File: Test2dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 6676ms, 85.06% of 7849ms total Dropped 592 nodes (cum <= 39.24ms) flat flat% sum% cum cum% 0 0% 0% 7814ms 99.55% __libc_start_call_main 0 0% 0% 7814ms 99.55% __libc_start_main_impl 0 0% 0% 7814ms 99.55% _start 0 0% 0% 7800ms 99.38% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 7800ms 99.38% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 7800ms 99.38% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 7800ms 99.38% main 0 0% 0% 7761ms 98.88% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 7760ms 98.87% CxxTest::TestRunner::runTest (inline) 0 0% 0% 7760ms 98.87% Test2DMonolayerRepresentativeSimulation::Test2DMonolayerRepresentativeSimulationForProfiling 0 0% 0% 7757ms 98.83% AbstractCellBasedSimulation::Solve 0 0% 0% 3327ms 42.39% AbstractCellBasedSimulation::UpdateCellPopulation 1ms 0.013% 0.013% 2867ms 36.53% MeshBasedCellPopulation::Update 3ms 0.038% 0.051% 2824ms 35.98% AbstractCellPopulation::WriteResultsToFiles 0 0% 0.051% 1597ms 20.35% OffLatticeSimulation::UpdateCellLocationsAndTopology 2ms 0.025% 0.076% 1444ms 18.40% ForwardEulerNumericalMethod::UpdateAllNodePositions 1ms 0.013% 0.089% 1432ms 18.24% MeshBasedCellPopulation::UpdateNodePairs 6ms 0.076% 0.17% 1383ms 17.62% AbstractNumericalMethod::ComputeForcesIncludingDamping 0 0% 0.17% 1375ms 17.52% MutableMesh::ReMesh 22ms 0.28% 0.45% 1235ms 15.73% MeshBasedCellPopulation::SpringIterator::operator++ 119ms 1.52% 1.96% 1027ms 13.08% TetrahedralMesh::EdgeIterator::operator++ 419ms 5.34% 7.30% 963ms 12.27% std::_Rb_tree::_M_lower_bound (inline) 7ms 0.089% 7.39% 947ms 12.07% AbstractTwoBodyInteractionForce::AddForceContribution 0 0% 7.39% 934ms 11.90% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 20ms 0.25% 7.64% 911ms 11.61% CellPropertyCollection::GetPropertiesType (inline) 280ms 3.57% 11.21% 905ms 11.53% __dynamic_cast 13ms 0.17% 11.38% 860ms 10.96% CellPopulationElementWriter::Visit 44ms 0.56% 11.94% 835ms 10.64% GeneralisedLinearSpringForce::CalculateForceBetweenNodes (partial-inline) 2ms 0.025% 11.96% 788ms 10.04% MeshBasedCellPopulation::AcceptCellWriter 30ms 0.38% 12.35% 727ms 9.26% AbstractCellPopulation::GetCellUsingLocationIndex 12ms 0.15% 12.50% 704ms 8.97% TetrahedralMesh::ImportFromMesher 8ms 0.1% 12.60% 698ms 8.89% AbstractCellProperty::IsSubType (inline) 2ms 0.025% 12.63% 617ms 7.86% std::ostream::operator<< (inline) 84ms 1.07% 13.70% 615ms 7.84% std::ostream::_M_insert 57ms 0.73% 14.42% 593ms 7.56% std::map::operator[] (partial-inline) 8ms 0.1% 14.52% 576ms 7.34% std::set::insert (inline) 10ms 0.13% 14.65% 568ms 7.24% std::_Rb_tree::_M_insert_unique 34ms 0.43% 15.08% 556ms 7.08% operator new 15ms 0.19% 15.28% 529ms 6.74% std::_Rb_tree::find (inline) 28ms 