File: Test3dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 63864ms, 87.91% of 72648ms total Dropped 867 nodes (cum <= 363.24ms) flat flat% sum% cum cum% 0 0% 0% 72585ms 99.91% __libc_start_call_main 0 0% 0% 72585ms 99.91% __libc_start_main_impl 0 0% 0% 72585ms 99.91% _start 0 0% 0% 72568ms 99.89% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 72568ms 99.89% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 72568ms 99.89% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 72568ms 99.89% main 0 0% 0% 72528ms 99.83% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 72528ms 99.83% CxxTest::TestRunner::runTest (inline) 0 0% 0% 72528ms 99.83% Test3dTissueRepresentativeSimulation::Test3DHoneycombMeshWithGhostNodes 1ms 0.0014% 0.0014% 72245ms 99.45% AbstractCellBasedSimulation::Solve 0 0% 0.0014% 60758ms 83.63% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0.0014% 60709ms 83.57% MeshBasedCellPopulation::Update 0 0% 0.0014% 37842ms 52.09% MeshBasedCellPopulation::TessellateIfNeeded 0 0% 0.0014% 37841ms 52.09% MeshBasedCellPopulation::CreateVoronoiTessellation (inline) 284ms 0.39% 0.39% 32579ms 44.85% VertexMesh::VertexMesh 0 0% 0.39% 18197ms 25.05% MutableMesh::ReMesh 541ms 0.74% 1.14% 14562ms 20.04% TetrahedralMesh::EdgeIterator::operator++ 0 0% 1.14% 12698ms 17.48% tetgen::tetrahedralize 0 0% 1.14% 12561ms 17.29% tetgen::tetgenmesh::delaunizevertices 7ms 0.0096% 1.15% 12557ms 17.28% tetgen::tetgenmesh::incrflipdelaunay 21ms 0.029% 1.18% 12149ms 16.72% std::set::insert (inline) 189ms 0.26% 1.44% 11650ms 16.04% std::_Rb_tree::_M_insert_unique 574ms 0.79% 2.23% 11086ms 15.26% tetgen::tetgenmesh::lawson 3148ms 4.33% 6.56% 11006ms 15.15% std::_Rb_tree::_M_lower_bound (inline) 502ms 0.69% 7.25% 10806ms 14.87% VertexElement::AddFace 237ms 0.33% 7.58% 10110ms 13.92% std::_Rb_tree::find (inline) 0 0% 7.58% 9532ms 13.12% std::set::count (inline) 8426ms 11.60% 19.17% 8426ms 11.60% std::_Rb_tree_increment 132ms 0.18% 19.36% 7337ms 10.10% std::less::operator() (inline) 7266ms 10.00% 29.36% 7266ms 10.00% std::operator< (inline) 279ms 0.38% 29.74% 6809ms 9.37% std::_Rb_tree::_M_insert_ (inline) 215ms 0.3% 30.04% 6754ms 9.30% operator new 1086ms 1.49% 31.53% 6482ms 8.92% __GI___libc_malloc 0 0% 31.53% 6176ms 8.50% OffLatticeSimulation::UpdateCellLocationsAndTopology 3ms 0.0041% 31.54% 6022ms 8.29% std::set_intersection (inline) 326ms 0.45% 31.99% 6019ms 8.29% std::__set_intersection 0 0% 31.99% 6001ms 8.26% ForwardEulerNumericalMethod::UpdateAllNodePositions 3ms 0.0041% 31.99% 5976ms 8.23% AbstractNumericalMethod::ComputeForcesIncludingDamping 10ms 0.014% 32.00% 5473ms 7.53% std::_Rb_tree::~_Rb_tree (inline) 2362ms 3.25% 35.25% 5461ms 7.52% std::_Rb_tree::_M_erase 26ms 0.036% 35.29% 5422ms 7.46% Node::AddElement 49ms 0.067% 35.36% 5407ms 7.44% std::__new_allocator::allocate (inline) 0 0% 35.36% 5391ms 7.42% std::set::~set (inline) 0 0% 35.36% 5375ms 7.40% std::allocator_traits::allocate (inline) 1ms 0.0014% 35.36% 5302ms 7.30% VertexMesh::~VertexMesh 194ms 0.27% 35.63% 5173ms 7.12% std::_Rb_tree_const_iterator::operator++ (inline) 0 0% 35.63% 5152ms 7.09% AbstractCellPopulation::WriteResultsToFiles 