File: Test2dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 6638ms, 84.52% of 7854ms total Dropped 590 nodes (cum <= 39.27ms) flat flat% sum% cum cum% 0 0% 0% 7813ms 99.48% __libc_start_call_main 0 0% 0% 7813ms 99.48% __libc_start_main_impl 0 0% 0% 7813ms 99.48% _start 0 0% 0% 7796ms 99.26% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 7796ms 99.26% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 7796ms 99.26% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 7796ms 99.26% main 0 0% 0% 7757ms 98.76% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 7757ms 98.76% CxxTest::TestRunner::runTest (inline) 0 0% 0% 7757ms 98.76% Test2DMonolayerRepresentativeSimulation::Test2DMonolayerRepresentativeSimulationForProfiling 0 0% 0% 7755ms 98.74% AbstractCellBasedSimulation::Solve 0 0% 0% 3311ms 42.16% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 2890ms 36.80% AbstractCellPopulation::WriteResultsToFiles 2ms 0.025% 0.025% 2863ms 36.45% MeshBasedCellPopulation::Update 3ms 0.038% 0.064% 1545ms 19.67% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 0.064% 1443ms 18.37% MeshBasedCellPopulation::UpdateNodePairs 0 0% 0.064% 1395ms 17.76% ForwardEulerNumericalMethod::UpdateAllNodePositions 1ms 0.013% 0.076% 1359ms 17.30% MutableMesh::ReMesh 7ms 0.089% 0.17% 1328ms 16.91% AbstractNumericalMethod::ComputeForcesIncludingDamping 13ms 0.17% 0.33% 1266ms 16.12% MeshBasedCellPopulation::SpringIterator::operator++ 114ms 1.45% 1.78% 1051ms 13.38% TetrahedralMesh::EdgeIterator::operator++ 442ms 5.63% 7.41% 981ms 12.49% std::_Rb_tree::_M_lower_bound (inline) 9ms 0.11% 7.52% 913ms 11.62% CellPropertyCollection::GetPropertiesType (inline) 0 0% 7.52% 909ms 11.57% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 2ms 0.025% 7.55% 895ms 11.40% AbstractTwoBodyInteractionForce::AddForceContribution 9ms 0.11% 7.66% 872ms 11.10% CellPopulationElementWriter::Visit 262ms 3.34% 11.00% 855ms 10.89% __dynamic_cast 54ms 0.69% 11.69% 799ms 10.17% AbstractVariableSizeTwoBodyInteractionForce::CalculateForceBetweenNodes 1ms 0.013% 11.70% 760ms 9.68% MeshBasedCellPopulation::AcceptCellWriter 12ms 0.15% 11.85% 736ms 9.37% TetrahedralMesh::ImportFromMesher 21ms 0.27% 12.12% 721ms 9.18% AbstractCellPopulation::GetCellUsingLocationIndex 6ms 0.076% 12.20% 700ms 8.91% AbstractCellProperty::IsSubType (inline) 3ms 0.038% 12.24% 650ms 8.28% std::ostream::operator<< (inline) 92ms 1.17% 13.41% 647ms 8.24% std::ostream::_M_insert 54ms 0.69% 14.09% 590ms 7.51% std::map::operator[] (partial-inline) 6ms 0.076% 14.17% 560ms 7.13% std::set::insert (inline) 37ms 0.47% 14.64% 555ms 7.07% operator new 14ms 0.18% 14.82% 554ms 7.05% std::_Rb_tree::_M_insert_unique 16ms 0.2% 15.02% 536ms 6.82% std::_Rb_tree::find (inline) 159ms 2.02% 17.05% 516ms 6.57% __GI___libc_malloc 40ms 0.51% 17.56% 503ms 6.40% std::__new_allocator::allocate (inline) 0 0% 17.56% 502ms 6.39% std::allocator_traits::allocate (inline) 0 0% 17.56% 496ms 6.32% std::_Rb_tree::lower_bound (inline) 0 0% 17.56% 496ms 6.32% std::map::lower_bound (inline) 0 0% 17.56% 495ms 6.30% std::set::count (inline) 2ms 0.025% 17.58% 491ms 6.25% triangulate 5ms 0.064% 17.65% 475ms 6.05% Cell::GetCellProliferativeType 5ms 0.064% 17.71% 472ms 6.01% LegacyCellProliferativeTypesWriter::VisitCell 471ms 6.00% 23.71% 471ms 6.00% __strcmp_avx2 199ms 2.53% 26.24% 443ms 5.64% __cxxabiv1::__si_class_type_info::__do_dyncast 6ms 0.076% 26.32% 434ms 5.53% AbstractCellBasedSimulation::DoCellBirth 0 0% 26.32% 423ms 5.39% NodeLocationWriter::Visit 0 0% 26.32% 423ms 5.39% delaunay 0 0% 26.32% 421ms 5.36% divconqdelaunay 0 0% 26.32% 420ms 5.35% std::_Rb_tree::_M_create_node (inline) 35ms 0.45% 26.76% 407ms 5.18% std::_Rb_tree::~_Rb_tree (inline) 9ms 0.11% 26.88% 404ms 5.14% Cell::GetMutationState 0 0% 26.88% 399ms 5.08% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 26.88% 389ms 4.95% std::_Rb_tree::_M_get_node (inline) 13ms 0.17% 27.04% 386ms 4.91% std::less::operator() (inline) 0 0% 27.04% 377ms 4.80% std::set::~set (inline) 373ms 4.75% 31.79% 373ms 4.75% std::operator< (inline) 32ms 0.41% 32.20% 366ms 4.66% std::num_put::_M_insert_float 70ms 0.89% 33.09% 365ms 4.65% std::_Rb_tree::_M_erase 18ms 0.23% 33.32% 358ms 4.56% std::_Rb_tree::_Rb_tree (partial-inline) 1ms 0.013% 33.33% 349ms 4.44% MeshBasedCellPopulation::GetDampingConstant 0 0% 33.33% 347ms 4.42% AbstractCentreBasedCellPopulation::GetDampingConstant 24ms 0.31% 33.64% 343ms 4.37% std::_Rb_tree::_M_insert_ (inline) 1ms 0.013% 33.65% 320ms 4.07% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 2ms 0.025% 33.68% 320ms 4.07% std::set::set (inline) 317ms 4.04% 37.71% 317ms 4.04% std::_Rb_tree::_S_right (inline) 0 0% 37.71% 315ms 4.01% AbstractCellBasedWriter::OpenOutputFileForAppend 0 0% 37.71% 312ms 3.97% OutputFileHandler::OpenOutputFile 46ms 0.59% 38.30% 309ms 3.93% std::_Rb_tree::_M_copy (inline) 119ms 1.52% 39.81% 306ms 3.90% __GI___libc_free 5ms 0.064% 39.88% 305ms 3.88% Element::Element 4ms 0.051% 39.93% 292ms 3.72% AbstractCellPopulation::IsCellAttachedToLocationIndex 5ms 0.064% 39.99% 288ms 3.67% Cell::ReadyToDivide 9ms 0.11% 40.11% 280ms 3.57% std::__new_allocator::deallocate (inline) 9ms 0.11% 40.22% 277ms 3.53% std::__cxx11::collate::do_transform 0 0% 40.22% 277ms 3.53% std::allocator_traits::deallocate (inline) 190ms 2.42% 42.64% 272ms 3.46% _int_malloc 0 0% 42.64% 268ms 3.41% std::_Rb_tree::_M_drop_node (inline) 15ms 0.19% 42.83% 266ms 3.39% divconqrecurse 6ms 0.076% 42.91% 263ms 3.35% ___vsnprintf 77ms 0.98% 43.89% 258ms 3.28% std::_Rb_tree::_M_clone_node (inline) 0 0% 43.89% 257ms 3.27% __vsnprintf_internal (inline) 3ms 0.038% 43.93% 253ms 3.22% CellProliferativeTypesWriter::VisitCell 34ms 0.43% 44.36% 252ms 3.21% __printf_buffer 56ms 0.71% 45.07% 243ms 3.09% mergehulls 2ms 0.025% 45.10% 241ms 3.07% AbstractCellProperty::IsType (inline) 0 0% 45.10% 217ms 2.76% std::_Rb_tree::_M_put_node (inline) 5ms 0.064% 45.16% 210ms 2.67% CellPropertyCollection::HasProperty 0 0% 45.16% 207ms 2.64% Cell::HasCellProperty (inline) 1ms 0.013% 45.17% 204ms 2.60% __printf_fp_spec (inline) 10ms 0.13% 45.30% 203ms 2.58% __printf_fp_l_buffer 3ms 0.038% 45.34% 197ms 2.51% Element::RegisterWithNodes (inline) 67ms 0.85% 46.19% 197ms 2.51% std::_Rb_tree::_M_get_insert_unique_pos (inline) 2ms 0.025% 46.22% 193ms 2.46% AbstractPhaseBasedCellCycleModel::ReadyToDivide 22ms 0.28% 46.50% 193ms 2.46% TetrahedralMesh::Clear 0 0% 46.50% 192ms 2.44% Node::AddElement 13ms 0.17% 46.66% 187ms 2.38% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 164ms 2.09% 48.75% 187ms 2.38% _int_free 86ms 1.09% 49.85% 181ms 2.30% __printf_fp_buffer_1 7ms 0.089% 49.94% 180ms 2.29% MeshBasedCellPopulation::SpringsEnd (inline) 47ms 0.6% 50.53% 170ms 2.16% AbstractCellProperty::IsSame 44ms 0.56% 51.09% 162ms 2.06% TetrahedralMesh::EdgesEnd (partial-inline) 2ms 0.025% 51.12% 152ms 1.94% OutputFileHandler::CommonConstructor 0 0% 51.12% 152ms 1.94% OutputFileHandler::OutputFileHandler 0 0% 51.12% 150ms 1.91% std::basic_ofstream::basic_ofstream (inline) 0 0% 51.12% 147ms 1.87% std::basic_ofstream::open (inline) 2ms 0.025% 51.15% 144ms 1.83% std::basic_filebuf::open 0 0% 51.15% 143ms 1.82% AbstractCellPopulation::CloseRoundRobinWritersFiles 0 0% 51.15% 143ms 1.82% OutputFileHandler::MakeFoldersAndReturnFullPath 1ms 0.013% 51.16% 141ms 1.80% std::basic_filebuf::close 0 0% 51.16% 140ms 1.78% AbstractCellBasedWriter::CloseFile 0 0% 51.16% 140ms 1.78% std::basic_ofstream::close (inline) 55ms 0.7% 51.86% 137ms 1.74% std::__ostream_insert 7ms 0.089% 51.95% 134ms 1.71% AbstractTetrahedralElement::CalculateJacobian 7ms 0.089% 52.04% 131ms 1.67% std::vector::push_back (inline) 0 0% 52.04% 128ms 1.63% FilesystemPermissions::SetFilePermissions (inline) 127ms 1.62% 53.65% 127ms 1.62% __GI_fchmodat 0 0% 53.65% 127ms 1.62% std::filesystem::permissions 35ms 0.45% 54.10% 127ms 1.62% std::num_put::_M_insert_int 14ms 0.18% 54.28% 124ms 1.58% AbstractCellPopulation::Iterator::IsRealCell (inline) 11ms 0.14% 54.42% 124ms 1.58% boost::numeric::ublas::c_vector::c_vector (inline) 27ms 0.34% 54.76% 123ms 1.57% std::type_info::operator== (inline) 0 0% 54.76% 122ms 1.55% AbstractCellPopulation::Iterator::operator++ (inline) 1ms 0.013% 54.77% 