File: Test2dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 6763ms, 85.39% of 7920ms total Dropped 590 nodes (cum <= 39.60ms) flat flat% sum% cum cum% 0 0% 0% 7885ms 99.56% __libc_start_call_main 0 0% 0% 7885ms 99.56% __libc_start_main_impl 0 0% 0% 7885ms 99.56% _start 0 0% 0% 7870ms 99.37% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 7870ms 99.37% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 7870ms 99.37% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 7870ms 99.37% main 0 0% 0% 7832ms 98.89% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 7831ms 98.88% CxxTest::TestRunner::runTest (inline) 0 0% 0% 7831ms 98.88% Test2DMonolayerRepresentativeSimulation::Test2DMonolayerRepresentativeSimulationForProfiling 0 0% 0% 7827ms 98.83% AbstractCellBasedSimulation::Solve 0 0% 0% 3345ms 42.23% AbstractCellBasedSimulation::UpdateCellPopulation 2ms 0.025% 0.025% 2907ms 36.70% MeshBasedCellPopulation::Update 1ms 0.013% 0.038% 2896ms 36.57% AbstractCellPopulation::WriteResultsToFiles 0 0% 0.038% 1576ms 19.90% OffLatticeSimulation::UpdateCellLocationsAndTopology 2ms 0.025% 0.063% 1441ms 18.19% MeshBasedCellPopulation::UpdateNodePairs 1ms 0.013% 0.076% 1422ms 17.95% ForwardEulerNumericalMethod::UpdateAllNodePositions 0 0% 0.076% 1403ms 17.71% MutableMesh::ReMesh 10ms 0.13% 0.2% 1367ms 17.26% AbstractNumericalMethod::ComputeForcesIncludingDamping 14ms 0.18% 0.38% 1279ms 16.15% MeshBasedCellPopulation::SpringIterator::operator++ 123ms 1.55% 1.93% 1042ms 13.16% TetrahedralMesh::EdgeIterator::operator++ 455ms 5.74% 7.68% 1009ms 12.74% std::_Rb_tree::_M_lower_bound (inline) 0 0% 7.68% 945ms 11.93% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 10ms 0.13% 7.80% 924ms 11.67% CellPropertyCollection::GetPropertiesType (inline) 268ms 3.38% 11.19% 910ms 11.49% __dynamic_cast 1ms 0.013% 11.20% 909ms 11.48% AbstractTwoBodyInteractionForce::AddForceContribution 7ms 0.088% 11.29% 868ms 10.96% CellPopulationElementWriter::Visit 21ms 0.27% 11.55% 801ms 10.11% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 3ms 0.038% 11.59% 785ms 9.91% MeshBasedCellPopulation::AcceptCellWriter 40ms 0.51% 12.10% 755ms 9.53% AbstractCellPopulation::GetCellUsingLocationIndex 2ms 0.025% 12.12% 717ms 9.05% AbstractCellProperty::IsSubType (inline) 4ms 0.051% 12.17% 714ms 9.02% TetrahedralMesh::ImportFromMesher 0 0% 12.17% 602ms 7.60% std::ostream::operator<< (inline) 81ms 1.02% 13.19% 601ms 7.59% std::ostream::_M_insert 50ms 0.63% 13.83% 594ms 7.50% std::map::operator[] (partial-inline) 35ms 0.44% 14.27% 569ms 7.18% operator new 17ms 0.21% 14.48% 559ms 7.06% std::_Rb_tree::find (inline) 6ms 0.076% 14.56% 548ms 6.92% std::set::insert (inline) 11ms 0.14% 14.70% 545ms 6.88% Cell::GetCellProliferativeType 4ms 0.051% 14.75% 542ms 6.84% std::_Rb_tree::_M_insert_unique 