File: Test3dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 60772ms, 88.51% of 68661ms total Dropped 895 nodes (cum <= 343.31ms) flat flat% sum% cum cum% 0 0% 0% 68596ms 99.91% __libc_start_call_main 0 0% 0% 68596ms 99.91% __libc_start_main_impl 0 0% 0% 68596ms 99.91% _start 0 0% 0% 68582ms 99.88% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 68582ms 99.88% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 68582ms 99.88% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 68582ms 99.88% main 0 0% 0% 68543ms 99.83% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 68543ms 99.83% CxxTest::TestRunner::runTest (inline) 0 0% 0% 68542ms 99.83% Test3dTissueRepresentativeSimulation::Test3DHoneycombMeshWithGhostNodes 0 0% 0% 68261ms 99.42% AbstractCellBasedSimulation::Solve 0 0% 0% 57370ms 83.56% AbstractCellBasedSimulation::UpdateCellPopulation 1ms 0.0015% 0.0015% 57316ms 83.48% MeshBasedCellPopulation::Update 1ms 0.0015% 0.0029% 34605ms 50.40% MeshBasedCellPopulation::CreateVoronoiTessellation (inline) 0 0% 0.0029% 34605ms 50.40% MeshBasedCellPopulation::TessellateIfNeeded 239ms 0.35% 0.35% 30248ms 44.05% VertexMesh::VertexMesh 1ms 0.0015% 0.35% 18334ms 26.70% MutableMesh::ReMesh 525ms 0.76% 1.12% 13536ms 19.71% TetrahedralMesh::EdgeIterator::operator++ 0 0% 1.12% 13231ms 19.27% tetgen::tetrahedralize 3ms 0.0044% 1.12% 13094ms 19.07% tetgen::tetgenmesh::delaunizevertices 4ms 0.0058% 1.13% 13091ms 19.07% tetgen::tetgenmesh::incrflipdelaunay 30ms 0.044% 1.17% 11773ms 17.15% std::set::insert (inline) 562ms 0.82% 1.99% 11609ms 16.91% tetgen::tetgenmesh::lawson 242ms 0.35% 2.34% 11309ms 16.47% std::_Rb_tree::_M_insert_unique 3004ms 4.38% 6.72% 10462ms 15.24% std::_Rb_tree::_M_lower_bound (inline) 388ms 0.57% 7.28% 10182ms 14.83% VertexElement::AddFace 210ms 0.31% 7.59% 9518ms 13.86% std::_Rb_tree::find (inline) 0 0% 7.59% 8984ms 13.08% std::set::count (inline) 7734ms 11.26% 18.85% 7734ms 11.26% std::_Rb_tree_increment 108ms 0.16% 19.01% 6942ms 10.11% std::less::operator() (inline) 6890ms 10.03% 29.04% 6890ms 10.03% std::operator< (inline) 267ms 0.39% 29.43% 6504ms 9.47% std::_Rb_tree::_M_insert_ (inline) 191ms 0.28% 29.71% 6221ms 9.06% operator new 1163ms 1.69% 31.41% 5954ms 8.67% __GI___libc_malloc 0 0% 31.41% 5865ms 8.54% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 31.41% 5702ms 8.30% ForwardEulerNumericalMethod::UpdateAllNodePositions 2ms 0.0029% 31.41% 5670ms 8.26% AbstractNumericalMethod::ComputeForcesIncludingDamping 1ms 0.0015% 31.41% 5446ms 7.93% std::set_intersection (inline) 327ms 0.48% 31.89% 5445ms 7.93% std::__set_intersection 49ms 0.071% 31.96% 5197ms 7.57% std::__new_allocator::allocate (inline) 0 0% 31.96% 5176ms 7.54% std::allocator_traits::allocate (inline) 33ms 0.048% 32.01% 5101ms 7.43% Node::AddElement 0 0% 32.01% 4864ms 7.08% AbstractCellPopulation::WriteResultsToFiles 2ms 0.0029% 32.01% 4862ms 7.08% std::_Rb_tree::~_Rb_tree (inline) 2059ms 3.00% 35.01% 4861ms 7.08% std::_Rb_tree::_M_erase 1325ms 1.93% 36.94% 4858ms 7.08% std::_Rb_tree::_M_get_insert_unique_pos 0 0% 36.94% 4785ms 6.97% std::set::~set (inline) 1ms 0.0015% 36.94% 4728ms 6.89% MeshBasedCellPopulation::UpdateNodePairs 