File: Test3dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 62191ms, 87.09% of 71407ms total Dropped 896 nodes (cum <= 357.04ms) flat flat% sum% cum cum% 0 0% 0% 71345ms 99.91% __libc_start_call_main 0 0% 0% 71345ms 99.91% __libc_start_main_impl 0 0% 0% 71345ms 99.91% _start 0 0% 0% 71327ms 99.89% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 71327ms 99.89% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 71327ms 99.89% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 71327ms 99.89% main 0 0% 0% 71281ms 99.82% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 71281ms 99.82% CxxTest::TestRunner::runTest (inline) 0 0% 0% 71281ms 99.82% Test3dTissueRepresentativeSimulation::Test3DHoneycombMeshWithGhostNodes 0 0% 0% 70993ms 99.42% AbstractCellBasedSimulation::Solve 0 0% 0% 60235ms 84.35% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 60184ms 84.28% MeshBasedCellPopulation::Update 0 0% 0% 34473ms 48.28% MeshBasedCellPopulation::CreateVoronoiTessellation (inline) 0 0% 0% 34473ms 48.28% MeshBasedCellPopulation::TessellateIfNeeded 269ms 0.38% 0.38% 30171ms 42.25% VertexMesh::VertexMesh 0 0% 0.38% 21047ms 29.47% MutableMesh::ReMesh 0 0% 0.38% 16265ms 22.78% tetgen::tetrahedralize 4ms 0.0056% 0.38% 16111ms 22.56% tetgen::tetgenmesh::delaunizevertices 12ms 0.017% 0.4% 16106ms 22.56% tetgen::tetgenmesh::incrflipdelaunay 618ms 0.87% 1.26% 14407ms 20.18% TetrahedralMesh::EdgeIterator::operator++ 520ms 0.73% 1.99% 14390ms 20.15% tetgen::tetgenmesh::lawson 28ms 0.039% 2.03% 11459ms 16.05% std::set::insert (inline) 296ms 0.41% 2.45% 11020ms 15.43% std::_Rb_tree::_M_insert_unique 442ms 0.62% 3.07% 10886ms 15.25% VertexElement::AddFace 3177ms 4.45% 7.51% 10723ms 15.02% std::_Rb_tree::_M_lower_bound (inline) 264ms 0.37% 7.88% 10060ms 14.09% std::_Rb_tree::find (inline) 0 0% 7.88% 9443ms 13.22% std::set::count (inline) 122ms 0.17% 8.06% 7189ms 10.07% std::less::operator() (inline) 7132ms 9.99% 18.04% 7132ms 9.99% std::operator< (inline) 6833ms 9.57% 27.61% 6833ms 9.57% std::_Rb_tree_increment 310ms 0.43% 28.05% 6491ms 9.09% std::_Rb_tree::_M_insert_ (inline) 182ms 0.25% 28.30% 6238ms 8.74% operator new 0 0% 28.30% 6231ms 8.73% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 28.30% 6057ms 8.48% ForwardEulerNumericalMethod::UpdateAllNodePositions 3ms 0.0042% 28.31% 6040ms 8.46% AbstractNumericalMethod::ComputeForcesIncludingDamping 1290ms 1.81% 30.11% 6001ms 8.40% __GI___libc_malloc 47ms 0.066% 30.18% 5206ms 7.29% std::__new_allocator::allocate (inline) 0 0% 30.18% 5189ms 7.27% std::allocator_traits::allocate (inline) 12ms 0.017% 30.19% 5059ms 7.08% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 0 0% 30.19% 5036ms 7.05% MeshBasedCellPopulation::UpdateNodePairs 4ms 0.0056% 30.20% 4993ms 6.99% std::set_intersection (inline) 289ms 0.4% 30.60% 4989ms 6.99% std::__set_intersection 4ms 0.0056% 30.61% 4969ms 6.96% std::_Rb_tree::~_Rb_tree (inline) 1824ms 2.55% 33.16% 4964ms 6.95% std::_Rb_tree::_M_erase 0 0% 33.16% 4910ms 6.88% std::set::~set (inline) 15ms 0.021% 33.19% 4861ms 6.81% MeshBasedCellPopulation::SpringIterator::operator++ 1373ms 1.92% 35.11% 4770ms 6.68% __GI___libc_free 1372ms 1.92% 37.03% 4500ms 6.30% std::_Rb_tree::_M_get_insert_unique_pos 60ms 0.084% 37.11% 4433ms 6.21% Node::AddElement 0 0% 37.11% 4366ms 6.11% AbstractCellPopulation::WriteResultsToFiles 3122ms 4.37% 41.49% 4347ms 6.09% _int_malloc 0 0% 41.49% 4330ms 6.06% VertexMesh::~VertexMesh 171ms 0.24% 41.73% 4224ms 5.92% std::_Rb_tree_const_iterator::operator++ (inline) 0 0% 41.73% 4188ms 5.86% std::_Rb_tree::_M_create_node (inline) 147ms 0.21% 41.93% 4156ms 5.82% std::__new_allocator::deallocate (inline) 0 0% 41.93% 4151ms 5.81% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 41.93% 4141ms 5.80% std::allocator_traits::deallocate (inline) 0 0% 41.93% 4132ms 5.79% std::_Rb_tree::_M_get_node (inline) 4059ms 5.68% 47.62% 4059ms 5.68% std::_Rb_tree::_S_right (inline) 121ms 0.17% 47.79% 3857ms 5.40% tetgen::tetgenmesh::insphere_sos 9ms 0.013% 47.80% 3851ms 5.39% TetrahedralMesh::ImportFromMesher 3440ms 4.82% 52.62% 3723ms 5.21% tetgen::insphere 123ms 0.17% 52.79% 3523ms 4.93% tetgen::tetgenmesh::flip23 1434ms 2.01% 54.80% 3392ms 4.75% _int_free 74ms 0.1% 54.90% 3366ms 4.71% MutableElement::AddNode 198ms 0.28% 55.18% 3110ms 4.36% VertexMesh::GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex 4ms 0.0056% 55.18% 3020ms 4.23% MeshBasedCellPopulationWithGhostNodes::WriteVtkResultsToFile 227ms 0.32% 55.50% 2978ms 4.17% Node::~Node 0 0% 55.50% 2929ms 4.10% std::_Rb_tree_iterator::operator++ (inline) 198ms 0.28% 55.78% 2756ms 3.86% VertexMesh::Clear 132ms 0.18% 55.96% 2615ms 3.66% tetgen::tetgenmesh::flip32 0 0% 55.96% 2306ms 3.23% std::_Rb_tree::_M_drop_node (inline) 0 0% 55.96% 2294ms 3.21% std::_Rb_tree::_M_put_node (inline) 2233ms 3.13% 59.09% 2233ms 3.13% Node::GetIndex 2114ms 2.96% 62.05% 2114ms 2.96% std::_Rb_tree_insert_and_rebalance 217ms 0.3% 62.35% 2060ms 2.88% tetgen::tetgenmesh::enqueueflipface 1364ms 1.91% 64.26% 1968ms 2.76% malloc_consolidate 5ms 0.007% 64.27% 1918ms 2.69% Element::Element 34ms 0.048% 64.32% 1881ms 2.63% std::_Vector_base::_M_deallocate (inline) 0 0% 64.32% 1793ms 2.51% std::vector::~vector (inline) 2ms 0.0028% 64.32% 1722ms 2.41% std::_Vector_base::~_Vector_base (inline) 2ms 0.0028% 64.32% 1680ms 2.35% _int_free_maybe_consolidate 1521ms 2.13% 66.45% 1596ms 2.24% tetgen::orient3d 9ms 0.013% 66.47% 1568ms 2.20% Element::RegisterWithNodes (inline) 93ms 0.13% 66.60% 1518ms 2.13% TetrahedralMesh::Clear 1439ms 2.02% 68.61% 1439ms 2.02% unlink_chunk 34ms 0.048% 68.66% 1385ms 1.94% tetgen::tetgenmesh::locate 77ms 0.11% 68.77% 1317ms 1.84% std::map::operator[] 86ms 0.12% 68.89% 1310ms 1.83% tetgen::tetgenmesh::preciselocate 78ms 0.11% 69.00% 1276ms 1.79% std::vector::_M_realloc_insert 1055ms 1.48% 70.47% 1263ms 1.77% AbstractElement::GetNodeGlobalIndex 2ms 0.0028% 70.48% 1188ms 1.66% VertexMesh::GenerateVerticesFromElementCircumcentres 0 0% 70.48% 1145ms 1.60% std::_Rb_tree::lower_bound (inline) 0 0% 70.48% 1145ms 1.60% std::map::lower_bound (inline) 1ms 0.0014% 70.48% 1078ms 1.51% VoronoiDataWriter::Visit 1074ms 1.50% 71.98% 1074ms 1.50% tetgen::tetgenmesh::oppo 114ms 0.16% 72.14% 1060ms 1.48% std::vector::push_back (inline) 0 0% 72.14% 1057ms 1.48% std::_Vector_base::_M_allocate (inline) 972ms 1.36% 73.50% 972ms 1.36% tetgen::tetgenmesh::triface::triface 0 0% 73.50% 896ms 1.25% TetrahedralMesh::RefreshJacobianCachedData 370ms 0.52% 74.02% 858ms 1.20% tetgen::tetgenmesh::sym 807ms 1.13% 75.15% 807ms 1.13% [libchaste_mesh.so] 777ms 1.09% 76.24% 777ms 1.09% AbstractElement::IsDeleted 775ms 1.09% 77.33% 775ms 1.09% Node::rGetLocation 9ms 0.013% 77.34% 770ms 1.08% AbstractTetrahedralElement::CalculateInverseJacobian 336ms 0.47% 77.81% 767ms 1.07% AbstractElement::GetNodeLocation 2ms 0.0028% 77.81% 751ms 1.05% AbstractTwoBodyInteractionForce::AddForceContribution 8ms 0.011% 77.82% 712ms 1% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 19ms 0.027% 77.85% 699ms 0.98% AbstractTetrahedralElement::CalculateJacobian 696ms 0.97% 78.82% 696ms 0.97% tetgen::tetgenmesh::triface::operator= 663ms 0.93% 79.75% 663ms 0.93% std::vector::size (inline) 248ms 0.35% 80.10% 663ms 0.93% tetgen::tetgenmesh::bond 34ms 0.048% 80.15% 650ms 0.91% tetgen::tetgenmesh::queue::push 15ms 0.021% 80.17% 639ms 0.89% boost::numeric::ublas::vector_assign (inline) 386ms 0.54% 80.71% 633ms 0.89% tetgen::tetgenmesh::fnextself 39ms 0.055% 80.76% 631ms 0.88% __atan2 374ms 0.52% 81.29% 616ms 0.86% tetgen::tetgenmesh::link::add 0 0% 81.29% 609ms 0.85% std::set::find (inline) 9ms 0.013% 81.30% 593ms 0.83% boost::numeric::ublas::c_vector::c_vector (inline) 475ms 0.67% 81.97% 586ms 0.82% __ieee754_atan2_fma 43ms 0.06% 82.03% 570ms 0.8% tetgen::tetgenmesh::enextfnext 46ms 0.064% 82.09% 565ms 0.79% tetgen::tetgenmesh::enext2fnext 564ms 0.79% 82.88% 564ms 0.79% tetgen::tetgenmesh::org 17ms 0.024% 82.90% 557ms 0.78% Element::CalculateCircumsphere 0 0% 82.90% 539ms 0.75% boost::numeric::ublas::inner_prod (inline) 1ms 0.0014% 82.91% 534ms 0.75% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 45ms 0.063% 82.97% 533ms 0.75% boost::numeric::ublas::vector_scalar_binary::evaluate 510ms 0.71% 83.68% 510ms 0.71% tetgen::tetgenmesh::decode 42ms 0.059% 83.74% 505ms 0.71% AbstractTetrahedralElement::RefreshJacobian 495ms 0.69% 84.43% 495ms 0.69% tetgen::tetgenmesh::pointmark 24ms 0.034% 84.47% 466ms 0.65% VertexMesh::CalculateUnitNormalToFaceWithArea 0 0% 84.47% 459ms 0.64% std::insert_iterator::operator= (inline) 199ms 0.28% 84.75% 431ms 0.6% boost::numeric::ublas::vector_inner_prod::apply (inline) 213ms 0.3% 85.04% 425ms 0.6% AbstractTetrahedralMesh::GetElement 26ms 0.036% 85.08% 416ms 0.58% std::_Rb_tree_iterator::operator-- (inline) 7ms 0.0098% 85.09% 411ms 0.58% CellPropertyCollection::GetPropertiesType (inline) 7ms 0.0098% 85.10% 411ms 0.58% boost::numeric::ublas::c_vector::operator= (inline) 109ms 0.15% 85.25% 409ms 0.57% boost::numeric::ublas::indexing_vector_assign 407ms 0.57% 85.82% 407ms 0.57% boost::numeric::ublas::c_vector::operator() 0 0% 85.82% 406ms 0.57% std::_Rb_tree::_M_insert_unique_ (inline) 402ms 0.56% 86.39% 402ms 0.56% tetgen::tetgenmesh::encode 7ms 0.0098% 86.40% 401ms 0.56% VertexElement::~VertexElement 123ms 0.17% 86.57% 399ms 0.56% __dynamic_cast 0 0% 86.57% 397ms 0.56% VertexMeshWriter::WriteVtkUsingMesh 7ms 0.0098% 86.58% 396ms 0.55% Cell::GetCellId 0 0% 86.58% 396ms 0.55% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 368ms 0.52% 87.09% 368ms 0.52% std::_Rb_tree_decrement