File: Test3dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 53807ms, 86.37% of 62296ms total Dropped 873 nodes (cum <= 311.48ms) flat flat% sum% cum cum% 0 0% 0% 62240ms 99.91% __libc_start_call_main 0 0% 0% 62240ms 99.91% __libc_start_main_impl 0 0% 0% 62240ms 99.91% _start 0 0% 0% 62222ms 99.88% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 62222ms 99.88% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 62222ms 99.88% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 62222ms 99.88% main 0 0% 0% 62180ms 99.81% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 62180ms 99.81% CxxTest::TestRunner::runTest (inline) 0 0% 0% 62180ms 99.81% Test3dTissueRepresentativeSimulation::Test3DHoneycombMeshWithGhostNodes 0 0% 0% 61904ms 99.37% AbstractCellBasedSimulation::Solve 0 0% 0% 52765ms 84.70% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 52721ms 84.63% MeshBasedCellPopulation::Update 0 0% 0% 28741ms 46.14% MeshBasedCellPopulation::CreateVoronoiTessellation (inline) 0 0% 0% 28741ms 46.14% MeshBasedCellPopulation::TessellateIfNeeded 218ms 0.35% 0.35% 25628ms 41.14% VertexMesh::VertexMesh 1ms 0.0016% 0.35% 19936ms 32.00% MutableMesh::ReMesh 0 0% 0.35% 15920ms 25.56% tetgen::tetrahedralize 2ms 0.0032% 0.35% 15769ms 25.31% tetgen::tetgenmesh::delaunizevertices 11ms 0.018% 0.37% 15762ms 25.30% tetgen::tetgenmesh::incrflipdelaunay 511ms 0.82% 1.19% 14081ms 22.60% tetgen::tetgenmesh::lawson 606ms 0.97% 2.17% 12355ms 19.83% TetrahedralMesh::EdgeIterator::operator++ 30ms 0.048% 2.21% 10003ms 16.06% std::set::insert (inline) 359ms 0.58% 2.79% 9811ms 15.75% VertexElement::AddFace 222ms 0.36% 3.15% 9545ms 15.32% std::_Rb_tree::_M_insert_unique 3191ms 5.12% 8.27% 9103ms 14.61% std::_Rb_tree::_M_lower_bound (inline) 277ms 0.44% 8.71% 8663ms 13.91% std::_Rb_tree::find (inline) 0 0% 8.71% 8048ms 12.92% std::set::count (inline) 103ms 0.17% 8.88% 5757ms 9.24% std::less::operator() (inline) 5706ms 9.16% 18.04% 5706ms 9.16% std::operator< (inline) 319ms 0.51% 18.55% 5678ms 9.11% std::_Rb_tree::_M_insert_ (inline) 0 0% 18.55% 5436ms 8.73% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 18.55% 5303ms 8.51% ForwardEulerNumericalMethod::UpdateAllNodePositions 4ms 0.0064% 18.56% 5283ms 8.48% AbstractNumericalMethod::ComputeForcesIncludingDamping 5063ms 8.13% 26.68% 5063ms 8.13% std::_Rb_tree_increment 144ms 0.23% 26.92% 5043ms 8.10% operator new 1180ms 1.89% 28.81% 4822ms 7.74% __GI___libc_malloc 12ms 0.019% 28.83% 4464ms 7.17% std::_Rb_tree::~_Rb_tree (inline) 1287ms 2.07% 30.89% 4448ms 7.14% std::_Rb_tree::_M_erase 5ms 0.008% 30.90% 4421ms 7.10% MeshBasedCellPopulation::UpdateNodePairs 0 0% 30.90% 4414ms 7.09% std::set::~set (inline) 4ms 0.0064% 30.91% 4399ms 7.06% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 37ms 0.059% 30.97% 4336ms 6.96% std::__new_allocator::allocate (inline) 0 0% 30.97% 4321ms 6.94% std::allocator_traits::allocate (inline) 18ms 0.029% 31.00% 4261ms 6.84% MeshBasedCellPopulation::SpringIterator::operator++ 1561ms 2.51% 33.50% 4173ms 6.70% __GI___libc_free 77ms 0.12% 33.63% 3941ms 6.33% std::__new_allocator::deallocate (inline) 0 0% 33.63% 3912ms 6.28% std::allocator_traits::deallocate (inline) 1ms 0.0016% 33.63% 3909ms 6.27% std::set_intersection (inline) 246ms 0.39% 34.02% 3908ms 6.27% std::__set_intersection 1326ms 2.13% 36.15% 3894ms 