File: Test3dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 58868ms, 87.41% of 67350ms total Dropped 866 nodes (cum <= 336.75ms) flat flat% sum% cum cum% 0 0% 0% 67297ms 99.92% __libc_start_call_main 0 0% 0% 67297ms 99.92% __libc_start_main_impl 0 0% 0% 67297ms 99.92% _start 0 0% 0% 67280ms 99.90% main 0 0% 0% 67279ms 99.89% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 67279ms 99.89% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 67279ms 99.89% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 67240ms 99.84% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 67240ms 99.84% CxxTest::TestRunner::runTest (inline) 0 0% 0% 67240ms 99.84% Test3dTissueRepresentativeSimulation::Test3DHoneycombMeshWithGhostNodes 0 0% 0% 66953ms 99.41% AbstractCellBasedSimulation::Solve 0 0% 0% 55958ms 83.09% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 55910ms 83.01% MeshBasedCellPopulation::Update 0 0% 0% 33803ms 50.19% MeshBasedCellPopulation::CreateVoronoiTessellation (inline) 0 0% 0% 33803ms 50.19% MeshBasedCellPopulation::TessellateIfNeeded 260ms 0.39% 0.39% 29376ms 43.62% VertexMesh::VertexMesh 0 0% 0.39% 17678ms 26.25% MutableMesh::ReMesh 547ms 0.81% 1.20% 13671ms 20.30% TetrahedralMesh::EdgeIterator::operator++ 0 0% 1.20% 12727ms 18.90% tetgen::tetrahedralize 1ms 0.0015% 1.20% 12588ms 18.69% tetgen::tetgenmesh::delaunizevertices 6ms 0.0089% 1.21% 12585ms 18.69% tetgen::tetgenmesh::incrflipdelaunay 33ms 0.049% 1.26% 11274ms 16.74% std::set::insert (inline) 530ms 0.79% 2.04% 11244ms 16.69% tetgen::tetgenmesh::lawson 197ms 0.29% 2.34% 10799ms 16.03% std::_Rb_tree::_M_insert_unique 3056ms 4.54% 6.87% 10423ms 15.48% std::_Rb_tree::_M_lower_bound (inline) 465ms 0.69% 7.56% 10046ms 14.92% VertexElement::AddFace 234ms 0.35% 7.91% 9582ms 14.23% std::_Rb_tree::find (inline) 0 0% 7.91% 9060ms 13.45% std::set::count (inline) 7533ms 11.18% 19.10% 7533ms 11.18% std::_Rb_tree_increment 102ms 0.15% 19.25% 6893ms 10.23% std::less::operator() (inline) 6862ms 10.19% 29.44% 6862ms 10.19% std::operator< (inline) 257ms 0.38% 29.82% 6242ms 9.27% std::_Rb_tree::_M_insert_ (inline) 236ms 0.35% 30.17% 5942ms 8.82% operator new 0 0% 30.17% 5934ms 8.81% OffLatticeSimulation::UpdateCellLocationsAndTopology 2ms 0.003% 30.17% 5761ms 8.55% ForwardEulerNumericalMethod::UpdateAllNodePositions 3ms 0.0045% 30.18% 5729ms 8.51% AbstractNumericalMethod::ComputeForcesIncludingDamping 1030ms 1.53% 31.71% 5641ms 8.38% __GI___libc_malloc 6ms 0.0089% 31.71% 5067ms 7.52% std::set_intersection (inline) 285ms 0.42% 32.14% 5061ms 7.51% std::__set_intersection 5ms 0.0074% 32.15% 4973ms 7.38% std::_Rb_tree::~_Rb_tree (inline) 2151ms 3.19% 35.34% 4968ms 7.38% std::_Rb_tree::_M_erase 43ms 0.064% 35.40% 4942ms 7.34% std::__new_allocator::allocate (inline) 0 0% 35.40% 4926ms 7.31% std::allocator_traits::allocate (inline) 0 0% 35.40% 4901ms 7.28% AbstractCellPopulation::WriteResultsToFiles 0 0% 35.40% 4901ms 7.28% std::set::~set (inline) 30ms 0.045% 35.45% 4840ms 7.19% Node::AddElement 1ms 0.0015% 35.45% 4774ms 7.09% MeshBasedCellPopulation::UpdateNodePairs 6ms 0.0089% 35.46% 4772ms 7.09% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 1275ms 1.89% 37.35% 4661ms 6.92% std::_Rb_tree::_M_get_insert_unique_pos 15ms 0.022% 37.37% 4607ms 6.84% MeshBasedCellPopulation::SpringIterator::operator++ 1269ms 1.88% 39.26% 4487ms 6.66% __GI___libc_free 0 0% 39.26% 4472ms 6.64% VertexMesh::~VertexMesh 4442ms 6.60% 45.85% 4442ms 6.60% std::_Rb_tree::_S_right (inline) 171ms 0.25% 46.11% 4342ms 6.45% std::_Rb_tree_const_iterator::operator++ (inline) 3136ms 4.66% 50.76% 4281ms 6.36% _int_malloc 10ms 0.015% 50.78% 4028ms 5.98% TetrahedralMesh::ImportFromMesher 0 0% 50.78% 3909ms 5.80% std::_Rb_tree::_M_create_node (inline) 0 0% 50.78% 3874ms 5.75% std::_Rb_tree::_Alloc_node::operator() (inline) 111ms 0.16% 50.94% 3874ms 5.75% std::__new_allocator::deallocate (inline) 0 0% 50.94% 3856ms 5.73% std::allocator_traits::deallocate (inline) 0 0% 50.94% 3852ms 5.72% std::_Rb_tree::_M_get_node (inline) 218ms 0.32% 51.27% 3662ms 5.44% VertexMesh::GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex 72ms 0.11% 51.37% 3586ms 5.32% MutableElement::AddNode 103ms 0.15% 51.53% 3559ms 5.28% tetgen::tetgenmesh::insphere_sos 0 0% 51.53% 3471ms 5.15% std::_Rb_tree_iterator::operator++ (inline) 3147ms 4.67% 56.20% 3443ms 5.11% tetgen::insphere 6ms 0.0089% 56.21% 3420ms 5.08% MeshBasedCellPopulationWithGhostNodes::WriteVtkResultsToFile 1204ms 1.79% 58.00% 3213ms 4.77% _int_free 209ms 0.31% 58.31% 3056ms 4.54% Node::~Node 244ms 0.36% 58.67% 2842ms 4.22% VertexMesh::Clear 213ms 0.32% 58.98% 2723ms 4.04% tetgen::tetgenmesh::flip23 2217ms 3.29% 62.28% 2217ms 3.29% std::_Rb_tree_insert_and_rebalance 2116ms 3.14% 65.42% 2116ms 3.14% Node::GetIndex 5ms 0.0074% 65.43% 2057ms 3.05% Element::Element 1316ms 1.95% 67.38% 2006ms 2.98% malloc_consolidate 0 0% 67.38% 1981ms 2.94% std::_Rb_tree::_M_drop_node (inline) 0 0% 67.38% 1968ms 2.92% std::_Rb_tree::_M_put_node (inline) 17ms 0.025% 67.40% 1905ms 2.83% std::_Vector_base::_M_deallocate (inline) 0 0% 67.40% 1805ms 2.68% std::vector::~vector (inline) 152ms 0.23% 67.63% 1776ms 2.64% tetgen::tetgenmesh::flip32 0 0% 67.63% 1752ms 2.60% std::_Vector_base::~_Vector_base (inline) 0 0% 67.63% 1738ms 2.58% Element::RegisterWithNodes (inline) 6ms 0.0089% 67.64% 1734ms 2.57% _int_free_maybe_consolidate 228ms 0.34% 67.98% 1604ms 2.38% TetrahedralMesh::Clear 1466ms 2.18% 70.15% 1466ms 2.18% unlink_chunk 76ms 0.11% 70.27% 1398ms 2.08% std::map::operator[] 1326ms 1.97% 72.24% 1392ms 2.07% tetgen::orient3d 0 0% 72.24% 1271ms 1.89% VertexMesh::GenerateVerticesFromElementCircumcentres 175ms 0.26% 72.50% 1269ms 1.88% tetgen::tetgenmesh::enqueueflipface 74ms 0.11% 72.61% 1245ms 1.85% std::vector::_M_realloc_insert 0 0% 72.61% 1243ms 1.85% std::_Rb_tree::lower_bound (inline) 0 0% 72.61% 1243ms 1.85% std::map::lower_bound (inline) 0 0% 72.61% 1215ms 1.80% VoronoiDataWriter::Visit 34ms 0.05% 72.66% 1134ms 1.68% tetgen::tetgenmesh::locate 966ms 1.43% 74.09% 1109ms 1.65% AbstractElement::GetNodeGlobalIndex 6ms 0.0089% 74.10% 1080ms 1.60% std::_Vector_base::_M_allocate (inline) 94ms 0.14% 74.24% 1053ms 1.56% tetgen::tetgenmesh::preciselocate 115ms 0.17% 74.41% 1025ms 1.52% std::vector::push_back (inline) 0 0% 74.41% 898ms 1.33% TetrahedralMesh::RefreshJacobianCachedData 875ms 1.30% 75.71% 875ms 1.30% tetgen::tetgenmesh::triface::triface 407ms 0.6% 76.31% 838ms 1.24% AbstractElement::GetNodeLocation 779ms 1.16% 77.47% 779ms 1.16% Node::rGetLocation 6ms 0.0089% 77.48% 775ms 1.15% AbstractTetrahedralElement::CalculateInverseJacobian 774ms 1.15% 78.63% 774ms 1.15% AbstractElement::IsDeleted 1ms 0.0015% 78.63% 740ms 1.10% AbstractTwoBodyInteractionForce::AddForceContribution 15ms 0.022% 78.65% 720ms 1.07% AbstractTetrahedralElement::CalculateJacobian 712ms 1.06% 79.71% 712ms 1.06% [libchaste_mesh.so] 357ms 0.53% 80.24% 699ms 1.04% tetgen::tetgenmesh::fnextself 14ms 0.021% 80.26% 688ms 1.02% AbstractVariableSizeTwoBodyInteractionForce::CalculateForceBetweenNodes 16ms 0.024% 80.28% 680ms 1.01% boost::numeric::ublas::vector_assign (inline) 16ms 0.024% 80.31% 676ms 1.00% boost::numeric::ublas::c_vector::c_vector (inline) 644ms 0.96% 81.26% 644ms 0.96% tetgen::tetgenmesh::triface::operator= 641ms 0.95% 82.22% 641ms 0.95% tetgen::tetgenmesh::oppo 48ms 0.071% 82.29% 621ms 0.92% __atan2 13ms 0.019% 82.31% 618ms 0.92% Element::CalculateCircumsphere 453ms 0.67% 82.98% 572ms 0.85% __ieee754_atan2_fma 49ms 0.073% 83.05% 560ms 0.83% AbstractTetrahedralElement::RefreshJacobian 522ms 0.78% 83.83% 522ms 0.78% std::vector::size (inline) 0 0% 83.83% 518ms 0.77% std::set::find (inline) 0 0% 83.83% 490ms 0.73% boost::numeric::ublas::inner_prod (inline) 7ms 0.01% 83.84% 487ms 0.72% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 38ms 0.056% 83.89% 487ms 0.72% tetgen::tetgenmesh::enext2fnext 0 0% 83.89% 481ms 0.71% std::insert_iterator::operator= (inline) 31ms 0.046% 83.94% 480ms 0.71% boost::numeric::ublas::vector_scalar_binary::evaluate 49ms 0.073% 84.01% 464ms 0.69% tetgen::tetgenmesh::enextfnext 134ms 0.2% 84.21% 444ms 0.66% boost::numeric::ublas::indexing_vector_assign 20ms 0.03% 84.24% 437ms 0.65% VertexMesh::CalculateUnitNormalToFaceWithArea 231ms 0.34% 84.58% 433ms 0.64% AbstractTetrahedralMesh::GetElement 267ms 0.4% 84.98% 419ms 0.62% tetgen::tetgenmesh::sym 0 0% 84.98% 417ms 0.62% std::_Rb_tree::_M_insert_unique_ (inline) 194ms 0.29% 85.27% 406ms 0.6% boost::numeric::ublas::vector_inner_prod::apply (inline) 0 0% 85.27% 404ms 0.6% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 0 0% 85.27% 401ms 0.6% VertexMeshWriter::WriteVtkUsingMesh 34ms 0.05% 85.32% 394ms 0.59% tetgen::tetgenmesh::queue::push 5ms 0.0074% 85.33% 392ms 0.58% boost::numeric::ublas::c_vector::operator= (inline) 7ms 0.01% 85.34% 390ms 0.58% CellPropertyCollection::GetPropertiesType (inline) 3ms 0.0045% 85.34% 377ms 0.56% Cell::GetCellId 25ms 0.037% 85.38% 375ms 0.56% std::_Rb_tree_iterator::operator-- (inline) 374ms 0.56% 85.93% 374ms 0.56% boost::numeric::ublas::c_vector::operator() 368ms 0.55% 86.48% 368ms 0.55% tetgen::tetgenmesh::org 251ms 0.37% 86.85% 360ms 0.53% tetgen::tetgenmesh::link::add 12ms 0.018% 86.87% 359ms 0.53% VertexElement::~VertexElement 9ms 0.013% 86.88% 355ms 0.53% std::vector::insert (inline) 249ms 0.37% 87.25% 342ms 0.51% tetgen::tetgenmesh::bond 103ms 0.15% 87.41% 339ms 0.5% __dynamic_cast