File: Test3dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 54316ms, 86.53% of 62774ms total Dropped 874 nodes (cum <= 313.87ms) flat flat% sum% cum cum% 0 0% 0% 62720ms 99.91% __libc_start_call_main 0 0% 0% 62720ms 99.91% __libc_start_main_impl 0 0% 0% 62720ms 99.91% _start 0 0% 0% 62703ms 99.89% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 62703ms 99.89% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 62703ms 99.89% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 62703ms 99.89% main 0 0% 0% 62658ms 99.82% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 62658ms 99.82% CxxTest::TestRunner::runTest (inline) 0 0% 0% 62658ms 99.82% Test3dTissueRepresentativeSimulation::Test3DHoneycombMeshWithGhostNodes 0 0% 0% 62371ms 99.36% AbstractCellBasedSimulation::Solve 0 0% 0% 53303ms 84.91% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 53253ms 84.83% MeshBasedCellPopulation::Update 0 0% 0% 28880ms 46.01% MeshBasedCellPopulation::TessellateIfNeeded 0 0% 0% 28879ms 46.00% MeshBasedCellPopulation::CreateVoronoiTessellation (inline) 211ms 0.34% 0.34% 25433ms 40.52% VertexMesh::VertexMesh 0 0% 0.34% 20336ms 32.40% MutableMesh::ReMesh 0 0% 0.34% 16276ms 25.93% tetgen::tetrahedralize 3ms 0.0048% 0.34% 16133ms 25.70% tetgen::tetgenmesh::delaunizevertices 15ms 0.024% 0.36% 16124ms 25.69% tetgen::tetgenmesh::incrflipdelaunay 516ms 0.82% 1.19% 14481ms 23.07% tetgen::tetgenmesh::lawson 632ms 1.01% 2.19% 12280ms 19.56% TetrahedralMesh::EdgeIterator::operator++ 37ms 0.059% 2.25% 10135ms 16.15% std::set::insert (inline) 349ms 0.56% 2.81% 9719ms 15.48% VertexElement::AddFace 270ms 0.43% 3.24% 9672ms 15.41% std::_Rb_tree::_M_insert_unique 3181ms 5.07% 8.31% 8905ms 14.19% std::_Rb_tree::_M_lower_bound (inline) 249ms 0.4% 8.70% 8439ms 13.44% std::_Rb_tree::find (inline) 0 0% 8.70% 7829ms 12.47% std::set::count (inline) 339ms 0.54% 9.24% 5805ms 9.25% std::_Rb_tree::_M_insert_ (inline) 119ms 0.19% 9.43% 5652ms 9.00% std::less::operator() (inline) 5583ms 8.89% 18.33% 5583ms 8.89% std::operator< (inline) 1ms 0.0016% 18.33% 5452ms 8.69% OffLatticeSimulation::UpdateCellLocationsAndTopology 1ms 0.0016% 18.33% 5320ms 8.47% ForwardEulerNumericalMethod::UpdateAllNodePositions 1ms 0.0016% 18.33% 5295ms 8.44% AbstractNumericalMethod::ComputeForcesIncludingDamping 180ms 0.29% 18.62% 5261ms 8.38% operator new 5051ms 8.05% 26.66% 5051ms 8.05% std::_Rb_tree_increment 1268ms 2.02% 28.68% 4999ms 7.96% __GI___libc_malloc 36ms 0.057% 28.74% 4523ms 7.21% std::__new_allocator::allocate (inline) 0 0% 28.74% 4502ms 7.17% std::allocator_traits::allocate (inline) 1ms 0.0016% 28.74% 4426ms 7.05% MeshBasedCellPopulation::UpdateNodePairs 7ms 0.011% 28.75% 4376ms 6.97% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 9ms 0.014% 28.77% 4332ms 6.90% std::_Rb_tree::~_Rb_tree (inline) 1555ms 2.48% 31.25% 4318ms 6.88% std::_Rb_tree::_M_erase 10ms 0.016% 31.26% 4284ms 6.82% MeshBasedCellPopulation::SpringIterator::operator++ 0 0% 31.26% 4272ms 6.81% std::set::~set (inline) 1190ms 1.90% 33.16% 4093ms 6.52% __GI___libc_free 9ms 0.014% 33.17% 3963ms 6.31% std::set_intersection (inline) 252ms 0.4% 33.57% 3954ms 6.30% std::__set_intersection 1342ms 2.14% 35.71% 3880ms 6.18% std::_Rb_tree::_M_get_insert_unique_pos 133ms 0.21% 35.92% 3856ms 6.14% tetgen::tetgenmesh::insphere_sos 3422ms 5.45% 41.37% 3707ms 5.91% tetgen::insphere 0 0% 41.37% 