File: Test3dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 53479ms, 86.97% of 61493ms total Dropped 880 nodes (cum <= 307.46ms) flat flat% sum% cum cum% 0 0% 0% 61411ms 99.87% __libc_start_call_main 0 0% 0% 61411ms 99.87% __libc_start_main_impl 0 0% 0% 61411ms 99.87% _start 0 0% 0% 61395ms 99.84% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 61395ms 99.84% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 61395ms 99.84% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 61395ms 99.84% main 0 0% 0% 61355ms 99.78% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 61355ms 99.78% CxxTest::TestRunner::runTest (inline) 0 0% 0% 61355ms 99.78% Test3dTissueRepresentativeSimulation::Test3DHoneycombMeshWithGhostNodes 0 0% 0% 61085ms 99.34% AbstractCellBasedSimulation::Solve 0 0% 0% 52029ms 84.61% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 51978ms 84.53% MeshBasedCellPopulation::Update 0 0% 0% 30533ms 49.65% MeshBasedCellPopulation::CreateVoronoiTessellation (inline) 0 0% 0% 30533ms 49.65% MeshBasedCellPopulation::TessellateIfNeeded 249ms 0.4% 0.4% 26780ms 43.55% VertexMesh::VertexMesh 0 0% 0.4% 17565ms 28.56% MutableMesh::ReMesh 0 0% 0.4% 12949ms 21.06% tetgen::tetrahedralize 2ms 0.0033% 0.41% 12809ms 20.83% tetgen::tetgenmesh::delaunizevertices 6ms 0.0098% 0.42% 12803ms 20.82% tetgen::tetgenmesh::incrflipdelaunay 561ms 0.91% 1.33% 12102ms 19.68% TetrahedralMesh::EdgeIterator::operator++ 582ms 0.95% 2.28% 11434ms 18.59% tetgen::tetgenmesh::lawson 31ms 0.05% 2.33% 10690ms 17.38% std::set::insert (inline) 202ms 0.33% 2.66% 10185ms 16.56% std::_Rb_tree::_M_insert_unique 413ms 0.67% 3.33% 9587ms 15.59% VertexElement::AddFace 3012ms 4.90% 8.23% 8966ms 14.58% std::_Rb_tree::_M_lower_bound (inline) 219ms 0.36% 8.58% 8392ms 13.65% std::_Rb_tree::find (inline) 0 0% 8.58% 7816ms 12.71% std::set::count (inline) 286ms 0.47% 9.05% 6068ms 9.87% std::_Rb_tree::_M_insert_ (inline) 108ms 0.18% 9.22% 5759ms 9.37% std::less::operator() (inline) 5697ms 9.26% 18.49% 5697ms 9.26% std::operator< (inline) 200ms 0.33% 18.81% 5560ms 9.04% operator new 5507ms 8.96% 27.77% 5507ms 8.96% std::_Rb_tree_increment 1ms 0.0016% 27.77% 5360ms 8.72% OffLatticeSimulation::UpdateCellLocationsAndTopology 1141ms 1.86% 29.62% 5290ms 8.60% __GI___libc_malloc 1ms 0.0016% 29.63% 5213ms 8.48% ForwardEulerNumericalMethod::UpdateAllNodePositions 7ms 0.011% 29.64% 5185ms 8.43% AbstractNumericalMethod::ComputeForcesIncludingDamping 55ms 0.089% 29.73% 4697ms 7.64% std::__new_allocator::allocate (inline) 0 0% 29.73% 4670ms 7.59% std::allocator_traits::allocate (inline) 8ms 0.013% 29.74% 4519ms 7.35% std::_Rb_tree::~_Rb_tree (inline) 1863ms 3.03% 32.77% 4508ms 7.33% std::_Rb_tree::_M_erase 0 0% 32.77% 4451ms 7.24% std::set::~set (inline) 5ms 0.0081% 32.78% 4440ms 7.22% std::set_intersection (inline) 302ms 0.49% 33.27% 4435ms 7.21% std::__set_intersection 4ms 0.0065% 33.28% 4284ms 6.97% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 2ms 0.0033% 33.28% 4251ms 6.91% MeshBasedCellPopulation::UpdateNodePairs 1272ms 2.07% 35.35% 4240ms 6.90% std::_Rb_tree::_M_get_insert_unique_pos 34ms 0.055% 35.40% 4222ms 6.87% Node::AddElement 9ms 0.015% 35.42% 4108ms 6.68% MeshBasedCellPopulation::SpringIterator::operator++ 1337ms 2.17% 37.59% 4095ms 6.66% __GI___libc_free 2809ms 4.57% 42.16% 3821ms 6.21% _int_malloc 0 0% 42.16% 3803ms 6.18% std::_Rb_tree::_M_create_node (inline) 0 0% 42.16% 3779ms 6.15% VertexMesh::~VertexMesh 0 0% 42.16% 3758ms 6.11% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 42.16% 3757ms 6.11% std::_Rb_tree::_M_get_node (inline) 19ms 0.031% 42.19% 3738ms 6.08% TetrahedralMesh::ImportFromMesher 181ms 0.29% 42.48% 3655ms 5.94% std::_Rb_tree_const_iterator::operator++ (inline) 3618ms 5.88% 48.37% 3618ms 5.88% std::_Rb_tree::_S_right (inline) 115ms 0.19% 48.56% 3577ms 5.82% tetgen::tetgenmesh::insphere_sos 129ms 0.21% 48.76% 3566ms 5.80% std::__new_allocator::deallocate (inline) 0 0% 48.76% 3547ms 5.77% std::allocator_traits::deallocate (inline) 0 0% 48.76% 3522ms 5.73% AbstractCellPopulation::WriteResultsToFiles 3151ms 5.12% 53.89% 3445ms 5.60% tetgen::insphere 76ms 0.12% 54.01% 3243ms 5.27% MutableElement::AddNode 180ms 0.29% 54.31% 2768ms 4.50% tetgen::tetgenmesh::flip23 1030ms 1.67% 55.98% 2757ms 4.48% _int_free 158ms 0.26% 56.24% 2669ms 4.34% Node::~Node 197ms 0.32% 56.56% 2435ms 3.96% VertexMesh::Clear 5ms 0.0081% 56.57% 2332ms 3.79% MeshBasedCellPopulationWithGhostNodes::WriteVtkResultsToFile 220ms 0.36% 56.92% 2330ms 3.79% VertexMesh::GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex 1ms 0.0016% 56.93% 2126ms 3.46% std::_Rb_tree_iterator::operator++ (inline) 2100ms 3.42% 60.34% 2100ms 3.42% std::_Rb_tree_insert_and_rebalance 147ms 0.24% 60.58% 1921ms 3.12% tetgen::tetgenmesh::flip32 0 0% 60.58% 1914ms 3.11% std::_Rb_tree::_M_drop_node (inline) 0 0% 60.58% 1898ms 3.09% std::_Rb_tree::_M_put_node (inline) 3ms 0.0049% 60.58% 1825ms 2.97% Element::Element 1758ms 2.86% 63.44% 1758ms 2.86% Node::GetIndex 1144ms 1.86% 65.30% 1690ms 2.75% malloc_consolidate 23ms 0.037% 65.34% 1671ms 2.72% std::_Vector_base::_M_deallocate (inline) 0 0% 65.34% 1545ms 2.51% std::vector::~vector (inline) 227ms 0.37% 65.71% 1512ms 2.46% TetrahedralMesh::Clear 4ms 0.0065% 65.72% 1488ms 2.42% Element::RegisterWithNodes (inline) 0 0% 65.72% 1471ms 2.39% std::_Vector_base::~_Vector_base (inline) 6ms 0.0098% 65.73% 1456ms 2.37% _int_free_maybe_consolidate 1287ms 2.09% 67.82% 1365ms 2.22% tetgen::orient3d 183ms 0.3% 68.12% 1323ms 2.15% tetgen::tetgenmesh::enqueueflipface 1290ms 2.10% 70.21% 1290ms 2.10% unlink_chunk 54ms 0.088% 70.30% 1151ms 1.87% std::vector::_M_realloc_insert 35ms 0.057% 70.36% 1137ms 1.85% tetgen::tetgenmesh::locate 60ms 0.098% 70.46% 1112ms 1.81% std::map::operator[] 5ms 0.0081% 70.46% 1094ms 1.78% VertexMesh::GenerateVerticesFromElementCircumcentres 87ms 0.14% 70.61% 1049ms 1.71% tetgen::tetgenmesh::preciselocate 848ms 1.38% 71.99% 1006ms 1.64% AbstractElement::GetNodeGlobalIndex 0 0% 71.99% 964ms 1.57% std::_Rb_tree::lower_bound (inline) 0 0% 71.99% 964ms 1.57% std::map::lower_bound (inline) 1ms 0.0016% 71.99% 948ms 1.54% VoronoiDataWriter::Visit 940ms 1.53% 73.52% 940ms 1.53% tetgen::tetgenmesh::triface::triface 131ms 0.21% 73.73% 931ms 1.51% std::vector::push_back (inline) 4ms 0.0065% 73.74% 917ms 1.49% std::_Vector_base::_M_allocate (inline) 2ms 0.0033% 73.74% 856ms 1.39% TetrahedralMesh::RefreshJacobianCachedData 413ms 0.67% 74.41% 757ms 1.23% tetgen::tetgenmesh::fnextself 337ms 0.55% 74.96% 749ms 1.22% AbstractElement::GetNodeLocation 12ms 0.02% 74.98% 743ms 1.21% AbstractTetrahedralElement::CalculateInverseJacobian 2ms 0.0033% 74.98% 723ms 1.18% AbstractTwoBodyInteractionForce::AddForceContribution 20ms 0.033% 75.01% 703ms 1.14% AbstractTetrahedralElement::CalculateJacobian 11ms 0.018% 75.03% 690ms 1.12% boost::numeric::ublas::vector_assign (inline) 16ms 0.026% 75.06% 682ms 1.11% AbstractVariableSizeTwoBodyInteractionForce::CalculateForceBetweenNodes 679ms 1.10% 76.16% 679ms 1.10% tetgen::tetgenmesh::oppo 670ms 1.09% 77.25% 670ms 1.09% Node::rGetLocation 9ms 0.015% 77.27% 669ms 1.09% boost::numeric::ublas::c_vector::c_vector (inline) 668ms 1.09% 78.35% 668ms 1.09% tetgen::tetgenmesh::triface::operator= 630ms 1.02% 79.38% 630ms 1.02% AbstractElement::IsDeleted 630ms 1.02% 80.40% 630ms 1.02% [libchaste_mesh.so] 51ms 0.083% 80.48% 572ms 0.93% __atan2 0 0% 80.48% 570ms 0.93% std::set::find (inline) 20ms 0.033% 80.52% 557ms 0.91% Element::CalculateCircumsphere 35ms 0.057% 80.57% 546ms 0.89% AbstractTetrahedralElement::RefreshJacobian 541ms 0.88% 81.45% 541ms 0.88% std::vector::size (inline) 426ms 0.69% 82.15% 521ms 0.85% __ieee754_atan2_fma 0 0% 82.15% 518ms 0.84% std::insert_iterator::operator= (inline) 46ms 0.075% 82.22% 502ms 0.82% tetgen::tetgenmesh::enextfnext 0 0% 82.22% 488ms 0.79% boost::numeric::ublas::inner_prod (inline) 4ms 0.0065% 82.23% 487ms 0.79% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 52ms 0.085% 82.31% 483ms 0.79% boost::numeric::ublas::vector_scalar_binary::evaluate 49ms 0.08% 82.39% 480ms 0.78% tetgen::tetgenmesh::enext2fnext 314ms 0.51% 82.90% 468ms 0.76% tetgen::tetgenmesh::sym 0 0% 82.90% 452ms 0.74% std::_Rb_tree::_M_insert_unique_ (inline) 116ms 0.19% 83.09% 438ms 0.71% boost::numeric::ublas::indexing_vector_assign 1ms 0.0016% 83.09% 435ms 0.71% CellPropertyCollection::GetPropertiesType (inline) 21ms 0.034% 83.13% 421ms 0.68% VertexMesh::CalculateUnitNormalToFaceWithArea 310ms 0.5% 83.63% 419ms 0.68% tetgen::tetgenmesh::bond 3ms 0.0049% 83.64% 407ms 0.66% Cell::GetCellId 99ms 0.16% 83.80% 405ms 0.66% __dynamic_cast 6ms 0.0098% 83.81% 405ms 0.66% boost::numeric::ublas::c_vector::operator= (inline) 19ms 0.031% 83.84% 405ms 0.66% std::_Rb_tree_iterator::operator-- (inline) 0 0% 83.84% 402ms 0.65% VertexMeshWriter::WriteVtkUsingMesh 224ms 0.36% 84.20% 388ms 0.63% AbstractTetrahedralMesh::GetElement 15ms 0.024% 84.23% 374ms 0.61% std::vector::insert (inline) 373ms 0.61% 84.83% 373ms 0.61% boost::numeric::ublas::c_vector::operator() 373ms 0.61% 85.44% 373ms 0.61% tetgen::tetgenmesh::org 370ms 0.6% 86.04% 370ms 0.6% std::_Rb_tree_decrement 169ms 0.27% 86.32% 368ms 0.6% boost::numeric::ublas::vector_inner_prod::apply (inline) 32ms 0.052% 86.37% 357ms 0.58% tetgen::tetgenmesh::queue::push 2ms 0.0033% 86.37% 348ms 0.57% AbstractCellProperty::IsSubType (inline) 0 0% 86.37% 345ms 0.56% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 6ms 0.0098% 86.38% 336ms 0.55% AbstractTetrahedralElement::AbstractTetrahedralElement 4ms 0.0065% 86.39% 334ms 0.54% VertexElement::~VertexElement 221ms 0.36% 86.75% 321ms 0.52% tetgen::tetgenmesh::link::add 136ms 0.22% 86.97% 319ms 0.52% Inverse