boost::detail::shared_count::shared_count (inline) 63ms 0.8% 77.44% 63ms 0.8% boost::shared_ptr::operator-> (inline) 0 0% 77.44% 62ms 0.79% FilesystemPermissions::CreateDirectoryWithPermissions (inline) 3ms 0.038% 77.48% 62ms 0.79% std::filesystem::create_directory 57ms 0.72% 78.20% 62ms 0.79% vertexsort 28ms 0.35% 78.55% 59ms 0.75% AbstractTetrahedralMesh::GetElement 3ms 0.038% 78.59% 59ms 0.75% std::filesystem::status 57ms 0.72% 79.31% 57ms 0.72% [libchaste_mesh.so] 57ms 0.72% 80.04% 57ms 0.72% __GI___fstatat64 56ms 0.71% 80.74% 56ms 0.71% [libstdc++.so.6.0.33] 35ms 0.44% 81.19% 53ms 0.67% boost::numeric::ublas::c_matrix::operator() 52ms 0.66% 81.85% 52ms 0.66% counterclockwise 1ms 0.013% 81.86% 51ms 0.65% TetrahedralMesh::EdgeIterator::GetNodeA 0 0% 81.86% 50ms 0.63% BoundaryNodeWriter::Visit 6ms 0.076% 81.94% 49ms 0.62% Node::ConstructNodeAttributes (inline) 2ms 0.025% 81.96% 49ms 0.62% std::__new_allocator::construct (inline) 0 0% 81.96% 49ms 0.62% std::allocator_traits::construct (inline) 0 0% 81.96% 48ms 0.61% std::_Rb_tree::_M_construct_node (inline) 0 0% 81.96% 48ms 0.61% std::_Rb_tree::_M_destroy_node (inline) 0 0% 81.96% 48ms 0.61% std::__new_allocator::destroy (inline) 0 0% 81.96% 48ms 0.61% std::allocator_traits::destroy (inline) 19ms 0.24% 82.20% 47ms 0.6% AbstractCellCycleModel::GetAge 8ms 0.1% 82.30% 47ms 0.6% Inverse 2ms 0.025% 82.33% 47ms 0.6% Node::ClearAppliedForce 47ms 0.6% 82.92% 47ms 0.6% boost::numeric::ublas::c_vector::operator() (partial-inline) 0 0% 82.92% 47ms 0.6% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 82.92% 47ms 0.6% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 0 0% 82.92% 46ms 0.58% std::vector::vector (inline) 45ms 0.57% 83.49% 45ms 0.57% std::vector::size (inline) 0 0% 83.49% 44ms 0.56% std::_Vector_base::_Vector_base (inline) 0 0% 83.49% 44ms 0.56% std::map::map (inline) 3ms 0.038% 83.53% 43ms 0.54% std::_Rb_tree::_M_emplace_hint_unique 0 0% 83.53% 43ms 0.54% std::_Vector_base::_M_create_storage (inline) 0 0% 83.53% 42ms 0.53% AbstractCentreBasedCellPopulation::CreateCellPair 14ms 0.18% 83.71% 42ms 0.53% Determinant (inline) 42ms 0.53% 84.24% 42ms 0.53% std::ostream::sentry::sentry 0 0% 84.24% 41ms 0.52% MeshBasedCellPopulation::SpringIterator::GetNodeB (inline) 0 0% 84.24% 41ms 0.52% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 0 0% 84.24% 40ms 0.51% boost::numeric::ublas::norm_2 (inline) 16ms 0.2% 84.44% 40ms 0.51% boost::numeric::ublas::vector_norm_2::apply (inline)