3700ms 5.89% std::_Rb_tree::_M_create_node (inline) 0 0% 41.37% 3663ms 5.84% std::_Rb_tree::_M_get_node (inline) 0 0% 41.37% 3660ms 5.83% std::_Rb_tree::_Alloc_node::operator() (inline) 148ms 0.24% 41.61% 3608ms 5.75% tetgen::tetgenmesh::flip23 133ms 0.21% 41.82% 3593ms 5.72% std::__new_allocator::deallocate (inline) 0 0% 41.82% 3575ms 5.70% std::allocator_traits::deallocate (inline) 0 0% 41.82% 3473ms 5.53% VertexMesh::~VertexMesh 0 0% 41.82% 3455ms 5.50% AbstractCellPopulation::WriteResultsToFiles 2508ms 4.00% 45.82% 3371ms 5.37% _int_malloc 50ms 0.08% 45.90% 3300ms 5.26% Node::AddElement 199ms 0.32% 46.21% 3248ms 5.17% std::_Rb_tree_const_iterator::operator++ (inline) 1ms 0.0016% 46.21% 3232ms 5.15% TetrahedralMesh::ImportFromMesher 2970ms 4.73% 50.95% 2970ms 4.73% std::_Rb_tree::_S_right (inline) 1393ms 2.22% 53.17% 2901ms 4.62% _int_free 65ms 0.1% 53.27% 2638ms 4.20% MutableElement::AddNode 146ms 0.23% 53.50% 2542ms 4.05% tetgen::tetgenmesh::flip32 167ms 0.27% 53.77% 2511ms 4.00% Node::~Node 4ms 0.0064% 53.77% 2338ms 3.72% MeshBasedCellPopulationWithGhostNodes::WriteVtkResultsToFile 191ms 0.3% 54.08% 2307ms 3.68% VertexMesh::GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex 150ms 0.24% 54.32% 2306ms 3.67% VertexMesh::Clear 3ms 0.0048% 54.32% 2132ms 3.40% std::_Rb_tree_iterator::operator++ (inline) 0 0% 54.32% 2115ms 3.37% std::_Rb_tree::_M_drop_node (inline) 0 0% 54.32% 2103ms 3.35% std::_Rb_tree::_M_put_node (inline) 241ms 0.38% 54.71% 1885ms 3.00% tetgen::tetgenmesh::enqueueflipface 1880ms 2.99% 57.70% 1880ms 2.99% std::_Rb_tree_insert_and_rebalance 1511ms 2.41% 60.11% 1614ms 2.57% tetgen::orient3d 1544ms 2.46% 62.57% 1544ms 2.46% Node::GetIndex 44ms 0.07% 62.64% 1516ms 2.42% std::_Vector_base::_M_deallocate (inline) 7ms 0.011% 62.65% 1502ms 2.39% Element::Element 986ms 1.57% 64.22% 1428ms 2.27% malloc_consolidate 0 0% 64.22% 1418ms 2.26% std::vector::~vector (inline) 90ms 0.14% 64.36% 1390ms 2.21% TetrahedralMesh::Clear 2ms 0.0032% 64.37% 1325ms 2.11% std::_Vector_base::~_Vector_base (inline) 26ms 0.041% 64.41% 1323ms 2.11% tetgen::tetgenmesh::locate 7ms 0.011% 64.42% 1248ms 1.99% _int_free_maybe_consolidate 83ms 0.13% 64.55% 1244ms 1.98% tetgen::tetgenmesh::preciselocate 4ms 0.0064% 64.56% 1146ms 1.83% Element::RegisterWithNodes (inline) 1108ms 1.77% 66.32% 1108ms 1.77% tetgen::tetgenmesh::triface::triface 57ms 0.091% 66.41% 1105ms 1.76% std::vector::_M_realloc_insert 81ms 0.13% 66.54% 1062ms 1.69% std::map::operator[] 1055ms 1.68% 68.22% 1055ms 1.68% unlink_chunk 833ms 1.33% 69.55% 1045ms 1.66% AbstractElement::GetNodeGlobalIndex 3ms 0.0048% 69.55% 909ms 1.45% VertexMesh::GenerateVerticesFromElementCircumcentres 0 0% 69.55% 897ms 1.43% std::_Rb_tree::lower_bound (inline) 0 0% 69.55% 897ms 1.43% std::map::lower_bound (inline) 889ms 1.42% 70.97% 889ms 1.42% tetgen::tetgenmesh::oppo 106ms 0.17% 71.14% 879ms 1.40% std::vector::push_back (inline) 0 0% 71.14% 874ms 1.39% VoronoiDataWriter::Visit 5ms 0.008% 71.15% 844ms 1.34% std::_Vector_base::_M_allocate (inline) 0 0% 71.15% 808ms 1.29% TetrahedralMesh::RefreshJacobianCachedData 806ms 1.28% 72.43% 806ms 1.28% tetgen::tetgenmesh::triface::operator= 776ms 1.24% 73.67% 776ms 1.24% [libchaste_mesh.so] 315ms 0.5% 74.17% 772ms 1.23% tetgen::tetgenmesh::sym 13ms 0.021% 74.19% 752ms 1.20% AbstractTetrahedralElement::CalculateInverseJacobian 2ms 0.0032% 74.19% 743ms 1.18% AbstractTwoBodyInteractionForce::AddForceContribution 21ms 0.033% 74.23% 704ms 1.12% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 441ms 0.7% 74.93% 693ms 1.10% tetgen::tetgenmesh::fnextself 25ms 0.04% 74.97% 674ms 1.07% AbstractTetrahedralElement::CalculateJacobian 13ms 0.021% 74.99% 659ms 1.05% boost::numeric::ublas::vector_assign (inline) 63ms 0.1% 75.09% 655ms 1.04% tetgen::tetgenmesh::enext2fnext 14ms 0.022% 75.11% 620ms 0.99% boost::numeric::ublas::c_vector::c_vector (inline) 55ms 0.088% 75.20% 616ms 0.98% tetgen::tetgenmesh::enextfnext 60ms 0.096% 75.30% 610ms 0.97% __atan2 53ms 0.084% 75.38% 606ms 0.97% tetgen::tetgenmesh::queue::push 0 0% 75.38% 604ms 0.96% std::set::find (inline) 262ms 0.42% 75.80% 574ms 0.91% AbstractElement::GetNodeLocation 221ms 0.35% 76.15% 557ms 0.89% tetgen::tetgenmesh::bond 364ms 0.58% 76.73% 553ms 0.88% tetgen::tetgenmesh::link::add 432ms 0.69% 77.42% 545ms 0.87% __ieee754_atan2_fma 544ms 0.87% 78.28% 544ms 0.87% std::vector::size (inline) 0 0% 78.28% 537ms 0.86% boost::numeric::ublas::inner_prod (inline) 535ms 0.85% 79.14% 535ms 0.85% AbstractElement::IsDeleted 52ms 0.083% 79.22% 533ms 0.85% boost::numeric::ublas::vector_scalar_binary::evaluate 0 0% 79.22% 533ms 0.85% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 518ms 0.83% 80.04% 518ms 0.83% tetgen::tetgenmesh::org 503ms 0.8% 80.85% 503ms 0.8% Node::rGetLocation 486ms 0.77% 81.62% 486ms 0.77% tetgen::tetgenmesh::decode 0 0% 81.62% 480ms 0.76% std::insert_iterator::operator= (inline) 57ms 0.091% 81.71% 474ms 0.76% AbstractTetrahedralElement::RefreshJacobian 473ms 0.75% 82.46% 473ms 0.75% tetgen::tetgenmesh::pointmark 250ms 0.4% 82.86% 469ms 0.75% AbstractTetrahedralMesh::GetElement 18ms 0.029% 82.89% 452ms 0.72% Element::CalculateCircumsphere 84ms 0.13% 83.02% 448ms 0.71% tetgen::tetgenmesh::queue::pop 13ms 0.021% 83.05% 426ms 0.68% boost::numeric::ublas::c_vector::operator= (inline) 1ms 0.0016% 83.05% 425ms 0.68% std::_Rb_tree::_M_insert_unique_ (inline) 410ms 0.65% 83.70% 410ms 0.65% boost::numeric::ublas::c_vector::operator() 110ms 0.18% 83.88% 410ms 0.65% boost::numeric::ublas::indexing_vector_assign 189ms 0.3% 84.18% 410ms 0.65% boost::numeric::ublas::vector_inner_prod::apply (inline) 2ms 0.0032% 84.18% 409ms 0.65% CellPropertyCollection::GetPropertiesType (inline) 11ms 0.018% 84.20% 409ms 0.65% VertexElement::~VertexElement 16ms 0.025% 84.22% 405ms 0.65% VertexMesh::CalculateUnitNormalToFaceWithArea 29ms 0.046% 84.27% 405ms 0.65% std::_Rb_tree_iterator::operator-- (inline) 3ms 0.0048% 84.27% 393ms 0.63% Cell::GetCellId 117ms 0.19% 84.46% 386ms 0.61% __dynamic_cast 0 0% 84.46% 385ms 0.61% VertexMeshWriter::WriteVtkUsingMesh 188ms 0.3% 84.76% 363ms 0.58% tetgen::tetgenmesh::link::deletenode 13ms 0.021% 84.78% 362ms 0.58% std::vector::insert (inline) 111ms 0.18% 84.96% 354ms 0.56% Inverse 7ms 0.011% 84.97% 350ms 0.56% AbstractTetrahedralElement::AbstractTetrahedralElement 349ms 0.56% 85.52% 349ms 0.56% std::_Rb_tree_decrement 260ms 0.41% 85.94% 330ms 0.53% boost::numeric::ublas::c_matrix::operator() 0 0% 85.94% 329ms 0.52% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 326ms 0.52% 86.46% 326ms 0.52% tetgen::tetgenmesh::encode 1ms 0.0016% 86.46% 316ms 0.5% AbstractCellProperty::IsSubType (inline) 42ms 0.067% 86.53% 314ms 0.5% boost::numeric::ublas::vector_reference::operator() (inline)