File: Test2dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 6537ms, 83.71% of 7809ms total Dropped 587 nodes (cum <= 39.05ms) flat flat% sum% cum cum% 0 0% 0% 7774ms 99.55% __libc_start_call_main 0 0% 0% 7774ms 99.55% __libc_start_main_impl 0 0% 0% 7774ms 99.55% _start 0 0% 0% 7755ms 99.31% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 7755ms 99.31% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 7755ms 99.31% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 7755ms 99.31% main 0 0% 0% 7716ms 98.81% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 7716ms 98.81% CxxTest::TestRunner::runTest (inline) 0 0% 0% 7716ms 98.81% Test2DMonolayerRepresentativeSimulation::Test2DMonolayerRepresentativeSimulationForProfiling 0 0% 0% 7713ms 98.77% AbstractCellBasedSimulation::Solve 0 0% 0% 3354ms 42.95% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 2933ms 37.56% MeshBasedCellPopulation::Update 2ms 0.026% 0.026% 2808ms 35.96% AbstractCellPopulation::WriteResultsToFiles 0 0% 0.026% 1539ms 19.71% OffLatticeSimulation::UpdateCellLocationsAndTopology 1ms 0.013% 0.038% 1469ms 18.81% MutableMesh::ReMesh 3ms 0.038% 0.077% 1420ms 18.18% MeshBasedCellPopulation::UpdateNodePairs 0 0% 0.077% 1378ms 17.65% ForwardEulerNumericalMethod::UpdateAllNodePositions 6ms 0.077% 0.15% 1316ms 16.85% AbstractNumericalMethod::ComputeForcesIncludingDamping 15ms 0.19% 0.35% 1235ms 15.82% MeshBasedCellPopulation::SpringIterator::operator++ 103ms 1.32% 1.66% 1010ms 12.93% TetrahedralMesh::EdgeIterator::operator++ 443ms 5.67% 7.34% 952ms 12.19% std::_Rb_tree::_M_lower_bound (inline) 3ms 0.038% 7.38% 929ms 11.90% AbstractTwoBodyInteractionForce::AddForceContribution 11ms 0.14% 7.52% 905ms 11.59% CellPopulationElementWriter::Visit 2ms 0.026% 7.54% 887ms 11.36% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 242ms 3.10% 10.64% 868ms 11.12% __dynamic_cast 59ms 0.76% 11.40% 819ms 10.49% GeneralisedLinearSpringForce::CalculateForceBetweenNodes (partial-inline) 7ms 0.09% 11.49% 794ms 10.17% CellPropertyCollection::GetPropertiesType (inline) 8ms 0.1% 11.59% 749ms 9.59% TetrahedralMesh::ImportFromMesher 31ms 0.4% 11.99% 746ms 9.55% AbstractCellPopulation::GetCellUsingLocationIndex 6ms 0.077% 12.06% 745ms 9.54% MeshBasedCellPopulation::AcceptCellWriter 2ms 0.026% 12.09% 656ms 8.40% AbstractCellProperty::IsSubType (inline) 38ms 0.49% 12.58% 602ms 7.71% operator new 0 0% 12.58% 597ms 7.65% std::ostream::operator<< (inline) 101ms 1.29% 13.87% 595ms 7.62% std::ostream::_M_insert 66ms 0.85% 14.71% 570ms 7.30% std::map::operator[] (partial-inline) 4ms 0.051% 14.77% 554ms 7.09% triangulate 201ms 2.57% 17.34% 550ms 7.04% __GI___libc_malloc 23ms 0.29% 17.63% 537ms 6.88% std::_Rb_tree::find (inline) 22ms 0.28% 17.92% 536ms 6.86% std::__new_allocator::allocate (inline) 0 0% 17.92% 535ms 6.85% std::allocator_traits::allocate (inline) 7ms 0.09% 18.00% 509ms 6.52% std::set::insert (inline) 2ms 0.026% 18.03% 505ms 6.47% LegacyCellProliferativeTypesWriter::VisitCell 505ms 6.47% 24.50% 505ms 6.47% __strcmp_avx2 14ms 0.18% 24.68% 502ms 6.43% std::_Rb_tree::_M_insert_unique 0 0% 24.68% 490ms 6.27% std::set::count (inline) 0 0% 24.68% 485ms 6.21% delaunay 1ms 0.013% 24.69% 483ms 6.19% divconqdelaunay 0 0% 24.69% 455ms 5.83% std::_Rb_tree::lower_bound (inline) 0 0% 24.69% 455ms 5.83% std::map::lower_bound (inline) 209ms 2.68% 27.37% 454ms 5.81% __cxxabiv1::__si_class_type_info::__do_dyncast 31ms 0.4% 27.76% 450ms 5.76% std::_Rb_tree::~_Rb_tree (inline) 3ms 0.038% 27.80% 448ms 5.74% Cell::GetCellProliferativeType 0 0% 27.80% 424ms 5.43% std::set::~set (inline) 77ms 0.99% 28.79% 418ms 5.35% std::_Rb_tree::_M_erase 0 0% 28.79% 411ms 5.26% std::_Rb_tree::_M_create_node (inline) 5ms 0.064% 28.85% 405ms 5.19% AbstractCellBasedSimulation::DoCellBirth 0 0% 28.85% 390ms 4.99% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 28.85% 389ms 4.98% std::_Rb_tree::_M_get_node (inline) 5ms 0.064% 28.92% 376ms 4.81% Cell::GetMutationState 10ms 0.13% 29.04% 362ms 4.64% std::less::operator() (inline) 352ms 4.51% 33.55% 352ms 4.51% std::operator< (inline) 22ms 0.28% 33.83% 349ms 4.47% std::_Rb_tree::_Rb_tree (partial-inline) 2ms 0.026% 33.86% 344ms 4.41% NodeLocationWriter::Visit 113ms 1.45% 35.31% 339ms 4.34% __GI___libc_free 6ms 0.077% 35.38% 328ms 4.20% Element::Element 0 0% 35.38% 322ms 4.12% std::_Rb_tree::_M_drop_node (inline) 12ms 0.15% 35.54% 316ms 4.05% std::__new_allocator::deallocate (inline) 3ms 0.038% 35.57% 313ms 4.01% std::set::set (inline) 0 0% 35.57% 311ms 3.98% std::allocator_traits::deallocate (inline) 32ms 0.41% 35.98% 311ms 3.98% std::num_put::_M_insert_float 2ms 0.026% 36.01% 308ms 3.94% MeshBasedCellPopulation::GetDampingConstant 1ms 0.013% 36.02% 306ms 3.92% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 3ms 0.038% 36.06% 305ms 3.91% AbstractCentreBasedCellPopulation::GetDampingConstant 0 0% 36.06% 304ms 3.89% AbstractCellBasedWriter::OpenOutputFileForAppend 0 0% 36.06% 302ms 3.87% OutputFileHandler::OpenOutputFile 22ms 0.28% 36.34% 299ms 3.83% std::_Rb_tree::_M_insert_ (inline) 13ms 0.17% 36.51% 297ms 3.80% AbstractCellPopulation::IsCellAttachedToLocationIndex 30ms 0.38% 36.89% 293ms 3.75% std::_Rb_tree::_M_copy (inline) 10ms 0.13% 37.02% 290ms 3.71% divconqrecurse 281ms 3.60% 40.62% 281ms 3.60% std::_Rb_tree::_S_right (inline) 7ms 0.09% 40.71% 275ms 3.52% Cell::ReadyToDivide 163ms 2.09% 42.80% 274ms 3.51% _int_malloc 84ms 1.08% 43.87% 272ms 3.48% mergehulls 63ms 0.81% 44.68% 259ms 3.32% std::_Rb_tree::_M_clone_node (inline) 0 0% 44.68% 257ms 3.29% std::_Rb_tree::_M_put_node (inline) 0 0% 44.68% 247ms 3.16% AbstractCellProperty::IsType (inline) 6ms 0.077% 44.76% 239ms 3.06% std::__cxx11::collate::do_transform 2ms 0.026% 44.78% 226ms 2.89% CellPropertyCollection::HasProperty 0 0% 44.78% 225ms 2.88% Cell::HasCellProperty (inline) 188ms 2.41% 47.19% 224ms 2.87% _int_free 0 0% 47.19% 220ms 2.82% ___vsnprintf 1ms 0.013% 47.20% 220ms 2.82% __vsnprintf_internal (inline) 21ms 0.27% 47.47% 217ms 2.78% __printf_buffer 8ms 0.1% 47.57% 204ms 2.61% Element::RegisterWithNodes (inline) 1ms 0.013% 47.59% 198ms 2.54% CellProliferativeTypesWriter::VisitCell 13ms 0.17% 47.75% 197ms 2.52% MeshBasedCellPopulation::SpringsEnd (inline) 3ms 0.038% 47.79% 195ms 2.50% Node::AddElement 9ms 0.12% 47.91% 191ms 2.45% TetrahedralMesh::Clear 70ms 0.9% 48.80% 189ms 2.42% std::_Rb_tree::_M_get_insert_unique_pos (inline) 1ms 0.013% 48.82% 186ms 2.38% AbstractPhaseBasedCellCycleModel::ReadyToDivide 42ms 0.54% 49.35% 183ms 2.34% AbstractCellProperty::IsSame 7ms 0.09% 49.44% 183ms 2.34% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 13ms 0.17% 49.61% 181ms 2.32% __printf_fp_l_buffer 0 0% 49.61% 181ms 2.32% __printf_fp_spec (inline) 19ms 0.24% 49.85% 174ms 2.23% AbstractTetrahedralElement::CalculateJacobian 0 0% 49.85% 163ms 2.09% std::basic_ofstream::basic_ofstream (inline) 88ms 1.13% 50.98% 162ms 2.07% __printf_fp_buffer_1 2ms 0.026% 51.01% 158ms 2.02% std::basic_filebuf::open 0 0% 51.01% 158ms 2.02% std::basic_ofstream::open (inline) 0 0% 51.01% 155ms 1.98% OutputFileHandler::CommonConstructor 0 0% 51.01% 155ms 1.98% OutputFileHandler::OutputFileHandler 0 0% 51.01% 146ms 1.87% OutputFileHandler::MakeFoldersAndReturnFullPath 0 0% 51.01% 146ms 1.87% std::_Vector_base::_M_allocate (inline) 20ms 0.26% 51.26% 143ms 1.83% boost::detail::shared_count::~shared_count (inline) 0 0% 51.26% 143ms 1.83% boost::shared_ptr::~shared_ptr (inline) 33ms 0.42% 51.68% 141ms 1.81% std::type_info::operator== (inline) 1ms 0.013% 51.70% 139ms 1.78% TetrahedralMesh::RefreshJacobianCachedData 25ms 0.32% 52.02% 138ms 1.77% TetrahedralMesh::EdgesEnd (partial-inline) 49ms 0.63% 52.64% 137ms 1.75% std::__ostream_insert 32ms 0.41% 53.05% 137ms 1.75% std::num_put::_M_insert_int 19ms 0.24% 53.30% 134ms 1.72% MeshBasedCellPopulation::SpringIterator::SpringIterator 1ms 0.013% 53.31% 132ms 1.69% std::__basic_file::open 0 0% 53.31% 131ms 1.68% _IO_new_fopen 0 0% 53.31% 131ms 1.68% __fopen_internal (inline) 0 0% 53.31% 130ms 1.66% _IO_new_file_fopen 1ms 0.013% 53.32% 130ms 1.66% __GI__IO_file_open 1ms 0.013% 53.34% 128ms 1.64% AbstractCellBasedWriter::CloseFile 0 0% 53.34% 128ms 1.64% AbstractCellPopulation::CloseRoundRobinWritersFiles 8ms 0.1% 53.44% 128ms 1.64% AbstractTetrahedralElement::CalculateInverseJacobian 2ms 0.026% 53.46% 128ms 1.64% std::basic_filebuf::close 0 0% 53.46% 127ms 1.63% std::basic_ofstream::close (inline) 15ms 0.19% 53.66% 126ms 1.61% AbstractTetrahedralElement::RefreshJacobian 4ms 0.051% 53.71% 126ms 1.61% boost::numeric::ublas::vector_assign (inline) 5ms 0.064% 53.77% 123ms 1.58% AbstractTetrahedralElement::AbstractTetrahedralElement 3ms 0.038% 53.81% 121ms 1.55% boost::numeric::ublas::c_vector::c_vector (inline) 120ms 1.54% 55.35% 120ms 1.54% incircle 1ms 0.013% 55.36% 118ms 1.51% alternateaxes 4ms 0.051% 55.41% 117ms 1.50% std::vector::push_back (inline) 1ms 0.013% 55.42% 116ms 1.49% std::operator<< (inline) 109ms 1.40% 56.82% 116ms 1.49% vertexmedian 115ms 1.47% 58.29% 115ms 1.47% __libc_open64 0 0% 58.29% 115ms 1.47% std::filesystem::permissions 0 0% 58.29% 114ms 1.46% FilesystemPermissions::SetFilePermissions (inline) 3ms 0.038% 58.33% 114ms 1.46% Node::~Node 113ms 1.45% 59.78% 113ms 1.45% TetrahedralMesh::EdgeIterator::operator!= (partial-inline) 112ms 1.43% 61.21% 112ms 1.43% __GI_fchmodat 105ms 1.34% 62.56% 110ms 1.41% boost::detail::sp_counted_base::release 10ms 0.13% 62.68% 110ms 1.41% std::vector::_M_realloc_insert 71ms 0.91% 63.59% 106ms 1.36% TetrahedralMesh::EdgeIterator::EdgeIterator (partial-inline) 5ms 0.064% 63.66% 102ms 1.31% AbstractCellPopulation::Iterator::IsRealCell (inline) 0 0% 63.66% 101ms 1.29% AbstractCellPopulation::Iterator::operator++ (inline) 100ms 1.28% 64.94% 100ms 1.28% [libchaste_cell_based.so] 21ms 0.27% 65.21% 93ms 1.19% boost::numeric::ublas::indexing_vector_assign 68ms 0.87% 66.08% 90ms 1.15% malloc_consolidate 59ms 0.76% 66.83% 90ms 1.15% std::basic_filebuf::xsputn 1ms 0.013% 66.85% 89ms 1.14% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 39ms 0.5% 67.35% 89ms 1.14% AbstractElement::GetNodeLocation 1ms 0.013% 67.36% 88ms 1.13% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (partial-inline) 53ms 0.68% 68.04% 88ms 1.13% boost::shared_ptr::shared_ptr (inline) 1ms 0.013% 68.05% 88ms 1.13% std::basic_filebuf::_M_terminate_output 2ms 0.026% 68.08% 88ms 1.13% std::basic_filebuf::overflow 1ms 0.013% 68.09% 86ms 1.10% std::basic_filebuf::_M_convert_to_external 84ms 1.08% 69.16% 84ms 1.08% __GI___libc_write 0 0% 69.16% 84ms 1.08% std::__basic_file::xsputn 83ms 1.06% 70.23% 83ms 1.06% std::_Rb_tree_insert_and_rebalance 0 0% 70.23% 78ms 1% FilesystemPermissions::CreateDirectoryWithPermissions (inline) 0 0% 70.23% 77ms 0.99% std::filesystem::create_directory 2ms 0.026% 70.25% 76ms 0.97% std::filesystem::status 1ms 0.013% 70.27% 75ms 0.96% AbstractCellPopulation::GetLocationIndexUsingCell 75ms 0.96% 71.23% 75ms 0.96% std::_Rb_tree_increment 74ms 0.95% 72.17% 74ms 0.95% __GI___fstatat64 4ms 0.051% 72.22% 72ms 0.92% TetrahedralMesh::EdgeIterator::GetNodeA 5ms 0.064% 72.29% 71ms 0.91% std::_Rb_tree_const_iterator::operator++ (inline) 70ms 0.9% 73.18% 70ms 0.9% std::vector::size (inline) 0 0% 73.18% 70ms 0.9% std::vector::vector (inline) 69ms 0.88% 74.07% 69ms 0.88% Node::GetIndex 0 0% 74.07% 67ms 0.86% std::_Vector_base::_Vector_base (inline) 0 0% 74.07% 67ms 0.86% tcache_get (inline) 67ms 0.86% 74.93% 67ms 0.86% tcache_get_n (inline) 0 0% 74.93% 66ms 0.85% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 74.93% 66ms 0.85% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 0 0% 74.93% 66ms 0.85% std::_Vector_base::_M_create_storage (inline) 51ms 0.65% 75.58% 66ms 0.85% std::num_put::do_put 0 0% 75.58% 65ms 0.83% std::_Rb_tree::_M_destroy_node (inline) 0 0% 75.58% 65ms 0.83% std::__new_allocator::destroy (inline) 0 0% 75.58% 65ms 0.83% std::allocator_traits::destroy (inline) 40ms 0.51% 76.09% 65ms 0.83% std::basic_streambuf::xsputn 64ms 0.82% 76.91% 64ms 0.82% [libstdc++.so.6.0.33] 64ms 0.82% 77.73% 64ms 0.82% counterclockwise 0 0% 77.73% 63ms 0.81% Cell::GetCellId 38ms 0.49% 78.22% 62ms 0.79% boost::numeric::ublas::c_matrix::operator() (partial-inline) 1ms 0.013% 78.23% 61ms 0.78% TetrahedralMesh::EdgeIterator::GetNodeB 55ms 0.7% 78.93% 61ms 0.78% vertexsort 44ms 0.56% 79.50% 60ms 0.77% AbstractElement::GetNodeGlobalIndex 0 0% 79.50% 60ms 0.77% CellPropertyCollection::~CellPropertyCollection (inline) 55ms 0.7% 80.20% 55ms 0.7% __memcpy_avx_unaligned_erms 1ms 0.013% 80.22% 55ms 0.7% std::_Vector_base::_M_deallocate (inline) 0 0% 80.22% 51ms 0.65% boost::numeric::ublas::norm_2 (inline) 16ms 0.2% 80.42% 51ms 0.65% boost::numeric::ublas::vector_norm_2::apply (inline) 4ms 0.051% 80.47% 49ms 0.63% std::_Rb_tree::_M_emplace_hint_unique 48ms 0.61% 81.09% 48ms 0.61% Node::rGetLocation 0 0% 81.09% 47ms 0.6% BoundaryNodeWriter::Visit 12ms 0.15% 81.24% 46ms 0.59% Determinant (inline) 9ms 0.12% 81.35% 45ms 0.58% CellPropertyCollection::AddProperty 1ms 0.013% 81.37% 45ms 0.58% Node::ClearAppliedForce 2ms 0.026% 81.39% 44ms 0.56% AbstractTetrahedralElement::~AbstractTetrahedralElement (inline) 22ms 0.28% 81.67% 44ms 0.56% AbstractTetrahedralMesh::GetElement 3ms 0.038% 81.71% 44ms 0.56% Node::ConstructNodeAttributes (inline) 44ms 0.56% 82.28% 44ms 0.56% boost::numeric::ublas::c_vector::operator() (partial-inline) 42ms 0.54% 82.81% 42ms 0.54% [libchaste_mesh.so] 42ms 0.54% 83.35% 42ms 0.54% __GI___mkdir 24ms 0.31% 83.66% 42ms 0.54% hack_digit 4ms 0.051% 83.71% 40ms 0.51% Element::~Element