File: Test3dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 51086ms, 86.69% of 58928ms total Dropped 865 nodes (cum <= 294.64ms) flat flat% sum% cum cum% 0 0% 0% 58859ms 99.88% __libc_start_call_main 0 0% 0% 58859ms 99.88% __libc_start_main_impl 0 0% 0% 58859ms 99.88% _start 0 0% 0% 58843ms 99.86% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 58843ms 99.86% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 58843ms 99.86% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 58843ms 99.86% main 0 0% 0% 58806ms 99.79% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 58806ms 99.79% CxxTest::TestRunner::runTest (inline) 0 0% 0% 58806ms 99.79% Test3dTissueRepresentativeSimulation::Test3DHoneycombMeshWithGhostNodes 1ms 0.0017% 0.0017% 58543ms 99.35% AbstractCellBasedSimulation::Solve 0 0% 0.0017% 49944ms 84.75% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0.0017% 49891ms 84.66% MeshBasedCellPopulation::Update 0 0% 0.0017% 29230ms 49.60% MeshBasedCellPopulation::CreateVoronoiTessellation (inline) 0 0% 0.0017% 29230ms 49.60% MeshBasedCellPopulation::TessellateIfNeeded 221ms 0.38% 0.38% 25507ms 43.29% VertexMesh::VertexMesh 0 0% 0.38% 16876ms 28.64% MutableMesh::ReMesh 0 0% 0.38% 12786ms 21.70% tetgen::tetrahedralize 4ms 0.0068% 0.38% 12652ms 21.47% tetgen::tetgenmesh::delaunizevertices 10ms 0.017% 0.4% 12646ms 21.46% tetgen::tetgenmesh::incrflipdelaunay 561ms 0.95% 1.35% 11648ms 19.77% TetrahedralMesh::EdgeIterator::operator++ 545ms 0.92% 2.28% 11193ms 18.99% tetgen::tetgenmesh::lawson 32ms 0.054% 2.33% 10031ms 17.02% std::set::insert (inline) 191ms 0.32% 2.66% 9524ms 16.16% std::_Rb_tree::_M_insert_unique 380ms 0.64% 3.30% 9303ms 15.79% VertexElement::AddFace 3029ms 5.14% 8.44% 8721ms 14.80% std::_Rb_tree::_M_lower_bound (inline) 245ms 0.42% 8.86% 8193ms 13.90% std::_Rb_tree::find (inline) 0 0% 8.86% 7560ms 12.83% std::set::count (inline) 272ms 0.46% 9.32% 5609ms 9.52% std::_Rb_tree::_M_insert_ (inline) 134ms 0.23% 9.55% 5538ms 9.40% std::less::operator() (inline) 5461ms 9.27% 18.81% 5461ms 9.27% std::operator< (inline) 187ms 0.32% 19.13% 5195ms 8.82% operator new 0 0% 19.13% 5132ms 8.71% OffLatticeSimulation::UpdateCellLocationsAndTopology 5038ms 8.55% 27.68% 5038ms 8.55% std::_Rb_tree_increment 1ms 0.0017% 27.68% 5011ms 8.50% ForwardEulerNumericalMethod::UpdateAllNodePositions 6ms 0.01% 27.69% 4986ms 8.46% AbstractNumericalMethod::ComputeForcesIncludingDamping 1077ms 1.83% 29.52% 4927ms 8.36% __GI___libc_malloc 48ms 0.081% 29.60% 4337ms 7.36% std::__new_allocator::allocate (inline) 10ms 0.017% 29.62% 4322ms 7.33% std::_Rb_tree::~_Rb_tree (inline) 1642ms 2.79% 32.40% 4311ms 7.32% std::_Rb_tree::_M_erase 0 0% 32.40% 4311ms 7.32% std::allocator_traits::allocate (inline) 0 0% 32.40% 4265ms 7.24% std::set::~set (inline) 2ms 0.0034% 32.41% 4143ms 7.03% MeshBasedCellPopulation::UpdateNodePairs 11ms 0.019% 32.43% 4134ms 7.02% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 4ms 0.0068% 32.43% 4107ms 6.97% std::set_intersection (inline) 253ms 0.43% 32.86% 4103ms 6.96% std::__set_intersection 1137ms 1.93% 34.79% 4101ms 6.96% __GI___libc_free 1225ms 2.08% 36.87% 4031ms 6.84% std::_Rb_tree::_M_get_insert_unique_pos 13ms 0.022% 36.89% 3998ms 