169ms 2.13% 16.88% 530ms 6.69% __GI___libc_malloc 1ms 0.013% 16.89% 523ms 6.60% triangulate 510ms 6.44% 23.33% 510ms 6.44% __strcmp_avx2 30ms 0.38% 23.71% 508ms 6.41% std::__new_allocator::allocate (inline) 0 0% 23.71% 502ms 6.34% std::allocator_traits::allocate (inline) 0 0% 23.71% 495ms 6.25% std::_Rb_tree::lower_bound (inline) 0 0% 23.71% 495ms 6.25% std::map::lower_bound (inline) 0 0% 23.71% 494ms 6.24% std::set::count (inline) 3ms 0.038% 23.75% 482ms 6.09% LegacyCellProliferativeTypesWriter::VisitCell 201ms 2.54% 26.29% 476ms 6.01% __cxxabiv1::__si_class_type_info::__do_dyncast 1ms 0.013% 26.30% 472ms 5.96% delaunay 1ms 0.013% 26.31% 471ms 5.95% divconqdelaunay 0 0% 26.31% 432ms 5.45% std::_Rb_tree::_M_create_node (inline) 5ms 0.063% 26.38% 424ms 5.35% AbstractCellBasedSimulation::DoCellBirth 42ms 0.53% 26.91% 406ms 5.13% std::_Rb_tree::~_Rb_tree (inline) 0 0% 26.91% 404ms 5.10% std::_Rb_tree::_Alloc_node::operator() (inline) 4ms 0.051% 26.96% 390ms 4.92% NodeLocationWriter::Visit 5ms 0.063% 27.02% 388ms 4.90% Cell::GetMutationState 0 0% 27.02% 386ms 4.87% std::_Rb_tree::_M_get_node (inline) 0 0% 27.02% 377ms 4.76% std::set::~set (inline) 73ms 0.92% 27.94% 361ms 4.56% std::_Rb_tree::_M_erase 13ms 0.16% 28.11% 361ms 4.56% std::less::operator() (inline) 348ms 4.39% 32.50% 348ms 4.39% std::operator< (inline) 4ms 0.051% 32.55% 344ms 4.34% AbstractCentreBasedCellPopulation::GetDampingConstant 0 0% 32.55% 344ms 4.34% MeshBasedCellPopulation::GetDampingConstant 28ms 0.35% 32.90% 343ms 4.33% std::_Rb_tree::_M_insert_ (inline) 27ms 0.34% 33.24% 334ms 4.22% std::_Rb_tree::_Rb_tree (partial-inline) 21ms 0.27% 33.51% 334ms 4.22% std::num_put::_M_insert_float 330ms 4.17% 37.68% 330ms 4.17% std::_Rb_tree::_S_right (inline) 0 0% 37.68% 328ms 4.14% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 0 0% 37.68% 325ms 4.10% AbstractCellBasedWriter::OpenOutputFileForAppend 1ms 0.013% 37.69% 321ms 4.05% OutputFileHandler::OpenOutputFile 94ms 1.19% 38.88% 320ms 4.04% __GI___libc_free 2ms 0.025% 38.90% 301ms 3.80% std::set::set (inline) 10ms 0.13% 39.03% 295ms 3.72% AbstractCellPopulation::IsCellAttachedToLocationIndex 5ms 0.063% 39.09% 292ms 3.69% Element::Element 30ms 0.38% 39.47% 282ms 3.56% std::_Rb_tree::_M_copy (inline) 180ms 2.27% 41.74% 280ms 3.54% _int_malloc 2ms 0.025% 41.77% 271ms 3.42% Cell::ReadyToDivide 0 0% 41.77% 269ms 3.40% std::_Rb_tree::_M_drop_node (inline) 8ms 0.1% 41.87% 269ms 3.40% std::__new_allocator::deallocate (inline) 0 0% 41.87% 267ms 3.37% std::allocator_traits::deallocate (inline) 6ms 0.076% 41.94% 265ms 3.35% std::__cxx11::collate::do_transform 3ms 0.038% 41.98% 263ms 3.32% CellProliferativeTypesWriter::VisitCell 6ms 0.076% 42.06% 251ms 3.17% divconqrecurse 71ms 0.9% 42.95% 250ms 3.16% std::_Rb_tree::_M_clone_node (inline) 2ms 0.025% 42.98% 248ms 3.13% ___vsnprintf 0 0% 42.98% 246ms 3.11% __vsnprintf_internal (inline) 59ms 0.74% 43.72% 241ms 3.04% mergehulls 32ms 0.4% 44.13% 240ms 3.03% __printf_buffer 200ms 2.53% 46.65% 226ms 2.85% _int_free 0 0% 46.65% 216ms 2.73% std::_Rb_tree::_M_put_node (inline) 4ms 0.051% 46.70% 199ms 2.51% AbstractCellProperty::IsType (inline) 11ms 0.14% 46.84% 198ms 2.50% TetrahedralMesh::Clear 3ms 0.038% 46.88% 195ms 2.46% AbstractPhaseBasedCellCycleModel::ReadyToDivide 84ms 1.06% 47.94% 195ms 2.46% std::_Rb_tree::_M_get_insert_unique_pos (inline) 7ms 0.088% 48.03% 190ms 2.40% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 7ms 0.088% 48.12% 189ms 2.39% __printf_fp_l_buffer 0 0% 48.12% 189ms 2.39% __printf_fp_spec (inline) 11ms 0.14% 48.26% 188ms 2.37% MeshBasedCellPopulation::SpringsEnd (inline) 7ms 0.088% 48.35% 187ms 2.36% Element::RegisterWithNodes (inline) 8ms 0.1% 48.45% 181ms 2.29% CellPropertyCollection::HasProperty 0 0% 48.45% 180ms 2.27% Cell::HasCellProperty (inline) 2ms 0.025% 48.47% 179ms 2.26% Node::AddElement 94ms 1.19% 49.66% 176ms 2.22% __printf_fp_buffer_1 12ms 0.15% 49.81% 168ms 2.12% AbstractTetrahedralElement::CalculateJacobian 78ms 0.98% 50.80% 164ms 2.07% std::__ostream_insert 0 0% 50.80% 164ms 2.07% std::basic_ofstream::basic_ofstream (inline) 43ms 0.54% 51.34% 162ms 2.05% TetrahedralMesh::EdgesEnd (partial-inline) 1ms 0.013% 51.35% 158ms 1.99% std::basic_ofstream::open (inline) 3ms 0.038% 51.39% 156ms 1.97% std::basic_filebuf::open 5ms 0.063% 51.45% 152ms 1.92% boost::numeric::ublas::vector_assign (inline) 34ms 0.43% 51.88% 142ms 1.79% AbstractCellProperty::IsSame 1ms 0.013% 51.89% 140ms 1.77% TetrahedralMesh::RefreshJacobianCachedData 3ms 0.038% 51.93% 140ms 1.77% boost::numeric::ublas::c_vector::c_vector (inline) 1ms 0.013% 51.94% 137ms 1.73% OutputFileHandler::CommonConstructor 0 0% 51.94% 137ms 1.73% OutputFileHandler::OutputFileHandler 5ms 0.063% 52.01% 136ms 1.72% std::operator<< (inline) 0 0% 52.01% 132ms 1.67% OutputFileHandler::MakeFoldersAndReturnFullPath 37ms 0.47% 52.47% 132ms 1.67% std::num_put::_M_insert_int 12ms 0.15% 52.63% 131ms 1.65% AbstractTetrahedralElement::RefreshJacobian 0 0% 52.63% 130ms 1.64% AbstractCellPopulation::CloseRoundRobinWritersFiles 2ms 0.025% 52.65% 130ms 1.64% AbstractTetrahedralElement::CalculateInverseJacobian 0 0% 52.65% 129ms 1.63% AbstractCellBasedWriter::CloseFile 3ms 0.038% 52.69% 129ms 1.63% alternateaxes 1ms 0.013% 52.70% 129ms 1.63% std::basic_ofstream::close (inline) 0 0% 52.70% 128ms 1.62% std::basic_filebuf::close 17ms 0.21% 52.92% 125ms 1.58% AbstractCellPopulation::Iterator::IsRealCell (inline) 117ms 1.48% 54.39% 125ms 1.58% vertexmedian 0 0% 54.39% 124ms 1.57% FilesystemPermissions::SetFilePermissions (inline) 123ms 1.55% 55.95% 123ms 1.55% __GI_fchmodat 