File: Test3dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 42398ms, 87.15% of 48650ms total Dropped 827 nodes (cum <= 243.25ms) flat flat% sum% cum cum% 0 0% 0% 48598ms 99.89% __libc_start_call_main 0 0% 0% 48598ms 99.89% __libc_start_main_impl 0 0% 0% 48598ms 99.89% _start 0 0% 0% 48584ms 99.86% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 48584ms 99.86% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 48584ms 99.86% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 48584ms 99.86% main 0 0% 0% 48544ms 99.78% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 48544ms 99.78% CxxTest::TestRunner::runTest (inline) 0 0% 0% 48543ms 99.78% Test3dTissueRepresentativeSimulation::Test3DHoneycombMeshWithGhostNodes 0 0% 0% 48335ms 99.35% AbstractCellBasedSimulation::Solve 0 0% 0% 41103ms 84.49% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 41065ms 84.41% MeshBasedCellPopulation::Update 0 0% 0% 22069ms 45.36% MeshBasedCellPopulation::TessellateIfNeeded 0 0% 0% 22067ms 45.36% MeshBasedCellPopulation::CreateVoronoiTessellation (inline) 158ms 0.32% 0.32% 19810ms 40.72% VertexMesh::VertexMesh 0 0% 0.32% 15782ms 32.44% MutableMesh::ReMesh 0 0% 0.32% 12585ms 25.87% tetgen::tetrahedralize 0 0% 0.32% 12472ms 25.64% tetgen::tetgenmesh::delaunizevertices 2ms 0.0041% 0.33% 12470ms 25.63% tetgen::tetgenmesh::incrflipdelaunay 407ms 0.84% 1.17% 11195ms 23.01% tetgen::tetgenmesh::lawson 495ms 1.02% 2.18% 9690ms 19.92% TetrahedralMesh::EdgeIterator::operator++ 30ms 0.062% 2.24% 7940ms 16.32% std::set::insert (inline) 281ms 0.58% 2.82% 7730ms 15.89% VertexElement::AddFace 162ms 0.33% 3.16% 7565ms 15.55% std::_Rb_tree::_M_insert_unique 2546ms 5.23% 8.39% 7181ms 14.76% std::_Rb_tree::_M_lower_bound (inline) 186ms 0.38% 8.77% 6730ms 13.83% std::_Rb_tree::find (inline) 0 0% 8.77% 6260ms 12.87% std::set::count (inline) 248ms 0.51% 9.28% 4637ms 9.53% std::_Rb_tree::_M_insert_ (inline) 114ms 0.23% 9.51% 4535ms 9.32% std::less::operator() (inline) 4472ms 9.19% 18.71% 4472ms 9.19% std::operator< (inline) 0 0% 18.71% 4257ms 8.75% OffLatticeSimulation::UpdateCellLocationsAndTopology 115ms 0.24% 18.94% 4169ms 8.57% operator new 0 0% 18.94% 4139ms 8.51% ForwardEulerNumericalMethod::UpdateAllNodePositions 3ms 0.0062% 18.95% 4124ms 8.48% AbstractNumericalMethod::ComputeForcesIncludingDamping 4090ms 8.41% 27.36% 4090ms 8.41% std::_Rb_tree_increment 1183ms 2.43% 29.79% 3996ms 8.21% __GI___libc_malloc 33ms 0.068% 29.86% 3641ms 7.48% std::__new_allocator::allocate (inline) 0 0% 29.86% 3620ms 7.44% std::allocator_traits::allocate (inline) 0 0% 29.86% 3493ms 7.18% MeshBasedCellPopulation::UpdateNodePairs 7ms 0.014% 29.87% 3433ms 7.06% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 6ms 0.012% 29.88% 3373ms 6.93% MeshBasedCellPopulation::SpringIterator::operator++ 7ms 0.014% 29.90% 3211ms 6.60% std::_Rb_tree::~_Rb_tree (inline) 1185ms 2.44% 32.33% 3204ms 6.59% std::_Rb_tree::_M_erase 0 0% 32.33% 3182ms 6.54% std::set::~set (inline) 1ms 0.0021% 32.34% 3094ms 6.36% std::set_intersection (inline) 178ms 0.37% 32.70% 3093ms 6.36% std::__set_intersection 0 0% 32.70% 2998ms 6.16% std::_Rb_tree::_M_create_node (inline) 1020ms 2.10% 34.80% 2991ms 6.15% std::_Rb_tree::_M_get_insert_unique_pos 0 0% 34.80% 2967ms 6.10% std::_Rb_tree::_M_get_node (inline) 0 0% 34.80% 2966ms 6.10% std::_Rb_tree::_Alloc_node::operator() (inline) 86ms 0.18% 34.97% 2935ms 