File: Test3dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 50003ms, 86.85% of 57576ms total Dropped 852 nodes (cum <= 287.88ms) flat flat% sum% cum cum% 0 0% 0% 57512ms 99.89% __libc_start_call_main 0 0% 0% 57512ms 99.89% __libc_start_main_impl 0 0% 0% 57512ms 99.89% _start 0 0% 0% 57497ms 99.86% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 57497ms 99.86% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 57497ms 99.86% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 57497ms 99.86% main 0 0% 0% 57459ms 99.80% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 57459ms 99.80% CxxTest::TestRunner::runTest (inline) 0 0% 0% 57459ms 99.80% Test3dTissueRepresentativeSimulation::Test3DHoneycombMeshWithGhostNodes 0 0% 0% 57203ms 99.35% AbstractCellBasedSimulation::Solve 0 0% 0% 48567ms 84.35% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 48520ms 84.27% MeshBasedCellPopulation::Update 0 0% 0% 27948ms 48.54% MeshBasedCellPopulation::CreateVoronoiTessellation (inline) 0 0% 0% 27948ms 48.54% MeshBasedCellPopulation::TessellateIfNeeded 212ms 0.37% 0.37% 24604ms 42.73% VertexMesh::VertexMesh 0 0% 0.37% 16841ms 29.25% MutableMesh::ReMesh 0 0% 0.37% 12697ms 22.05% tetgen::tetrahedralize 1ms 0.0017% 0.37% 12566ms 21.83% tetgen::tetgenmesh::delaunizevertices 10ms 0.017% 0.39% 12562ms 21.82% tetgen::tetgenmesh::incrflipdelaunay 545ms 0.95% 1.33% 11453ms 19.89% TetrahedralMesh::EdgeIterator::operator++ 569ms 0.99% 2.32% 11203ms 19.46% tetgen::tetgenmesh::lawson 27ms 0.047% 2.37% 9849ms 17.11% std::set::insert (inline) 207ms 0.36% 2.73% 9343ms 16.23% std::_Rb_tree::_M_insert_unique 392ms 0.68% 3.41% 9183ms 15.95% VertexElement::AddFace 3043ms 5.29% 8.69% 8554ms 14.86% std::_Rb_tree::_M_lower_bound (inline) 263ms 0.46% 9.15% 8084ms 14.04% std::_Rb_tree::find (inline) 0 0% 9.15% 7470ms 12.97% std::set::count (inline) 280ms 0.49% 9.64% 5592ms 9.71% std::_Rb_tree::_M_insert_ (inline) 104ms 0.18% 9.82% 5354ms 9.30% std::less::operator() (inline) 5305ms 9.21% 19.03% 5305ms 9.21% std::operator< (inline) 0 0% 19.03% 5203ms 9.04% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 19.03% 5078ms 8.82% ForwardEulerNumericalMethod::UpdateAllNodePositions 4ms 0.0069% 19.04% 5056ms 8.78% AbstractNumericalMethod::ComputeForcesIncludingDamping 212ms 0.37% 19.41% 4913ms 8.53% operator new 4785ms 8.31% 27.72% 4785ms 8.31% std::_Rb_tree_increment 1054ms 1.83% 29.55% 4614ms 8.01% __GI___libc_malloc 9ms 0.016% 29.56% 4262ms 7.40% std::_Rb_tree::~_Rb_tree (inline) 1660ms 2.88% 32.45% 4249ms 7.38% std::_Rb_tree::_M_erase 39ms 0.068% 32.52% 4200ms 7.29% std::__new_allocator::allocate (inline) 0 0% 32.52% 4199ms 7.29% std::set::~set (inline) 0 0% 32.52% 4166ms 7.24% std::allocator_traits::allocate (inline) 0 0% 32.52% 4068ms 7.07% MeshBasedCellPopulation::UpdateNodePairs 6ms 0.01% 32.53% 4049ms 7.03% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 11ms 0.019% 32.54% 3930ms 6.83% MeshBasedCellPopulation::SpringIterator::operator++ 1ms 0.0017% 32.55% 3877ms 6.73% std::set_intersection (inline) 260ms 0.45% 33.00% 3876ms 6.73% std::__set_intersection 1268ms 2.20% 35.20% 3857ms 6.70% std::_Rb_tree::_M_get_insert_unique_pos 1100ms 1.91% 37.11% 3726ms 6.47% __GI___libc_free 19ms 0.033% 37.14% 3592ms 6.24% Node::AddElement 111ms 0.19% 37.34% 3527ms 