File: Test2dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 6681ms, 84.75% of 7883ms total Dropped 596 nodes (cum <= 39.41ms) flat flat% sum% cum cum% 0 0% 0% 7849ms 99.57% __libc_start_call_main 0 0% 0% 7849ms 99.57% __libc_start_main_impl 0 0% 0% 7849ms 99.57% _start 0 0% 0% 7835ms 99.39% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 7835ms 99.39% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 7835ms 99.39% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 7835ms 99.39% main 0 0% 0% 7798ms 98.92% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 7798ms 98.92% CxxTest::TestRunner::runTest (inline) 0 0% 0% 7798ms 98.92% Test2DMonolayerRepresentativeSimulation::Test2DMonolayerRepresentativeSimulationForProfiling 0 0% 0% 7795ms 98.88% AbstractCellBasedSimulation::Solve 0 0% 0% 3291ms 41.75% AbstractCellBasedSimulation::UpdateCellPopulation 1ms 0.013% 0.013% 2883ms 36.57% AbstractCellPopulation::WriteResultsToFiles 2ms 0.025% 0.038% 2842ms 36.05% MeshBasedCellPopulation::Update 2ms 0.025% 0.063% 1605ms 20.36% OffLatticeSimulation::UpdateCellLocationsAndTopology 2ms 0.025% 0.089% 1442ms 18.29% ForwardEulerNumericalMethod::UpdateAllNodePositions 2ms 0.025% 0.11% 1405ms 17.82% MutableMesh::ReMesh 1ms 0.013% 0.13% 1380ms 17.51% MeshBasedCellPopulation::UpdateNodePairs 2ms 0.025% 0.15% 1376ms 17.46% AbstractNumericalMethod::ComputeForcesIncludingDamping 21ms 0.27% 0.42% 1211ms 15.36% MeshBasedCellPopulation::SpringIterator::operator++ 432ms 5.48% 5.90% 1011ms 12.83% std::_Rb_tree::_M_lower_bound (inline) 133ms 1.69% 7.59% 979ms 12.42% TetrahedralMesh::EdgeIterator::operator++ 3ms 0.038% 7.62% 953ms 12.09% AbstractTwoBodyInteractionForce::AddForceContribution 2ms 0.025% 7.65% 931ms 11.81% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 5ms 0.063% 7.71% 901ms 11.43% CellPopulationElementWriter::Visit 10ms 0.13% 7.84% 897ms 11.38% CellPropertyCollection::GetPropertiesType (inline) 267ms 3.39% 11.23% 882ms 11.19% __dynamic_cast 43ms 0.55% 11.77% 850ms 10.78% GeneralisedLinearSpringForce::CalculateForceBetweenNodes (partial-inline) 33ms 0.42% 12.19% 809ms 10.26% AbstractCellPopulation::GetCellUsingLocationIndex 7ms 0.089% 12.28% 774ms 9.82% MeshBasedCellPopulation::AcceptCellWriter 11ms 0.14% 12.42% 718ms 9.11% TetrahedralMesh::ImportFromMesher 6ms 0.076% 12.50% 698ms 8.85% AbstractCellProperty::IsSubType (inline) 48ms 0.61% 13.10% 638ms 8.09% std::map::operator[] (partial-inline) 0 0% 13.10% 578ms 7.33% std::ostream::operator<< (inline) 97ms 1.23% 14.33% 576ms 7.31% std::ostream::_M_insert 0 0% 14.33% 535ms 6.79% std::_Rb_tree::lower_bound (inline) 0 0% 14.33% 535ms 6.79% std::map::lower_bound (inline) 0 0% 14.33% 534ms 6.77% triangulate 41ms 0.52% 14.85% 532ms 6.75% operator new 21ms 0.27% 15.12% 528ms 6.70% std::_Rb_tree::find (inline) 5ms 0.063% 15.18% 514ms 6.52% Cell::GetCellProliferativeType 502ms 6.37% 21.55% 502ms 6.37% __strcmp_avx2 7ms 0.089% 21.64% 498ms 6.32% std::set::insert (inline) 164ms 2.08% 23.72% 492ms 6.24% __GI___libc_malloc 8ms 0.1% 23.82% 491ms 6.23% std::_Rb_tree::_M_insert_unique 5ms 0.063% 23.89% 477ms 6.05% LegacyCellProliferativeTypesWriter::VisitCell 0 0% 23.89% 476ms 6.04% std::set::count (inline) 32ms 0.41% 24.29% 473ms 6.00% std::__new_allocator::allocate (inline) 0 0% 24.29% 469ms 5.95% std::allocator_traits::allocate (inline) 0 0% 24.29% 465ms 5.90% delaunay 0 0% 24.29% 464ms 5.89% divconqdelaunay 193ms 2.45% 26.74% 443ms 5.62% __cxxabiv1::__si_class_type_info::__do_dyncast 34ms 0.43% 27.17% 440ms 5.58% std::_Rb_tree::~_Rb_tree (inline) 2ms 0.025% 27.20% 433ms 5.49% AbstractCellBasedSimulation::DoCellBirth 0 0% 27.20% 412ms 5.23% std::set::~set (inline) 81ms 1.03% 28.23% 406ms 5.15% std::_Rb_tree::_M_erase 0 0% 28.23% 404ms 5.12% std::_Rb_tree::_M_create_node (inline) 6ms 0.076% 28.30% 388ms 4.92% Cell::GetMutationState 0 0% 28.30% 380ms 4.82% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 28.30% 373ms 4.73% std::_Rb_tree::_M_get_node (inline) 18ms 0.23% 28.53% 370ms 4.69% std::less::operator() (inline) 3ms 0.038% 28.57% 366ms 4.64% NodeLocationWriter::Visit 364ms 4.62% 33.19% 364ms 4.62% std::_Rb_tree::_S_right (inline) 352ms 4.47% 37.65% 352ms 4.47% std::operator< (inline) 20ms 0.25% 37.90% 348ms 4.41% std::_Rb_tree::_Rb_tree (partial-inline) 0 0% 37.90% 333ms 4.22% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 0 0% 37.90% 332ms 4.21% AbstractCellBasedWriter::OpenOutputFileForAppend 0 0% 37.90% 329ms 4.17% OutputFileHandler::OpenOutputFile 2ms 0.025% 37.93% 325ms 4.12% AbstractCentreBasedCellPopulation::GetDampingConstant 0 0% 37.93% 325ms 4.12% MeshBasedCellPopulation::GetDampingConstant 20ms 0.25% 38.18% 319ms 4.05% std::num_put::_M_insert_float 2ms 0.025% 38.21% 315ms 4.00% std::set::set (inline) 96ms 1.22% 39.43% 302ms 3.83% __GI___libc_free 7ms 0.089% 39.52% 300ms 3.81% AbstractCellPopulation::IsCellAttachedToLocationIndex 4ms 0.051% 39.57% 300ms 3.81% Element::Element 38ms 0.48% 40.05% 300ms 3.81% std::_Rb_tree::_M_copy (inline) 21ms 0.27% 40.31% 300ms 3.81% std::_Rb_tree::_M_insert_ (inline) 0 0% 40.31% 299ms 3.79% std::_Rb_tree::_M_drop_node (inline) 1ms 0.013% 40.33% 279ms 3.54% Cell::ReadyToDivide 9ms 0.11% 40.44% 277ms 3.51% std::__new_allocator::deallocate (inline) 0 0% 40.44% 273ms 3.46% std::allocator_traits::deallocate (inline) 8ms 0.1% 40.54% 267ms 3.39% divconqrecurse 79ms 1.00% 41.55% 259ms 3.29% std::_Rb_tree::_M_clone_node (inline) 170ms 2.16% 43.70% 256ms 3.25% _int_malloc 3ms 0.038% 43.74% 251ms 3.18% std::__cxx11::collate::do_transform 2ms 0.025% 43.77% 248ms 3.15% CellProliferativeTypesWriter::VisitCell 76ms 0.96% 44.73% 248ms 3.15% mergehulls 2ms 0.025% 44.75% 237ms 3.01% ___vsnprintf 1ms 0.013% 44.77% 235ms 2.98% __vsnprintf_internal (inline) 0 0% 44.77% 233ms 2.96% std::_Rb_tree::_M_put_node (inline) 32ms 0.41% 45.17% 228ms 2.89% __printf_buffer 2ms 0.025% 45.20% 214ms 2.71% AbstractCellProperty::IsType (inline) 0 0% 45.20% 214ms 2.71% Cell::HasCellProperty (inline) 4ms 0.051% 45.25% 214ms 2.71% CellPropertyCollection::HasProperty 27ms 0.34% 45.59% 213ms 2.70% TetrahedralMesh::Clear 174ms 2.21% 47.80% 204ms 2.59% _int_free 5ms 0.063% 47.86% 198ms 2.51% Element::RegisterWithNodes (inline) 5ms 0.063% 47.93% 191ms 2.42% Node::AddElement 2ms 0.025% 47.95% 189ms 2.40% AbstractPhaseBasedCellCycleModel::ReadyToDivide 15ms 0.19% 48.14% 184ms 2.33% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 60ms 0.76% 48.90% 183ms 2.32% std::_Rb_tree::_M_get_insert_unique_pos (inline) 11ms 0.14% 49.04% 177ms 2.25% MeshBasedCellPopulation::SpringsEnd (inline) 2ms 0.025% 49.07% 176ms 2.23% __printf_fp_spec (inline) 9ms 0.11% 49.18% 174ms 2.21% __printf_fp_l_buffer 47ms 0.6% 49.78% 169ms 2.14% AbstractCellProperty::IsSame 4ms 0.051% 49.83% 166ms 2.11% boost::numeric::ublas::vector_assign (inline) 16ms 0.2% 50.03% 161ms 2.04% AbstractTetrahedralElement::CalculateJacobian 5ms 0.063% 50.10% 161ms 2.04% boost::numeric::ublas::c_vector::c_vector (inline) 40ms 0.51% 50.60% 156ms 1.98% TetrahedralMesh::EdgesEnd (partial-inline) 79ms 1.00% 51.60% 156ms 1.98% __printf_fp_buffer_1 0 0% 51.60% 155ms 1.97% std::basic_ofstream::basic_ofstream (inline) 0 0% 51.60% 148ms 1.88% std::basic_ofstream::open (inline) 0 0% 51.60% 147ms 1.86% std::basic_filebuf::open 61ms 0.77% 52.38% 137ms 1.74% std::__ostream_insert 0 0% 52.38% 135ms 1.71% OutputFileHandler::CommonConstructor 0 0% 52.38% 135ms 1.71% OutputFileHandler::OutputFileHandler 0 0% 52.38% 134ms 1.70% FilesystemPermissions::SetFilePermissions (inline) 0 0% 52.38% 134ms 1.70% TetrahedralMesh::RefreshJacobianCachedData 133ms 1.69% 54.07% 133ms 1.69% __GI_fchmodat 0 0% 54.07% 133ms 1.69% std::filesystem::permissions 11ms 0.14% 54.21% 132ms 1.67% Node::~Node 1ms 0.013% 54.22% 130ms 1.65% OutputFileHandler::MakeFoldersAndReturnFullPath 44ms 0.56% 54.78% 128ms 1.62% boost::numeric::ublas::indexing_vector_assign 15ms 0.19% 54.97% 127ms 1.61% AbstractCellPopulation::Iterator::IsRealCell (inline) 0 0% 54.97% 127ms 1.61% AbstractCellPopulation::Iterator::operator++ (inline) 10ms 0.13% 55.09% 127ms 1.61% boost::detail::shared_count::~shared_count (inline) 0 0% 55.09% 127ms 1.61% boost::shared_ptr::~shared_ptr (inline) 1ms 0.013% 55.11% 125ms 1.59% AbstractTetrahedralElement::CalculateInverseJacobian 12ms 0.15% 55.26% 125ms 1.59% std::_Rb_tree_const_iterator::operator++ (inline) 32ms 0.41% 55.66% 122ms 1.55% std::type_info::operator== (inline) 1ms 0.013% 55.68% 119ms 1.51% AbstractCellPopulation::CloseRoundRobinWritersFiles 118ms 1.50% 57.17% 118ms 1.50% std::_Rb_tree_increment 0 0% 57.17% 116ms 1.47% AbstractCellBasedWriter::CloseFile 15ms 0.19% 57.36% 116ms 1.47% AbstractTetrahedralElement::RefreshJacobian 0 0% 57.36% 116ms 1.47% std::__basic_file::open 1ms 0.013% 57.38% 116ms 1.47% std::basic_filebuf::close 0 0% 57.38% 116ms 1.47% std::basic_ofstream::close (inline) 0 0% 57.38% 115ms 1.46% _IO_new_fopen 0 0% 57.38% 115ms 1.46% __fopen_internal (inline) 3ms 0.038% 57.41% 114ms 1.45% alternateaxes 114ms 1.45% 58.86% 114ms 1.45% boost::detail::sp_counted_base::release 0 0% 58.86% 113ms 1.43% _IO_new_file_fopen 1ms 0.013% 58.87% 113ms 1.43% __GI__IO_file_open 100ms 1.27% 60.14% 110ms 1.40% vertexmedian 53ms 0.67% 60.81% 109ms 1.38% boost::shared_ptr::shared_ptr (inline) 5ms 0.063% 60.88% 109ms 1.38% std::operator<< (inline) 3ms 0.038% 60.92% 106ms 1.34% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (partial-inline) 2ms 0.025% 60.94% 106ms 1.34% AbstractTetrahedralElement::AbstractTetrahedralElement 18ms 0.23% 61.17% 102ms 1.29% std::num_put::_M_insert_int 10ms 0.13% 61.30% 101ms 1.28% MeshBasedCellPopulation::SpringIterator::SpringIterator 101ms 1.28% 62.58% 101ms 1.28% incircle 1ms 0.013% 62.59% 99ms 1.26% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 98ms 1.24% 63.83% 99ms 1.26% __libc_open64 2ms 0.025% 63.86% 98ms 1.24% std::_Vector_base::_M_allocate (inline) 4ms 0.051% 63.91% 98ms 1.24% std::vector::push_back (inline) 66ms 0.84% 64.75% 97ms 1.23% TetrahedralMesh::EdgeIterator::EdgeIterator (partial-inline) 95ms 1.21% 65.95% 95ms 1.21% std::_Rb_tree_insert_and_rebalance 94ms 1.19% 67.14% 94ms 1.19% [libchaste_cell_based.so] 4ms 0.051% 67.20% 90ms 1.14% AbstractCellPopulation::GetLocationIndexUsingCell 41ms 0.52% 67.72% 88ms 1.12% AbstractElement::GetNodeLocation 0 0% 67.72% 86ms 1.09% std::basic_filebuf::_M_terminate_output 11ms 0.14% 67.85% 86ms 1.09% std::vector::_M_realloc_insert 85ms 1.08% 68.93% 85ms 1.08% __GI___libc_write 1ms 0.013% 68.95% 85ms 1.08% std::__basic_file::xsputn 0 0% 68.95% 85ms 1.08% std::basic_filebuf::_M_convert_to_external 0 0% 68.95% 85ms 1.08% std::basic_filebuf::overflow 66ms 0.84% 69.78% 80ms 1.01% std::basic_streambuf::xsputn 1ms 0.013% 69.80% 78ms 0.99% Cell::GetCellId 77ms 0.98% 70.77% 77ms 0.98% TetrahedralMesh::EdgeIterator::operator!