6.78% MeshBasedCellPopulation::SpringIterator::operator++ 27ms 0.046% 36.94% 3782ms 6.42% Node::AddElement 0 0% 36.94% 3750ms 6.36% VertexMesh::~VertexMesh 133ms 0.23% 37.16% 3645ms 6.19% std::__new_allocator::deallocate (inline) 0 0% 37.16% 3628ms 6.16% std::allocator_traits::deallocate (inline) 2641ms 4.48% 41.65% 3525ms 5.98% _int_malloc 118ms 0.2% 41.85% 3498ms 5.94% tetgen::tetgenmesh::insphere_sos 0 0% 41.85% 3494ms 5.93% std::_Rb_tree::_M_create_node (inline) 0 0% 41.85% 3455ms 5.86% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 41.85% 3451ms 5.86% std::_Rb_tree::_M_get_node (inline) 3421ms 5.81% 47.65% 3421ms 5.81% std::_Rb_tree::_S_right (inline) 3097ms 5.26% 52.91% 3368ms 5.72% tetgen::insphere 169ms 0.29% 53.19% 3366ms 5.71% std::_Rb_tree_const_iterator::operator++ (inline) 0 0% 53.19% 3306ms 5.61% AbstractCellPopulation::WriteResultsToFiles 11ms 0.019% 53.21% 3269ms 5.55% TetrahedralMesh::ImportFromMesher 62ms 0.11% 53.32% 2968ms 5.04% MutableElement::AddNode 1233ms 2.09% 55.41% 2956ms 5.02% _int_free 196ms 0.33% 55.74% 2737ms 4.64% tetgen::tetgenmesh::flip23 174ms 0.3% 56.04% 2476ms 4.20% Node::~Node 191ms 0.32% 56.36% 2327ms 3.95% VertexMesh::Clear 2ms 0.0034% 56.37% 2180ms 3.70% MeshBasedCellPopulationWithGhostNodes::WriteVtkResultsToFile 204ms 0.35% 56.71% 2135ms 3.62% VertexMesh::GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex 1966ms 3.34% 60.05% 1966ms 3.34% std::_Rb_tree_insert_and_rebalance 0 0% 60.05% 1949ms 3.31% std::_Rb_tree_iterator::operator++ (inline) 0 0% 60.05% 1943ms 3.30% std::_Rb_tree::_M_drop_node (inline) 0 0% 60.05% 1929ms 3.27% std::_Rb_tree::_M_put_node (inline) 168ms 0.29% 60.33% 1887ms 3.20% tetgen::tetgenmesh::flip32 22ms 0.037% 60.37% 1721ms 2.92% std::_Vector_base::_M_deallocate (inline) 1147ms 1.95% 62.32% 1711ms 2.90% malloc_consolidate 0 0% 62.32% 1581ms 2.68% std::vector::~vector (inline) 5ms 0.0085% 62.33% 1574ms 2.67% Element::Element 1534ms 2.60% 64.93% 1534ms 2.60% Node::GetIndex 0 0% 64.93% 1521ms 2.58% std::_Vector_base::~_Vector_base (inline) 8ms 0.014% 64.94% 1502ms 2.55% _int_free_maybe_consolidate 1322ms 2.24% 67.19% 1419ms 2.41% tetgen::orient3d 186ms 0.32% 67.50% 1331ms 2.26% TetrahedralMesh::Clear 4ms 0.0068% 67.51% 1292ms 2.19% Element::RegisterWithNodes (inline) 184ms 0.31% 67.82% 1237ms 2.10% tetgen::tetgenmesh::enqueueflipface 42ms 0.071% 67.89% 1230ms 2.09% tetgen::tetgenmesh::locate 1173ms 1.99% 69.88% 1173ms 1.99% unlink_chunk 5ms 0.0085% 69.89% 1150ms 1.95% VertexMesh::GenerateVerticesFromElementCircumcentres 98ms 0.17% 70.06% 1139ms 1.93% tetgen::tetgenmesh::preciselocate 47ms 0.08% 70.14% 1102ms 1.87% std::vector::_M_realloc_insert 58ms 0.098% 70.23% 1094ms 1.86% std::map::operator[] 0 0% 70.23% 963ms 1.63% std::_Rb_tree::lower_bound (inline) 0 0% 70.23% 963ms 1.63% std::map::lower_bound (inline) 825ms 1.40% 71.63% 954ms 1.62% AbstractElement::GetNodeGlobalIndex 914ms 1.55% 73.19% 914ms 1.55% tetgen::tetgenmesh::triface::triface 112ms 0.19% 73.38% 892ms 1.51% std::vector::push_back (inline) 0 0% 73.38% 888ms 1.51% VoronoiDataWriter::Visit 4ms 0.0068% 73.38% 864ms 1.47% std::_Vector_base::_M_allocate (inline) 475ms 0.81% 74.19% 851ms 1.44% tetgen::tetgenmesh::fnextself 0 0% 74.19% 