File: Test3dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 51069ms, 87.03% of 58677ms total Dropped 830 nodes (cum <= 293.38ms) flat flat% sum% cum cum% 0 0% 0% 58620ms 99.90% __libc_start_call_main 0 0% 0% 58620ms 99.90% __libc_start_main_impl 0 0% 0% 58620ms 99.90% _start 0 0% 0% 58605ms 99.88% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 58605ms 99.88% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 58605ms 99.88% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 58605ms 99.88% main 0 0% 0% 58569ms 99.82% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 58569ms 99.82% CxxTest::TestRunner::runTest (inline) 0 0% 0% 58569ms 99.82% Test3dTissueRepresentativeSimulation::Test3DHoneycombMeshWithGhostNodes 0 0% 0% 58313ms 99.38% AbstractCellBasedSimulation::Solve 0 0% 0% 47988ms 81.78% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 47941ms 81.70% MeshBasedCellPopulation::Update 0 0% 0% 27220ms 46.39% MeshBasedCellPopulation::TessellateIfNeeded 0 0% 0% 27218ms 46.39% MeshBasedCellPopulation::CreateVoronoiTessellation (inline) 207ms 0.35% 0.35% 24067ms 41.02% VertexMesh::VertexMesh 0 0% 0.35% 16651ms 28.38% MutableMesh::ReMesh 0 0% 0.35% 12747ms 21.72% tetgen::tetrahedralize 0 0% 0.35% 12609ms 21.49% tetgen::tetgenmesh::delaunizevertices 10ms 0.017% 0.37% 12606ms 21.48% tetgen::tetgenmesh::incrflipdelaunay 615ms 1.05% 1.42% 12382ms 21.10% TetrahedralMesh::EdgeIterator::operator++ 534ms 0.91% 2.33% 11199ms 19.09% tetgen::tetgenmesh::lawson 3023ms 5.15% 7.48% 10021ms 17.08% std::_Rb_tree::_M_lower_bound (inline) 35ms 0.06% 7.54% 9445ms 16.10% std::set::insert (inline) 238ms 0.41% 7.95% 9309ms 15.86% std::_Rb_tree::find (inline) 293ms 0.5% 8.44% 9018ms 15.37% VertexElement::AddFace 206ms 0.35% 8.80% 8907ms 15.18% std::_Rb_tree::_M_insert_unique 0 0% 8.80% 8738ms 14.89% std::set::count (inline) 110ms 0.19% 8.98% 6648ms 11.33% std::less::operator() (inline) 6602ms 11.25% 20.23% 6602ms 11.25% std::operator< (inline) 5907ms 10.07% 30.30% 5907ms 10.07% std::_Rb_tree_increment 0 0% 30.30% 5471ms 9.32% OffLatticeSimulation::UpdateCellLocationsAndTopology 275ms 0.47% 30.77% 5344ms 9.11% std::_Rb_tree::_M_insert_ (inline) 0 0% 30.77% 5343ms 9.11% ForwardEulerNumericalMethod::UpdateAllNodePositions 1ms 0.0017% 30.77% 5315ms 9.06% AbstractNumericalMethod::ComputeForcesIncludingDamping 192ms 0.33% 31.10% 4737ms 8.07% operator new 0 0% 31.10% 4717ms 8.04% AbstractCellPopulation::WriteResultsToFiles 1102ms 1.88% 32.98% 4471ms 7.62% __GI___libc_malloc 1ms 0.0017% 32.98% 4399ms 7.50% MeshBasedCellPopulation::UpdateNodePairs 5ms 0.0085% 32.99% 4384ms 7.47% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 18ms 0.031% 33.02% 4262ms 7.26% MeshBasedCellPopulation::SpringIterator::operator++ 47ms 0.08% 33.10% 4058ms 6.92% std::__new_allocator::allocate (inline) 9ms 0.015% 33.11% 4034ms 6.87% std::_Rb_tree::~_Rb_tree (inline) 0 0% 33.11% 4034ms 6.87% std::allocator_traits::allocate (inline) 1576ms 2.69% 35.80% 4023ms 6.86% std::_Rb_tree::_M_erase 0 0% 35.80% 3975ms 6.77% std::set::~set (inline) 1194ms 2.03% 37.83% 3698ms 6.30% std::_Rb_tree::_M_get_insert_unique_pos 240ms 0.41% 38.24% 3635ms 6.19% VertexMesh::GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex 117ms 0.2% 38.44% 3482ms 5.93% tetgen::tetgenmesh::insphere_sos 972ms 1.66% 40.10% 3477ms 5.93% __GI___libc_free 2ms 0.0034% 40.10% 3422ms 5.83% std::set_intersection (inline) 225ms 0.38% 40.49% 3420ms 5.83% std::__set_intersection 1ms 0.0017% 40.49% 3410ms 5.81% std::_Rb_tree_iterator::operator++ (inline) 1ms 0.0017% 40.49% 3357ms 5.72% MeshBasedCellPopulationWithGhostNodes::WriteVtkResultsToFile 3065ms 5.22% 45.71% 3349ms 5.71% tetgen::insphere 0 0% 45.71% 3269ms 5.57% std::_Rb_tree::_M_create_node (inline) 0 0% 45.71% 3241ms 5.52% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 45.71% 3236ms 5.51% std::_Rb_tree::_M_get_node (inline) 3184ms 5.43% 51.14% 3184ms 5.43% std::_Rb_tree::_S_right (inline) 0 0% 51.14% 3173ms 5.41% VertexMesh::~VertexMesh 16ms 0.027% 51.17% 3147ms 5.36% Node::AddElement 8ms 0.014% 51.18% 3136ms 5.34% TetrahedralMesh::ImportFromMesher 148ms 0.25% 51.43% 3114ms 5.31% std::__new_allocator::deallocate (inline) 0 0% 51.43% 3093ms 5.27% std::allocator_traits::deallocate (inline) 2204ms 3.76% 55.19% 3018ms 5.14% _int_malloc 152ms 0.26% 55.45% 2735ms 4.66% std::_Rb_tree_const_iterator::operator++ (inline) 192ms 0.33% 55.77% 2715ms 4.63% tetgen::tetgenmesh::flip23 1151ms 1.96% 57.74% 2501ms 4.26% _int_free 78ms 0.13% 57.87% 2293ms 3.91% MutableElement::AddNode 149ms 0.25% 58.12% 2278ms 3.88% Node::~Node 179ms 0.31% 58.43% 2162ms 3.68% VertexMesh::Clear 155ms 0.26% 58.69% 1951ms 3.32% tetgen::tetgenmesh::flip32 1893ms 3.23% 61.92% 1893ms 3.23% std::_Rb_tree_insert_and_rebalance 0 0% 61.92% 1841ms 3.14% std::_Rb_tree::_M_drop_node (inline) 0 0% 61.92% 1830ms 3.12% std::_Rb_tree::_M_put_node (inline) 6ms 0.01% 61.93% 1627ms 2.77% Element::Element 1585ms 2.70% 64.63% 1585ms 2.70% Node::GetIndex 1268ms 2.16% 66.79% 1355ms 2.31% tetgen::orient3d 805ms 1.37% 68.16% 1321ms 2.25% malloc_consolidate 198ms 0.34% 68.50% 1292ms 2.20% tetgen::tetgenmesh::enqueueflipface 1ms 0.0017% 68.50% 1289ms 2.20% Element::RegisterWithNodes (inline) 21ms 0.036% 68.54% 1284ms 2.19% std::_Vector_base::_M_deallocate (inline) 58ms 0.099% 68.64% 1248ms 2.13% std::map::operator[] 0 0% 68.64% 1247ms 2.13% std::vector::~vector (inline) 152ms 0.26% 68.90% 1203ms 2.05% TetrahedralMesh::Clear 38ms 0.065% 68.96% 1201ms 2.05% tetgen::tetgenmesh::locate 6ms 0.01% 68.97% 1142ms 1.95% _int_free_maybe_consolidate 0 0% 68.97% 1131ms 1.93% std::_Rb_tree::lower_bound (inline) 0 0% 68.97% 1131ms 1.93% std::map::lower_bound (inline) 99ms 0.17% 69.14% 1126ms 1.92% tetgen::tetgenmesh::preciselocate 0 0% 69.14% 1119ms 1.91% VoronoiDataWriter::Visit 1ms 0.0017% 69.14% 1112ms 1.90% std::_Vector_base::~_Vector_base (inline) 1017ms 1.73% 70.87% 1017ms 1.73% unlink_chunk 56ms 0.095% 70.97% 1013ms 1.73% std::vector::_M_realloc_insert 8ms 0.014% 70.98% 940ms 1.60% VertexMesh::GenerateVerticesFromElementCircumcentres 890ms 1.52% 72.50% 890ms 1.52% tetgen::tetgenmesh::triface::triface 119ms 0.2% 72.70% 865ms 1.47% std::vector::push_back (inline) 8ms 0.014% 72.72% 806ms 1.37% std::_Vector_base::_M_allocate (inline) 464ms 0.79% 73.51% 806ms 1.37% tetgen::tetgenmesh::fnextself 2ms 0.0034% 73.51% 741ms 1.26% TetrahedralMesh::RefreshJacobianCachedData 0 0% 73.51% 724ms 1.23% AbstractTwoBodyInteractionForce::AddForceContribution 