File: Test2dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 5944ms, 82.96% of 7165ms total Dropped 589 nodes (cum <= 35.83ms) flat flat% sum% cum cum% 0 0% 0% 7129ms 99.50% __libc_start_call_main 0 0% 0% 7129ms 99.50% __libc_start_main_impl 0 0% 0% 7129ms 99.50% _start 0 0% 0% 7115ms 99.30% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 7115ms 99.30% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 7115ms 99.30% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 7115ms 99.30% main 0 0% 0% 7080ms 98.81% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 7080ms 98.81% CxxTest::TestRunner::runTest (inline) 0 0% 0% 7080ms 98.81% Test2DMonolayerRepresentativeSimulation::Test2DMonolayerRepresentativeSimulationForProfiling 1ms 0.014% 0.014% 7077ms 98.77% AbstractCellBasedSimulation::Solve 1ms 0.014% 0.028% 2839ms 39.62% AbstractCellPopulation::WriteResultsToFiles 1ms 0.014% 0.042% 2729ms 38.09% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0.042% 2279ms 31.81% MeshBasedCellPopulation::Update 0 0% 0.042% 1499ms 20.92% OffLatticeSimulation::UpdateCellLocationsAndTopology 1ms 0.014% 0.056% 1399ms 19.53% MutableMesh::ReMesh 0 0% 0.056% 1376ms 19.20% ForwardEulerNumericalMethod::UpdateAllNodePositions 6ms 0.084% 0.14% 1330ms 18.56% AbstractNumericalMethod::ComputeForcesIncludingDamping 3ms 0.042% 0.18% 950ms 13.26% AbstractTwoBodyInteractionForce::AddForceContribution 265ms 3.70% 3.88% 919ms 12.83% __dynamic_cast 12ms 0.17% 4.05% 891ms 12.44% CellPropertyCollection::GetPropertiesType (inline) 8ms 0.11% 4.16% 887ms 12.38% CellPopulationElementWriter::Visit 2ms 0.028% 4.19% 880ms 12.28% AbstractCentreBasedCellPopulation::AcceptCellWritersAcrossPopulation 34ms 0.47% 4.66% 861ms 12.02% GeneralisedLinearSpringForce::CalculateForceBetweenNodes (partial-inline) 4ms 0.056% 4.72% 844ms 11.78% MeshBasedCellPopulation::UpdateNodePairs 33ms 0.46% 5.18% 758ms 10.58% AbstractCellPopulation::GetCellUsingLocationIndex 3ms 0.042% 5.22% 749ms 10.45% MeshBasedCellPopulation::AcceptCellWriter 9ms 0.13% 5.35% 749ms 10.45% TetrahedralMesh::ImportFromMesher 5ms 0.07% 5.42% 704ms 9.83% AbstractCellProperty::IsSubType (inline) 28ms 0.39% 5.81% 632ms 8.82% MeshBasedCellPopulation::SpringIterator::operator++ 42ms 0.59% 6.39% 600ms 8.37% std::map::operator[] (partial-inline) 2ms 0.028% 6.42% 592ms 8.26% std::ostream::operator<< (inline) 79ms 1.10% 7.52% 590ms 8.23% std::ostream::_M_insert 531ms 7.41% 14.93% 531ms 7.41% __strcmp_avx2 249ms 3.48% 18.41% 528ms 7.37% std::_Rb_tree::_M_lower_bound (inline) 2ms 0.028% 18.44% 526ms 7.34% Cell::GetCellProliferativeType 2ms 0.028% 18.46% 502ms 7.01% triangulate 0 0% 18.46% 500ms 6.98% std::_Rb_tree::lower_bound (inline) 0 0% 18.46% 500ms 6.98% std::map::lower_bound (inline) 30ms 0.42% 18.88% 493ms 6.88% operator new 196ms 2.74% 21.62% 467ms 6.52% __cxxabiv1::__si_class_type_info::__do_dyncast 3ms 0.042% 21.66% 460ms 6.42% LegacyCellProliferativeTypesWriter::VisitCell 163ms 2.27% 23.94% 458ms 6.39% __GI___libc_malloc 27ms 0.38% 24.31% 443ms 6.18% std::__new_allocator::allocate (inline) 1ms 0.014% 24.33% 438ms 6.11% delaunay 0 0% 24.33% 438ms 6.11% std::allocator_traits::allocate (inline) 6ms 0.084% 24.41% 435ms 6.07% AbstractCellBasedSimulation::DoCellBirth 3ms 0.042% 24.45% 435ms 6.07% divconqdelaunay 1ms 0.014% 24.47% 399ms 5.57% NodeLocationWriter::Visit 3ms 0.042% 24.51% 371ms 5.18% Cell::GetMutationState 45ms 0.63% 25.14% 361ms 5.04% TetrahedralMesh::EdgeIterator::operator++ 27ms 0.38% 25.51% 358ms 5.00% std::_Rb_tree::~_Rb_tree (inline) 27ms 0.38% 25.89% 350ms 4.88% std::num_put::_M_insert_float 0 0% 25.89% 335ms 4.68% std::set::~set (inline) 73ms 1.02% 26.91% 331ms 4.62% std::_Rb_tree::_M_erase 0 0% 26.91% 330ms 4.61% std::_Rb_tree::_M_create_node (inline) 97ms 1.35% 28.26% 314ms 4.38% __GI___libc_free 307ms 4.28% 32.55% 307ms 4.28% std::_Rb_tree::_S_right (inline) 1ms 0.014% 32.56% 306ms 4.27% std::set::set (inline) 16ms 0.22% 32.78% 304ms 4.24% std::_Rb_tree::_Rb_tree 0 0% 32.78% 299ms 4.17% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 0 0% 32.78% 298ms 4.16% AbstractCellBasedWriter::OpenOutputFileForAppend 5ms 0.07% 32.85% 297ms 4.15% Cell::ReadyToDivide 0 0% 32.85% 295ms 4.12% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 32.85% 294ms 4.10% OutputFileHandler::OpenOutputFile 3ms 0.042% 32.90% 292ms 4.08% AbstractCentreBasedCellPopulation::GetDampingConstant 0 0% 32.90% 292ms 4.08% MeshBasedCellPopulation::GetDampingConstant 0 0% 32.90% 291ms 4.06% std::_Rb_tree::_M_get_node (inline) 9ms 0.13% 33.02% 284ms 3.96% AbstractCellPopulation::IsCellAttachedToLocationIndex 2ms 0.028% 33.05% 281ms 3.92% std::__cxx11::collate::do_transform 2ms 0.028% 33.08% 280ms 3.91% Element::Element 17ms 0.24% 33.31% 275ms 3.84% std::__new_allocator::deallocate (inline) 35ms 0.49% 33.80% 273ms 3.81% std::_Rb_tree::_M_copy (inline) 0 0% 33.80% 272ms 3.80% std::allocator_traits::deallocate (inline) 8ms 0.11% 33.91% 269ms 3.75% ___vsnprintf 15ms 0.21% 34.12% 269ms 3.75% divconqrecurse 2ms 0.028% 34.15% 261ms 3.64% __vsnprintf_internal (inline) 1ms 0.014% 34.17% 253ms 3.53% CellProliferativeTypesWriter::VisitCell 23ms 0.32% 34.49% 252ms 3.52% __printf_buffer 75ms 1.05% 35.53% 244ms 3.41% mergehulls 0 0% 35.53% 241ms 3.36% std::_Rb_tree::_M_drop_node (inline) 2ms 0.028% 35.56% 234ms 3.27% std::_Rb_tree::_M_insert_unique (inline) 0 0% 35.56% 234ms 3.27% std::set::insert (inline) 66ms 0.92% 36.48% 232ms 3.24% std::_Rb_tree::_M_clone_node (inline) 21ms 0.29% 36.78% 230ms 3.21% TetrahedralMesh::Clear 174ms 2.43% 39.20% 217ms 3.03% _int_free 160ms 2.23% 41.44% 217ms 3.03% _int_malloc 1ms 0.014% 41.45% 209ms 2.92% AbstractPhaseBasedCellCycleModel::ReadyToDivide 9ms 0.13% 41.58% 207ms 2.89% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 4ms 0.056% 41.63% 206ms 2.88% AbstractCellProperty::IsType (inline) 4ms 0.056% 41.69% 206ms 2.88% __printf_fp_spec (inline) 0 0% 41.69% 204ms 2.85% Cell::HasCellProperty (inline) 5ms 0.07% 41.76% 204ms 2.85% CellPropertyCollection::HasProperty 15ms 0.21% 41.97% 202ms 2.82% __printf_fp_l_buffer 6ms 0.084% 42.05% 195ms 2.72% Element::RegisterWithNodes (inline) 13ms 0.18% 42.23% 193ms 2.69% MeshBasedCellPopulation::SpringsEnd 0 0% 42.23% 188ms 2.62% std::_Rb_tree::_M_put_node (inline) 3ms 0.042% 42.27% 185ms 2.58% Node::AddElement 99ms 1.38% 43.66% 182ms 2.54% __printf_fp_buffer_1 17ms 0.24% 43.89% 182ms 2.54% std::_Rb_tree::_M_insert_ (inline) 0 0% 43.89% 155ms 2.16% std::basic_ofstream::basic_ofstream (inline) 40ms 0.56% 44.45% 151ms 2.11% AbstractCellProperty::IsSame 0 0% 44.45% 150ms 2.09% AbstractCellBasedWriter::CloseFile 0 0% 44.45% 150ms 2.09% AbstractCellPopulation::CloseRoundRobinWritersFiles 0 0% 44.45% 150ms 2.09% std::basic_filebuf::close 0 0% 44.45% 150ms 2.09% std::basic_ofstream::close (inline) 1ms 0.014% 44.47% 149ms 2.08% std::basic_filebuf::open 0 0% 44.47% 149ms 2.08% std::basic_ofstream::open (inline) 2ms 0.028% 44.49% 147ms 2.05% boost::numeric::ublas::vector_assign (inline) 6ms 0.084% 44.58% 143ms 2.00% boost::numeric::ublas::c_vector::c_vector (inline) 2ms 0.028% 44.61% 142ms 1.98% OutputFileHandler::OutputFileHandler 13ms 0.18% 44.79% 141ms 1.97% AbstractTetrahedralElement::CalculateJacobian 26ms 0.36% 45.15% 141ms 1.97% TetrahedralMesh::EdgesEnd (partial-inline) 0 0% 45.15% 140ms 1.95% OutputFileHandler::CommonConstructor 60ms 0.84% 45.99% 137ms 1.91% std::__ostream_insert 0 0% 45.99% 136ms 1.90% TetrahedralMesh::RefreshJacobianCachedData 0 0% 45.99% 135ms 1.88% OutputFileHandler::MakeFoldersAndReturnFullPath 11ms 0.15% 46.14% 128ms 1.79% Node::~Node 0 0% 46.14% 128ms 1.79% std::_Hashtable::count (inline) 1ms 0.014% 46.15% 128ms 1.79% std::_Hashtable::find (inline) 0 0% 46.15% 128ms 1.79% std::unordered_set::count (inline) 0 0% 46.15% 127ms 1.77% _IO_new_fopen 0 0% 46.15% 127ms 1.77% __fopen_internal (inline) 0 0% 46.15% 127ms 1.77% std::__basic_file::open 4ms 0.056% 46.21% 126ms 1.76% std::vector::push_back (inline) 7ms 0.098% 46.31% 124ms 1.73% AbstractTetrahedralElement::CalculateInverseJacobian 34ms 0.47% 46.78% 124ms 1.73% MeshBasedCellPopulation::SpringIterator::SpringIterator 0 0% 46.78% 124ms 1.73% _IO_new_file_fopen 0 0% 46.78% 124ms 1.73% __GI__IO_file_open 0 0% 46.78% 119ms 1.66% FilesystemPermissions::SetFilePermissions (inline) 0 0% 46.78% 119ms 1.66% std::filesystem::permissions 5ms 0.07% 46.85% 118ms 1.65% std::vector::_M_realloc_insert 116ms 1.62% 48.47% 116ms 1.62% __GI_fchmodat 9ms 0.13% 48.60% 116ms 1.62% std::_Rb_tree_const_iterator::operator++ (inline) 2ms 0.028% 48.63% 115ms 1.61% std::basic_filebuf::_M_terminate_output 114ms 1.59% 50.22% 114ms 1.59% std::_Rb_tree_increment 29ms 0.4% 50.62% 114ms 1.59% std::num_put::_M_insert_int 113ms 1.58% 52.20% 113ms 1.58% incircle 0 0% 52.20% 113ms 1.58% std::basic_filebuf::overflow 29ms 0.4% 52.60% 112ms 1.56% boost::numeric::ublas::indexing_vector_assign 2ms 0.028% 52.63% 112ms 1.56% std::basic_filebuf::_M_convert_to_external 111ms 1.55% 54.18% 111ms 1.55% __libc_open64 1ms 0.014% 54.19% 111ms 1.55% std::operator<< (inline) 22ms 0.31% 54.50% 111ms 1.55% std::type_info::operator== (inline) 50ms 0.7% 55.20% 110ms 1.54% boost::shared_ptr::shared_ptr (inline) 1ms 0.014% 55.21% 109ms 1.52% std::__basic_file::xsputn 107ms 1.49% 56.71% 108ms 1.51% __GI___libc_write 15ms 0.21% 56.92% 103ms 1.44% AbstractCellPopulation::Iterator::IsRealCell (inline) 1ms 0.014% 56.93% 103ms 1.44% AbstractCellPopulation::Iterator::operator++ (inline) 43ms 0.6% 57.53% 99ms 1.38% std::_Hashtable::_M_find_before_node (inline) 0 0% 57.53% 99ms 1.38% std::_Hashtable::_M_find_node (inline) 3ms 0.042% 57.57% 99ms 1.38% std::_Vector_base::_M_allocate (inline) 7ms 0.098% 57.67% 97ms 1.35% boost::detail::shared_count::~shared_count (inline) 0 0% 57.67% 97ms 1.35% boost::shared_ptr::~shared_ptr (inline) 8ms 0.11% 57.78% 96ms 1.34% AbstractTetrahedralElement::RefreshJacobian 4ms 0.056% 57.84% 96ms 1.34% alternateaxes 0 0% 57.84% 96ms 1.34% std::_Hashtable::_M_insert (inline) 8ms 0.11% 57.95% 96ms 1.34% std::_Hashtable::_M_insert_unique_aux (inline) 0 0% 57.95% 96ms 1.34% std::__detail::_Insert_base::insert (inline) 0 0% 57.95% 96ms 1.34% std::unordered_set::insert (inline) 2ms 0.028% 57.98% 94ms 1.31% AbstractTetrahedralElement::AbstractTetrahedralElement 49ms 0.68% 58.66% 93ms 1.30% TetrahedralMesh::EdgeIterator::EdgeIterator 0 0% 58.66% 92ms 1.28% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 0 0% 58.66% 92ms 1.28% std::_Hashtable::~_Hashtable (inline) 0 0% 58.66% 92ms 1.28% std::unordered_set::~unordered_set (inline) 80ms 1.12% 59.78% 90ms 1.26% vertexmedian 87ms 1.21% 60.99% 88ms 1.23% boost::detail::sp_counted_base::release 9ms 0.13% 61.12% 88ms 1.23% std::_Hashtable::_M_insert_unique 82ms 1.14% 62.26% 82ms 1.14% TetrahedralMesh::EdgeIterator::operator!= (partial-inline) 0 0% 62.26% 80ms 1.12% Cell::GetCellId 79ms 1.10% 63.36% 79ms 1.10% [libchaste_cell_based.so] 1ms 0.014% 63.38% 77ms 1.07% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 0 0% 63.38% 77ms 1.07% FilesystemPermissions::CreateDirectoryWithPermissions (inline) 0 0% 63.38% 77ms 1.07% std::filesystem::create_directory 33ms 0.46% 63.84% 76ms 1.06% AbstractElement::GetNodeLocation 54ms 0.75% 64.59% 73ms 1.02% std::basic_streambuf::xsputn 5ms 0.07% 64.66% 72ms 1.00% TetrahedralMesh::EdgeIterator::GetNodeB 0 0% 64.66% 72ms 1.00% tcache_get (inline) 72ms 1.00% 65.67% 72ms 1.00% tcache_get_n (inline) 48ms 0.67% 66.34% 71ms 0.99% std::basic_filebuf::xsputn 5ms 0.07% 66.41% 70ms 0.98% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 70ms 0.98% 67.38% 70ms 0.98% Node::GetIndex 0 0% 67.38% 68ms 0.95% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 67.38% 68ms 0.95% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 3ms 0.042% 67.42% 67ms 0.94% std::filesystem::status 66ms 0.92% 68.35% 66ms 0.92% std::vector::size (inline) 51ms 0.71% 69.06% 65ms 0.91% AbstractElement::GetNodeGlobalIndex 65ms 0.91% 69.97% 65ms 0.91% __memcpy_avx_unaligned_erms 64ms 0.89% 70.86% 64ms 0.89% __GI___fstatat64 2ms 0.028% 70.89% 63ms 0.88% TetrahedralMesh::EdgeIterator::GetNodeA 60ms 0.84% 71.72% 63ms 0.88% vertexsort 0 0% 71.72% 62ms 0.87% MeshBasedCellPopulation::SpringIterator::~SpringIterator (inline) 6ms 0.084% 71.81% 61ms 0.85% std::_Hashtable::clear (inline) 1ms 0.014% 71.82% 60ms 0.84% AbstractCellPopulation::GetLocationIndexUsingCell 60ms 0.84% 72.66% 60ms 0.84% boost::detail::shared_count::shared_count (inline) 7ms 0.098% 72.76% 58ms 0.81% Node::ConstructNodeAttributes (inline) 58ms 0.81% 73.57% 58ms 0.81% [libchaste_mesh.so] 1ms 0.014% 73.58% 58ms 0.81% std::_Rb_tree::_M_emplace_hint_unique 6ms 0.084% 73.66% 57ms 0.8% CellPropertyCollection::AddProperty 55ms 0.77% 74.43% 55ms 0.77% boost::numeric::ublas::c_vector::operator() (partial-inline) 36ms 0.5% 74.93% 55ms 0.77% malloc_consolidate 54ms 0.75% 75.69% 54ms 0.75% counterclockwise 4ms 0.056% 75.74% 54ms 0.75% std::__detail::_Hashtable_base::_M_equals (inline) 1ms 0.014% 75.76% 53ms 0.74% Node::ClearAppliedForce 34ms 0.47% 76.23% 53ms 0.74% boost::numeric::ublas::c_matrix::operator() 0 0% 76.23% 53ms 0.74% std::_Rb_tree::_M_destroy_node (inline) 0 0% 76.23% 53ms 0.74% std::__new_allocator::destroy (inline) 0 0% 76.23% 53ms 0.74% std::allocator_traits::destroy (inline) 4ms 0.056% 76.29% 52ms 0.73% Element::~Element 44ms 0.61% 76.90% 52ms 0.73% std::num_put::do_put 0 0% 76.90% 51ms 0.71% AbstractCentreBasedCellPopulation::CreateCellPair 0 0% 76.90% 50ms 0.7% AbstractTetrahedralElement::~AbstractTetrahedralElement (inline) 24ms 0.33% 77.24% 50ms 0.7% std::_Rb_tree::_M_get_insert_unique_pos (inline) 50ms 0.7% 77.93% 50ms 0.7% std::_Rb_tree_insert_and_rebalance 21ms 0.29% 78.23% 48ms 0.67% AbstractTetrahedralMesh::GetNumAllElements 0 0% 78.23% 48ms 0.67% boost::numeric::ublas::norm_2 (inline) 16ms 0.22% 78.45% 48ms 0.67% boost::numeric::ublas::vector_norm_2::apply (inline) 48ms 0.67% 79.12% 48ms 0.67% boost::shared_ptr::operator-> (inline) 0 0% 79.12% 47ms 0.66% CellPropertyCollection::~CellPropertyCollection (inline) 14ms 0.2% 79.32% 46ms 0.64% Determinant (inline) 31ms 0.43% 79.75% 46ms 0.64% hack_digit 2ms 0.028% 79.78% 45ms 0.63% std::_Vector_base::_M_deallocate (inline) 0 0% 79.78% 45ms 0.63% std::__detail::_AllocNode::operator() (inline) 0 0% 79.78% 45ms 0.63% std::__detail::_Hashtable_alloc::_M_allocate_node (inline) 45ms 0.63% 80.40% 45ms 0.63% std::__detail::_Hashtable_base::_S_equals (inline) 0 0% 80.40% 44ms 0.61% std::__detail::_NodeBuilder::_S_build (inline) 2ms 0.028% 80.43% 43ms 0.6% std::__new_allocator::construct (inline) 0 0% 80.43% 43ms 0.6% std::allocator_traits::construct (inline) 0 0% 80.43% 42ms 0.59% MeshBasedCellPopulation::SpringIterator::GetNodeB (inline) 42ms 0.59% 81.02% 42ms 0.59% Node::IsDeleted 42ms 0.59% 81.61% 42ms 0.59% [libstdc++.so.6.0.33] 42ms 0.59% 82.19% 42ms 0.59% __GI___mkdir 1ms 0.014% 82.21% 40ms 0.56% BoundaryNodeWriter::Visit 23ms 0.32% 82.53% 40ms 0.56% CellPropertyCollection::GetProperty 0 0% 82.53% 39ms 0.54% AbstractCentreBasedCellPopulation::IsMarkedSpring 10ms 0.14% 82.67% 39ms 0.54% Inverse 0 0% 82.67% 39ms 0.54% std::_Rb_tree::_M_construct_node (inline) 16ms 0.22% 82.89% 38ms 0.53% AbstractCellCycleModel::GetAge 5ms 0.07% 82.96% 37ms 0.52% NodeAttributes::NodeAttributes 0 0% 82.96% 36ms 0.5% MeshBasedCellPopulation::SpringIterator::GetNodeA (inline)