File: Test3dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 54441ms, 87.31% of 62354ms total Dropped 836 nodes (cum <= 311.77ms) flat flat% sum% cum cum% 0 0% 0% 62298ms 99.91% __libc_start_call_main 0 0% 0% 62298ms 99.91% __libc_start_main_impl 0 0% 0% 62298ms 99.91% _start 0 0% 0% 62283ms 99.89% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 62283ms 99.89% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 62283ms 99.89% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 62283ms 99.89% main 0 0% 0% 62247ms 99.83% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 62247ms 99.83% CxxTest::TestRunner::runTest (inline) 0 0% 0% 62247ms 99.83% Test3dTissueRepresentativeSimulation::Test3DHoneycombMeshWithGhostNodes 0 0% 0% 61983ms 99.41% AbstractCellBasedSimulation::Solve 0 0% 0% 51360ms 82.37% AbstractCellBasedSimulation::UpdateCellPopulation 1ms 0.0016% 0.0016% 51313ms 82.29% MeshBasedCellPopulation::Update 0 0% 0.0016% 29497ms 47.31% MeshBasedCellPopulation::CreateVoronoiTessellation (inline) 0 0% 0.0016% 29497ms 47.31% MeshBasedCellPopulation::TessellateIfNeeded 230ms 0.37% 0.37% 25998ms 41.69% VertexMesh::VertexMesh 0 0% 0.37% 17582ms 28.20% MutableMesh::ReMesh 571ms 0.92% 1.29% 12905ms 20.70% TetrahedralMesh::EdgeIterator::operator++ 0 0% 1.29% 12892ms 20.68% tetgen::tetrahedralize 1ms 0.0016% 1.29% 12754ms 20.45% tetgen::tetgenmesh::delaunizevertices 5ms 0.008% 1.30% 12750ms 20.45% tetgen::tetgenmesh::incrflipdelaunay 551ms 0.88% 2.18% 11345ms 18.19% tetgen::tetgenmesh::lawson 39ms 0.063% 2.24% 10418ms 16.71% std::set::insert (inline) 3022ms 4.85% 7.09% 9958ms 15.97% std::_Rb_tree::_M_lower_bound (inline) 227ms 0.36% 7.45% 9899ms 15.88% std::_Rb_tree::_M_insert_unique 370ms 0.59% 8.05% 9484ms 15.21% VertexElement::AddFace 259ms 0.42% 8.46% 9268ms 14.86% std::_Rb_tree::find (inline) 0 0% 8.46% 8716ms 13.98% std::set::count (inline) 120ms 0.19% 8.65% 6631ms 10.63% std::less::operator() (inline) 6570ms 10.54% 19.19% 6570ms 10.54% std::operator< (inline) 6370ms 10.22% 29.41% 6370ms 10.22% std::_Rb_tree_increment 259ms 0.42% 29.82% 5965ms 9.57% std::_Rb_tree::_M_insert_ (inline) 1ms 0.0016% 29.82% 5654ms 9.07% OffLatticeSimulation::UpdateCellLocationsAndTopology 215ms 0.34% 30.17% 5518ms 8.85% operator new 1ms 0.0016% 30.17% 5505ms 8.83% ForwardEulerNumericalMethod::UpdateAllNodePositions 3ms 0.0048% 30.17% 5483ms 8.79% AbstractNumericalMethod::ComputeForcesIncludingDamping 1150ms 1.84% 32.02% 5226ms 8.38% __GI___libc_malloc 0 0% 32.02% 4826ms 7.74% AbstractCellPopulation::WriteResultsToFiles 44ms 0.071% 32.09% 4650ms 7.46% std::__new_allocator::allocate (inline) 0 0% 32.09% 4633ms 7.43% std::allocator_traits::allocate (inline) 0 0% 32.09% 4560ms 7.31% MeshBasedCellPopulation::UpdateNodePairs 8ms 0.013% 32.10% 4555ms 7.31% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 7ms 0.011% 32.11% 4442ms 7.12% std::_Rb_tree::~_Rb_tree (inline) 1739ms 2.79% 34.90% 4433ms 7.11% std::_Rb_tree::_M_erase 15ms 0.024% 34.93% 4421ms 7.09% MeshBasedCellPopulation::SpringIterator::operator++ 0 0% 34.93% 4379ms 7.02% std::set::~set (inline) 1187ms 1.90% 36.83% 4039ms 6.48% std::_Rb_tree::_M_get_insert_unique_pos 1339ms 2.15% 38.98% 3986ms 6.39% __GI___libc_free 1ms 0.0016% 38.98% 3956ms 6.34% std::set_intersection (inline) 248ms 0.4% 39.38% 3955ms 6.34% std::__set_intersection 25ms 0.04% 39.42% 3947ms 6.33% Node::AddElement 7ms 0.011% 39.43% 3836ms 6.15% TetrahedralMesh::ImportFromMesher 0 0% 39.43% 3765ms 6.04% std::_Rb_tree::_M_create_node (inline) 0 0% 39.43% 3731ms 5.98% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 39.43% 3721ms 5.97% std::_Rb_tree::_M_get_node (inline) 2727ms 4.37% 43.80% 3714ms 5.96% _int_malloc 257ms 0.41% 44.21% 3665ms 5.88% VertexMesh::GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex 105ms 0.17% 44.38% 3550ms 5.69% std::__new_allocator::deallocate (inline) 3535ms 5.67% 50.05% 3535ms 5.67% std::_Rb_tree::_S_right (inline) 0 0% 50.05% 3530ms 5.66% VertexMesh::~VertexMesh 0 0% 50.05% 3523ms 5.65% std::allocator_traits::deallocate (inline) 112ms 0.18% 50.23% 3456ms 5.54% tetgen::tetgenmesh::insphere_sos 2ms 0.0032% 50.23% 3422ms 5.49% std::_Rb_tree_iterator::operator++ (inline) 6ms 0.0096% 50.24% 3411ms 5.47% MeshBasedCellPopulationWithGhostNodes::WriteVtkResultsToFile 3037ms 4.87% 55.11% 3327ms 5.34% tetgen::insphere 163ms 0.26% 55.38% 3231ms 5.18% std::_Rb_tree_const_iterator::operator++ (inline) 66ms 0.11% 55.48% 2841ms 4.56% MutableElement::AddNode 206ms 0.33% 55.81% 2677ms 4.29% tetgen::tetgenmesh::flip23 1094ms 1.75% 57.57% 2646ms 4.24% _int_free 181ms 0.29% 57.86% 2581ms 4.14% Node::~Node 192ms 0.31% 58.16% 2347ms 3.76% VertexMesh::Clear 0 0% 58.16% 2055ms 3.30% std::_Rb_tree::_M_drop_node (inline) 2054ms 3.29% 61.46% 2054ms 3.29% std::_Rb_tree_insert_and_rebalance 0 0% 61.46% 2038ms 3.27% std::_Rb_tree::_M_put_node (inline) 2ms 0.0032% 61.46% 1928ms 3.09% Element::Element 153ms 0.25% 61.71% 1847ms 2.96% tetgen::tetgenmesh::flip32 1756ms 2.82% 64.52% 1756ms 2.82% Node::GetIndex 3ms 0.0048% 64.53% 1589ms 2.55% Element::RegisterWithNodes (inline) 996ms 1.60% 66.13% 1560ms 2.50% malloc_consolidate 25ms 0.04% 66.17% 1510ms 2.42% std::_Vector_base::_M_deallocate (inline) 203ms 0.33% 66.49% 1502ms 2.41% TetrahedralMesh::Clear 1359ms 2.18% 68.67% 1439ms 2.31% tetgen::orient3d 0 0% 68.67% 1394ms 2.24% std::vector::~vector (inline) 7ms 0.011% 68.68% 1329ms 2.13% _int_free_maybe_consolidate 1ms 0.0016% 68.68% 1327ms 2.13% std::_Vector_base::~_Vector_base (inline) 163ms 0.26% 68.95% 1303ms 2.09% tetgen::tetgenmesh::enqueueflipface 47ms 0.075% 69.02% 1226ms 1.97% std::map::operator[] 1203ms 1.93% 70.95% 1203ms 1.93% unlink_chunk 34ms 0.055% 71.00% 1168ms 1.87% tetgen::tetgenmesh::locate 0 0% 71.00% 1161ms 1.86% VoronoiDataWriter::Visit 62ms 0.099% 71.10% 1138ms 1.83% std::vector::_M_realloc_insert 0 0% 71.10% 1112ms 1.78% std::_Rb_tree::lower_bound (inline) 0 0% 71.10% 1112ms 1.78% std::map::lower_bound (inline) 102ms 0.16% 71.27% 1090ms 1.75% tetgen::tetgenmesh::preciselocate 6ms 0.0096% 71.28% 1024ms 1.64% VertexMesh::GenerateVerticesFromElementCircumcentres 141ms 0.23% 71.50% 968ms 1.55% std::vector::push_back (inline) 3ms 0.0048% 71.51% 915ms 1.47% std::_Vector_base::_M_allocate (inline) 721ms 1.16% 72.66% 900ms 1.44% AbstractElement::GetNodeGlobalIndex 850ms 1.36% 74.03% 850ms 1.36% tetgen::tetgenmesh::triface::triface 1ms 0.0016% 74.03% 826ms 1.32% TetrahedralMesh::RefreshJacobianCachedData 738ms 1.18% 75.21% 738ms 1.18% tetgen::tetgenmesh::oppo 1ms 0.0016% 75.21% 731ms 1.17% AbstractTwoBodyInteractionForce::AddForceContribution 9ms 0.014% 75.23% 723ms 1.16% AbstractTetrahedralElement::CalculateInverseJacobian 309ms 0.5% 75.72% 716ms 1.15% AbstractElement::GetNodeLocation 688ms 1.10% 76.83% 688ms 1.10% [libchaste_mesh.so] 393ms 0.63% 77.46% 687ms 1.10% tetgen::tetgenmesh::fnextself 9ms 0.014% 77.47% 681ms 1.09% AbstractTetrahedralElement::CalculateJacobian 23ms 0.037% 77.51% 676ms 1.08% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 669ms 1.07% 78.58% 669ms 1.07% tetgen::tetgenmesh::triface::operator= 15ms 0.024% 78.61% 644ms 1.03% boost::numeric::ublas::c_vector::c_vector (inline) 11ms 0.018% 78.62% 640ms 1.03% boost::numeric::ublas::vector_assign (inline) 616ms 0.99% 79.61% 616ms 0.99% Node::rGetLocation 39ms 0.063% 79.67% 604ms 0.97% __atan2 582ms 0.93% 80.61% 582ms 0.93% AbstractElement::IsDeleted 466ms 0.75% 81.35% 565ms 0.91% __ieee754_atan2_fma 0 0% 81.35% 549ms 0.88% std::set::find (inline) 545ms 0.87% 82.23% 545ms 0.87% std::vector::size (inline) 47ms 0.075% 82.30% 529ms 0.85% AbstractTetrahedralElement::RefreshJacobian 17ms 0.027% 82.33% 525ms 0.84% Element::CalculateCircumsphere 0 0% 82.33% 513ms 0.82% std::insert_iterator::operator= (inline) 45ms 0.072% 82.40% 482ms 0.77% tetgen::tetgenmesh::enext2fnext 0 0% 82.40% 481ms 0.77% boost::numeric::ublas::inner_prod (inline) 2ms 0.0032% 82.41% 479ms 0.77% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 32ms 0.051% 82.46% 477ms 0.76% boost::numeric::ublas::vector_scalar_binary::evaluate 294ms 0.47% 82.93% 453ms 0.73% tetgen::tetgenmesh::sym 0 0% 82.93% 450ms 0.72% std::_Rb_tree::_M_insert_unique_ (inline) 34ms 0.055% 82.98% 448ms 0.72% tetgen::tetgenmesh::enextfnext 0 0% 82.98% 416ms 0.67% CellPropertyCollection::GetPropertiesType (inline) 28ms 0.045% 83.03% 413ms 0.66% tetgen::tetgenmesh::queue::push 104ms 0.17% 83.20% 409ms 0.66% boost::numeric::ublas::indexing_vector_assign 189ms 0.3% 83.50% 405ms 0.65% boost::numeric::ublas::vector_inner_prod::apply (inline) 1ms 0.0016% 83.50% 391ms 0.63% Cell::GetCellId 0 0% 83.50% 391ms 0.63% VertexMeshWriter::WriteVtkUsingMesh 88ms 0.14% 83.64% 391ms 0.63% __dynamic_cast 253ms 0.41% 84.05% 384ms 0.62% tetgen::tetgenmesh::link::add 217ms 0.35% 84.40% 382ms 0.61% AbstractTetrahedralMesh::GetElement 376ms 0.6% 85.00% 376ms 0.6% boost::numeric::ublas::c_vector::operator() 15ms 0.024% 85.02% 371ms 0.59% VertexMesh::CalculateUnitNormalToFaceWithArea 370ms 0.59% 85.62% 370ms 0.59% tetgen::tetgenmesh::org 0 0% 85.62% 369ms 0.59% boost::numeric::ublas::c_vector::operator= (inline) 17ms 0.027% 85.64% 363ms 0.58% std::_Rb_tree_iterator::operator-- (inline) 16ms 0.026% 85.67% 347ms 0.56% std::vector::insert (inline) 4ms 0.0064% 85.68% 339ms 0.54% AbstractTetrahedralElement::AbstractTetrahedralElement 0 0% 85.68% 335ms 0.54% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 0 0% 85.68% 332ms 0.53% AbstractCellProperty::IsSubType (inline) 0 0% 85.68% 326ms 0.52% tcache_get (inline) 326ms 0.52% 86.20% 326ms 0.52% tcache_get_n (inline) 143ms 0.23% 86.43% 321ms 0.51% Inverse 2ms 0.0032% 86.43% 321ms 0.51% VertexElement::~VertexElement 321ms 0.51% 86.95% 321ms 0.51% std::_Rb_tree_decrement 227ms 0.36% 87.31% 317ms 0.51% tetgen::tetgenmesh::bond