= (partial-inline) 61ms 0.77% 71.55% 72ms 0.91% vertexsort 2ms 0.025% 71.57% 70ms 0.89% TetrahedralMesh::EdgeIterator::GetNodeA 0 0% 71.57% 69ms 0.88% tcache_get (inline) 69ms 0.88% 72.45% 69ms 0.88% tcache_get_n (inline) 67ms 0.85% 73.30% 67ms 0.85% counterclockwise 44ms 0.56% 73.86% 67ms 0.85% std::basic_filebuf::xsputn 0 0% 73.86% 66ms 0.84% std::_Rb_tree::_M_destroy_node (inline) 0 0% 73.86% 66ms 0.84% std::__new_allocator::destroy (inline) 0 0% 73.86% 66ms 0.84% std::allocator_traits::destroy (inline) 48ms 0.61% 74.46% 65ms 0.82% malloc_consolidate 1ms 0.013% 74.48% 64ms 0.81% FilesystemPermissions::CreateDirectoryWithPermissions (inline) 10ms 0.13% 74.60% 63ms 0.8% CellPropertyCollection::AddProperty 9ms 0.11% 74.72% 63ms 0.8% TetrahedralMesh::EdgeIterator::GetNodeB 1ms 0.013% 74.73% 63ms 0.8% std::filesystem::create_directory 63ms 0.8% 75.53% 63ms 0.8% std::vector::size (inline) 61ms 0.77% 76.30% 61ms 0.77% Node::GetIndex 42ms 0.53% 76.84% 61ms 0.77% boost::numeric::ublas::c_matrix::operator() (partial-inline) 0 0% 76.84% 60ms 0.76% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 76.84% 60ms 0.76% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 2ms 0.025% 76.86% 58ms 0.74% std::filesystem::status 2ms 0.025% 76.89% 56ms 0.71% BoundaryNodeWriter::Visit 53ms 0.67% 77.56% 56ms 0.71% boost::detail::shared_count::shared_count (inline) 40ms 0.51% 78.07% 55ms 0.7% AbstractElement::GetNodeGlobalIndex 55ms 0.7% 78.76% 55ms 0.7% __GI___fstatat64 55ms 0.7% 79.46% 55ms 0.7% __memcpy_avx_unaligned_erms 55ms 0.7% 80.16% 55ms 0.7% boost::numeric::ublas::c_vector::operator() 1ms 0.013% 80.17% 55ms 0.7% std::_Rb_tree::_M_emplace_hint_unique 54ms 0.69% 80.86% 54ms 0.69% [libchaste_mesh.so] 42ms 0.53% 81.39% 54ms 0.69% std::num_put::do_put 5ms 0.063% 81.45% 53ms 0.67% Node::ConstructNodeAttributes (inline) 1ms 0.013% 81.47% 52ms 0.66% AbstractCentreBasedCellPopulation::CreateCellPair 18ms 0.23% 81.69% 52ms 0.66% Determinant (inline) 0 0% 81.69% 49ms 0.62% Node::ClearAppliedForce 0 0% 81.69% 48ms 0.61% std::vector::vector (inline) 0 0% 81.69% 47ms 0.6% std::map::find (inline) 0 0% 81.69% 46ms 0.58% std::_Vector_base::_Vector_base (inline) 0 0% 81.69% 45ms 0.57% boost::numeric::ublas::norm_2 (inline) 12ms 0.15% 81.85% 45ms 0.57% boost::numeric::ublas::vector_norm_2::apply (inline) 45ms 0.57% 82.42% 45ms 0.57% boost::shared_ptr::operator-> (inline) 30ms 0.38% 82.80% 44ms 0.56% AbstractTetrahedralMesh::GetElement 14ms 0.18% 82.98% 44ms 0.56% AbstractTetrahedralMesh::GetNumAllElements 18ms 0.23% 83.20% 43ms 0.55% AbstractCellCycleModel::GetAge 43ms 0.55% 83.75% 43ms 0.55% Node::IsDeleted 0 0% 83.75% 43ms 0.55% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 25ms 0.32% 84.07% 43ms 0.55% hack_digit 4ms 0.051% 84.12% 43ms 0.55% std::_Vector_base::_M_deallocate (inline) 0 0% 84.12% 42ms 0.53% std::_Vector_base::_M_create_storage (inline) 0 0% 84.12% 41ms 0.52% MeshBasedCellPopulation::SpringIterator::~SpringIterator (inline) 7ms 0.089% 84.21% 40ms 0.51% Inverse 3ms 0.038% 84.24% 40ms 0.51% std::__new_allocator::construct (inline) 0 0% 84.24% 40ms 0.51% std::allocator_traits::construct (inline) 40ms 0.51% 84.75% 40ms 0.51% std::ostream::sentry::sentry