6.03% tetgen::tetgenmesh::insphere_sos 958ms 1.97% 36.94% 2929ms 6.02% __GI___libc_free 0 0% 36.94% 2856ms 5.87% AbstractCellPopulation::WriteResultsToFiles 2609ms 5.36% 42.31% 2834ms 5.83% tetgen::insphere 102ms 0.21% 42.52% 2723ms 5.60% tetgen::tetgenmesh::flip23 7ms 0.014% 42.53% 2604ms 5.35% TetrahedralMesh::ImportFromMesher 132ms 0.27% 42.80% 2542ms 5.23% std::_Rb_tree_const_iterator::operator++ (inline) 97ms 0.2% 43.00% 2529ms 5.20% std::__new_allocator::deallocate (inline) 0 0% 43.00% 2521ms 5.18% std::allocator_traits::deallocate (inline) 1834ms 3.77% 46.77% 2511ms 5.16% _int_malloc 30ms 0.062% 46.83% 2480ms 5.10% Node::AddElement 0 0% 46.83% 2272ms 4.67% VertexMesh::~VertexMesh 2270ms 4.67% 51.50% 2270ms 4.67% std::_Rb_tree::_S_right (inline) 104ms 0.21% 51.71% 2037ms 4.19% tetgen::tetgenmesh::flip32 54ms 0.11% 51.82% 1982ms 4.07% MutableElement::AddNode 991ms 2.04% 53.86% 1970ms 4.05% _int_free 3ms 0.0062% 53.87% 1954ms 4.02% MeshBasedCellPopulationWithGhostNodes::WriteVtkResultsToFile 129ms 0.27% 54.13% 1914ms 3.93% VertexMesh::GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex 121ms 0.25% 54.38% 1828ms 3.76% Node::~Node 0 0% 54.38% 1797ms 3.69% std::_Rb_tree_iterator::operator++ (inline) 0 0% 54.38% 1586ms 3.26% std::_Rb_tree::_M_drop_node (inline) 0 0% 54.38% 1577ms 3.24% std::_Rb_tree::_M_put_node (inline) 143ms 0.29% 54.67% 1550ms 3.19% VertexMesh::Clear 1473ms 3.03% 57.70% 1473ms 3.03% std::_Rb_tree_insert_and_rebalance 152ms 0.31% 58.01% 1466ms 3.01% tetgen::tetgenmesh::enqueueflipface 1287ms 2.65% 60.66% 1287ms 2.65% Node::GetIndex 1188ms 2.44% 63.10% 1262ms 2.59% tetgen::orient3d 72ms 0.15% 63.25% 1226ms 2.52% TetrahedralMesh::Clear 6ms 0.012% 63.26% 1158ms 2.38% Element::Element 21ms 0.043% 63.31% 1045ms 2.15% tetgen::tetgenmesh::locate 75ms 0.15% 63.46% 984ms 2.02% tetgen::tetgenmesh::preciselocate 18ms 0.037% 63.50% 962ms 1.98% std::_Vector_base::_M_deallocate (inline) 580ms 1.19% 64.69% 951ms 1.95% malloc_consolidate 0 0% 64.69% 919ms 1.89% std::vector::~vector (inline) 54ms 0.11% 64.80% 895ms 1.84% std::map::operator[] 4ms 0.0082% 64.81% 892ms 1.83% Element::RegisterWithNodes (inline) 892ms 1.83% 66.64% 892ms 1.83% tetgen::tetgenmesh::triface::triface 51ms 0.1% 66.75% 858ms 1.76% std::vector::_M_realloc_insert 829ms 1.70% 68.45% 829ms 1.70% unlink_chunk 1ms 0.0021% 68.45% 827ms 1.70% std::_Vector_base::~_Vector_base (inline) 5ms 0.01% 68.46% 800ms 1.64% _int_free_maybe_consolidate 628ms 1.29% 69.75% 784ms 1.61% AbstractElement::GetNodeGlobalIndex 0 0% 69.75% 783ms 1.61% std::_Rb_tree::lower_bound (inline) 0 0% 69.75% 783ms 1.61% std::map::lower_bound (inline) 771ms 1.58% 71.34% 771ms 1.58% tetgen::tetgenmesh::oppo 0 0% 71.34% 707ms 1.45% VoronoiDataWriter::Visit 84ms 0.17% 71.51% 677ms 1.39% std::vector::push_back (inline) 664ms 1.36% 72.88% 664ms 1.36% [libchaste_mesh.so] 3ms 0.0062% 72.88% 656ms 1.35% std::_Vector_base::_M_allocate (inline) 254ms 0.52% 73.40% 650ms 1.34% tetgen::tetgenmesh::sym 1ms 0.0021% 73.41% 637ms 1.31% VertexMesh::GenerateVerticesFromElementCircumcentres 0 0% 73.41% 580ms 1.19% TetrahedralMesh::RefreshJacobianCachedData 338ms 0.69% 74.10% 573ms 1.18% tetgen::tetgenmesh::fnextself 0 0% 74.10% 561ms 1.15% AbstractTwoBodyInteractionForce::AddForceContribution 7ms 0.014% 74.12% 529ms 1.09% AbstractTetrahedralElement::CalculateInverseJacobian 529ms 1.09% 75.20% 529ms 1.09% tetgen::tetgenmesh::triface::operator= 11ms 0.023% 75.23% 528ms 1.09% AbstractVariableSizeTwoBodyInteractionForce::CalculateForceBetweenNodes 11ms 0.023% 75.25% 512ms 1.05% AbstractTetrahedralElement::CalculateJacobian 44ms 0.09% 75.34% 489ms 1.01% tetgen::tetgenmesh::enextfnext 10ms 0.021% 75.36% 480ms 0.99% boost::numeric::ublas::vector_assign (inline) 196ms 0.4% 75.76% 479ms 0.98% tetgen::tetgenmesh::bond 42ms 0.086% 75.85% 471ms 0.97% __atan2 31ms 0.064% 75.91% 461ms 0.95% tetgen::tetgenmesh::queue::push 0 0% 75.91% 460ms 0.95% std::set::find (inline) 6ms 0.012% 75.92% 455ms 0.94% boost::numeric::ublas::c_vector::c_vector (inline) 451ms 0.93% 76.85% 451ms 0.93% std::vector::size (inline) 47ms 0.097% 76.95% 449ms 0.92% tetgen::tetgenmesh::enext2fnext 190ms 0.39% 77.34% 434ms 0.89% AbstractElement::GetNodeLocation 255ms 0.52% 77.86% 429ms 0.88% tetgen::tetgenmesh::link::add 323ms 0.66% 78.53% 426ms 0.88% __ieee754_atan2_fma 417ms 0.86% 79.38% 417ms 0.86% tetgen::tetgenmesh::decode 409ms 0.84% 80.22% 409ms 0.84% Node::rGetLocation 403ms 0.83% 81.05% 403ms 0.83% tetgen::tetgenmesh::org 392ms 0.81% 81.86% 392ms 0.81% AbstractElement::IsDeleted 0 0% 81.86% 384ms 0.79% std::insert_iterator::operator= (inline) 0 0% 81.86% 383ms 0.79% boost::numeric::ublas::inner_prod (inline) 1ms 0.0021% 81.86% 380ms 0.78% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 27ms 0.055% 81.92% 379ms 0.78% boost::numeric::ublas::vector_scalar_binary::evaluate 29ms 0.06% 81.98% 355ms 0.73% AbstractTetrahedralElement::RefreshJacobian 92ms 0.19% 82.16% 347ms 0.71% tetgen::tetgenmesh::queue::pop 0 0% 82.16% 342ms 0.7% std::_Rb_tree::_M_insert_unique_ (inline) 163ms 0.34% 82.50% 335ms 0.69% AbstractTetrahedralMesh::GetElement 10ms 0.021% 82.52% 334ms 0.69% Element::CalculateCircumsphere 333ms 0.68% 83.20% 333ms 0.68% tetgen::tetgenmesh::pointmark 13ms 0.027% 83.23% 330ms 0.68% VertexMesh::CalculateUnitNormalToFaceWithArea 18ms 0.037% 83.27% 326ms 0.67% std::_Rb_tree_iterator::operator-- (inline) 4ms 0.0082% 83.28% 319ms 0.66% CellPropertyCollection::GetPropertiesType (inline) 0 0% 83.28% 319ms 0.66% VertexMeshWriter::WriteVtkUsingMesh 73ms 0.15% 83.43% 311ms 0.64% __dynamic_cast 116ms 0.24% 83.66% 307ms 0.63% boost::numeric::ublas::vector_inner_prod::apply (inline) 1ms 0.0021% 83.67% 306ms 0.63% Cell::GetCellId 2ms 0.0041% 83.67% 305ms 0.63% boost::numeric::ublas::c_vector::operator= (inline) 296ms 0.61% 84.28% 296ms 0.61% boost::numeric::ublas::c_vector::operator() 76ms 0.16% 84.44% 291ms 0.6% boost::numeric::ublas::indexing_vector_assign 5ms 0.01% 84.45% 287ms 0.59% VertexElement::~VertexElement 0 0% 84.45% 286ms 0.59% AbstractTetrahedralElement::~AbstractTetrahedralElement (inline) 1ms 0.0021% 84.45% 286ms 0.59% Element::~Element 11ms 0.023% 84.47% 286ms 0.59% std::vector::insert (inline) 285ms 0.59% 85.06% 285ms 0.59% std::_Rb_tree_decrement 272ms 0.56% 85.62% 272ms 0.56% tetgen::tetgenmesh::encode 0 0% 85.62% 270ms 0.55% tcache_get (inline) 270ms 0.55% 86.17% 270ms 0.55% tcache_get_n (inline) 0 0% 86.17% 267ms 0.55% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 1ms 0.0021% 86.17% 266ms 0.55% AbstractCellProperty::IsSubType (inline) 3ms 0.0062% 86.18% 263ms 0.54% AbstractTetrahedralElement::AbstractTetrahedralElement 261ms 0.54% 86.72% 261ms 0.54% tetgen::tetgenmesh::face::face 211ms 0.43% 87.15% 252ms 0.52% tetgen::tetgenmesh::link::deletenode