File: Test3dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 51899ms, 86.90% of 59722ms total Dropped 895 nodes (cum <= 298.61ms) flat flat% sum% cum cum% 0 0% 0% 59676ms 99.92% __libc_start_call_main 0 0% 0% 59676ms 99.92% __libc_start_main_impl 0 0% 0% 59676ms 99.92% _start 0 0% 0% 59659ms 99.89% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 59659ms 99.89% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 59659ms 99.89% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 59659ms 99.89% main 0 0% 0% 59618ms 99.83% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 59618ms 99.83% CxxTest::TestRunner::runTest (inline) 0 0% 0% 59618ms 99.83% Test3dTissueRepresentativeSimulation::Test3DHoneycombMeshWithGhostNodes 0 0% 0% 59344ms 99.37% AbstractCellBasedSimulation::Solve 0 0% 0% 50490ms 84.54% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 50431ms 84.44% MeshBasedCellPopulation::Update 0 0% 0% 26623ms 44.58% MeshBasedCellPopulation::TessellateIfNeeded 0 0% 0% 26622ms 44.58% MeshBasedCellPopulation::CreateVoronoiTessellation (inline) 201ms 0.34% 0.34% 24090ms 40.34% VertexMesh::VertexMesh 0 0% 0.34% 19919ms 33.35% MutableMesh::ReMesh 0 0% 0.34% 16284ms 27.27% tetgen::tetrahedralize 4ms 0.0067% 0.34% 16134ms 27.02% tetgen::tetgenmesh::delaunizevertices 11ms 0.018% 0.36% 16129ms 27.01% tetgen::tetgenmesh::incrflipdelaunay 534ms 0.89% 1.26% 14483ms 24.25% tetgen::tetgenmesh::lawson 625ms 1.05% 2.30% 11885ms 19.90% TetrahedralMesh::EdgeIterator::operator++ 35ms 0.059% 2.36% 9502ms 15.91% std::set::insert (inline) 326ms 0.55% 2.91% 9490ms 15.89% VertexElement::AddFace 195ms 0.33% 3.23% 9066ms 15.18% std::_Rb_tree::_M_insert_unique 3272ms 5.48% 8.71% 8895ms 14.89% std::_Rb_tree::_M_lower_bound (inline) 254ms 0.43% 9.14% 8393ms 14.05% std::_Rb_tree::find (inline) 0 0% 9.14% 7816ms 13.09% std::set::count (inline) 118ms 0.2% 9.33% 5607ms 9.39% std::less::operator() (inline) 5545ms 9.28% 18.62% 5545ms 9.28% std::operator< (inline) 335ms 0.56% 19.18% 5422ms 9.08% std::_Rb_tree::_M_insert_ (inline) 0 0% 19.18% 5270ms 8.82% OffLatticeSimulation::UpdateCellLocationsAndTopology 1ms 0.0017% 19.18% 5163ms 8.65% ForwardEulerNumericalMethod::UpdateAllNodePositions 0 0% 19.18% 5131ms 8.59% AbstractNumericalMethod::ComputeForcesIncludingDamping 4774ms 7.99% 27.18% 4774ms 7.99% std::_Rb_tree_increment 152ms 0.25% 27.43% 4693ms 7.86% operator new 1207ms 2.02% 29.45% 4427ms 7.41% __GI___libc_malloc 0 0% 29.45% 4265ms 7.14% MeshBasedCellPopulation::UpdateNodePairs 5ms 0.0084% 29.46% 4230ms 7.08% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 35ms 0.059% 29.52% 4126ms 6.91% std::__new_allocator::allocate (inline) 15ms 0.025% 29.54% 4118ms 6.90% MeshBasedCellPopulation::SpringIterator::operator++ 0 0% 29.54% 4113ms 6.89% std::allocator_traits::allocate (inline) 118ms 0.2% 29.74% 3868ms 6.48% tetgen::tetgenmesh::insphere_sos 4ms 0.0067% 29.75% 3806ms 6.37% std::_Rb_tree::~_Rb_tree (inline) 1253ms 2.10% 31.85% 3800ms 6.36% std::_Rb_tree::_M_erase 0 0% 31.85% 3771ms 6.31% std::set::~set (inline) 3446ms 5.77% 37.62% 3738ms 6.26% tetgen::insphere 1274ms 2.13% 39.75% 3696ms 6.19% std::_Rb_tree::_M_get_insert_unique_pos 3ms 0.005% 39.75% 3655ms 6.12% std::set_intersection (inline) 232ms 0.39% 40.14% 3652ms 6.11% std::__set_intersection 140ms 0.23% 40.38% 3622ms 6.06% tetgen::tetgenmesh::flip23 1030ms 1.72% 42.10% 3496ms 5.85% __GI___libc_free 0 0% 42.10% 3429ms 5.74% AbstractCellPopulation::WriteResultsToFiles 0 0% 42.10% 3378ms 5.66% std::_Rb_tree::_M_create_node (inline) 0 0% 42.10% 3353ms 5.61% std::_Rb_tree::_M_get_node (inline) 0 0% 42.10% 3344ms 5.60% std::_Rb_tree::_Alloc_node::operator() (inline) 153ms 0.26% 42.36% 3146ms 5.27% std::__new_allocator::deallocate (inline) 0 0% 42.36% 3134ms 5.25% std::allocator_traits::deallocate (inline) 202ms 0.34% 42.70% 2999ms 5.02% std::_Rb_tree_const_iterator::operator++ (inline) 45ms 0.075% 42.77% 2891ms 4.84% Node::AddElement 2144ms 3.59% 46.36% 2861ms 4.79% _int_malloc 8ms 0.013% 46.37% 2854ms 4.78% TetrahedralMesh::ImportFromMesher 2680ms 4.49% 50.86% 2680ms 4.49% std::_Rb_tree::_S_right (inline) 130ms 0.22% 51.08% 2608ms 4.37% tetgen::tetgenmesh::flip32 0 0% 51.08% 2550ms 4.27% VertexMesh::~VertexMesh 1339ms 2.24% 53.32% 2460ms 4.12% _int_free 88ms 0.15% 53.47% 2378ms 3.98% MutableElement::AddNode 6ms 0.01% 53.48% 2338ms 3.91% MeshBasedCellPopulationWithGhostNodes::WriteVtkResultsToFile 218ms 0.37% 53.84% 2316ms 3.88% VertexMesh::GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex 2ms 0.0033% 53.85% 2115ms 3.54% std::_Rb_tree_iterator::operator++ (inline) 0 0% 53.85% 2036ms 3.41% std::_Rb_tree::_M_drop_node (inline) 0 0% 53.85% 2019ms 3.38% std::_Rb_tree::_M_put_node (inline) 132ms 0.22% 54.07% 1931ms 3.23% Node::~Node 224ms 0.38% 54.44% 1855ms 3.11% tetgen::tetgenmesh::enqueueflipface 1775ms 2.97% 57.42% 1775ms 2.97% std::_Rb_tree_insert_and_rebalance 142ms 0.24% 57.65% 1709ms 2.86% VertexMesh::Clear 1530ms 2.56% 60.22% 1603ms 2.68% tetgen::orient3d 1423ms 2.38% 62.60% 1423ms 2.38% Node::GetIndex 5ms 0.0084% 62.61% 1374ms 2.30% Element::Element 35ms 0.059% 62.67% 1359ms 2.28% tetgen::tetgenmesh::locate 95ms 0.16% 62.82% 1284ms 2.15% tetgen::tetgenmesh::preciselocate 84ms 0.14% 62.97% 1211ms 2.03% TetrahedralMesh::Clear 26ms 0.044% 63.01% 1141ms 1.91% std::_Vector_base::_M_deallocate (inline) 69ms 0.12% 63.12% 1101ms 1.84% std::map::operator[] 702ms 1.18% 64.30% 1096ms 1.84% malloc_consolidate 0 0% 64.30% 1035ms 1.73% std::vector::~vector (inline) 1029ms 1.72% 66.02% 1029ms 1.72% tetgen::tetgenmesh::triface::triface 5ms 0.0084% 66.03% 1025ms 1.72% Element::RegisterWithNodes (inline) 67ms 0.11% 66.14% 1023ms 1.71% std::vector::_M_realloc_insert 0 0% 66.14% 963ms 1.61% std::_Rb_tree::lower_bound (inline) 0 0% 66.14% 963ms 1.61% std::map::lower_bound (inline) 1ms 0.0017% 66.14% 957ms 1.60% std::_Vector_base::~_Vector_base (inline) 7ms 0.012% 66.16% 949ms 1.59% _int_free_maybe_consolidate 725ms 1.21% 67.37% 931ms 1.56% AbstractElement::GetNodeGlobalIndex 923ms 1.55% 68.92% 923ms 1.55% tetgen::tetgenmesh::oppo 877ms 1.47% 70.38% 877ms 1.47% unlink_chunk 861ms 1.44% 71.83% 861ms 1.44% tetgen::tetgenmesh::triface::operator= 0 0% 71.83% 860ms 1.44% VoronoiDataWriter::Visit 310ms 0.52% 72.35% 830ms 1.39% tetgen::tetgenmesh::sym 119ms 0.2% 72.54% 825ms 1.38% std::vector::push_back (inline) 5ms 0.0084% 72.55% 765ms 1.28% std::_Vector_base::_M_allocate (inline) 761ms 1.27% 73.83% 761ms 1.27% [libchaste_mesh.so] 4ms 0.0067% 73.83% 757ms 1.27% VertexMesh::GenerateVerticesFromElementCircumcentres 0 0% 73.83% 755ms 1.26% TetrahedralMesh::RefreshJacobianCachedData 0 0% 73.83% 738ms 1.24% AbstractTwoBodyInteractionForce::AddForceContribution 8ms 0.013% 73.85% 693ms 1.16% AbstractTetrahedralElement::CalculateInverseJacobian 14ms 0.023% 73.87% 689ms 1.15% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 11ms 0.018% 73.89% 640ms 1.07% AbstractTetrahedralElement::CalculateJacobian 221ms 0.37% 74.26% 631ms 1.06% tetgen::tetgenmesh::bond 42ms 0.07% 74.33% 627ms 1.05% __atan2 399ms 0.67% 75.00% 619ms 1.04% tetgen::tetgenmesh::fnextself 63ms 0.11% 75.10% 611ms 1.02% tetgen::tetgenmesh::enext2fnext 15ms 0.025% 75.13% 604ms 1.01% boost::numeric::ublas::vector_assign (inline) 442ms 0.74% 75.87% 585ms 0.98% __ieee754_atan2_fma 63ms 0.11% 75.97% 583ms 0.98% tetgen::tetgenmesh::enextfnext 0 0% 75.97% 576ms 0.96% std::set::find (inline) 40ms 0.067% 76.04% 576ms 0.96% tetgen::tetgenmesh::queue::push 13ms 0.022% 76.06% 571ms 0.96% boost::numeric::ublas::c_vector::c_vector (inline) 0 0% 76.06% 540ms 0.9% boost::numeric::ublas::inner_prod (inline) 39ms 0.065% 76.13% 538ms 0.9% boost::numeric::ublas::vector_scalar_binary::evaluate 0 0% 76.13% 538ms 0.9% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 537ms 0.9% 77.03% 537ms 0.9% tetgen::tetgenmesh::decode 350ms 0.59% 77.61% 536ms 0.9% tetgen::tetgenmesh::link::add 234ms 0.39% 78.00% 530ms 0.89% AbstractElement::GetNodeLocation 525ms 0.88% 78.88% 525ms 0.88% std::vector::size (inline) 507ms 0.85% 79.73% 507ms 0.85% tetgen::tetgenmesh::org 479ms 0.8% 80.53% 479ms 0.8% Node::rGetLocation 0 0% 80.53% 462ms 0.77% std::insert_iterator::operator= (inline) 45ms 0.075% 80.61% 447ms 0.75% AbstractTetrahedralElement::RefreshJacobian 437ms 0.73% 81.34% 437ms 0.73% AbstractElement::IsDeleted 185ms 0.31% 81.65% 435ms 0.73% boost::numeric::ublas::vector_inner_prod::apply (inline) 50ms 0.084% 81.74% 421ms 0.7% tetgen::tetgenmesh::queue::pop 113ms 0.19% 81.92% 417ms 0.7% __dynamic_cast 7ms 0.012% 81.94% 415ms 0.69% CellPropertyCollection::GetPropertiesType (inline) 4ms 0.0067% 81.94% 412ms 0.69% Cell::GetCellId 19ms 0.032% 81.97% 412ms 0.69% std::_Rb_tree_iterator::operator-- (inline) 19ms 0.032% 82.01% 406ms 0.68% Element::CalculateCircumsphere 403ms 0.67% 82.68% 403ms 0.67% boost::numeric::ublas::c_vector::operator() 401ms 0.67% 83.35% 401ms 0.67% tetgen::tetgenmesh::encode 0 0% 83.35% 400ms 0.67% std::_Rb_tree::_M_insert_unique_ (inline) 211ms 0.35% 83.71% 387ms 0.65% AbstractTetrahedralMesh::GetElement 0 0% 83.71% 386ms 0.65% VertexMeshWriter::WriteVtkUsingMesh 9ms 0.015% 83.72% 386ms 0.65% boost::numeric::ublas::c_vector::operator= (inline) 385ms 0.64% 84.37% 385ms 0.64% tetgen::tetgenmesh::pointmark 92ms 0.15% 84.52% 376ms 0.63% boost::numeric::ublas::indexing_vector_assign 23ms 0.039% 84.56% 375ms 0.63% VertexMesh::CalculateUnitNormalToFaceWithArea 204ms 0.34% 84.90% 367ms 0.61% tetgen::tetgenmesh::link::deletenode 365ms 0.61% 85.51% 365ms 0.61% std::_Rb_tree_decrement 17ms 0.028% 85.54% 350ms 0.59% std::vector::insert (inline) 5ms 0.0084% 85.55% 344ms 0.58% AbstractTetrahedralElement::AbstractTetrahedralElement 2ms 0.0033% 85.55% 338ms 0.57% AbstractCellProperty::IsSubType (inline) 130ms 0.22% 85.77% 323ms 0.54% Inverse 15ms 0.025% 85.79% 321ms 0.54% VertexElement::~VertexElement 307ms 0.51% 86.31% 307ms 0.51% tetgen::tetgenmesh::face::face 0 0% 86.31% 306ms 0.51% tcache_get (inline) 306ms 0.51% 86.82% 306ms 0.51% tcache_get_n (inline) 48ms 0.08% 86.90% 305ms 0.51% boost::numeric::ublas::vector_reference::operator() (inline)