120ms 1.53% TetrahedralMesh::RefreshJacobianCachedData 1ms 0.013% 54.79% 119ms 1.52% boost::numeric::ublas::vector_assign (inline) 7ms 0.089% 54.88% 117ms 1.49% std::vector::_M_realloc_insert 3ms 0.038% 54.91% 116ms 1.48% std::_Vector_base::_M_allocate (inline) 115ms 1.46% 56.38% 115ms 1.46% incircle 1ms 0.013% 56.39% 113ms 1.44% std::__basic_file::open 0 0% 56.39% 112ms 1.43% _IO_new_fopen 2ms 0.025% 56.42% 112ms 1.43% __fopen_internal (inline) 4ms 0.051% 56.47% 112ms 1.43% std::operator<< (inline) 9ms 0.11% 56.58% 110ms 1.40% std::_Rb_tree_const_iterator::operator++ (inline) 110ms 1.40% 57.98% 110ms 1.40% std::_Rb_tree_increment 8ms 0.1% 58.09% 108ms 1.38% AbstractTetrahedralElement::AbstractTetrahedralElement 0 0% 58.09% 107ms 1.36% Cell::GetCellId 0 0% 58.09% 107ms 1.36% _IO_new_file_fopen 1ms 0.013% 58.10% 106ms 1.35% __GI__IO_file_open 7ms 0.089% 58.19% 105ms 1.34% AbstractTetrahedralElement::CalculateInverseJacobian 13ms 0.17% 58.35% 105ms 1.34% boost::detail::shared_count::~shared_count (inline) 0 0% 58.35% 105ms 1.34% boost::shared_ptr::~shared_ptr (inline) 105ms 1.34% 59.69% 105ms 1.34% std::_Rb_tree_insert_and_rebalance 17ms 0.22% 59.91% 104ms 1.32% MeshBasedCellPopulation::SpringIterator::SpringIterator 5ms 0.064% 59.97% 103ms 1.31% Node::~Node 100ms 1.27% 61.24% 100ms 1.27% [libchaste_cell_based.so] 2ms 0.025% 61.27% 100ms 1.27% std::basic_filebuf::_M_terminate_output 2ms 0.025% 61.29% 100ms 1.27% std::basic_filebuf::overflow 60ms 0.76% 62.06% 99ms 1.26% TetrahedralMesh::EdgeIterator::EdgeIterator (partial-inline) 98ms 1.25% 63.31% 99ms 1.26% __libc_open64 16ms 0.2% 63.51% 98ms 1.25% AbstractTetrahedralElement::RefreshJacobian 0 0% 63.51% 98ms 1.25% std::__basic_file::xsputn 0 0% 63.51% 98ms 1.25% std::basic_filebuf::_M_convert_to_external 97ms 1.24% 64.74% 97ms 1.24% __GI___libc_write 1ms 0.013% 64.76% 94ms 1.20% alternateaxes 27ms 0.34% 65.10% 92ms 1.17% boost::numeric::ublas::indexing_vector_assign 84ms 1.07% 66.17% 92ms 1.17% vertexmedian 2ms 0.025% 66.20% 91ms 1.16% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (partial-inline) 1ms 0.013% 66.21% 91ms 1.16% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 43ms 0.55% 66.76% 91ms 1.16% boost::shared_ptr::shared_ptr (inline) 88ms 1.12% 67.88% 88ms 1.12% boost::detail::sp_counted_base::release 57ms 0.73% 68.60% 82ms 1.04% std::basic_filebuf::xsputn 11ms 0.14% 68.74% 80ms 1.02% CellPropertyCollection::AddProperty 0 0% 68.74% 80ms 1.02% std::filesystem::status 0 0% 68.74% 78ms 0.99% tcache_get (inline) 78ms 0.99% 69.74% 78ms 0.99% tcache_get_n (inline) 2ms 0.025% 69.76% 76ms 0.97% AbstractCellPopulation::GetLocationIndexUsingCell 75ms 0.95% 70.72% 75ms 0.95% __GI___fstatat64 74ms 0.94% 71.66% 74ms 0.94% Node::GetIndex 50ms 0.64% 72.29% 74ms 0.94% std::basic_streambuf::xsputn 0 0% 72.29% 73ms 0.93% FilesystemPermissions::CreateDirectoryWithPermissions (inline) 73ms 0.93% 73.22% 73ms 0.93% counterclockwise 0 0% 73.22% 73ms 0.93% std::filesystem::create_directory 56ms 0.71% 73.94% 72ms 0.92% AbstractElement::GetNodeGlobalIndex 47ms 0.6% 74.54% 70ms 0.89% malloc_consolidate 0 0% 74.54% 69ms 0.88% AbstractCentreBasedCellPopulation::CreateCellPair 32ms 0.41% 74.94% 67ms 0.85% AbstractElement::GetNodeLocation 67ms 0.85% 75.80% 67ms 0.85% __memcpy_avx_unaligned_erms 67ms 0.85% 76.65% 67ms 0.85% std::vector::size (inline) 64ms 0.81% 77.46% 64ms 0.81% TetrahedralMesh::EdgeIterator::operator!= (partial-inline) 3ms 0.038% 77.50% 63ms 0.8% std::_Vector_base::_M_deallocate (inline) 50ms 0.64% 78.14% 57ms 0.73% vertexsort 0 0% 78.14% 55ms 0.7% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 2ms 0.025% 78.16% 54ms 0.69% TetrahedralMesh::EdgeIterator::GetNodeA 37ms 0.47% 78.64% 54ms 0.69% hack_digit 2ms 0.025% 78.66% 53ms 0.67% TetrahedralMesh::EdgeIterator::GetNodeB 52ms 0.66% 79.32% 52ms 0.66% Node::IsDeleted 52ms 0.66% 79.98% 52ms 0.66% std::ostream::sentry::sentry 0 0% 79.98% 52ms 0.66% std::vector::vector (inline) 0 0% 79.98% 51ms 0.65% MeshBasedCellPopulation::SpringIterator::~SpringIterator (inline) 0 0% 79.98% 51ms 0.65% std::_Rb_tree::_M_destroy_node (inline) 0 0% 79.98% 51ms 0.65% std::__new_allocator::destroy (inline) 0 0% 79.98% 51ms 0.65% std::allocator_traits::destroy (inline) 46ms 0.59% 80.57% 48ms 0.61% boost::detail::shared_count::shared_count (inline) 0 0% 80.57% 48ms 0.61% std::_Vector_base::_Vector_base (inline) 42ms 0.53% 81.11% 48ms 0.61% std::num_put::do_put 4ms 0.051% 81.16% 47ms 0.6% Node::ConstructNodeAttributes (inline) 47ms 0.6% 81.75% 47ms 0.6% [libstdc++.so.6.0.33] 19ms 0.24% 82.00% 46ms 0.59% AbstractTetrahedralMesh::GetElement 46ms 0.59% 82.58% 46ms 0.59% [libchaste_mesh.so] 28ms 0.36% 82.94% 46ms 0.59% boost::numeric::ublas::c_matrix::operator() (partial-inline) 0 0% 82.94% 46ms 0.59% std::_Vector_base::_M_create_storage (inline) 6ms 0.076% 83.02% 45ms 0.57% Element::~Element 0 0% 83.02% 45ms 0.57% Node::ClearAppliedForce 16ms 0.2% 83.22% 43ms 0.55% Determinant (inline) 43ms 0.55% 83.77% 43ms 0.55% boost::numeric::ublas::c_vector::operator() (inline) 42ms 0.53% 84.30% 42ms 0.53% boost::shared_ptr::operator-> (inline) 0 0% 84.30% 40ms 0.51% AbstractCentreBasedCellPopulation::IsMarkedSpring 1ms 0.013% 84.31% 40ms 0.51% AbstractTetrahedralElement::~AbstractTetrahedralElement (inline) 13ms 0.17% 84.48% 40ms 0.51% AbstractTetrahedralMesh::GetNumAllElements 3ms 0.038% 84.52% 40ms 0.51% std::_Rb_tree::_M_emplace_hint_unique 0 0% 84.52% 40ms 0.51% std::map::map (inline)