6.25% std::_Rb_tree::_M_get_insert_unique_pos 97ms 0.16% 36.31% 3764ms 6.04% tetgen::tetgenmesh::insphere_sos 3384ms 5.43% 41.74% 3658ms 5.87% tetgen::insphere 0 0% 41.74% 3558ms 5.71% std::_Rb_tree::_M_create_node (inline) 0 0% 41.74% 3541ms 5.68% AbstractCellPopulation::WriteResultsToFiles 0 0% 41.74% 3528ms 5.66% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 41.74% 3518ms 5.65% std::_Rb_tree::_M_get_node (inline) 139ms 0.22% 41.96% 3511ms 5.64% tetgen::tetgenmesh::flip23 48ms 0.077% 42.04% 3434ms 5.51% Node::AddElement 2411ms 3.87% 45.91% 3302ms 5.30% _int_malloc 26ms 0.042% 45.95% 3227ms 5.18% TetrahedralMesh::ImportFromMesher 185ms 0.3% 46.25% 3182ms 5.11% std::_Rb_tree_const_iterator::operator++ (inline) 0 0% 46.25% 3132ms 5.03% VertexMesh::~VertexMesh 3032ms 4.87% 51.12% 3032ms 4.87% std::_Rb_tree::_S_right (inline) 74ms 0.12% 51.23% 2721ms 4.37% MutableElement::AddNode 1278ms 2.05% 53.29% 2608ms 4.19% _int_free 0 0% 53.29% 2606ms 4.18% std::_Rb_tree::_M_drop_node (inline) 0 0% 53.29% 2590ms 4.16% std::_Rb_tree::_M_put_node (inline) 143ms 0.23% 53.52% 2505ms 4.02% tetgen::tetgenmesh::flip32 3ms 0.0048% 53.52% 2413ms 3.87% MeshBasedCellPopulationWithGhostNodes::WriteVtkResultsToFile 218ms 0.35% 53.87% 2388ms 3.83% VertexMesh::GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex 149ms 0.24% 54.11% 2349ms 3.77% Node::~Node 0 0% 54.11% 2185ms 3.51% std::_Rb_tree_iterator::operator++ (inline) 140ms 0.22% 54.33% 2107ms 3.38% VertexMesh::Clear 240ms 0.39% 54.72% 1941ms 3.12% tetgen::tetgenmesh::enqueueflipface 1899ms 3.05% 57.77% 1899ms 3.05% std::_Rb_tree_insert_and_rebalance 1579ms 2.53% 60.30% 1651ms 2.65% tetgen::orient3d 1604ms 2.57% 62.88% 1604ms 2.57% Node::GetIndex 3ms 0.0048% 62.88% 1517ms 2.44% Element::Element 104ms 0.17% 63.05% 1363ms 2.19% TetrahedralMesh::Clear 47ms 0.075% 63.12% 1357ms 2.18% tetgen::tetgenmesh::locate 23ms 0.037% 63.16% 1345ms 2.16% std::_Vector_base::_M_deallocate (inline) 901ms 1.45% 64.61% 1321ms 2.12% malloc_consolidate 0 0% 64.61% 1268ms 2.04% std::vector::~vector (inline) 87ms 0.14% 64.75% 1263ms 2.03% tetgen::tetgenmesh::preciselocate 6ms 0.0096% 64.76% 1192ms 1.91% Element::RegisterWithNodes (inline) 3ms 0.0048% 64.76% 1176ms 1.89% std::_Vector_base::~_Vector_base (inline) 6ms 0.0096% 64.77% 1117ms 1.79% _int_free_maybe_consolidate 74ms 0.12% 64.89% 1079ms 1.73% std::map::operator[] 59ms 0.095% 64.98% 1055ms 1.69% std::vector::_M_realloc_insert 1040ms 1.67% 66.65% 1040ms 1.67% tetgen::tetgenmesh::oppo 834ms 1.34% 67.99% 1027ms 1.65% AbstractElement::GetNodeGlobalIndex 1016ms 1.63% 69.62% 1016ms 1.63% unlink_chunk 943ms 1.51% 71.14% 943ms 1.51% tetgen::tetgenmesh::triface::triface 0 0% 71.14% 933ms 1.50% std::_Rb_tree::lower_bound (inline) 0 0% 71.14% 933ms 1.50% std::map::lower_bound (inline) 0 0% 71.14% 890ms 1.43% VoronoiDataWriter::Visit 116ms 0.19% 71.32% 870ms 1.40% std::vector::push_back (inline) 4ms 0.0064% 71.33% 858ms 1.38% VertexMesh::GenerateVerticesFromElementCircumcentres 11ms 0.018% 71.35% 814ms 1.31% std::_Vector_base::_M_allocate (inline) 0 0% 71.35% 767ms 1.23% TetrahedralMesh::RefreshJacobianCachedData 759ms 1.22% 72.57% 759ms 1.22% [libchaste_mesh.so] 284ms 0.46% 73.02% 756ms 1.21% tetgen::tetgenmesh::sym 0 0% 73.02% 712ms 1.14% AbstractTwoBodyInteractionForce::AddForceContribution 8ms 0.013% 73.04% 690ms 1.11% AbstractTetrahedralElement::CalculateInverseJacobian 15ms 0.024% 73.06% 671ms 1.08% AbstractVariableSizeTwoBodyInteractionForce::CalculateForceBetweenNodes 36ms 0.058% 73.12% 664ms 1.07% tetgen::tetgenmesh::queue::push 50ms 0.08% 73.20% 663ms 1.06% __atan2 663ms 1.06% 74.26% 663ms 1.06% tetgen::tetgenmesh::triface::operator= 15ms 0.024% 74.29% 636ms 1.02% AbstractTetrahedralElement::CalculateJacobian 408ms 0.65% 74.94% 628ms 1.01% tetgen::tetgenmesh::link::add 8ms 0.013% 74.95% 626ms 1.00% boost::numeric::ublas::vector_assign (inline) 0 0% 74.95% 608ms 0.98% std::set::find (inline) 64ms 0.1% 75.06% 605ms 0.97% tetgen::tetgenmesh::enext2fnext 476ms 0.76% 75.82% 603ms 0.97% __ieee754_atan2_fma 351ms 0.56% 76.38% 603ms 0.97% tetgen::tetgenmesh::fnextself 10ms 0.016% 76.40% 599ms 0.96% boost::numeric::ublas::c_vector::c_vector (inline) 231ms 0.37% 76.77% 573ms 0.92% tetgen::tetgenmesh::bond 242ms 0.39% 77.16% 554ms 0.89% AbstractElement::GetNodeLocation 50ms 0.08% 77.24% 546ms 0.88% tetgen::tetgenmesh::enextfnext 545ms 0.87% 78.11% 545ms 0.87% std::vector::size (inline) 538ms 0.86% 78.98% 538ms 0.86% AbstractElement::IsDeleted 537ms 0.86% 79.84% 537ms 0.86% Node::rGetLocation 0 0% 79.84% 506ms 0.81% boost::numeric::ublas::inner_prod (inline) 50ms 0.08% 79.92% 504ms 0.81% boost::numeric::ublas::vector_scalar_binary::evaluate 0 0% 79.92% 504ms 0.81% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 0 0% 79.92% 499ms 0.8% std::insert_iterator::operator= (inline) 497ms 0.8% 80.72% 497ms 0.8% tetgen::tetgenmesh::decode 45ms 0.072% 80.79% 461ms 0.74% AbstractTetrahedralElement::RefreshJacobian 456ms 0.73% 81.52% 456ms 0.73% tetgen::tetgenmesh::org 444ms 0.71% 82.23% 444ms 0.71% operator delete 0 0% 82.23% 426ms 0.68% std::_Rb_tree::_M_insert_unique_ (inline) 11ms 0.018% 82.25% 425ms 0.68% Element::CalculateCircumsphere 412ms 0.66% 82.91% 412ms 0.66% tetgen::tetgenmesh::pointmark 182ms 0.29% 83.21% 411ms 0.66% AbstractTetrahedralMesh::GetElement 13ms 0.021% 83.23% 405ms 0.65% VertexMesh::CalculateUnitNormalToFaceWithArea 5ms 0.008% 83.23% 402ms 0.65% CellPropertyCollection::GetPropertiesType (inline) 2ms 0.0032% 83.24% 396ms 0.64% Cell::GetCellId 24ms 0.039% 83.28% 393ms 0.63% std::_Rb_tree_iterator::operator-- (inline) 0 0% 83.28% 389ms 0.62% VertexMeshWriter::WriteVtkUsingMesh 88ms 0.14% 83.42% 386ms 0.62% __dynamic_cast 2ms 0.0032% 83.42% 382ms 0.61% boost::numeric::ublas::c_vector::operator= (inline) 103ms 0.17% 83.59% 380ms 0.61% boost::numeric::ublas::indexing_vector_assign 150ms 0.24% 83.83% 378ms 0.61% boost::numeric::ublas::vector_inner_prod::apply (inline) 368ms 0.59% 84.42% 368ms 0.59% boost::numeric::ublas::c_vector::operator() 10ms 0.016% 84.43% 362ms 0.58% VertexElement::~VertexElement 343ms 0.55% 84.98% 343ms 0.55% std::_Rb_tree_decrement 0 0% 84.98% 339ms 0.54% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 80ms 0.13% 85.11% 330ms 0.53% tetgen::tetgenmesh::queue::pop 13ms 0.021% 85.13% 329ms 0.53% std::vector::insert (inline) 1ms 0.0016% 85.14% 325ms 0.52% AbstractCellProperty::IsSubType (inline) 125ms 0.2% 85.34% 323ms 0.52% Inverse 4ms 0.0064% 85.34% 322ms 0.52% AbstractTetrahedralElement::AbstractTetrahedralElement 322ms 0.52% 85.86% 322ms 0.52% tetgen::tetgenmesh::face::face 320ms 0.51% 86.37% 320ms 0.51% tetgen::tetgenmesh::encode