6.13% tetgen::tetgenmesh::insphere_sos 0 0% 37.34% 3401ms 5.91% std::_Rb_tree::_M_create_node (inline) 3114ms 5.41% 42.75% 3400ms 5.91% tetgen::insphere 0 0% 42.75% 3367ms 5.85% VertexMesh::~VertexMesh 0 0% 42.75% 3365ms 5.84% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 42.75% 3345ms 5.81% std::_Rb_tree::_M_get_node (inline) 15ms 0.026% 42.77% 3338ms 5.80% TetrahedralMesh::ImportFromMesher 135ms 0.23% 43.01% 3335ms 5.79% std::__new_allocator::deallocate (inline) 0 0% 43.01% 3319ms 5.76% std::allocator_traits::deallocate (inline) 0 0% 43.01% 3289ms 5.71% AbstractCellPopulation::WriteResultsToFiles 2411ms 4.19% 47.19% 3233ms 5.62% _int_malloc 194ms 0.34% 47.53% 3138ms 5.45% std::_Rb_tree_const_iterator::operator++ (inline) 3130ms 5.44% 52.97% 3130ms 5.44% std::_Rb_tree::_S_right (inline) 68ms 0.12% 53.08% 2785ms 4.84% MutableElement::AddNode 208ms 0.36% 53.45% 2706ms 4.70% tetgen::tetgenmesh::flip23 1205ms 2.09% 55.54% 2623ms 4.56% _int_free 182ms 0.32% 55.85% 2451ms 4.26% Node::~Node 178ms 0.31% 56.16% 2232ms 3.88% VertexMesh::Clear 1ms 0.0017% 56.17% 2188ms 3.80% MeshBasedCellPopulationWithGhostNodes::WriteVtkResultsToFile 191ms 0.33% 56.50% 2139ms 3.72% VertexMesh::GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex 2027ms 3.52% 60.02% 2027ms 3.52% std::_Rb_tree_insert_and_rebalance 1ms 0.0017% 60.02% 1957ms 3.40% std::_Rb_tree_iterator::operator++ (inline) 0 0% 60.02% 1944ms 3.38% std::_Rb_tree::_M_drop_node (inline) 0 0% 60.02% 1931ms 3.35% std::_Rb_tree::_M_put_node (inline) 166ms 0.29% 60.31% 1842ms 3.20% tetgen::tetgenmesh::flip32 4ms 0.0069% 60.32% 1602ms 2.78% Element::Element 1429ms 2.48% 62.80% 1429ms 2.48% Node::GetIndex 1317ms 2.29% 65.08% 1418ms 2.46% tetgen::orient3d 22ms 0.038% 65.12% 1410ms 2.45% std::_Vector_base::_M_deallocate (inline) 949ms 1.65% 66.77% 1397ms 2.43% malloc_consolidate 194ms 0.34% 67.11% 1388ms 2.41% TetrahedralMesh::Clear 174ms 0.3% 67.41% 1346ms 2.34% tetgen::tetgenmesh::enqueueflipface 0 0% 67.41% 1331ms 2.31% std::vector::~vector (inline) 4ms 0.0069% 67.42% 1283ms 2.23% Element::RegisterWithNodes (inline) 0 0% 67.42% 1250ms 2.17% std::_Vector_base::~_Vector_base (inline) 9ms 0.016% 67.43% 1203ms 2.09% _int_free_maybe_consolidate 31ms 0.054% 67.49% 1159ms 2.01% tetgen::tetgenmesh::locate 98ms 0.17% 67.66% 1093ms 1.90% tetgen::tetgenmesh::preciselocate 72ms 0.13% 67.78% 1063ms 1.85% std::vector::_M_realloc_insert 38ms 0.066% 67.85% 1035ms 1.80% std::map::operator[] 1009ms 1.75% 69.60% 1009ms 1.75% unlink_chunk 778ms 1.35% 70.95% 932ms 1.62% AbstractElement::GetNodeGlobalIndex 0 0% 70.95% 923ms 1.60% std::_Rb_tree::lower_bound (inline) 0 0% 70.95% 923ms 1.60% std::map::lower_bound (inline) 920ms 1.60% 72.55% 920ms 1.60% tetgen::tetgenmesh::triface::triface 1ms 0.0017% 72.55% 877ms 1.52% VertexMesh::GenerateVerticesFromElementCircumcentres 1ms 0.0017% 72.55% 869ms 1.51% VoronoiDataWriter::Visit 96ms 0.17% 72.72% 850ms 1.48% std::vector::push_back (inline) 0 0% 72.72% 842ms 1.46% AbstractTwoBodyInteractionForce::AddForceContribution 5ms 0.0087% 72.73% 826ms 1.43% std::_Vector_base::_M_allocate (inline) 10ms 0.017% 72.75% 801ms 1.39% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 0 0% 72.75% 791ms 1.37% TetrahedralMesh::RefreshJacobianCachedData 12ms 0.021% 72.77% 720ms 1.25% AbstractTetrahedralElement::CalculateInverseJacobian 18ms 0.031% 72.80% 714ms 1.24% boost::numeric::ublas::vector_assign (inline) 694ms 1.21% 74.00% 694ms 1.21% tetgen::tetgenmesh::oppo 687ms 1.19% 75.20% 687ms 1.19% [libchaste_mesh.so] 8ms 0.014% 75.21% 672ms 1.17% boost::numeric::ublas::c_vector::c_vector (inline) 15ms 0.026% 75.24% 655ms 1.14% AbstractTetrahedralElement::CalculateJacobian 322ms 0.56% 75.80% 644ms 1.12% tetgen::tetgenmesh::fnextself 286ms 0.5% 76.29% 624ms 1.08% AbstractElement::GetNodeLocation 0 0% 76.29% 612ms 1.06% std::set::find (inline) 608ms 1.06% 77.35% 608ms 1.06% tetgen::tetgenmesh::triface::operator= 48ms 0.083% 77.43% 585ms 1.02% __atan2 558ms 0.97% 78.40% 558ms 0.97% Node::rGetLocation 429ms 0.75% 79.15% 537ms 0.93% __ieee754_atan2_fma 7ms 0.012% 79.16% 515ms 0.89% CellPropertyCollection::GetPropertiesType (inline) 0 0% 79.16% 510ms 0.89% std::insert_iterator::operator= (inline) 508ms 0.88% 80.04% 508ms 0.88% std::vector::size (inline) 1ms 0.0017% 80.04% 494ms 0.86% Cell::GetCellId 13ms 0.023% 80.06% 491ms 0.85% Element::CalculateCircumsphere 490ms 0.85% 80.92% 490ms 0.85% AbstractElement::IsDeleted 0 0% 80.92% 484ms 0.84% boost::numeric::ublas::inner_prod (inline) 89ms 0.15% 81.07% 481ms 0.84% __dynamic_cast 6ms 0.01% 81.08% 480ms 0.83% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 36ms 0.063% 81.14% 474ms 0.82% boost::numeric::ublas::vector_scalar_binary::evaluate 43ms 0.075% 81.22% 472ms 0.82% AbstractTetrahedralElement::RefreshJacobian 312ms 0.54% 81.76% 472ms 0.82% tetgen::tetgenmesh::sym 115ms 0.2% 81.96% 448ms 0.78% boost::numeric::ublas::indexing_vector_assign 41ms 0.071% 82.03% 448ms 0.78% tetgen::tetgenmesh::enextfnext 1ms 0.0017% 82.03% 447ms 0.78% std::_Rb_tree::_M_insert_unique_ (inline) 436ms 0.76% 82.79% 436ms 0.76% boost::numeric::ublas::c_vector::operator() 48ms 0.083% 82.87% 414ms 0.72% tetgen::tetgenmesh::enext2fnext 2ms 0.0035% 82.88% 409ms 0.71% AbstractCellProperty::IsSubType (inline) 11ms 0.019% 82.90% 402ms 0.7% VertexMesh::CalculateUnitNormalToFaceWithArea 0 0% 82.90% 401ms 0.7% VertexMeshWriter::WriteVtkUsingMesh 29ms 0.05% 82.95% 391ms 0.68% tetgen::tetgenmesh::queue::push 205ms 0.36% 83.30% 388ms 0.67% AbstractTetrahedralMesh::GetElement 23ms 0.04% 83.34% 388ms 0.67% std::_Rb_tree_iterator::operator-- (inline) 2ms 0.0035% 83.35% 384ms 0.67% boost::numeric::ublas::c_vector::operator= (inline) 170ms 0.3% 83.64% 377ms 0.65% boost::numeric::ublas::vector_inner_prod::apply (inline) 230ms 0.4% 84.04% 371ms 0.64% tetgen::tetgenmesh::bond 249ms 0.43% 84.47% 359ms 0.62% tetgen::tetgenmesh::link::add 350ms 0.61% 85.08% 350ms 0.61% std::_Rb_tree_decrement 348ms 0.6% 85.69% 348ms 0.6% tetgen::tetgenmesh::org 12ms 0.021% 85.71% 333ms 0.58% std::vector::insert (inline) 11ms 0.019% 85.72% 326ms 0.57% VertexElement::~VertexElement 48ms 0.083% 85.81% 322ms 0.56% boost::numeric::ublas::vector_reference::operator() (inline) 150ms 0.26% 86.07% 319ms 0.55% Inverse 9ms 0.016% 86.08% 315ms 0.55% AbstractTetrahedralElement::AbstractTetrahedralElement 0 0% 86.08% 312ms 0.54% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 140ms 0.24% 86.33% 305ms 0.53% __cxxabiv1::__si_class_type_info::__do_dyncast 0 0% 86.33% 299ms 0.52% tcache_get (inline) 299ms 0.52% 86.85% 299ms 0.52% tcache_get_n (inline)