3701ms 5.09% 40.72% 5046ms 6.95% _int_malloc 5027ms 6.92% 47.64% 5027ms 6.92% std::_Rb_tree::_S_right (inline) 1ms 0.0014% 47.64% 5021ms 6.91% MeshBasedCellPopulation::UpdateNodePairs 1309ms 1.80% 49.44% 5008ms 6.89% __GI___libc_free 4ms 0.0055% 49.45% 4984ms 6.86% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 1226ms 1.69% 51.14% 4980ms 6.85% std::_Rb_tree::_M_get_insert_unique_pos 12ms 0.017% 51.15% 4835ms 6.66% MeshBasedCellPopulation::SpringIterator::operator++ 13ms 0.018% 51.17% 4399ms 6.06% TetrahedralMesh::ImportFromMesher 126ms 0.17% 51.34% 4373ms 6.02% std::__new_allocator::deallocate (inline) 0 0% 51.34% 4357ms 6.00% std::_Rb_tree::_M_create_node (inline) 0 0% 51.34% 4351ms 5.99% std::allocator_traits::deallocate (inline) 0 0% 51.34% 4320ms 5.95% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 51.34% 4302ms 5.92% std::_Rb_tree::_M_get_node (inline) 78ms 0.11% 51.45% 4074ms 5.61% MutableElement::AddNode 244ms 0.34% 51.79% 3764ms 5.18% VertexMesh::GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex 1273ms 1.75% 53.54% 3697ms 5.09% _int_free 3ms 0.0041% 53.54% 3573ms 4.92% MeshBasedCellPopulationWithGhostNodes::WriteVtkResultsToFile 0 0% 53.54% 3553ms 4.89% std::_Rb_tree_iterator::operator++ (inline) 265ms 0.36% 53.91% 3488ms 4.80% Node::~Node 90ms 0.12% 54.03% 3414ms 4.70% tetgen::tetgenmesh::insphere_sos 3037ms 4.18% 58.21% 3314ms 4.56% tetgen::insphere 283ms 0.39% 58.60% 3274ms 4.51% VertexMesh::Clear 2673ms 3.68% 62.28% 2673ms 3.68% Node::GetIndex 187ms 0.26% 62.54% 2654ms 3.65% tetgen::tetgenmesh::flip23 1669ms 2.30% 64.84% 2429ms 3.34% malloc_consolidate 2332ms 3.21% 68.05% 2332ms 3.21% std::_Rb_tree_insert_and_rebalance 14ms 0.019% 68.07% 2331ms 3.21% std::_Vector_base::_M_deallocate (inline) 4ms 0.0055% 68.07% 2224ms 3.06% Element::Element 0 0% 68.07% 2181ms 3.00% std::vector::~vector (inline) 10ms 0.014% 68.09% 2153ms 2.96% _int_free_maybe_consolidate 1ms 0.0014% 68.09% 2146ms 2.95% std::_Vector_base::~_Vector_base (inline) 0 0% 68.09% 2049ms 2.82% std::_Rb_tree::_M_drop_node (inline) 0 0% 68.09% 2034ms 2.80% std::_Rb_tree::_M_put_node (inline) 2ms 0.0028% 68.09% 1868ms 2.57% Element::RegisterWithNodes (inline) 159ms 0.22% 68.31% 1824ms 2.51% tetgen::tetgenmesh::flip32 1729ms 2.38% 70.69% 1729ms 2.38% unlink_chunk 264ms 0.36% 71.05% 1690ms 2.33% TetrahedralMesh::Clear 8ms 0.011% 71.06% 1589ms 2.19% VertexMesh::GenerateVerticesFromElementCircumcentres 1395ms 1.92% 72.98% 1483ms 2.04% tetgen::orient3d 51ms 0.07% 73.05% 1424ms 1.96% std::map::operator[] 2ms 0.0028% 73.06% 1304ms 1.79% VoronoiDataWriter::Visit 0 0% 73.06% 1296ms 1.78% std::_Rb_tree::lower_bound (inline) 0 0% 73.06% 1296ms 1.78% std::map::lower_bound (inline) 81ms 0.11% 73.17% 1284ms 1.77% std::vector::_M_realloc_insert 186ms 0.26% 73.42% 1280ms 1.76% tetgen::tetgenmesh::enqueueflipface 1136ms 1.56% 74.99% 1275ms 1.76% AbstractElement::GetNodeGlobalIndex 40ms 0.055% 75.04% 1237ms 1.70% tetgen::tetgenmesh::locate 98ms 0.13% 75.18% 1149ms 1.58% tetgen::tetgenmesh::preciselocate 3ms 0.0041% 75.18% 1076ms 1.48% std::_Vector_base::_M_allocate (inline) 1ms 0.0014% 75.18% 1061ms 1.46% TetrahedralMesh::RefreshJacobianCachedData 120ms 0.17% 75.35% 1059ms 1.46% std::vector::push_back (inline) 461ms 0.63% 75.98% 1028ms 1.42% AbstractElement::GetNodeLocation 991ms 1.36% 77.35% 991ms 1.36% Node::rGetLocation 961ms 1.32% 78.67% 961ms 1.32% AbstractElement::IsDeleted 901ms 1.24% 79.91% 901ms 1.24% tetgen::tetgenmesh::triface::triface 10ms 0.014% 79.92% 873ms 1.20% AbstractTetrahedralElement::CalculateInverseJacobian 11ms 0.015% 79.94% 833ms 1.15% AbstractTetrahedralElement::CalculateJacobian 1ms 0.0014% 79.94% 752ms 1.04% AbstractTwoBodyInteractionForce::AddForceContribution 16ms 0.022% 79.96% 727ms 1.00% Element::CalculateCircumsphere 17ms 0.023% 79.99% 709ms 0.98% boost::numeric::ublas::vector_assign (inline) 14ms 0.019% 80.00% 700ms 0.96% AbstractVariableSizeTwoBodyInteractionForce::CalculateForceBetweenNodes 375ms 0.52% 80.52% 700ms 0.96% tetgen::tetgenmesh::fnextself 665ms 0.92% 81.44% 665ms 0.92% tetgen::tetgenmesh::oppo 51ms 0.07% 81.51% 657ms 0.9% AbstractTetrahedralElement::RefreshJacobian 7ms 0.0096% 81.52% 654ms 0.9% boost::numeric::ublas::c_vector::c_vector (inline) 638ms 0.88% 82.39% 638ms 0.88% [libchaste_mesh.so] 624ms 0.86% 83.25% 624ms 0.86% std::vector::size (inline) 606ms 0.83% 84.09% 606ms 0.83% tetgen::tetgenmesh::triface::operator= 36ms 0.05% 84.14% 591ms 0.81% __atan2 0 0% 84.14% 569ms 0.78% std::set::find (inline) 462ms 0.64% 84.77% 554ms 0.76% __ieee754_atan2_fma 24ms 0.033% 84.81% 548ms 0.75% VertexMesh::CalculateUnitNormalToFaceWithArea 0 0% 84.81% 512ms 0.7% boost::numeric::ublas::inner_prod (inline) 28ms 0.039% 84.84% 509ms 0.7% boost::numeric::ublas::vector_scalar_binary::evaluate 0 0% 84.84% 509ms 0.7% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 0 0% 84.84% 501ms 0.69% std::insert_iterator::operator= (inline) 45ms 0.062% 84.91% 475ms 0.65% tetgen::tetgenmesh::enext2fnext 59ms 0.081% 84.99% 466ms 0.64% tetgen::tetgenmesh::enextfnext 0 0% 84.99% 460ms 0.63% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 0 0% 84.99% 454ms 0.62% std::_Rb_tree::_M_insert_unique_ (inline) 315ms 0.43% 85.42% 454ms 0.62% tetgen::tetgenmesh::sym 131ms 0.18% 85.60% 445ms 0.61% boost::numeric::ublas::indexing_vector_assign 436ms 0.6% 86.20% 436ms 0.6% boost::numeric::ublas::c_vector::operator() 3ms 0.0041% 86.21% 422ms 0.58% CellPropertyCollection::GetPropertiesType (inline) 205ms 0.28% 86.49% 421ms 0.58% boost::numeric::ublas::vector_inner_prod::apply (inline) 0 0% 86.49% 405ms 0.56% VertexMeshWriter::WriteVtkUsingMesh 26ms 0.036% 86.52% 403ms 0.55% std::_Rb_tree_iterator::operator-- (inline) 2ms 0.0028% 86.53% 402ms 0.55% Cell::GetCellId 95ms 0.13% 86.66% 402ms 0.55% __dynamic_cast 212ms 0.29% 86.95% 394ms 0.54% AbstractTetrahedralMesh::GetElement 3ms 0.0041% 86.95% 389ms 0.54% VertexMesh::GetVolumeOfElement 5ms 0.0069% 86.96% 384ms 0.53% boost::numeric::ublas::c_vector::operator= (inline) 374ms 0.51% 87.48% 374ms 0.51% tetgen::tetgenmesh::org 12ms 0.017% 87.49% 371ms 0.51% std::vector::insert (inline) 269ms 0.37% 87.86% 369ms 0.51% tetgen::tetgenmesh::bond 8ms 0.011% 87.87% 368ms 0.51% VertexElement::~VertexElement 26ms 0.036% 87.91% 368ms 0.51% tetgen::tetgenmesh::queue::push