5ms 0.0073% 36.95% 4714ms 6.87% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 213ms 0.31% 37.26% 4661ms 6.79% std::_Rb_tree_const_iterator::operator++ (inline) 4576ms 6.66% 43.92% 4576ms 6.66% std::_Rb_tree::_S_right (inline) 15ms 0.022% 43.94% 4560ms 6.64% MeshBasedCellPopulation::SpringIterator::operator++ 1306ms 1.90% 45.84% 4461ms 6.50% __GI___libc_free 3227ms 4.70% 50.54% 4428ms 6.45% _int_malloc 0 0% 50.54% 4394ms 6.40% VertexMesh::~VertexMesh 0 0% 50.54% 4150ms 6.04% std::_Rb_tree::_M_create_node (inline) 12ms 0.017% 50.56% 4131ms 6.02% TetrahedralMesh::ImportFromMesher 0 0% 50.56% 4116ms 5.99% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 50.56% 4104ms 5.98% std::_Rb_tree::_M_get_node (inline) 97ms 0.14% 50.70% 3847ms 5.60% std::__new_allocator::deallocate (inline) 0 0% 50.70% 3828ms 5.58% std::allocator_traits::deallocate (inline) 81ms 0.12% 50.82% 3818ms 5.56% MutableElement::AddNode 223ms 0.32% 51.15% 3583ms 5.22% VertexMesh::GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex 103ms 0.15% 51.30% 3530ms 5.14% tetgen::tetgenmesh::insphere_sos 3140ms 4.57% 55.87% 3417ms 4.98% tetgen::insphere 4ms 0.0058% 55.87% 3383ms 4.93% MeshBasedCellPopulationWithGhostNodes::WriteVtkResultsToFile 0 0% 55.87% 3381ms 4.92% std::_Rb_tree_iterator::operator++ (inline) 1167ms 1.70% 57.57% 3154ms 4.59% _int_free 195ms 0.28% 57.86% 2999ms 4.37% Node::~Node 259ms 0.38% 58.24% 2782ms 4.05% VertexMesh::Clear 209ms 0.3% 58.54% 2684ms 3.91% tetgen::tetgenmesh::flip23 2240ms 3.26% 61.80% 2240ms 3.26% std::_Rb_tree_insert_and_rebalance 2190ms 3.19% 64.99% 2190ms 3.19% Node::GetIndex 2ms 0.0029% 64.99% 2130ms 3.10% Element::Element 167ms 0.24% 65.24% 2031ms 2.96% tetgen::tetgenmesh::flip32 1354ms 1.97% 67.21% 2012ms 2.93% malloc_consolidate 0 0% 67.21% 1941ms 2.83% std::_Rb_tree::_M_drop_node (inline) 0 0% 67.21% 1929ms 2.81% std::_Rb_tree::_M_put_node (inline) 23ms 0.033% 67.24% 1922ms 2.80% std::_Vector_base::_M_deallocate (inline) 0 0% 67.24% 1805ms 2.63% std::vector::~vector (inline) 7ms 0.01% 67.25% 1798ms 2.62% Element::RegisterWithNodes (inline) 0 0% 67.25% 1757ms 2.56% std::_Vector_base::~_Vector_base (inline) 5ms 0.0073% 67.26% 1723ms 2.51% _int_free_maybe_consolidate 235ms 0.34% 67.60% 1577ms 2.30% TetrahedralMesh::Clear 1408ms 2.05% 69.65% 1507ms 2.19% tetgen::orient3d 1498ms 2.18% 71.84% 1498ms 2.18% unlink_chunk 53ms 0.077% 71.91% 1405ms 2.05% std::map::operator[] 200ms 0.29% 72.20% 1341ms 1.95% tetgen::tetgenmesh::enqueueflipface 5ms 0.0073% 72.21% 1275ms 1.86% VertexMesh::GenerateVerticesFromElementCircumcentres 63ms 0.092% 72.30% 1269ms 1.85% std::vector::_M_realloc_insert 0 0% 72.30% 1267ms 1.85% std::_Rb_tree::lower_bound (inline) 0 0% 72.30% 1267ms 1.85% std::map::lower_bound (inline) 34ms 0.05% 72.35% 1250ms 1.82% tetgen::tetgenmesh::locate 0 0% 72.35% 1224ms 1.78% VoronoiDataWriter::Visit 94ms 0.14% 72.49% 1174ms 1.71% tetgen::tetgenmesh::preciselocate 983ms 1.43% 73.92% 1160ms 1.69% AbstractElement::GetNodeGlobalIndex 6ms 0.0087% 73.93% 1078ms 1.57% std::_Vector_base::_M_allocate (inline) 116ms 0.17% 74.10% 1044ms 1.52% std::vector::push_back (inline) 981ms 1.43% 75.53% 981ms 