805ms 1.37% TetrahedralMesh::RefreshJacobianCachedData 19ms 0.032% 74.22% 735ms 1.25% boost::numeric::ublas::vector_assign (inline) 9ms 0.015% 74.24% 714ms 1.21% AbstractTetrahedralElement::CalculateInverseJacobian 11ms 0.019% 74.26% 703ms 1.19% boost::numeric::ublas::c_vector::c_vector (inline) 1ms 0.0017% 74.26% 693ms 1.18% AbstractTwoBodyInteractionForce::AddForceContribution 299ms 0.51% 74.76% 678ms 1.15% AbstractElement::GetNodeLocation 672ms 1.14% 75.90% 672ms 1.14% [libchaste_mesh.so] 12ms 0.02% 75.92% 656ms 1.11% AbstractVariableSizeTwoBodyInteractionForce::CalculateForceBetweenNodes 0 0% 75.92% 630ms 1.07% std::set::find (inline) 44ms 0.075% 76.00% 623ms 1.06% __atan2 12ms 0.02% 76.02% 593ms 1.01% AbstractTetrahedralElement::CalculateJacobian 593ms 1.01% 77.03% 593ms 1.01% tetgen::tetgenmesh::triface::operator= 592ms 1.00% 78.03% 592ms 1.00% AbstractElement::IsDeleted 23ms 0.039% 78.07% 588ms 1% Element::CalculateCircumsphere 468ms 0.79% 78.86% 579ms 0.98% __ieee754_atan2_fma 573ms 0.97% 79.84% 573ms 0.97% tetgen::tetgenmesh::oppo 60ms 0.1% 79.94% 564ms 0.96% tetgen::tetgenmesh::enextfnext 529ms 0.9% 80.84% 529ms 0.9% std::vector::size (inline) 528ms 0.9% 81.73% 528ms 0.9% Node::rGetLocation 0 0% 81.73% 497ms 0.84% std::insert_iterator::operator= (inline) 30ms 0.051% 81.78% 496ms 0.84% tetgen::tetgenmesh::enext2fnext 40ms 0.068% 81.85% 462ms 0.78% AbstractTetrahedralElement::RefreshJacobian 113ms 0.19% 82.04% 457ms 0.78% boost::numeric::ublas::indexing_vector_assign 312ms 0.53% 82.57% 457ms 0.78% tetgen::tetgenmesh::sym 0 0% 82.57% 453ms 0.77% std::_Rb_tree::_M_insert_unique_ (inline) 0 0% 82.57% 424ms 0.72% boost::numeric::ublas::inner_prod (inline) 2ms 0.0034% 82.58% 423ms 0.72% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 32ms 0.054% 82.63% 421ms 0.71% boost::numeric::ublas::vector_scalar_binary::evaluate 16ms 0.027% 82.66% 410ms 0.7% VertexMesh::CalculateUnitNormalToFaceWithArea 400ms 0.68% 83.34% 400ms 0.68% tetgen::tetgenmesh::org 2ms 0.0034% 83.34% 398ms 0.68% boost::numeric::ublas::c_vector::operator= (inline) 282ms 0.48% 83.82% 398ms 0.68% tetgen::tetgenmesh::bond 395ms 0.67% 84.49% 395ms 0.67% boost::numeric::ublas::c_vector::operator() 0 0% 84.49% 390ms 0.66% VertexMeshWriter::WriteVtkUsingMesh 92ms 0.16% 84.64% 390ms 0.66% __dynamic_cast 2ms 0.0034% 84.65% 387ms 0.66% CellPropertyCollection::GetPropertiesType (inline) 30ms 0.051% 84.70% 387ms 0.66% std::_Rb_tree_iterator::operator-- (inline) 1ms 0.0017% 84.70% 379ms 0.64% Cell::GetCellId 27ms 0.046% 84.75% 373ms 0.63% tetgen::tetgenmesh::queue::push 198ms 0.34% 85.08% 357ms 0.61% AbstractTetrahedralMesh::GetElement 13ms 0.022% 85.10% 347ms 0.59% std::vector::insert (inline) 233ms 0.4% 85.50% 345ms 0.59% tetgen::tetgenmesh::link::add 141ms 0.24% 85.74% 343ms 0.58% Inverse 13ms 0.022% 85.76% 341ms 0.58% VertexElement::~VertexElement 146ms 0.25% 86.01% 340ms 0.58% boost::numeric::ublas::vector_inner_prod::apply (inline) 336ms 0.57% 86.58% 336ms 0.57% std::_Rb_tree_decrement 4ms 0.0068% 86.59% 331ms 0.56% AbstractCellProperty::IsSubType (inline) 0 0% 86.59% 308ms 0.52% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 63ms 0.11% 86.69% 296ms 0.5% tetgen::tetgenmesh::queue::pop