0 0% 55.95% 123ms 1.55% std::filesystem::permissions 1ms 0.013% 55.96% 122ms 1.54% AbstractCellPopulation::Iterator::operator++ (inline) 13ms 0.16% 56.12% 117ms 1.48% boost::detail::shared_count::~shared_count (inline) 0 0% 56.12% 117ms 1.48% boost::shared_ptr::~shared_ptr (inline) 1ms 0.013% 56.14% 117ms 1.48% std::_Vector_base::_M_allocate (inline) 1ms 0.013% 56.15% 116ms 1.46% _IO_new_fopen 0 0% 56.15% 116ms 1.46% std::__basic_file::open 0 0% 56.15% 115ms 1.45% __fopen_internal (inline) 10ms 0.13% 56.28% 114ms 1.44% MeshBasedCellPopulation::SpringIterator::SpringIterator 7ms 0.088% 56.36% 114ms 1.44% std::vector::push_back (inline) 0 0% 56.36% 113ms 1.43% _IO_new_file_fopen 2ms 0.025% 56.39% 113ms 1.43% __GI__IO_file_open 112ms 1.41% 57.80% 112ms 1.41% incircle 8ms 0.1% 57.90% 111ms 1.40% Node::~Node 38ms 0.48% 58.38% 111ms 1.40% boost::numeric::ublas::indexing_vector_assign 12ms 0.15% 58.54% 110ms 1.39% std::_Rb_tree_const_iterator::operator++ (inline) 73ms 0.92% 59.46% 108ms 1.36% TetrahedralMesh::EdgeIterator::EdgeIterator (partial-inline) 37ms 0.47% 59.92% 108ms 1.36% boost::shared_ptr::shared_ptr (inline) 25ms 0.32% 60.24% 108ms 1.36% std::type_info::operator== (inline) 48ms 0.61% 60.85% 104ms 1.31% AbstractElement::GetNodeLocation 1ms 0.013% 60.86% 104ms 1.31% AbstractTetrahedralElement::AbstractTetrahedralElement 103ms 1.30% 62.16% 103ms 1.30% std::_Rb_tree_increment 9ms 0.11% 62.27% 103ms 1.30% std::vector::_M_realloc_insert 4ms 0.051% 62.32% 102ms 1.29% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (partial-inline) 101ms 1.28% 63.60% 101ms 1.28% __libc_open64 100ms 1.26% 64.86% 101ms 1.28% boost::detail::sp_counted_base::release 2ms 0.025% 64.89% 101ms 1.28% std::basic_filebuf::overflow 0 0% 64.89% 100ms 1.26% std::basic_filebuf::_M_terminate_output 99ms 1.25% 66.14% 99ms 1.25% __GI___libc_write 0 0% 66.14% 99ms 1.25% std::__basic_file::xsputn 0 0% 66.14% 99ms 1.25% std::basic_filebuf::_M_convert_to_external 2ms 0.025% 66.16% 92ms 1.16% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 92ms 1.16% 67.32% 92ms 1.16% std::_Rb_tree_insert_and_rebalance 2ms 0.025% 67.35% 90ms 1.14% AbstractCellPopulation::GetLocationIndexUsingCell 83ms 1.05% 68.40% 87ms 1.10% vertexsort 81ms 1.02% 69.42% 81ms 1.02% [libchaste_cell_based.so] 52ms 0.66% 70.08% 81ms 1.02% std::basic_filebuf::xsputn 57ms 0.72% 70.80% 79ms 1% malloc_consolidate 77ms 0.97% 71.77% 77ms 0.97% TetrahedralMesh::EdgeIterator::operator!= (partial-inline) 6ms 0.076% 71.84% 76ms 0.96% CellPropertyCollection::AddProperty 9ms 0.11% 71.96% 74ms 0.93% Node::ConstructNodeAttributes (inline) 74ms 0.93% 72.89% 74ms 0.93% Node::GetIndex 0 0% 72.89% 73ms 0.92% tcache_get (inline) 73ms 0.92% 73.81% 73ms 0.92% tcache_get_n (inline) 1ms 0.013% 73.83% 72ms 0.91% Cell::GetCellId 69ms 0.87% 74.70% 71ms 0.9% boost::detail::shared_count::shared_count (inline) 2ms 0.025% 74.72% 70ms 0.88% Node::ClearAppliedForce 54ms 0.68% 75.40% 70ms 0.88% std::basic_streambuf::xsputn 65ms 0.82% 76.22% 65ms 0.82% counterclockwise 2ms 0.025% 76.25% 64ms 0.81% TetrahedralMesh::EdgeIterator::GetNodeA 1ms 0.013% 76.26% 64ms 0.81% std::filesystem::status 0 0% 76.26% 63ms 0.8% FilesystemPermissions::CreateDirectoryWithPermissions (inline) 63ms 0.8% 77.06% 63ms 0.8% __GI___fstatat64 1ms 0.013% 77.07% 63ms 0.8% std::filesystem::create_directory 62ms 0.78% 77.85% 62ms 0.78% __memcpy_avx_unaligned_erms 46ms 0.58% 78.43% 60ms 0.76% std::num_put::do_put 6ms 0.076% 78.51% 59ms 0.74% TetrahedralMesh::EdgeIterator::GetNodeB 47ms 0.59% 79.10% 58ms 0.73% AbstractElement::GetNodeGlobalIndex 0 0% 79.10% 55ms 0.69% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 79.10% 55ms 0.69% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 55ms 0.69% 79.80% 55ms 0.69% std::vector::size (inline) 0 0% 79.80% 53ms 0.67% std::_Rb_tree::_M_destroy_node (inline) 0 0% 79.80% 53ms 0.67% std::__new_allocator::destroy (inline) 0 0% 79.80% 53ms 0.67% std::allocator_traits::destroy (inline) 52ms 0.66% 80.45% 52ms 0.66% [libchaste_mesh.so] 0 0% 80.45% 52ms 0.66% std::map::find (inline) 33ms 0.42% 80.87% 51ms 0.64% AbstractTetrahedralMesh::GetElement 4ms 0.051% 80.92% 51ms 0.64% std::_Vector_base::_M_deallocate (inline) 2ms 0.025% 80.95% 50ms 0.63% std::__new_allocator::construct (inline) 0 0% 80.95% 50ms 0.63% std::allocator_traits::construct (inline) 1ms 0.013% 80.96% 49ms 0.62% std::_Rb_tree::_M_emplace_hint_unique 23ms 0.29% 81.25% 48ms 0.61% boost::numeric::ublas::c_matrix::operator() (partial-inline) 1ms 0.013% 81.26% 47ms 0.59% AbstractCentreBasedCellPopulation::CreateCellPair 5ms 0.063% 81.33% 47ms 0.59% NodeAttributes::NodeAttributes 46ms 0.58% 81.91% 46ms 0.58% Node::rGetLocation 34ms 0.43% 82.34% 46ms 0.58% hack_digit 0 0% 82.34% 46ms 0.58% std::_Rb_tree::_M_construct_node (inline) 0 0% 82.34% 44ms 0.56% BoundaryNodeWriter::Visit 20ms 0.25% 82.59% 43ms 0.54% AbstractCellCycleModel::GetAge 0 0% 82.59% 43ms 0.54% CellPropertyCollection::~CellPropertyCollection (inline) 43ms 0.54% 83.13% 43ms 0.54% boost::numeric::ublas::c_vector::operator() (partial-inline) 43ms 0.54% 83.67% 43ms 0.54% std::ostream::sentry::sentry 0 0% 83.67% 41ms 0.52% std::vector::vector (inline) 0 0% 83.67% 40ms 0.51% AbstractCentreBasedCellPopulation::IsMarkedSpring 1ms 0.013% 83.69% 40ms 0.51% AbstractTetrahedralElement::~AbstractTetrahedralElement (inline) 15ms 0.19% 83.88% 40ms 0.51% AbstractTetrahedralMesh::GetNumAllElements 40ms 0.51% 84.38% 40ms 0.51% Node::IsDeleted 40ms 0.51% 84.89% 40ms 0.51% boost::numeric::ublas::same_impl_ex 40ms 0.51% 85.39% 40ms 0.51% boost::shared_ptr::operator-> (inline)