File: Test2dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 6815ms, 86.96% of 7837ms total Dropped 555 nodes (cum <= 39.19ms) flat flat% sum% cum cum% 0 0% 0% 7802ms 99.55% __libc_start_call_main 0 0% 0% 7802ms 99.55% __libc_start_main_impl 0 0% 0% 7802ms 99.55% _start 0 0% 0% 7788ms 99.37% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 7788ms 99.37% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 7788ms 99.37% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 7788ms 99.37% main 0 0% 0% 7746ms 98.84% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 7746ms 98.84% CxxTest::TestRunner::runTest (inline) 0 0% 0% 7746ms 98.84% Test2DMonolayerRepresentativeSimulation::Test2DMonolayerRepresentativeSimulationForProfiling 2ms 0.026% 0.026% 7743ms 98.80% AbstractCellBasedSimulation::Solve 1ms 0.013% 0.038% 3331ms 42.50% AbstractCellBasedSimulation::UpdateCellPopulation 1ms 0.013% 0.051% 2865ms 36.56% MeshBasedCellPopulation::Update 0 0% 0.051% 2770ms 35.35% AbstractCellPopulation::WriteResultsToFiles 2ms 0.026% 0.077% 1627ms 20.76% OffLatticeSimulation::UpdateCellLocationsAndTopology 1ms 0.013% 0.089% 1467ms 18.72% ForwardEulerNumericalMethod::UpdateAllNodePositions 4ms 0.051% 0.14% 1425ms 18.18% AbstractNumericalMethod::ComputeForcesIncludingDamping 0 0% 0.14% 1418ms 18.09% MutableMesh::ReMesh 0 0% 0.14% 1388ms 17.71% MeshBasedCellPopulation::UpdateNodePairs 21ms 0.27% 0.41% 1211ms 15.45% MeshBasedCellPopulation::SpringIterator::operator++ 5ms 0.064% 0.47% 1045ms 13.33% AbstractTwoBodyInteractionForce::AddForceContribution 95ms 1.21% 1.68% 978ms 12.48% TetrahedralMesh::EdgeIterator::operator++ 418ms 5.33% 7.02% 924ms 11.79% std::_Rb_tree::_M_lower_bound (inline) 73ms 0.93% 7.95% 917ms 11.70% GeneralisedLinearSpringForce::CalculateForceBetweenNodes (partial-inline) 250ms 3.19% 11.14% 904ms 11.54% __dynamic_cast 1ms 0.013% 11.15% 903ms 11.52% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 10ms 0.13% 11.28% 900ms 11.48% CellPropertyCollection::GetPropertiesType (inline) 9ms 0.11% 11.39% 875ms 11.16% CellPopulationElementWriter::Visit 4ms 0.051% 11.45% 779ms 9.94% MeshBasedCellPopulation::AcceptCellWriter 2ms 0.026% 11.47% 718ms 9.16% AbstractCellProperty::IsSubType (inline) 36ms 0.46% 11.93% 716ms 9.14% AbstractCellPopulation::GetCellUsingLocationIndex 9ms 0.11% 12.05% 678ms 8.65% TetrahedralMesh::ImportFromMesher 0 0% 12.05% 596ms 7.60% std::ostream::operator<< (inline) 81ms 1.03% 13.08% 595ms 7.59% std::ostream::_M_insert 2ms 0.026% 13.10% 571ms 7.29% triangulate 20ms 0.26% 13.36% 551ms 7.03% std::_Rb_tree::find (inline) 5ms 0.064% 13.42% 526ms 6.71% Cell::GetCellProliferativeType 58ms 0.74% 14.16% 522ms 6.66% std::map::operator[] (partial-inline) 513ms 6.55% 20.71% 513ms 6.55% __strcmp_avx2 37ms 0.47% 21.18% 504ms 6.43% operator new 0 0% 21.18% 503ms 6.42% delaunay 2ms 0.026% 21.21% 503ms 