8ms 0.014% 73.52% 696ms 1.19% AbstractTetrahedralElement::CalculateInverseJacobian 563ms 0.96% 74.48% 690ms 1.18% AbstractElement::GetNodeGlobalIndex 680ms 1.16% 75.64% 680ms 1.16% tetgen::tetgenmesh::oppo 18ms 0.031% 75.67% 677ms 1.15% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 659ms 1.12% 76.80% 659ms 1.12% [libchaste_mesh.so] 13ms 0.022% 76.82% 655ms 1.12% AbstractTetrahedralElement::CalculateJacobian 9ms 0.015% 76.83% 647ms 1.10% boost::numeric::ublas::vector_assign (inline) 252ms 0.43% 77.26% 644ms 1.10% AbstractElement::GetNodeLocation 11ms 0.019% 77.28% 631ms 1.08% boost::numeric::ublas::c_vector::c_vector (inline) 51ms 0.087% 77.37% 629ms 1.07% __atan2 486ms 0.83% 78.20% 578ms 0.99% __ieee754_atan2_fma 577ms 0.98% 79.18% 577ms 0.98% Node::rGetLocation 0 0% 79.18% 562ms 0.96% std::set::find (inline) 540ms 0.92% 80.10% 540ms 0.92% tetgen::tetgenmesh::triface::operator= 50ms 0.085% 80.19% 524ms 0.89% tetgen::tetgenmesh::enextfnext 0 0% 80.19% 521ms 0.89% std::insert_iterator::operator= (inline) 21ms 0.036% 80.22% 498ms 0.85% Element::CalculateCircumsphere 31ms 0.053% 80.28% 489ms 0.83% tetgen::tetgenmesh::enext2fnext 40ms 0.068% 80.34% 488ms 0.83% AbstractTetrahedralElement::RefreshJacobian 0 0% 80.34% 487ms 0.83% boost::numeric::ublas::inner_prod (inline) 5ms 0.0085% 80.35% 483ms 0.82% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 32ms 0.055% 80.41% 478ms 0.81% boost::numeric::ublas::vector_scalar_binary::evaluate 296ms 0.5% 80.91% 466ms 0.79% tetgen::tetgenmesh::sym 2ms 0.0034% 80.91% 464ms 0.79% std::_Rb_tree::_M_insert_unique_ (inline) 443ms 0.75% 81.67% 443ms 0.75% std::vector::size (inline) 100ms 0.17% 81.84% 410ms 0.7% boost::numeric::ublas::indexing_vector_assign 180ms 0.31% 82.15% 403ms 0.69% boost::numeric::ublas::vector_inner_prod::apply (inline) 36ms 0.061% 82.21% 399ms 0.68% std::_Rb_tree_iterator::operator-- (inline) 29ms 0.049% 82.26% 397ms 0.68% tetgen::tetgenmesh::queue::push 0 0% 82.26% 392ms 0.67% VertexMeshWriter::WriteVtkUsingMesh 392ms 0.67% 82.93% 392ms 0.67% boost::numeric::ublas::c_vector::operator() 229ms 0.39% 83.32% 388ms 0.66% AbstractTetrahedralMesh::GetElement 2ms 0.0034% 83.32% 381ms 0.65% boost::numeric::ublas::c_vector::operator= (inline) 378ms 0.64% 83.96% 378ms 0.64% tetgen::tetgenmesh::org 3ms 0.0051% 83.97% 371ms 0.63% CellPropertyCollection::GetPropertiesType (inline) 4ms 0.0068% 83.97% 369ms 0.63% Cell::GetCellId 249ms 0.42% 84.40% 368ms 0.63% tetgen::tetgenmesh::link::add 79ms 0.13% 84.53% 361ms 0.62% __dynamic_cast 351ms 0.6% 85.13% 351ms 0.6% AbstractElement::IsDeleted 342ms 0.58% 85.72% 342ms 0.58% std::_Rb_tree_decrement 5ms 0.0085% 85.72% 341ms 0.58% VertexElement::~VertexElement 243ms 0.41% 86.14% 339ms 0.58% tetgen::tetgenmesh::bond 12ms 0.02% 86.16% 336ms 0.57% VertexMesh::CalculateUnitNormalToFaceWithArea 2ms 0.0034% 86.16% 332ms 0.57% AbstractTetrahedralElement::AbstractTetrahedralElement 0 0% 86.16% 329ms 0.56% tcache_get (inline) 329ms 0.56% 86.72% 329ms 0.56% tcache_get_n (inline) 122ms 0.21% 86.93% 313ms 0.53% Inverse 61ms 0.1% 87.03% 310ms 0.53% boost::numeric::ublas::vector_reference::operator() (inline) 0 0% 87.03% 300ms 0.51% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline)