File: Test3dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 47458ms, 87.28% of 54374ms total Dropped 861 nodes (cum <= 271.87ms) flat flat% sum% cum cum% 0 0% 0% 54309ms 99.88% __libc_start_call_main 0 0% 0% 54309ms 99.88% __libc_start_main_impl 0 0% 0% 54309ms 99.88% _start 0 0% 0% 54295ms 99.85% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 54295ms 99.85% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 54295ms 99.85% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 54295ms 99.85% main 0 0% 0% 54259ms 99.79% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 54259ms 99.79% CxxTest::TestRunner::runTest (inline) 0 0% 0% 54259ms 99.79% Test3dTissueRepresentativeSimulation::Test3DHoneycombMeshWithGhostNodes 0 0% 0% 54012ms 99.33% AbstractCellBasedSimulation::Solve 0 0% 0% 45536ms 83.75% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 45483ms 83.65% MeshBasedCellPopulation::Update 0 0% 0% 25211ms 46.37% MeshBasedCellPopulation::CreateVoronoiTessellation (inline) 0 0% 0% 25211ms 46.37% MeshBasedCellPopulation::TessellateIfNeeded 204ms 0.38% 0.38% 22502ms 41.38% VertexMesh::VertexMesh 0 0% 0.38% 16666ms 30.65% MutableMesh::ReMesh 0 0% 0.38% 12958ms 23.83% tetgen::tetrahedralize 0 0% 0.38% 12826ms 23.59% tetgen::tetgenmesh::delaunizevertices 6ms 0.011% 0.39% 12822ms 23.58% tetgen::tetgenmesh::incrflipdelaunay 561ms 1.03% 1.42% 11376ms 20.92% tetgen::tetgenmesh::lawson 542ms 1% 2.41% 11059ms 20.34% TetrahedralMesh::EdgeIterator::operator++ 37ms 0.068% 2.48% 9247ms 17.01% std::set::insert (inline) 307ms 0.56% 3.05% 8796ms 16.18% VertexElement::AddFace 212ms 0.39% 3.44% 8742ms 16.08% std::_Rb_tree::_M_insert_unique 2956ms 5.44% 8.87% 8594ms 15.81% std::_Rb_tree::_M_lower_bound (inline) 230ms 0.42% 9.30% 8041ms 14.79% std::_Rb_tree::find (inline) 0 0% 9.30% 7489ms 13.77% std::set::count (inline) 118ms 0.22% 9.51% 5512ms 10.14% std::less::operator() (inline) 5450ms 10.02% 19.54% 5450ms 10.02% std::operator< (inline) 261ms 0.48% 20.02% 5207ms 9.58% std::_Rb_tree::_M_insert_ (inline) 0 0% 20.02% 4907ms 9.02% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 20.02% 4805ms 8.84% ForwardEulerNumericalMethod::UpdateAllNodePositions 4ms 0.0074% 20.02% 4770ms 8.77% AbstractNumericalMethod::ComputeForcesIncludingDamping 199ms 0.37% 20.39% 4456ms 8.20% operator new 1060ms 1.95% 22.34% 4195ms 7.72% __GI___libc_malloc 4168ms 7.67% 30.01% 4168ms 7.67% std::_Rb_tree_increment 2ms 0.0037% 30.01% 3993ms 7.34% MeshBasedCellPopulation::UpdateNodePairs 6ms 0.011% 30.02% 3927ms 7.22% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 45ms 0.083% 30.10% 3892ms 7.16% std::__new_allocator::allocate (inline) 0 0% 30.10% 3874ms 7.12% std::allocator_traits::allocate (inline) 6ms 0.011% 30.11% 3860ms 7.10% MeshBasedCellPopulation::SpringIterator::operator++ 16ms 0.029% 30.14% 3819ms 7.02% std::_Rb_tree::~_Rb_tree (inline) 1404ms 2.58% 32.73% 3802ms 6.99% std::_Rb_tree::_M_erase 0 0% 32.73% 3780ms 6.95% std::set::~set (inline) 1224ms 2.25% 34.98% 3602ms 6.62% std::_Rb_tree::_M_get_insert_unique_pos 116ms 0.21% 35.19% 3462ms 6.37% tetgen::tetgenmesh::insphere_sos 0 0% 35.19% 3381ms 6.22% AbstractCellPopulation::WriteResultsToFiles 3046ms 5.60% 40.79% 3332ms 6.13% tetgen::insphere 987ms 1.82% 42.61% 3327ms 6.12% __GI___libc_free 0 0% 42.61% 3163ms 5.82% std::_Rb_tree::_M_create_node (inline) 0 0% 42.61% 3136ms 5.77% std::_Rb_tree::_M_get_node (inline) 0 0% 42.61% 3135ms 5.77% std::_Rb_tree::_Alloc_node::operator() (inline) 30ms 0.055% 42.66% 3079ms 5.66% Node::AddElement 4ms 0.0074% 42.67% 3032ms 5.58% std::set_intersection (inline) 201ms 0.37% 43.04% 3028ms 5.57% std::__set_intersection 129ms 0.24% 43.28% 3013ms 5.54% std::__new_allocator::deallocate (inline) 0 0% 43.28% 2999ms 5.52% std::allocator_traits::deallocate (inline) 10ms 0.018% 43.29% 2957ms 5.44% TetrahedralMesh::ImportFromMesher 2183ms 4.01% 47.31% 2812ms 5.17% _int_malloc 2766ms 5.09% 52.40% 2766ms 5.09% std::_Rb_tree::_S_right (inline) 0 0% 52.40% 2722ms 5.01% VertexMesh::~VertexMesh 165ms 0.3% 52.70% 2686ms 4.94% tetgen::tetgenmesh::flip23 186ms 0.34% 53.04% 2367ms 4.35% std::_Rb_tree_const_iterator::operator++ (inline) 1179ms 2.17% 55.21% 2339ms 4.30% _int_free 211ms 0.39% 55.60% 2303ms 4.24% VertexMesh::GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex 78ms 0.14% 55.74% 2301ms 4.23% MutableElement::AddNode 1ms 0.0018% 55.74% 2286ms 4.20% MeshBasedCellPopulationWithGhostNodes::WriteVtkResultsToFile 1ms 0.0018% 55.75% 2103ms 3.87% std::_Rb_tree_iterator::operator++ (inline) 100ms 0.18% 55.93% 1979ms 3.64% Node::~Node 1869ms 3.44% 59.37% 1869ms 3.44% std::_Rb_tree_insert_and_rebalance 0 0% 59.37% 1865ms 3.43% std::_Rb_tree::_M_drop_node (inline) 0 0% 59.37% 1857ms 3.42% std::_Rb_tree::_M_put_node (inline) 142ms 0.26% 59.63% 1856ms 3.41% VertexMesh::Clear 156ms 0.29% 59.91% 1791ms 3.29% tetgen::tetgenmesh::flip32 6ms 0.011% 59.93% 1581ms 2.91% Element::Element 1401ms 2.58% 62.50% 1496ms 2.75% tetgen::orient3d 1263ms 2.32% 64.83% 1263ms 2.32% Node::GetIndex 2ms 0.0037% 64.83% 1248ms 2.30% Element::RegisterWithNodes (inline) 39ms 0.072% 64.90% 1235ms 2.27% tetgen::tetgenmesh::locate 187ms 0.34% 65.24% 1190ms 2.19% tetgen::tetgenmesh::enqueueflipface 18ms 0.033% 65.28% 1160ms 2.13% std::_Vector_base::_M_deallocate (inline) 89ms 0.16% 65.44% 1153ms 2.12% tetgen::tetgenmesh::preciselocate 659ms 1.21% 66.65% 1087ms 2.00% malloc_consolidate 0 0% 66.65% 1083ms 1.99% std::vector::~vector (inline) 69ms 0.13% 66.78% 1082ms 1.99% std::map::operator[] 131ms 0.24% 67.02% 1075ms 1.98% TetrahedralMesh::Clear 73ms 0.13% 67.16% 1000ms 1.84% std::vector::_M_realloc_insert 1ms 0.0018% 67.16% 981ms 1.80% std::_Vector_base::~_Vector_base (inline) 0 0% 67.16% 954ms 1.75% std::_Rb_tree::lower_bound (inline) 0 0% 67.16% 954ms 1.75% std::map::lower_bound (inline) 8ms 0.015% 67.17% 940ms 1.73% _int_free_maybe_consolidate 0 0% 67.17% 875ms 1.61% VoronoiDataWriter::Visit 834ms 1.53% 68.71% 834ms 1.53% unlink_chunk 102ms 0.19% 68.89% 811ms 1.49% std::vector::push_back (inline) 6ms 0.011% 68.90% 767ms 1.41% VertexMesh::GenerateVerticesFromElementCircumcentres 8ms 0.015% 68.92% 746ms 1.37% std::_Vector_base::_M_allocate (inline) 1ms 0.0018% 68.92% 739ms 1.36% TetrahedralMesh::RefreshJacobianCachedData 552ms 1.02% 69.94% 728ms 1.34% AbstractElement::GetNodeGlobalIndex 706ms 1.30% 71.23% 706ms 1.30% tetgen::tetgenmesh::triface::triface 2ms 0.0037% 71.24% 698ms 1.28% AbstractTwoBodyInteractionForce::AddForceContribution 460ms 0.85% 72.08% 696ms 1.28% tetgen::tetgenmesh::fnextself 12ms 0.022% 72.11% 672ms 1.24% AbstractTetrahedralElement::CalculateInverseJacobian 13ms 0.024% 72.13% 645ms 1.19% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 16ms 0.029% 72.16% 644ms 1.18% boost::numeric::ublas::vector_assign (inline) 643ms 1.18% 73.34% 643ms 1.18% tetgen::tetgenmesh::triface::operator= 15ms 0.028% 73.37% 639ms 1.18% AbstractTetrahedralElement::CalculateJacobian 637ms 1.17% 74.54% 637ms 1.17% [libchaste_mesh.so] 6ms 0.011% 74.55% 616ms 1.13% boost::numeric::ublas::c_vector::c_vector (inline) 49ms 0.09% 74.64% 572ms 1.05% __atan2 0 0% 74.64% 547ms 1.01% std::set::find (inline) 542ms 1% 75.64% 542ms 1% tetgen::tetgenmesh::oppo 218ms 0.4% 76.04% 540ms 0.99% AbstractElement::GetNodeLocation 407ms 0.75% 76.79% 522ms 0.96% __ieee754_atan2_fma 506ms 0.93% 77.72% 506ms 0.93% std::vector::size (inline) 0 0% 77.72% 504ms 0.93% boost::numeric::ublas::inner_prod (inline) 0 0% 77.72% 503ms 0.93% std::insert_iterator::operator= (inline) 6ms 0.011% 77.73% 500ms 0.92% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 39ms 0.072% 77.80% 494ms 0.91% boost::numeric::ublas::vector_scalar_binary::evaluate 45ms 0.083% 77.88% 467ms 0.86% tetgen::tetgenmesh::enext2fnext 46ms 0.085% 77.97% 464ms 0.85% tetgen::tetgenmesh::enextfnext 463ms 0.85% 78.82% 463ms 0.85% Node::rGetLocation 46ms 0.085% 78.91% 460ms 0.85% AbstractTetrahedralElement::RefreshJacobian 0 0% 78.91% 449ms 0.83% std::_Rb_tree::_M_insert_unique_ (inline) 26ms 0.048% 78.95% 437ms 0.8% tetgen::tetgenmesh::queue::push 114ms 0.21% 79.16% 433ms 0.8% boost::numeric::ublas::indexing_vector_assign 280ms 0.51% 79.68% 431ms 0.79% tetgen::tetgenmesh::sym 243ms 0.45% 80.12% 430ms 0.79% AbstractTetrahedralMesh::GetElement 427ms 0.79% 80.91% 427ms 0.79% boost::numeric::ublas::c_vector::operator() 417ms 0.77% 81.68% 417ms 0.77% tetgen::tetgenmesh::pointmark 19ms 0.035% 81.71% 414ms 0.76% Element::CalculateCircumsphere 6ms 0.011% 81.72% 410ms 0.75% boost::numeric::ublas::c_vector::operator= (inline) 345ms 0.63% 82.36% 410ms 0.75% tetgen::tetgenmesh::link::add 171ms 0.31% 82.67% 392ms 0.72% boost::numeric::ublas::vector_inner_prod::apply (inline) 0 0% 82.67% 387ms 0.71% VertexMeshWriter::WriteVtkUsingMesh 382ms 0.7% 83.37% 382ms 0.7% tetgen::tetgenmesh::org 26ms 0.048% 83.42% 381ms 0.7% std::_Rb_tree_iterator::operator-- (inline) 365ms 0.67% 84.09% 365ms 0.67% AbstractElement::IsDeleted 25ms 0.046% 84.14% 364ms 0.67% VertexMesh::CalculateUnitNormalToFaceWithArea 94ms 0.17% 84.31% 356ms 0.65% __dynamic_cast 4ms 0.0074% 84.32% 344ms 0.63% CellPropertyCollection::GetPropertiesType (inline) 3ms 0.0055% 84.33% 343ms 0.63% Cell::GetCellId 260ms 0.48% 84.80% 334ms 0.61% tetgen::tetgenmesh::bond 333ms 0.61% 85.42% 333ms 0.61% std::_Rb_tree_decrement 8ms 0.015% 85.43% 328ms 0.6% AbstractTetrahedralElement::AbstractTetrahedralElement 45ms 0.083% 85.51% 327ms 0.6% tetgen::tetgenmesh::queue::pop 50ms 0.092% 85.61% 322ms 0.59% boost::numeric::ublas::vector_reference::operator() (inline) 15ms 0.028% 85.63% 320ms 0.59% std::vector::insert (inline) 3ms 0.0055% 85.64% 317ms 0.58% VertexElement::~VertexElement 113ms 0.21% 85.85% 303ms 0.56% Inverse 2ms 0.0037% 85.85% 298ms 0.55% tcache_get (inline) 296ms 0.54% 86.39% 296ms 0.54% tcache_get_n (inline) 36ms 0.066% 86.46% 286ms 0.53% tetgen::insphereadapt 228ms 0.42% 86.88% 280ms 0.51% tetgen::tetgenmesh::link::deletenode 2ms 0.0037% 86.88% 277ms 0.51% AbstractCellProperty::IsSubType (inline) 216ms 0.4% 87.28% 274ms 0.5% boost::numeric::ublas::c_matrix::operator() 0 0% 87.28% 272ms 0.5% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline)