File: Test3dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 49551ms, 86.36% of 57374ms total Dropped 874 nodes (cum <= 286.87ms) flat flat% sum% cum cum% 0 0% 0% 57310ms 99.89% __libc_start_call_main 0 0% 0% 57310ms 99.89% __libc_start_main_impl 0 0% 0% 57310ms 99.89% _start 0 0% 0% 57295ms 99.86% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 57295ms 99.86% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 57295ms 99.86% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 57295ms 99.86% main 0 0% 0% 57256ms 99.79% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 57256ms 99.79% CxxTest::TestRunner::runTest (inline) 0 0% 0% 57256ms 99.79% Test3dTissueRepresentativeSimulation::Test3DHoneycombMeshWithGhostNodes 0 0% 0% 57005ms 99.36% AbstractCellBasedSimulation::Solve 0 0% 0% 48422ms 84.40% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 48374ms 84.31% MeshBasedCellPopulation::Update 0 0% 0% 27664ms 48.22% MeshBasedCellPopulation::CreateVoronoiTessellation (inline) 0 0% 0% 27664ms 48.22% MeshBasedCellPopulation::TessellateIfNeeded 226ms 0.39% 0.39% 24384ms 42.50% VertexMesh::VertexMesh 0 0% 0.39% 16951ms 29.54% MutableMesh::ReMesh 0 0% 0.39% 12657ms 22.06% tetgen::tetrahedralize 1ms 0.0017% 0.4% 12524ms 21.83% tetgen::tetgenmesh::delaunizevertices 8ms 0.014% 0.41% 12518ms 21.82% tetgen::tetgenmesh::incrflipdelaunay 579ms 1.01% 1.42% 11578ms 20.18% TetrahedralMesh::EdgeIterator::operator++ 592ms 1.03% 2.45% 11105ms 19.36% tetgen::tetgenmesh::lawson 20ms 0.035% 2.49% 9881ms 17.22% std::set::insert (inline) 235ms 0.41% 2.90% 9401ms 16.39% std::_Rb_tree::_M_insert_unique 403ms 0.7% 3.60% 9093ms 15.85% VertexElement::AddFace 3057ms 5.33% 8.93% 8616ms 15.02% std::_Rb_tree::_M_lower_bound (inline) 255ms 0.44% 9.37% 8133ms 14.18% std::_Rb_tree::find (inline) 0 0% 9.37% 7550ms 13.16% std::set::count (inline) 254ms 0.44% 9.81% 5639ms 9.83% std::_Rb_tree::_M_insert_ (inline) 117ms 0.2% 10.02% 5378ms 9.37% std::less::operator() (inline) 5321ms 9.27% 19.29% 5321ms 9.27% std::operator< (inline) 0 0% 19.29% 5140ms 8.96% OffLatticeSimulation::UpdateCellLocationsAndTopology 221ms 0.39% 19.68% 5079ms 8.85% operator new 0 0% 19.68% 5022ms 8.75% ForwardEulerNumericalMethod::UpdateAllNodePositions 2ms 0.0035% 19.68% 4990ms 8.70% AbstractNumericalMethod::ComputeForcesIncludingDamping 1126ms 1.96% 21.64% 4777ms 8.33% __GI___libc_malloc 4635ms 8.08% 29.72% 4635ms 8.08% std::_Rb_tree_increment 45ms 0.078% 29.80% 4348ms 7.58% std::__new_allocator::allocate (inline) 0 0% 29.80% 4320ms 7.53% std::allocator_traits::allocate (inline) 9ms 0.016% 29.81% 4236ms 7.38% std::_Rb_tree::~_Rb_tree (inline) 1619ms 2.82% 32.64% 4225ms 7.36% std::_Rb_tree::_M_erase 0 0% 32.64% 4180ms 7.29% std::set::~set (inline) 3ms 0.0052% 32.64% 4109ms 7.16% MeshBasedCellPopulation::UpdateNodePairs 9ms 0.016% 32.66% 4105ms 7.15% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 16ms 0.028% 32.69% 3960ms 6.90% MeshBasedCellPopulation::SpringIterator::operator++ 1240ms 2.16% 34.85% 3818ms 6.65% std::_Rb_tree::_M_get_insert_unique_pos 1142ms 1.99% 36.84% 3767ms 6.57% __GI___libc_free 3ms 0.0052% 36.84% 3653ms 6.37% std::set_intersection (inline) 262ms 0.46% 37.30% 3650ms 6.36% std::__set_intersection 31ms 0.054% 37.35% 3606ms 6.29% Node::AddElement 0 0% 37.35% 3536ms 6.16% std::_Rb_tree::_M_create_node (inline) 0 0% 37.35% 3509ms 6.12% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 37.35% 3488ms 6.08% std::_Rb_tree::_M_get_node (inline) 9ms 0.016% 37.37% 3477ms 6.06% TetrahedralMesh::ImportFromMesher 117ms 0.2% 37.57% 3437ms 5.99% tetgen::tetgenmesh::insphere_sos 2506ms 4.37% 41.94% 3339ms 5.82% _int_malloc 138ms 0.24% 42.18% 3335ms 5.81% std::__new_allocator::deallocate (inline) 0 0% 42.18% 3315ms 5.78% std::allocator_traits::deallocate (inline) 3043ms 5.30% 47.48% 3310ms 5.77% tetgen::insphere 0 0% 47.48% 3298ms 5.75% VertexMesh::~VertexMesh 0 0% 47.48% 3289ms 5.73% AbstractCellPopulation::WriteResultsToFiles 3125ms 5.45% 52.93% 3125ms 5.45% std::_Rb_tree::_S_right (inline) 166ms 0.29% 53.22% 2923ms 5.09% std::_Rb_tree_const_iterator::operator++ (inline) 84ms 0.15% 53.37% 2719ms 4.74% MutableElement::AddNode 208ms 0.36% 53.73% 2651ms 4.62% tetgen::tetgenmesh::flip23 1197ms 2.09% 55.82% 2621ms 4.57% _int_free 180ms 0.31% 56.13% 2400ms 4.18% Node::~Node 197ms 0.34% 56.47% 2179ms 3.80% VertexMesh::Clear 3ms 0.0052% 56.48% 2170ms 3.78% MeshBasedCellPopulationWithGhostNodes::WriteVtkResultsToFile 202ms 0.35% 56.83% 2158ms 3.76% VertexMesh::GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex 1ms 0.0017% 56.83% 1972ms 3.44% std::_Rb_tree_iterator::operator++ (inline) 0 0% 56.83% 1944ms 3.39% std::_Rb_tree::_M_drop_node (inline) 1939ms 3.38% 60.21% 1939ms 3.38% std::_Rb_tree_insert_and_rebalance 0 0% 60.21% 1928ms 3.36% std::_Rb_tree::_M_put_node (inline) 177ms 0.31% 60.52% 1791ms 3.12% tetgen::tetgenmesh::flip32 6ms 0.01% 60.53% 1705ms 2.97% Element::Element 1424ms 2.48% 63.01% 1424ms 2.48% Node::GetIndex 951ms 1.66% 64.67% 1406ms 2.45% malloc_consolidate 1316ms 2.29% 66.96% 1400ms 2.44% tetgen::orient3d 12ms 0.021% 66.99% 1399ms 2.44% std::_Vector_base::_M_deallocate (inline) 195ms 0.34% 67.32% 1393ms 2.43% TetrahedralMesh::Clear 6ms 0.01% 67.34% 1386ms 2.42% Element::RegisterWithNodes (inline) 0 0% 67.34% 1289ms 2.25% std::vector::~vector (inline) 166ms 0.29% 67.62% 1265ms 2.20% tetgen::tetgenmesh::enqueueflipface 1ms 0.0017% 67.63% 1223ms 2.13% std::_Vector_base::~_Vector_base (inline) 5ms 0.0087% 67.64% 1192ms 2.08% _int_free_maybe_consolidate 34ms 0.059% 67.69% 1184ms 2.06% tetgen::tetgenmesh::locate 71ms 0.12% 67.82% 1110ms 1.93% std::vector::_M_realloc_insert 95ms 0.17% 67.98% 1091ms 1.90% tetgen::tetgenmesh::preciselocate 70ms 0.12% 68.11% 1055ms 1.84% std::map::operator[] 1014ms 1.77% 69.87% 1014ms 1.77% unlink_chunk 775ms 1.35% 71.22% 944ms 1.65% AbstractElement::GetNodeGlobalIndex 0 0% 71.22% 927ms 1.62% std::_Rb_tree::lower_bound (inline) 0 0% 71.22% 927ms 1.62% std::map::lower_bound (inline) 5ms 0.0087% 71.23% 918ms 1.60% VertexMesh::GenerateVerticesFromElementCircumcentres 119ms 0.21% 71.44% 907ms 1.58% std::vector::push_back (inline) 890ms 1.55% 72.99% 890ms 1.55% tetgen::tetgenmesh::triface::triface 0 0% 72.99% 885ms 1.54% VoronoiDataWriter::Visit 13ms 0.023% 73.01% 845ms 1.47% std::_Vector_base::_M_allocate (inline) 2ms 0.0035% 73.02% 802ms 1.40% TetrahedralMesh::RefreshJacobianCachedData 731ms 1.27% 74.29% 731ms 1.27% tetgen::tetgenmesh::oppo 11ms 0.019% 74.31% 722ms 1.26% AbstractTetrahedralElement::CalculateInverseJacobian 0 0% 74.31% 721ms 1.26% AbstractTwoBodyInteractionForce::AddForceContribution 19ms 0.033% 74.34% 721ms 1.26% boost::numeric::ublas::vector_assign (inline) 16ms 0.028% 74.37% 683ms 1.19% AbstractTetrahedralElement::CalculateJacobian 14ms 0.024% 74.40% 677ms 1.18% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 11ms 0.019% 74.42% 673ms 1.17% boost::numeric::ublas::c_vector::c_vector (inline) 334ms 0.58% 75.00% 670ms 1.17% tetgen::tetgenmesh::fnextself 283ms 0.49% 75.49% 664ms 1.16% AbstractElement::GetNodeLocation 629ms 1.10% 76.59% 629ms 1.10% [libchaste_mesh.so] 0 0% 76.59% 580ms 1.01% std::set::find (inline) 49ms 0.085% 76.67% 573ms 1% __atan2 547ms 0.95% 77.63% 547ms 0.95% tetgen::tetgenmesh::triface::operator= 402ms 0.7% 78.33% 524ms 0.91% __ieee754_atan2_fma 49ms 0.085% 78.41% 514ms 0.9% AbstractTetrahedralElement::RefreshJacobian 15ms 0.026% 78.44% 514ms 0.9% Element::CalculateCircumsphere 511ms 0.89% 79.33% 511ms 0.89% std::vector::size (inline) 507ms 0.88% 80.21% 507ms 0.88% AbstractElement::IsDeleted 499ms 0.87% 81.08% 499ms 0.87% Node::rGetLocation 0 0% 81.08% 496ms 0.86% std::insert_iterator::operator= (inline) 0 0% 81.08% 487ms 0.85% boost::numeric::ublas::inner_prod (inline) 3ms 0.0052% 81.09% 481ms 0.84% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 31ms 0.054% 81.14% 478ms 0.83% boost::numeric::ublas::vector_scalar_binary::evaluate 127ms 0.22% 81.36% 461ms 0.8% boost::numeric::ublas::indexing_vector_assign 45ms 0.078% 81.44% 445ms 0.78% tetgen::tetgenmesh::enextfnext 0 0% 81.44% 436ms 0.76% std::_Rb_tree::_M_insert_unique_ (inline) 42ms 0.073% 81.51% 436ms 0.76% tetgen::tetgenmesh::enext2fnext 426ms 0.74% 82.26% 426ms 0.74% boost::numeric::ublas::c_vector::operator() 22ms 0.038% 82.30% 415ms 0.72% std::_Rb_tree_iterator::operator-- (inline) 278ms 0.48% 82.78% 415ms 0.72% tetgen::tetgenmesh::sym 25ms 0.044% 82.82% 401ms 0.7% VertexMesh::CalculateUnitNormalToFaceWithArea 4ms 0.007% 82.83% 399ms 0.7% CellPropertyCollection::GetPropertiesType (inline) 3ms 0.0052% 82.84% 397ms 0.69% boost::numeric::ublas::c_vector::operator= (inline) 178ms 0.31% 83.15% 397ms 0.69% boost::numeric::ublas::vector_inner_prod::apply (inline) 283ms 0.49% 83.64% 395ms 0.69% tetgen::tetgenmesh::bond 210ms 0.37% 84.00% 390ms 0.68% AbstractTetrahedralMesh::GetElement 0 0% 84.00% 390ms 0.68% VertexMeshWriter::WriteVtkUsingMesh 6ms 0.01% 84.02% 379ms 0.66% Cell::GetCellId 82ms 0.14% 84.16% 379ms 0.66% __dynamic_cast 369ms 0.64% 84.80% 369ms 0.64% std::_Rb_tree_decrement 23ms 0.04% 84.84% 364ms 0.63% tetgen::tetgenmesh::queue::push 361ms 0.63% 85.47% 361ms 0.63% tetgen::tetgenmesh::org 14ms 0.024% 85.50% 345ms 0.6% std::vector::insert (inline) 232ms 0.4% 85.90% 341ms 0.59% tetgen::tetgenmesh::link::add 63ms 0.11% 86.01% 322ms 0.56% boost::numeric::ublas::vector_reference::operator() (inline) 0 0% 86.01% 319ms 0.56% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 2ms 0.0035% 86.01% 313ms 0.55% AbstractTetrahedralElement::AbstractTetrahedralElement 3ms 0.0052% 86.02% 310ms 0.54% AbstractCellProperty::IsSubType (inline) 8ms 0.014% 86.03% 306ms 0.53% VertexElement::~VertexElement 118ms 0.21% 86.24% 305ms 0.53% Inverse 73ms 0.13% 86.36% 296ms 0.52% tetgen::tetgenmesh::queue::pop