0.36% 15.63% 526ms 6.70% std::__new_allocator::allocate (inline) 0 0% 15.63% 524ms 6.68% std::allocator_traits::allocate (inline) 0 0% 15.63% 523ms 6.66% triangulate 6ms 0.076% 15.71% 522ms 6.65% Cell::GetCellProliferativeType 164ms 2.09% 17.80% 511ms 6.51% __GI___libc_malloc 4ms 0.051% 17.85% 503ms 6.41% LegacyCellProliferativeTypesWriter::VisitCell 0 0% 17.85% 482ms 6.14% std::_Rb_tree::lower_bound (inline) 0 0% 17.85% 482ms 6.14% std::map::lower_bound (inline) 0 0% 17.85% 481ms 6.13% std::set::count (inline) 477ms 6.08% 23.93% 477ms 6.08% __strcmp_avx2 209ms 2.66% 26.59% 471ms 6.00% __cxxabiv1::__si_class_type_info::__do_dyncast 0 0% 26.59% 456ms 5.81% delaunay 0 0% 26.59% 455ms 5.80% divconqdelaunay 1ms 0.013% 26.60% 450ms 5.73% AbstractCellBasedSimulation::DoCellBirth 0 0% 26.60% 450ms 5.73% std::_Rb_tree::_M_create_node (inline) 0 0% 26.60% 419ms 5.34% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 26.60% 413ms 5.26% std::_Rb_tree::_M_get_node (inline) 2ms 0.025% 26.63% 388ms 4.94% Cell::GetMutationState 19ms 0.24% 26.87% 384ms 4.89% std::less::operator() (inline) 37ms 0.47% 27.34% 380ms 4.84% std::_Rb_tree::~_Rb_tree (inline) 1ms 0.013% 27.35% 377ms 4.80% NodeLocationWriter::Visit 23ms 0.29% 27.65% 375ms 4.78% std::_Rb_tree::_M_insert_ (inline) 365ms 4.65% 32.30% 365ms 4.65% std::operator< (inline) 0 0% 32.30% 360ms 4.59% std::set::~set (inline) 1ms 0.013% 32.31% 341ms 4.34% MeshBasedCellPopulation::GetDampingConstant 4ms 0.051% 32.36% 340ms 4.33% AbstractCentreBasedCellPopulation::GetDampingConstant 18ms 0.23% 32.59% 338ms 4.31% std::_Rb_tree::_Rb_tree (partial-inline) 82ms 1.04% 33.63% 333ms 4.24% std::_Rb_tree::_M_erase 6ms 0.076% 33.71% 330ms 4.20% Element::Element 19ms 0.24% 33.95% 322ms 4.10% std::num_put::_M_insert_float 312ms 3.98% 37.93% 312ms 3.98% std::_Rb_tree::_S_right (inline) 3ms 0.038% 37.97% 304ms 3.87% std::set::set (inline) 1ms 0.013% 37.98% 300ms 3.82% Cell::ReadyToDivide 40ms 0.51% 38.49% 291ms 3.71% std::_Rb_tree::_M_copy (inline) 101ms 1.29% 39.78% 274ms 3.49% __GI___libc_free 177ms 2.26% 42.03% 273ms 3.48% _int_malloc 10ms 0.13% 42.16% 271ms 3.45% AbstractCellPopulation::IsCellAttachedToLocationIndex 0 0% 42.16% 268ms 3.41% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 1ms 0.013% 42.17% 266ms 3.39% AbstractCellBasedWriter::OpenOutputFileForAppend 0 0% 42.17% 262ms 3.34% OutputFileHandler::OpenOutputFile 10ms 0.13% 42.30% 256ms 3.26% divconqrecurse 4ms 0.051% 42.35% 254ms 3.24% CellProliferativeTypesWriter::VisitCell 3ms 0.038% 42.39% 252ms 3.21% std::__cxx11::collate::do_transform 84ms 1.07% 43.46% 247ms 3.15% std::_Rb_tree::_M_clone_node (inline) 10ms 0.13% 43.59% 243ms 3.10% CellPropertyCollection::HasProperty 0 0% 43.59% 240ms 3.06% Cell::HasCellProperty (inline) 73ms 0.93% 44.52% 240ms 3.06% mergehulls 11ms 0.14% 44.66% 240ms 3.06% std::__new_allocator::deallocate (inline) 2ms 0.025% 44.68% 239ms 3.04% ___vsnprintf 0 0% 44.68% 237ms 3.02% __vsnprintf_internal (inline) 4ms 0.051% 44.73% 236ms 3.01% AbstractCellProperty::IsType (inline) 0 0% 44.73% 235ms 2.99% std::allocator_traits::deallocate (inline) 0 0% 44.73% 234ms 2.98% std::_Rb_tree::_M_drop_node (inline) 39ms 0.5% 45.23% 233ms 2.97% __printf_buffer 5ms 0.064% 45.29% 231ms 2.94% Element::RegisterWithNodes (inline) 3ms 0.038% 45.33% 226ms 2.88% Node::AddElement 5ms 0.064% 45.39% 196ms 2.50% AbstractPhaseBasedCellCycleModel::ReadyToDivide 0 0% 45.39% 192ms 2.45% std::_Rb_tree::_M_put_node (inline) 11ms 0.14% 45.53% 188ms 2.40% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 20ms 0.25% 45.79% 186ms 2.37% TetrahedralMesh::Clear 58ms 0.74% 46.53% 183ms 2.33% std::_Rb_tree::_M_get_insert_unique_pos (inline) 8ms 0.1% 46.63% 180ms 2.29% MeshBasedCellPopulation::SpringsEnd (inline) 1ms 0.013% 46.64% 176ms 2.24% __printf_fp_spec (inline) 6ms 0.076% 46.72% 175ms 2.23% __printf_fp_l_buffer 148ms 1.89% 48.60% 172ms 2.19% _int_free 57ms 0.73% 49.33% 167ms 2.13% AbstractCellProperty::IsSame 0 0% 49.33% 165ms 2.10% OutputFileHandler::CommonConstructor 0 0% 49.33% 165ms 2.10% OutputFileHandler::OutputFileHandler 85ms 1.08% 50.41% 159ms 2.03% __printf_fp_buffer_1 0 0% 50.41% 158ms 2.01% OutputFileHandler::MakeFoldersAndReturnFullPath 39ms 0.5% 50.91% 149ms 1.90% std::num_put::_M_insert_int 9ms 0.11% 51.03% 147ms 1.87% AbstractTetrahedralElement::CalculateJacobian 36ms 0.46% 51.48% 140ms 1.78% TetrahedralMesh::EdgesEnd (partial-inline) 5ms 0.064% 51.55% 137ms 1.75% boost::numeric::ublas::vector_assign (inline) 6ms 0.076% 51.62% 133ms 1.69% boost::numeric::ublas::c_vector::c_vector (inline) 0 0% 51.62% 131ms 1.67% AbstractCellBasedWriter::CloseFile 0 0% 51.62% 131ms 1.67% AbstractCellPopulation::CloseRoundRobinWritersFiles 1ms 0.013% 51.64% 131ms 1.67% std::basic_filebuf::close 0 0% 51.64% 131ms 1.67% std::basic_ofstream::close (inline) 25ms 0.32% 51.96% 130ms 1.66% AbstractCellPopulation::Iterator::IsRealCell (inline) 0 0% 51.96% 127ms 1.62% std::basic_ofstream::basic_ofstream (inline) 0 0% 51.96% 126ms 1.61% AbstractCellPopulation::Iterator::operator++ (inline) 20ms 0.25% 52.21% 125ms 1.59% MeshBasedCellPopulation::SpringIterator::SpringIterator 0 0% 52.21% 125ms 1.59% TetrahedralMesh::RefreshJacobianCachedData 50ms 0.64% 52.85% 125ms 1.59% std::__ostream_insert 0 0% 52.85% 124ms 1.58% std::basic_filebuf::open 0 0% 52.85% 124ms 1.58% std::basic_ofstream::open (inline) 123ms 1.57% 54.41% 123ms 1.57% std::_Rb_tree_increment 5ms 0.064% 54.48% 121ms 1.54% alternateaxes 1ms 0.013% 54.49% 120ms 1.53% AbstractTetrahedralElement::CalculateInverseJacobian 13ms 0.17% 54.66% 118ms 1.50% AbstractTetrahedralElement::RefreshJacobian 4ms 0.051% 54.71% 118ms 1.50% std::_Rb_tree_const_iterator::operator++ (inline) 0 0% 54.71% 115ms 1.47% FilesystemPermissions::SetFilePermissions (inline) 115ms 1.47% 56.17% 115ms 1.47% __GI_fchmodat 0 0% 56.17% 115ms 1.47% std::filesystem::permissions 109ms 1.39% 57.56% 115ms 1.47% vertexmedian 2ms 0.025% 57.59% 113ms 1.44% std::_Vector_base::_M_allocate (inline) 27ms 0.34% 57.93% 110ms 1.40% std::type_info::operator== (inline) 52ms 0.66% 58.59% 107ms 1.36% boost::shared_ptr::shared_ptr (inline) 74ms 0.94% 59.54% 104ms 1.33% TetrahedralMesh::EdgeIterator::EdgeIterator (partial-inline) 10ms 0.13% 59.66% 103ms 1.31% boost::detail::shared_count::~shared_count (inline) 0 0% 59.66% 103ms 1.31% boost::shared_ptr::~shared_ptr (inline) 103ms 1.31% 60.98% 103ms 1.31% std::_Rb_tree_insert_and_rebalance 4ms 0.051% 61.03% 101ms 1.29% AbstractTetrahedralElement::AbstractTetrahedralElement 5ms 0.064% 61.09% 100ms 1.27% Node::~Node 3ms 0.038% 61.13% 100ms 1.27% std::operator<< (inline) 1ms 0.013% 61.14% 98ms 1.25% std::__basic_file::open 97ms 1.24% 62.38% 97ms 1.24% [libchaste_cell_based.so] 0 0% 62.38% 97ms 1.24% _IO_new_fopen 0 0% 62.38% 97ms 1.24% __fopen_internal (inline) 70ms 0.89% 63.27% 97ms 1.24% std::basic_streambuf::xsputn 96ms 1.22% 64.49% 96ms 1.22% __GI___fstatat64 96ms 1.22% 65.72% 96ms 1.22% incircle 1ms 0.013% 65.73% 96ms 1.22% std::filesystem::status 30ms 0.38% 66.11% 95ms 1.21% boost::numeric::ublas::indexing_vector_assign 2ms 0.025% 66.14% 95ms 1.21% std::vector::push_back (inline) 0 0% 66.14% 94ms 1.20% _IO_new_file_fopen 1ms 0.013% 66.15% 94ms 1.20% __GI__IO_file_open 3ms 0.038% 66.19% 94ms 1.20% std::basic_filebuf::_M_convert_to_external 0 0% 66.19% 94ms 1.20% std::basic_filebuf::_M_terminate_output 0 0% 66.19% 94ms 1.20% std::basic_filebuf::overflow 92ms 1.17% 67.36% 92ms 1.17% __GI___libc_write 3ms 0.038% 67.40% 91ms 1.16% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (partial-inline) 0 0% 67.40% 91ms 1.16% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 0 0% 67.40% 91ms 1.16% std::__basic_file::xsputn 40ms 0.51% 67.91% 89ms 1.13% AbstractElement::GetNodeLocation 4ms 0.051% 67.96% 88ms 1.12% std::vector::_M_realloc_insert 85ms 1.08% 69.04% 86ms 1.10% boost::detail::sp_counted_base::release 0 0% 69.04% 84ms 1.07% FilesystemPermissions::CreateDirectoryWithPermissions (inline) 1ms 0.013% 69.05% 84ms 1.07% std::filesystem::create_directory 83ms 1.06% 70.11% 83ms 1.06% TetrahedralMesh::EdgeIterator::operator!= (partial-inline) 80ms 1.02% 71.13% 81ms 1.03% __libc_open64 2ms 0.025% 71.16% 77ms 0.98% AbstractCellPopulation::GetLocationIndexUsingCell 12ms 0.15% 71.31% 74ms 0.94% CellPropertyCollection::AddProperty 73ms 0.93% 72.24% 73ms 0.93% Node::GetIndex 55ms 0.7% 72.94% 73ms 0.93% malloc_consolidate 48ms 0.61% 73.55% 72ms 0.92% std::basic_filebuf::xsputn 69ms 0.88% 74.43% 69ms 0.88% counterclockwise 0 0% 74.43% 68ms 0.87% tcache_get (inline) 68ms 0.87% 75.30% 68ms 0.87% tcache_get_n (inline) 0 0% 75.30% 67ms 0.85% Cell::GetCellId 67ms 0.85% 76.15% 67ms 0.85% __memcpy_avx_unaligned_erms 0 0% 76.15% 66ms 0.84% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 76.15% 66ms 0.84% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 63ms 0.8% 76.95% 66ms 0.84% vertexsort 0 0% 76.95% 63ms 0.8% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 52ms 0.66% 77.61% 63ms 0.8% std::num_put::do_put 0 0% 77.61% 60ms 0.76% MeshBasedCellPopulation::SpringIterator::~SpringIterator (inline) 3ms 0.038% 77.65% 59ms 0.75% TetrahedralMesh::EdgeIterator::GetNodeA 58ms 0.74% 78.39% 58ms 0.74% Node::IsDeleted 5ms 0.064% 78.46% 58ms 0.74% TetrahedralMesh::EdgeIterator::GetNodeB 28ms 0.36% 78.81% 56ms 0.71% AbstractCellCycleModel::GetAge 31ms 0.39% 79.21% 56ms 0.71% AbstractTetrahedralMesh::GetElement 52ms 0.66% 79.87% 55ms 0.7% boost::detail::shared_count::shared_count (inline) 2ms 0.025% 79.90% 54ms 0.69% std::_Rb_tree::_M_emplace_hint_unique 6ms 0.076% 79.97% 53ms 0.68% Node::ConstructNodeAttributes (inline) 43ms 0.55% 80.52% 52ms 0.66% AbstractElement::GetNodeGlobalIndex 0 0% 80.52% 51ms 0.65% Node::ClearAppliedForce 0 0% 80.52% 51ms 0.65% boost::numeric::ublas::norm_2 (inline) 13ms 0.17% 80.69% 51ms 0.65% boost::numeric::ublas::vector_norm_2::apply (inline) 49ms 0.62% 81.31% 49ms 0.62% [libstdc++.so.6.0.33] 48ms 0.61% 81.92% 48ms 0.61% [libchaste_mesh.so] 21ms 0.27% 82.19% 46ms 0.59% boost::numeric::ublas::c_matrix::operator() (partial-inline) 46ms 0.59% 82.77% 46ms 0.59% boost::numeric::ublas::c_vector::operator() (partial-inline) 46ms 0.59% 83.36% 46ms 0.59% std::vector::size (inline) 0 0% 83.36% 45ms 0.57% std::vector::vector (inline) 44ms 0.56% 83.92% 44ms 0.56% boost::shared_ptr::operator-> (inline) 4ms 0.051% 83.97% 44ms 0.56% std::_Vector_base::_M_deallocate (inline) 42ms 0.54% 84.51% 42ms 0.54% AbstractElement::IsDeleted 42ms 0.54% 85.04% 42ms 0.54% Node::rGetLocation 0 0% 85.04% 42ms 0.54% std::_Rb_tree::_M_destroy_node (inline) 0 0% 85.04% 42ms 0.54% std::_Vector_base::_Vector_base (inline) 1ms 0.013% 85.06% 42ms 0.54% std::__new_allocator::construct (inline) 0 0% 85.06% 42ms 0.54% std::__new_allocator::destroy (inline) 0 0% 85.06% 42ms 0.54% std::allocator_traits::construct (inline) 0 0% 85.06% 42ms 0.54% std::allocator_traits::destroy (inline) 0 0% 85.06% 40ms 0.51% AbstractCentreBasedCellPopulation::IsMarkedSpring 0 0% 85.06% 40ms 0.51% std::_Vector_base::_M_create_storage (inline) 0 0% 85.06% 40ms 0.51% std::map::find (inline)