1.43% tetgen::tetgenmesh::triface::triface 0 0% 75.53% 942ms 1.37% TetrahedralMesh::RefreshJacobianCachedData 893ms 1.30% 76.83% 893ms 1.30% Node::rGetLocation 385ms 0.56% 77.39% 867ms 1.26% AbstractElement::GetNodeLocation 401ms 0.58% 77.97% 858ms 1.25% tetgen::tetgenmesh::fnextself 8ms 0.012% 77.98% 815ms 1.19% AbstractTetrahedralElement::CalculateInverseJacobian 811ms 1.18% 79.17% 811ms 1.18% tetgen::tetgenmesh::triface::operator= 11ms 0.016% 79.18% 772ms 1.12% AbstractTetrahedralElement::CalculateJacobian 738ms 1.07% 80.26% 738ms 1.07% AbstractElement::IsDeleted 0 0% 80.26% 738ms 1.07% AbstractTwoBodyInteractionForce::AddForceContribution 15ms 0.022% 80.28% 678ms 0.99% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 55ms 0.08% 80.36% 677ms 0.99% __atan2 650ms 0.95% 81.31% 650ms 0.95% [libchaste_mesh.so] 13ms 0.019% 81.32% 639ms 0.93% boost::numeric::ublas::vector_assign (inline) 15ms 0.022% 81.35% 634ms 0.92% boost::numeric::ublas::c_vector::c_vector (inline) 19ms 0.028% 81.37% 624ms 0.91% Element::CalculateCircumsphere 493ms 0.72% 82.09% 621ms 0.9% __ieee754_atan2_fma 44ms 0.064% 82.16% 603ms 0.88% AbstractTetrahedralElement::RefreshJacobian 580ms 0.84% 83.00% 580ms 0.84% tetgen::tetgenmesh::oppo 572ms 0.83% 83.83% 572ms 0.83% std::vector::size (inline) 47ms 0.068% 83.90% 539ms 0.79% tetgen::tetgenmesh::enextfnext 0 0% 83.90% 528ms 0.77% std::set::find (inline) 46ms 0.067% 83.97% 519ms 0.76% tetgen::tetgenmesh::enext2fnext 344ms 0.5% 84.47% 471ms 0.69% tetgen::tetgenmesh::sym 0 0% 84.47% 468ms 0.68% boost::numeric::ublas::inner_prod (inline) 6ms 0.0087% 84.48% 463ms 0.67% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 27ms 0.039% 84.52% 457ms 0.67% boost::numeric::ublas::vector_scalar_binary::evaluate 0 0% 84.52% 455ms 0.66% std::insert_iterator::operator= (inline) 27ms 0.039% 84.56% 449ms 0.65% VertexMesh::CalculateUnitNormalToFaceWithArea 107ms 0.16% 84.71% 420ms 0.61% boost::numeric::ublas::indexing_vector_assign 0 0% 84.71% 417ms 0.61% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 0 0% 84.71% 403ms 0.59% std::_Rb_tree::_M_insert_unique_ (inline) 17ms 0.025% 84.74% 402ms 0.59% std::_Rb_tree_iterator::operator-- (inline) 0 0% 84.74% 395ms 0.58% VertexMeshWriter::WriteVtkUsingMesh 391ms 0.57% 85.31% 391ms 0.57% tetgen::tetgenmesh::org 390ms 0.57% 85.88% 390ms 0.57% boost::numeric::ublas::c_vector::operator() 7ms 0.01% 85.89% 386ms 0.56% CellPropertyCollection::GetPropertiesType (inline) 205ms 0.3% 86.18% 385ms 0.56% AbstractTetrahedralMesh::GetElement 155ms 0.23% 86.41% 382ms 0.56% boost::numeric::ublas::vector_inner_prod::apply (inline) 7ms 0.01% 86.42% 375ms 0.55% boost::numeric::ublas::c_vector::operator= (inline) 25ms 0.036% 86.46% 375ms 0.55% tetgen::tetgenmesh::queue::push 275ms 0.4% 86.86% 369ms 0.54% tetgen::tetgenmesh::bond 365ms 0.53% 87.39% 365ms 0.53% tetgen::tetgenmesh::pointmark 104ms 0.15% 87.54% 364ms 0.53% __dynamic_cast 10ms 0.015% 87.55% 361ms 0.53% std::vector::insert (inline) 360ms 0.52% 88.08% 360ms 0.52% std::_Rb_tree_decrement 1ms 0.0015% 88.08% 358ms 0.52% Cell::GetCellId 287ms 0.42% 88.50% 347ms 0.51% tetgen::tetgenmesh::link::add 8ms 0.012% 88.51% 345ms 0.5% VertexMesh::GetVolumeOfElement