File: Test3dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 36789ms, 85.40% of 43078ms total Dropped 761 nodes (cum <= 215.39ms) flat flat% sum% cum cum% 0 0% 0% 43051ms 99.94% __libc_start_call_main 0 0% 0% 43051ms 99.94% __libc_start_main_impl 0 0% 0% 43051ms 99.94% _start 0 0% 0% 43038ms 99.91% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 43038ms 99.91% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 43038ms 99.91% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 43038ms 99.91% main 0 0% 0% 43003ms 99.83% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 43003ms 99.83% CxxTest::TestRunner::runTest (inline) 0 0% 0% 43003ms 99.83% Test3dTissueRepresentativeSimulation::Test3DHoneycombMeshWithGhostNodes 1ms 0.0023% 0.0023% 42841ms 99.45% AbstractCellBasedSimulation::Solve 0 0% 0.0023% 35881ms 83.29% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0.0023% 35843ms 83.20% MeshBasedCellPopulation::Update 0 0% 0.0023% 22252ms 51.66% MeshBasedCellPopulation::CreateVoronoiTessellation (inline) 0 0% 0.0023% 22252ms 51.66% MeshBasedCellPopulation::TessellateIfNeeded 213ms 0.49% 0.5% 20106ms 46.67% VertexMesh::VertexMesh 0 0% 0.5% 10577ms 24.55% MutableMesh::ReMesh 392ms 0.91% 1.41% 9516ms 22.09% TetrahedralMesh::EdgeIterator::operator++ 19ms 0.044% 1.45% 8331ms 19.34% std::set::insert (inline) 107ms 0.25% 1.70% 7900ms 18.34% std::_Rb_tree::_M_insert_unique 0 0% 1.70% 7823ms 18.16% tetgen::tetrahedralize 0 0% 1.70% 7746ms 17.98% tetgen::tetgenmesh::delaunizevertices 3ms 0.007% 1.71% 7745ms 17.98% tetgen::tetgenmesh::incrflipdelaunay 218ms 0.51% 2.21% 7641ms 17.74% VertexElement::AddFace 2969ms 6.89% 9.10% 7398ms 17.17% std::_Rb_tree::_M_lower_bound (inline) 124ms 0.29% 9.39% 7080ms 16.44% std::_Rb_tree::find (inline) 359ms 0.83% 10.23% 6805ms 15.80% tetgen::tetgenmesh::lawson 0 0% 10.23% 6636ms 15.40% std::set::count (inline) 236ms 0.55% 10.77% 5144ms 11.94% std::_Rb_tree::_M_insert_ (inline) 164ms 0.38% 11.15% 4953ms 11.50% operator new 1405ms 3.26% 14.42% 4736ms 10.99% __GI___libc_malloc 52ms 0.12% 14.54% 4287ms 9.95% std::__new_allocator::allocate (inline) 0 0% 14.54% 4266ms 9.90% std::allocator_traits::allocate (inline) 0 0% 14.54% 4176ms 9.69% OffLatticeSimulation::UpdateCellLocationsAndTopology 1ms 0.0023% 14.54% 4062ms 9.43% ForwardEulerNumericalMethod::UpdateAllNodePositions 1ms 0.0023% 14.54% 4045ms 9.39% AbstractNumericalMethod::ComputeForcesIncludingDamping 3979ms 9.24% 23.78% 3979ms 9.24% std::_Rb_tree_increment 57ms 0.13% 23.91% 3926ms 9.11% std::less::operator() (inline) 3910ms 9.08% 32.99% 3910ms 9.08% std::operator< (inline) 0 0% 32.99% 3477ms 8.07% std::_Rb_tree::_M_create_node (inline) 0 0% 32.99% 3450ms 8.01% std::_Rb_tree::_M_get_node (inline) 0 0% 32.99% 3441ms 7.99% std::_Rb_tree::_Alloc_node::operator() (inline) 199ms 0.46% 33.45% 3310ms 7.68% std::__set_intersection 0 0% 33.45% 3310ms 7.68% std::set_intersection (inline) 2ms 0.0046% 33.45% 3264ms 7.58% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 502ms 1.17% 34.62% 3263ms 7.57% __GI___libc_free 0 0% 34.62% 3259ms 7.57% MeshBasedCellPopulation::UpdateNodePairs 8ms 0.019% 34.64% 3170ms 7.36% MeshBasedCellPopulation::SpringIterator::operator++ 2546ms 5.91% 40.55% 3053ms 7.09% _int_malloc 65ms 0.15% 40.70% 2995ms 6.95% std::__new_allocator::deallocate (inline) 0 0% 40.70% 2985ms 6.93% std::allocator_traits::deallocate (inline) 994ms 2.31% 43.01% 2918ms 6.77% std::_Rb_tree::_M_get_insert_unique_pos 8ms 0.019% 43.02% 2803ms 6.51% std::_Rb_tree::~_Rb_tree (inline) 726ms 1.69% 44.71% 2790ms 6.48% std::_Rb_tree::_M_erase 65ms 0.15% 44.86% 2785ms 6.47% Node::AddElement 0 0% 44.86% 2770ms 6.43% std::set::~set (inline) 1384ms 3.21% 48.07% 2745ms 6.37% _int_free 170ms 0.39% 48.47% 2664ms 6.18% std::_Rb_tree_const_iterator::operator++ (inline) 0 0% 48.47% 2658ms 6.17% AbstractCellPopulation::WriteResultsToFiles 2468ms 5.73% 54.20% 2468ms 5.73% std::_Rb_tree::_S_right (inline) 0 0% 54.20% 2163ms 5.02% VertexMesh::~VertexMesh 5ms 0.012% 54.21% 2152ms 5.00% TetrahedralMesh::ImportFromMesher 46ms 0.11% 54.32% 2095ms 4.86% tetgen::tetgenmesh::insphere_sos 1881ms 4.37% 58.68% 2026ms 4.70% tetgen::insphere 46ms 0.11% 58.79% 1993ms 4.63% MutableElement::AddNode 207ms 0.48% 59.27% 1944ms 4.51% std::_Rb_tree_iterator::operator++ (inline) 2ms 0.0046% 59.27% 1933ms 4.49% VertexMesh::GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex 2ms 0.0046% 59.28% 1904ms 4.42% MeshBasedCellPopulationWithGhostNodes::WriteVtkResultsToFile 0 0% 59.28% 1754ms 4.07% std::_Rb_tree::_M_drop_node (inline) 0 0% 59.28% 1738ms 4.03% std::_Rb_tree::_M_put_node (inline) 1607ms 3.73% 63.01% 1607ms 3.73% [libchaste_mesh.so] 144ms 0.33% 63.34% 1582ms 3.67% tetgen::tetgenmesh::flip23 1524ms 3.54% 66.88% 1524ms 3.54% std::_Rb_tree_insert_and_rebalance 3ms 0.007% 66.89% 1386ms 3.22% Element::Element 757ms 1.76% 68.65% 1283ms 2.98% malloc_consolidate 15ms 0.035% 68.68% 1262ms 2.93% std::_Vector_base::_M_deallocate (inline) 4ms 0.0093% 68.69% 1183ms 2.75% Node::~Node 9ms 0.021% 68.71% 1173ms 2.72% Element::RegisterWithNodes (inline) 0 0% 68.71% 1149ms 2.67% std::vector::~vector (inline) 4ms 0.0093% 68.72% 1143ms 2.65% _int_free_maybe_consolidate 117ms 0.27% 68.99% 1141ms 2.65% tetgen::tetgenmesh::flip32 1ms 0.0023% 68.99% 1133ms 2.63% std::_Vector_base::~_Vector_base (inline) 3ms 0.007% 69.00% 1119ms 2.60% VertexMesh::Clear 1028ms 2.39% 71.39% 1064ms 2.47% tetgen::orient3d 1039ms 2.41% 73.80% 1039ms 2.41% Node::GetIndex 46ms 0.11% 73.91% 910ms 2.11% std::vector::_M_realloc_insert 834ms 1.94% 75.84% 834ms 1.94% unlink_chunk 2ms 0.0046% 75.85% 818ms 1.90% std::_Vector_base::_M_allocate (inline) 60ms 0.14% 75.99% 805ms 1.87% std::map::operator[] 24ms 0.056% 76.04% 804ms 1.87% tetgen::tetgenmesh::locate 4ms 0.0093% 76.05% 776ms 1.80% VertexMesh::GenerateVerticesFromElementCircumcentres 62ms 0.14% 76.19% 750ms 1.74% tetgen::tetgenmesh::preciselocate 128ms 0.3% 76.49% 728ms 1.69% tetgen::tetgenmesh::enqueueflipface 52ms 0.12% 76.61% 714ms 1.66% std::vector::push_back (inline) 0 0% 76.61% 682ms 1.58% std::_Rb_tree::lower_bound (inline) 0 0% 76.61% 682ms 1.58% std::map::lower_bound (inline) 0 0% 76.61% 607ms 1.41% VoronoiDataWriter::Visit 1ms 0.0023% 76.61% 588ms 1.36% TetrahedralMesh::RefreshJacobianCachedData 3ms 0.007% 76.62% 581ms 1.35% AbstractTwoBodyInteractionForce::AddForceContribution 11ms 0.026% 76.65% 559ms 1.30% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 335ms 0.78% 77.42% 519ms 1.20% AbstractElement::GetNodeGlobalIndex 5ms 0.012% 77.44% 513ms 1.19% AbstractTetrahedralElement::CalculateInverseJacobian 502ms 1.17% 78.60% 502ms 1.17% Node::rGetLocation 4ms 0.0093% 78.61% 502ms 1.17% TetrahedralMesh::Clear 231ms 0.54% 79.15% 457ms 1.06% AbstractElement::GetNodeLocation 3ms 0.007% 79.15% 446ms 1.04% AbstractTetrahedralElement::CalculateJacobian 0 0% 79.15% 440ms 1.02% std::set::find (inline) 0 0% 79.15% 437ms 1.01% std::insert_iterator::operator= (inline) 420ms 0.97% 80.13% 420ms 0.97% tetgen::tetgenmesh::oppo 250ms 0.58% 80.71% 410ms 0.95% tetgen::tetgenmesh::sym 5ms 0.012% 80.72% 402ms 0.93% boost::numeric::ublas::vector_assign (inline) 26ms 0.06% 80.78% 393ms 0.91% __atan2 5ms 0.012% 80.79% 387ms 0.9% boost::numeric::ublas::c_vector::c_vector (inline) 0 0% 80.79% 383ms 0.89% std::_Rb_tree::_M_insert_unique_ (inline) 330ms 0.77% 81.56% 365ms 0.85% __ieee754_atan2_fma 24ms 0.056% 81.61% 357ms 0.83% AbstractTetrahedralElement::RefreshJacobian 33ms 0.077% 81.69% 352ms 0.82% std::_Rb_tree_iterator::operator-- (inline) 15ms 0.035% 81.73% 339ms 0.79% Element::CalculateCircumsphere 320ms 0.74% 82.47% 320ms 0.74% std::vector::size (inline) 3ms 0.007% 82.48% 309ms 0.72% Cell::GetCellId 7ms 0.016% 82.49% 301ms 0.7% CellPropertyCollection::GetPropertiesType (inline) 299ms 0.69% 83.19% 299ms 0.69% std::_Rb_tree_decrement 217ms 0.5% 83.69% 286ms 0.66% tetgen::tetgenmesh::fnextself 11ms 0.026% 83.72% 283ms 0.66% std::vector::insert (inline) 27ms 0.063% 83.78% 271ms 0.63% tetgen::tetgenmesh::enext2fnext 0 0% 83.78% 268ms 0.62% VertexMeshWriter::WriteVtkUsingMesh 0 0% 83.78% 259ms 0.6% boost::numeric::ublas::inner_prod (inline) 1ms 0.0023% 83.78% 259ms 0.6% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 14ms 0.032% 83.81% 258ms 0.6% boost::numeric::ublas::vector_scalar_binary::evaluate 249ms 0.58% 84.39% 249ms 0.58% boost::numeric::ublas::c_vector::operator() 179ms 0.42% 84.81% 248ms 0.58% AbstractTetrahedralMesh::GetElement 17ms 0.039% 84.85% 242ms 0.56% tetgen::tetgenmesh::enextfnext 3ms 0.007% 84.85% 239ms 0.55% boost::numeric::ublas::c_vector::operator= (inline) 63ms 0.15% 85.00% 236ms 0.55% __dynamic_cast 12ms 0.028% 85.03% 230ms 0.53% boost::numeric::ublas::vector_reference::operator() (inline) 84ms 0.19% 85.22% 229ms 0.53% Inverse 45ms 0.1% 85.33% 229ms 0.53% boost::numeric::ublas::vector_inner_prod::apply (inline) 18ms 0.042% 85.37% 225ms 0.52% tetgen::tetgenmesh::queue::push 14ms 0.032% 85.40% 222ms 0.52% VertexMesh::CalculateUnitNormalToFaceWithArea