6.42% divconqdelaunay 0 0% 21.21% 502ms 6.41% std::set::count (inline) 5ms 0.064% 21.27% 495ms 6.32% std::set::insert (inline) 2ms 0.026% 21.30% 492ms 6.28% LegacyCellProliferativeTypesWriter::VisitCell 10ms 0.13% 21.42% 490ms 6.25% std::_Rb_tree::_M_insert_unique 29ms 0.37% 21.79% 480ms 6.12% std::__new_allocator::allocate (inline) 0 0% 21.79% 476ms 6.07% std::allocator_traits::allocate (inline) 210ms 2.68% 24.47% 466ms 5.95% __cxxabiv1::__si_class_type_info::__do_dyncast 156ms 1.99% 26.46% 457ms 5.83% __GI___libc_malloc 3ms 0.038% 26.50% 453ms 5.78% AbstractCellBasedSimulation::DoCellBirth 34ms 0.43% 26.94% 429ms 5.47% std::_Rb_tree::~_Rb_tree (inline) 0 0% 26.94% 422ms 5.38% std::_Rb_tree::_M_create_node (inline) 0 0% 26.94% 420ms 5.36% std::_Rb_tree::lower_bound (inline) 0 0% 26.94% 420ms 5.36% std::map::lower_bound (inline) 0 0% 26.94% 397ms 5.07% std::set::~set (inline) 0 0% 26.94% 396ms 5.05% std::_Rb_tree::_Alloc_node::operator() (inline) 93ms 1.19% 28.12% 391ms 4.99% std::_Rb_tree::_M_erase 0 0% 28.12% 381ms 4.86% std::_Rb_tree::_M_get_node (inline) 10ms 0.13% 28.25% 379ms 4.84% std::less::operator() (inline) 17ms 0.22% 28.47% 372ms 4.75% std::_Rb_tree::_Rb_tree (partial-inline) 1ms 0.013% 28.48% 371ms 4.73% Cell::GetMutationState 2ms 0.026% 28.51% 370ms 4.72% NodeLocationWriter::Visit 369ms 4.71% 33.21% 369ms 4.71% std::operator< (inline) 2ms 0.026% 33.24% 328ms 4.19% std::set::set (inline) 23ms 0.29% 33.53% 327ms 4.17% std::num_put::_M_insert_float 10ms 0.13% 33.66% 308ms 3.93% divconqrecurse 38ms 0.48% 34.15% 308ms 3.93% std::_Rb_tree::_M_copy (inline) 111ms 1.42% 35.56% 304ms 3.88% __GI___libc_free 5ms 0.064% 35.63% 300ms 3.83% Cell::ReadyToDivide 16ms 0.2% 35.83% 300ms 3.83% std::_Rb_tree::_M_insert_ (inline) 0 0% 35.83% 294ms 3.75% AbstractCellBasedWriter::OpenOutputFileForAppend 0 0% 35.83% 294ms 3.75% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 0 0% 35.83% 293ms 3.74% OutputFileHandler::OpenOutputFile 1ms 0.013% 35.84% 292ms 3.73% AbstractCentreBasedCellPopulation::GetDampingConstant 0 0% 35.84% 292ms 3.73% MeshBasedCellPopulation::GetDampingConstant 96ms 1.22% 37.07% 288ms 3.67% mergehulls 4ms 0.051% 37.12% 287ms 3.66% AbstractCellPopulation::IsCellAttachedToLocationIndex 2ms 0.026% 37.14% 286ms 3.65% Element::Element 0 0% 37.14% 278ms 3.55% std::_Rb_tree::_M_drop_node (inline) 18ms 0.23% 37.37% 277ms 3.53% std::__new_allocator::deallocate (inline) 275ms 3.51% 40.88% 275ms 3.51% std::_Rb_tree::_S_right (inline) 0 0% 40.88% 272ms 3.47% std::allocator_traits::deallocate (inline) 62ms 0.79% 41.67% 263ms 3.36% std::_Rb_tree::_M_clone_node (inline) 3ms 0.038% 41.71% 251ms 3.20% CellProliferativeTypesWriter::VisitCell 8ms 0.1% 41.81% 242ms 3.09% std::__cxx11::collate::do_transform 163ms 2.08% 43.89% 238ms 3.04% _int_malloc 1ms 0.013% 43.91% 230ms 2.93% ___vsnprintf 0 0% 43.91% 229ms 2.92% __vsnprintf_internal (inline) 30ms 0.38% 44.29% 228ms 2.91% __printf_buffer 3ms 0.038% 44.33% 225ms 2.87% boost::numeric::ublas::vector_assign (inline) 0 0% 44.33% 221ms 2.82% std::_Rb_tree::_M_put_node (inline) 0 0% 44.33% 216ms 2.76% Cell::HasCellProperty (inline) 5ms 0.064% 44.39% 215ms 2.74% CellPropertyCollection::HasProperty 3ms 0.038% 44.43% 208ms 2.65% AbstractCellProperty::IsType (inline) 3ms 0.038% 44.47% 202ms 2.58% boost::numeric::ublas::c_vector::c_vector (inline) 10ms 0.13% 44.60% 200ms 2.55% AbstractPhaseBasedCellCycleModel::ReadyToDivide 61ms 0.78% 45.37% 196ms 2.50% boost::numeric::ublas::indexing_vector_assign 19ms 0.24% 45.62% 195ms 2.49% TetrahedralMesh::Clear 6ms 0.077% 45.69% 192ms 2.45% Element::RegisterWithNodes (inline) 162ms 2.07% 47.76% 191ms 2.44% _int_free 13ms 0.17% 47.93% 187ms 2.39% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 8ms 0.1% 48.03% 185ms 2.36% __printf_fp_l_buffer 0 0% 48.03% 185ms 2.36% __printf_fp_spec (inline) 4ms 0.051% 48.08% 183ms 2.34% Node::AddElement 61ms 0.78% 48.86% 180ms 2.30% std::_Rb_tree::_M_get_insert_unique_pos (inline) 5ms 0.064% 48.92% 177ms 2.26% MeshBasedCellPopulation::SpringsEnd (inline) 102ms 1.30% 50.22% 167ms 2.13% __printf_fp_buffer_1 12ms 0.15% 50.38% 156ms 1.99% AbstractTetrahedralElement::CalculateJacobian 39ms 0.5% 50.87% 152ms 1.94% AbstractCellProperty::IsSame 0 0% 50.87% 152ms 1.94% std::basic_ofstream::basic_ofstream (inline) 1ms 0.013% 50.89% 151ms 1.93% TetrahedralMesh::RefreshJacobianCachedData 1ms 0.013% 50.90% 151ms 1.93% std::basic_filebuf::open 0 0% 50.90% 151ms 1.93% std::basic_ofstream::open (inline) 36ms 0.46% 51.36% 144ms 1.84% TetrahedralMesh::EdgesEnd (partial-inline) 0 0% 51.36% 139ms 1.77% OutputFileHandler::CommonConstructor 0 0% 51.36% 139ms 1.77% OutputFileHandler::OutputFileHandler 33ms 0.42% 51.78% 138ms 1.76% boost::detail::shared_count::~shared_count (inline) 0 0% 51.78% 138ms 1.76% boost::shared_ptr::~shared_ptr (inline) 45ms 0.57% 52.35% 137ms 1.75% std::__ostream_insert 5ms 0.064% 52.42% 136ms 1.74% AbstractTetrahedralElement::CalculateInverseJacobian 0 0% 52.42% 135ms 1.72% OutputFileHandler::MakeFoldersAndReturnFullPath 6ms 0.077% 52.49% 128ms 1.63% alternateaxes 12ms 0.15% 52.65% 122ms 1.56% MeshBasedCellPopulation::SpringIterator::SpringIterator 11ms 0.14% 52.79% 121ms 1.54% AbstractCellPopulation::Iterator::IsRealCell (inline) 114ms 1.45% 54.24% 121ms 1.54% vertexmedian 0 0% 54.24% 119ms 1.52% FilesystemPermissions::SetFilePermissions (inline) 2ms 0.026% 54.27% 119ms 1.52% std::__basic_file::open 1ms 0.013% 54.28% 119ms 1.52% std::filesystem::permissions 118ms 1.51% 55.79% 118ms 1.51% __GI_fchmodat 0 0% 55.79% 117ms 1.49% AbstractCellPopulation::Iterator::operator++ (inline) 5ms 0.064% 55.85% 117ms 1.49% std::vector::push_back (inline) 0 0% 55.85% 116ms 1.48% _IO_new_fopen 0 0% 55.85% 116ms 1.48% __fopen_internal (inline) 116ms 1.48% 57.33% 116ms 1.48% incircle 4ms 0.051% 57.38% 114ms 1.45% Node::~Node 1ms 0.013% 57.39% 114ms 1.45% _IO_new_file_fopen 32ms 0.41% 57.80% 114ms 1.45% std::num_put::_M_insert_int 14ms 0.18% 57.98% 113ms 1.44% AbstractTetrahedralElement::RefreshJacobian 7ms 0.089% 58.07% 113ms 1.44% std::_Rb_tree_const_iterator::operator++ (inline) 113ms 1.44% 59.51% 113ms 1.44% std::_Rb_tree_increment 1ms 0.013% 59.53% 113ms 1.44% std::operator<< (inline) 26ms 0.33% 59.86% 113ms 1.44% std::type_info::operator== (inline) 0 0% 59.86% 111ms 1.42% __GI__IO_file_open 51ms 0.65% 60.51% 107ms 1.37% boost::shared_ptr::shared_ptr (inline) 12ms 0.15% 60.66% 107ms 1.37% std::vector::_M_realloc_insert 0 0% 60.66% 105ms 1.34% AbstractCellBasedWriter::CloseFile 0 0% 60.66% 105ms 1.34% AbstractCellPopulation::CloseRoundRobinWritersFiles 105ms 1.34% 62.00% 105ms 1.34% __libc_open64 0 0% 62.00% 105ms 1.34% std::basic_ofstream::close (inline) 4ms 0.051% 62.05% 104ms 1.33% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (partial-inline) 1ms 0.013% 62.06% 104ms 1.33% std::basic_filebuf::close 102ms 1.30% 63.37% 102ms 1.30% boost::detail::sp_counted_base::release 1ms 0.013% 63.38% 101ms 1.29% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 70ms 0.89% 64.27% 100ms 1.28% TetrahedralMesh::EdgeIterator::EdgeIterator (partial-inline) 99ms 1.26% 65.54% 99ms 1.26% [libchaste_cell_based.so] 4ms 0.051% 65.59% 99ms 1.26% std::_Vector_base::_M_allocate (inline) 0 0% 65.59% 98ms 1.25% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 65.59% 98ms 1.25% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 0 0% 65.59% 96ms 1.22% AbstractTetrahedralElement::AbstractTetrahedralElement 95ms 1.21% 66.80% 95ms 1.21% boost::numeric::ublas::c_vector::operator() (partial-inline) 95ms 1.21% 68.01% 95ms 1.21% std::_Rb_tree_insert_and_rebalance 46ms 0.59% 68.60% 90ms 1.15% AbstractElement::GetNodeLocation 0 0% 68.60% 87ms 1.11% boost::numeric::ublas::norm_2 (inline) 20ms 0.26% 68.85% 87ms 1.11% boost::numeric::ublas::vector_norm_2::apply (inline) 4ms 0.051% 68.90% 84ms 1.07% AbstractCellPopulation::GetLocationIndexUsingCell 80ms 1.02% 69.92% 80ms 1.02% TetrahedralMesh::EdgeIterator::operator!= (partial-inline) 56ms 0.71% 70.64% 80ms 1.02% std::basic_filebuf::xsputn 56ms 0.71% 71.35% 78ms 1% std::basic_streambuf::xsputn 5ms 0.064% 71.42% 77ms 0.98% std::basic_filebuf::overflow 0 0% 71.42% 76ms 0.97% FilesystemPermissions::CreateDirectoryWithPermissions (inline) 0 0% 71.42% 76ms 0.97% std::filesystem::create_directory 75ms 0.96% 72.37% 75ms 0.96% counterclockwise 1ms 0.013% 72.39% 75ms 0.96% std::basic_filebuf::_M_terminate_output 73ms 0.93% 73.32% 73ms 0.93% __GI___libc_write 1ms 0.013% 73.33% 72ms 0.92% Cell::GetCellId 72ms 0.92% 74.25% 72ms 0.92% Node::GetIndex 0 0% 74.25% 72ms 0.92% std::__basic_file::xsputn 0 0% 74.25% 72ms 0.92% std::basic_filebuf::_M_convert_to_external 71ms 0.91% 75.16% 71ms 0.91% __GI___fstatat64 1ms 0.013% 75.17% 71ms 0.91% std::filesystem::status 4ms 0.051% 75.22% 70ms 0.89% TetrahedralMesh::EdgeIterator::GetNodeA 46ms 0.59% 75.81% 70ms 0.89% malloc_consolidate 61ms 0.78% 76.59% 61ms 0.78% __memcpy_avx_unaligned_erms 0 0% 76.59% 60ms 0.77% tcache_get (inline) 60ms 0.77% 77.35% 60ms 0.77% tcache_get_n (inline) 51ms 0.65% 78.00% 59ms 0.75% std::num_put::do_put 53ms 0.68% 78.68% 59ms 0.75% vertexsort 58ms 0.74% 79.42% 58ms 0.74% [libchaste_mesh.so] 4ms 0.051% 79.47% 57ms 0.73% CellPropertyCollection::AddProperty 0 0% 79.47% 57ms 0.73% std::_Rb_tree::_M_destroy_node (inline) 0 0% 79.47% 57ms 0.73% std::__new_allocator::destroy (inline) 0 0% 79.47% 57ms 0.73% std::allocator_traits::destroy (inline) 5ms 0.064% 79.53% 56ms 0.71% TetrahedralMesh::EdgeIterator::GetNodeB 54ms 0.69% 80.22% 56ms 0.71% boost::detail::shared_count::shared_count (inline) 44ms 0.56% 80.78% 55ms 0.7% AbstractElement::GetNodeGlobalIndex 54ms 0.69% 81.47% 54ms 0.69% std::ostream::sentry::sentry 36ms 0.46% 81.93% 53ms 0.68% boost::numeric::ublas::c_matrix::operator() 4ms 0.051% 81.98% 51ms 0.65% std::_Vector_base::_M_deallocate (inline) 50ms 0.64% 82.62% 50ms 0.64% [libstdc++.so.6.0.33] 0 0% 82.62% 50ms 0.64% boost::numeric::ublas::vector_reference::operator() (inline) 17ms 0.22% 82.84% 49ms 0.63% Determinant (inline) 25ms 0.32% 83.16% 48ms 0.61% AbstractTetrahedralMesh::GetElement 11ms 0.14% 83.30% 48ms 0.61% Inverse 0 0% 83.30% 48ms 0.61% MeshBasedCellPopulation::SpringIterator::~SpringIterator (inline) 48ms 0.61% 83.91% 48ms 0.61% boost::numeric::ublas::same_impl_ex 0 0% 83.91% 47ms 0.6% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 47ms 0.6% 84.51% 47ms 0.6% boost::shared_ptr::operator-> (inline) 0 0% 84.51% 46ms 0.59% BoundaryNodeWriter::Visit 0 0% 84.51% 46ms 0.59% std::map::find (inline) 0 0% 84.51% 46ms 0.59% std::map::map (inline) 1ms 0.013% 84.52% 45ms 0.57% std::__new_allocator::construct (inline) 0 0% 84.52% 45ms 0.57% std::allocator_traits::construct (inline) 17ms 0.22% 84.74% 44ms 0.56% NodeAttributes::AddAppliedForceContribution 0 0% 84.74% 44ms 0.56% std::_Rb_tree::_M_emplace_hint_unique 22ms 0.28% 85.02% 43ms 0.55% AbstractCellCycleModel::GetAge 0 0% 85.02% 43ms 0.55% AbstractCentreBasedCellPopulation::CreateCellPair 0 0% 85.02% 43ms 0.55% std::_Rb_tree::_Rb_tree_impl::_Rb_tree_impl (inline) 3ms 0.038% 85.06% 43ms 0.55% std::_Rb_tree_header::_Rb_tree_header (inline) 0 0% 85.06% 42ms 0.54% Node::ClearAppliedForce 1ms 0.013% 85.07% 42ms 0.54% Node::ConstructNodeAttributes (inline) 26ms 0.33% 85.40% 42ms 0.54% hack_digit 42ms 0.54% 85.94% 42ms 0.54% std::vector::size (inline) 0 0% 85.94% 41ms 0.52% std::_Rb_tree::_M_construct_node (inline) 40ms 0.51% 86.45% 40ms 0.51% Node::IsDeleted 40ms 0.51% 86.96% 40ms 0.51% std::_Rb_tree_header::_M_reset (inline)