File: Test3dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 48715ms, 87.09% of 55937ms total Dropped 873 nodes (cum <= 279.69ms) flat flat% sum% cum cum% 0 0% 0% 55880ms 99.90% __libc_start_call_main 0 0% 0% 55880ms 99.90% __libc_start_main_impl 0 0% 0% 55880ms 99.90% _start 0 0% 0% 55866ms 99.87% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 55866ms 99.87% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 55866ms 99.87% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 55866ms 99.87% main 0 0% 0% 55831ms 99.81% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 55831ms 99.81% CxxTest::TestRunner::runTest (inline) 0 0% 0% 55830ms 99.81% Test3dTissueRepresentativeSimulation::Test3DHoneycombMeshWithGhostNodes 0 0% 0% 55582ms 99.37% AbstractCellBasedSimulation::Solve 0 0% 0% 47029ms 84.07% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 46986ms 84.00% MeshBasedCellPopulation::Update 0 0% 0% 26264ms 46.95% MeshBasedCellPopulation::TessellateIfNeeded 0 0% 0% 26262ms 46.95% MeshBasedCellPopulation::CreateVoronoiTessellation (inline) 188ms 0.34% 0.34% 23321ms 41.69% VertexMesh::VertexMesh 0 0% 0.34% 17094ms 30.56% MutableMesh::ReMesh 0 0% 0.34% 13070ms 23.37% tetgen::tetrahedralize 0 0% 0.34% 12937ms 23.13% tetgen::tetgenmesh::delaunizevertices 11ms 0.02% 0.36% 12933ms 23.12% tetgen::tetgenmesh::incrflipdelaunay 516ms 0.92% 1.28% 11510ms 20.58% tetgen::tetgenmesh::lawson 564ms 1.01% 2.29% 11132ms 19.90% TetrahedralMesh::EdgeIterator::operator++ 29ms 0.052% 2.34% 9742ms 17.42% std::set::insert (inline) 263ms 0.47% 2.81% 9280ms 16.59% std::_Rb_tree::_M_insert_unique 366ms 0.65% 3.46% 9059ms 16.20% VertexElement::AddFace 2905ms 5.19% 8.66% 8469ms 15.14% std::_Rb_tree::_M_lower_bound (inline) 211ms 0.38% 9.03% 7849ms 14.03% std::_Rb_tree::find (inline) 0 0% 9.03% 7288ms 13.03% std::set::count (inline) 291ms 0.52% 9.55% 5578ms 9.97% std::_Rb_tree::_M_insert_ (inline) 119ms 0.21% 9.77% 5360ms 9.58% std::less::operator() (inline) 5299ms 9.47% 19.24% 5299ms 9.47% std::operator< (inline) 0 0% 19.24% 5016ms 8.97% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 19.24% 4887ms 8.74% ForwardEulerNumericalMethod::UpdateAllNodePositions 4ms 0.0072% 19.25% 4862ms 8.69% AbstractNumericalMethod::ComputeForcesIncludingDamping 207ms 0.37% 19.62% 4727ms 8.45% operator new 1104ms 1.97% 21.59% 4444ms 7.94% __GI___libc_malloc 4432ms 7.92% 29.51% 4432ms 7.92% std::_Rb_tree_increment 51ms 0.091% 29.60% 4133ms 7.39% std::__new_allocator::allocate (inline) 0 0% 29.60% 4110ms 7.35% std::allocator_traits::allocate (inline) 5ms 0.0089% 29.61% 4046ms 7.23% std::_Rb_tree::~_Rb_tree (inline) 1550ms 2.77% 32.38% 4037ms 7.22% std::_Rb_tree::_M_erase 0 0% 32.38% 3998ms 7.15% std::set::~set (inline) 4ms 0.0072% 32.39% 3994ms 7.14% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 2ms 0.0036% 32.40% 3971ms 7.10% MeshBasedCellPopulation::UpdateNodePairs 9ms 0.016% 32.41% 3829ms 6.85% MeshBasedCellPopulation::SpringIterator::operator++ 1224ms 2.19% 34.60% 3728ms 6.66% std::_Rb_tree::_M_get_insert_unique_pos 104ms 0.19% 34.79% 3554ms 6.35% tetgen::tetgenmesh::insphere_sos 3127ms 5.59% 40.38% 3437ms 6.14% tetgen::insphere 1115ms 1.99% 42.37% 3427ms 6.13% __GI___libc_free 3ms 0.0054% 42.37% 3391ms 6.06% std::set_intersection (inline) 1ms 0.0018% 42.38% 3388ms 6.06% AbstractCellPopulation::WriteResultsToFiles 255ms 0.46% 42.83% 3388ms 6.06% std::__set_intersection 0 0% 42.83% 3357ms 6.00% std::_Rb_tree::_M_create_node (inline) 0 0% 42.83% 3330ms 5.95% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 42.83% 3310ms 5.92% std::_Rb_tree::_M_get_node (inline) 12ms 0.021% 42.85% 3263ms 5.83% TetrahedralMesh::ImportFromMesher 26ms 0.046% 42.90% 3197ms 5.72% Node::AddElement 96ms 0.17% 43.07% 3025ms 5.41% std::__new_allocator::deallocate (inline) 0 0% 43.07% 3010ms 5.38% std::allocator_traits::deallocate (inline) 2248ms 4.02% 47.09% 2980ms 5.33% _int_malloc 0 0% 47.09% 2958ms 5.29% VertexMesh::~VertexMesh 2949ms 5.27% 52.36% 2949ms 5.27% std::_Rb_tree::_S_right (inline) 196ms 0.35% 52.71% 2728ms 4.88% tetgen::tetgenmesh::flip23 228ms 0.41% 53.12% 2714ms 4.85% std::_Rb_tree_const_iterator::operator++ (inline) 77ms 0.14% 53.26% 2415ms 4.32% MutableElement::AddNode 1115ms 1.99% 55.25% 2311ms 4.13% _int_free 158ms 0.28% 55.53% 2307ms 4.12% Node::~Node 2ms 0.0036% 55.54% 2270ms 4.06% MeshBasedCellPopulationWithGhostNodes::WriteVtkResultsToFile 218ms 0.39% 55.93% 2256ms 4.03% VertexMesh::GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex 180ms 0.32% 56.25% 2049ms 3.66% VertexMesh::Clear 2049ms 3.66% 59.91% 2049ms 3.66% std::_Rb_tree_insert_and_rebalance 1ms 0.0018% 59.91% 2048ms 3.66% std::_Rb_tree_iterator::operator++ (inline) 163ms 0.29% 60.21% 1959ms 3.50% tetgen::tetgenmesh::flip32 0 0% 60.21% 1858ms 3.32% std::_Rb_tree::_M_drop_node (inline) 0 0% 60.21% 1848ms 3.30% std::_Rb_tree::_M_put_node (inline) 5ms 0.0089% 60.21% 1563ms 2.79% Element::Element 1393ms 2.49% 62.70% 1472ms 2.63% tetgen::orient3d 194ms 0.35% 63.05% 1385ms 2.48% TetrahedralMesh::Clear 199ms 0.36% 63.41% 1282ms 2.29% tetgen::tetgenmesh::enqueueflipface 7ms 0.013% 63.42% 1257ms 2.25% Element::RegisterWithNodes (inline) 1190ms 2.13% 65.55% 1190ms 2.13% Node::GetIndex 787ms 1.41% 66.95% 1186ms 2.12% malloc_consolidate 24ms 0.043% 67.00% 1183ms 2.11% tetgen::tetgenmesh::locate 12ms 0.021% 67.02% 1174ms 2.10% std::_Vector_base::_M_deallocate (inline) 95ms 0.17% 67.19% 1121ms 2.00% tetgen::tetgenmesh::preciselocate 0 0% 67.19% 1109ms 1.98% std::vector::~vector (inline) 72ms 0.13% 67.32% 1097ms 1.96% std::map::operator[] 48ms 0.086% 67.40% 1018ms 1.82% std::vector::_M_realloc_insert 1ms 0.0018% 67.40% 1016ms 1.82% std::_Vector_base::~_Vector_base (inline) 17ms 0.03% 67.43% 1008ms 1.80% _int_free_maybe_consolidate 986ms 1.76% 69.20% 986ms 1.76% tetgen::tetgenmesh::triface::triface 0 0% 69.20% 952ms 1.70% std::_Rb_tree::lower_bound (inline) 0 0% 69.20% 952ms 1.70% std::map::lower_bound (inline) 0 0% 69.20% 891ms 1.59% VoronoiDataWriter::Visit 871ms 1.56% 70.75% 871ms 1.56% unlink_chunk 692ms 1.24% 71.99% 868ms 1.55% AbstractElement::GetNodeGlobalIndex 110ms 0.2% 72.19% 817ms 1.46% std::vector::push_back (inline) 4ms 0.0072% 72.20% 810ms 1.45% VertexMesh::GenerateVerticesFromElementCircumcentres 4ms 0.0072% 72.20% 804ms 1.44% std::_Vector_base::_M_allocate (inline) 775ms 1.39% 73.59% 775ms 1.39% tetgen::tetgenmesh::triface::operator= 313ms 0.56% 74.15% 765ms 1.37% tetgen::tetgenmesh::fnextself 0 0% 74.15% 739ms 1.32% TetrahedralMesh::RefreshJacobianCachedData 2ms 0.0036% 74.15% 713ms 1.27% AbstractTwoBodyInteractionForce::AddForceContribution 8ms 0.014% 74.17% 685ms 1.22% AbstractTetrahedralElement::CalculateInverseJacobian 14ms 0.025% 74.19% 680ms 1.22% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 19ms 0.034% 74.22% 673ms 1.20% boost::numeric::ublas::vector_assign (inline) 667ms 1.19% 75.42% 667ms 1.19% [libchaste_mesh.so] 11ms 0.02% 75.44% 644ms 1.15% boost::numeric::ublas::c_vector::c_vector (inline) 20ms 0.036% 75.47% 600ms 1.07% AbstractTetrahedralElement::CalculateJacobian 47ms 0.084% 75.56% 585ms 1.05% __atan2 0 0% 75.56% 559ms 1% std::set::find (inline) 548ms 0.98% 76.54% 548ms 0.98% tetgen::tetgenmesh::oppo 222ms 0.4% 76.93% 542ms 0.97% AbstractElement::GetNodeLocation 425ms 0.76% 77.69% 538ms 0.96% __ieee754_atan2_fma 49ms 0.088% 77.78% 521ms 0.93% tetgen::tetgenmesh::enext2fnext 494ms 0.88% 78.66% 494ms 0.88% std::vector::size (inline) 57ms 0.1% 78.77% 493ms 0.88% tetgen::tetgenmesh::enextfnext 0 0% 78.77% 467ms 0.83% std::insert_iterator::operator= (inline) 460ms 0.82% 79.59% 460ms 0.82% Node::rGetLocation 36ms 0.064% 79.65% 455ms 0.81% tetgen::tetgenmesh::queue::push 0 0% 79.65% 454ms 0.81% boost::numeric::ublas::inner_prod (inline) 2ms 0.0036% 79.66% 451ms 0.81% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 296ms 0.53% 80.18% 450ms 0.8% tetgen::tetgenmesh::sym 23ms 0.041% 80.23% 449ms 0.8% boost::numeric::ublas::vector_scalar_binary::evaluate 116ms 0.21% 80.43% 443ms 0.79% boost::numeric::ublas::indexing_vector_assign 14ms 0.025% 80.46% 439ms 0.78% Element::CalculateCircumsphere 23ms 0.041% 80.50% 434ms 0.78% std::_Rb_tree_iterator::operator-- (inline) 32ms 0.057% 80.56% 427ms 0.76% AbstractTetrahedralElement::RefreshJacobian 351ms 0.63% 81.18% 418ms 0.75% tetgen::tetgenmesh::link::add 409ms 0.73% 81.92% 409ms 0.73% boost::numeric::ublas::c_vector::operator() 3ms 0.0054% 81.92% 407ms 0.73% CellPropertyCollection::GetPropertiesType (inline) 76ms 0.14% 82.06% 406ms 0.73% __dynamic_cast 0 0% 82.06% 403ms 0.72% std::_Rb_tree::_M_insert_unique_ (inline) 397ms 0.71% 82.77% 397ms 0.71% AbstractElement::IsDeleted 392ms 0.7% 83.47% 392ms 0.7% std::_Rb_tree_decrement 0 0% 83.47% 391ms 0.7% VertexMeshWriter::WriteVtkUsingMesh 3ms 0.0054% 83.47% 391ms 0.7% boost::numeric::ublas::c_vector::operator= (inline) 15ms 0.027% 83.50% 387ms 0.69% VertexMesh::CalculateUnitNormalToFaceWithArea 1ms 0.0018% 83.50% 384ms 0.69% Cell::GetCellId 217ms 0.39% 83.89% 377ms 0.67% AbstractTetrahedralMesh::GetElement 165ms 0.29% 84.18% 368ms 0.66% boost::numeric::ublas::vector_inner_prod::apply (inline) 368ms 0.66% 84.84% 368ms 0.66% tetgen::tetgenmesh::org 256ms 0.46% 85.30% 342ms 0.61% tetgen::tetgenmesh::bond 2ms 0.0036% 85.30% 334ms 0.6% tcache_get (inline) 143ms 0.26% 85.56% 333ms 0.6% Inverse 10ms 0.018% 85.58% 333ms 0.6% std::vector::insert (inline) 5ms 0.0089% 85.59% 332ms 0.59% AbstractCellProperty::IsSubType (inline) 332ms 0.59% 86.18% 332ms 0.59% tcache_get_n (inline) 329ms 0.59% 86.77% 329ms 0.59% tetgen::tetgenmesh::pointmark 62ms 0.11% 86.88% 311ms 0.56% boost::numeric::ublas::vector_reference::operator() (inline) 39ms 0.07% 86.95% 309ms 0.55% tetgen::insphereadapt 70ms 0.13% 87.07% 309ms 0.55% tetgen::tetgenmesh::queue::pop 6ms 0.011% 87.08% 305ms 0.55% VertexElement::~VertexElement 3ms 0.0054% 87.09% 299ms 0.53% AbstractTetrahedralElement::AbstractTetrahedralElement 0 0% 87.09% 287ms 0.51% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline)