File: Test3dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 61934ms, 88.41% of 70057ms total Dropped 893 nodes (cum <= 350.29ms) flat flat% sum% cum cum% 0 0% 0% 69995ms 99.91% __libc_start_call_main 0 0% 0% 69995ms 99.91% __libc_start_main_impl 0 0% 0% 69995ms 99.91% _start 0 0% 0% 69979ms 99.89% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 69979ms 99.89% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 69979ms 99.89% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 69979ms 99.89% main 0 0% 0% 69941ms 99.83% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 69941ms 99.83% CxxTest::TestRunner::runTest (inline) 0 0% 0% 69941ms 99.83% Test3dTissueRepresentativeSimulation::Test3DHoneycombMeshWithGhostNodes 0 0% 0% 69672ms 99.45% AbstractCellBasedSimulation::Solve 0 0% 0% 58521ms 83.53% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 58475ms 83.47% MeshBasedCellPopulation::Update 1ms 0.0014% 0.0014% 35995ms 51.38% MeshBasedCellPopulation::TessellateIfNeeded 0 0% 0.0014% 35994ms 51.38% MeshBasedCellPopulation::CreateVoronoiTessellation (inline) 277ms 0.4% 0.4% 31116ms 44.42% VertexMesh::VertexMesh 0 0% 0.4% 17928ms 25.59% MutableMesh::ReMesh 538ms 0.77% 1.16% 14066ms 20.08% TetrahedralMesh::EdgeIterator::operator++ 0 0% 1.16% 12842ms 18.33% tetgen::tetrahedralize 2ms 0.0029% 1.17% 12711ms 18.14% tetgen::tetgenmesh::delaunizevertices 10ms 0.014% 1.18% 12702ms 18.13% tetgen::tetgenmesh::incrflipdelaunay 25ms 0.036% 1.22% 11843ms 16.90% std::set::insert (inline) 198ms 0.28% 1.50% 11355ms 16.21% std::_Rb_tree::_M_insert_unique 569ms 0.81% 2.31% 11252ms 16.06% tetgen::tetgenmesh::lawson 3050ms 4.35% 6.67% 10698ms 15.27% std::_Rb_tree::_M_lower_bound (inline) 442ms 0.63% 7.30% 10405ms 14.85% VertexElement::AddFace 225ms 0.32% 7.62% 9827ms 14.03% std::_Rb_tree::find (inline) 0 0% 7.62% 9303ms 13.28% std::set::count (inline) 7832ms 11.18% 18.80% 7832ms 11.18% std::_Rb_tree_increment 110ms 0.16% 18.95% 7164ms 10.23% std::less::operator() (inline) 7127ms 10.17% 29.13% 7127ms 10.17% std::operator< (inline) 262ms 0.37% 29.50% 6659ms 9.51% std::_Rb_tree::_M_insert_ (inline) 210ms 0.3% 29.80% 6466ms 9.23% operator new 1132ms 1.62% 31.42% 6209ms 8.86% __GI___libc_malloc 1ms 0.0014% 31.42% 6043ms 8.63% OffLatticeSimulation::UpdateCellLocationsAndTopology 2ms 0.0029% 31.42% 5876ms 8.39% ForwardEulerNumericalMethod::UpdateAllNodePositions 6ms 0.0086% 31.43% 5843ms 8.34% AbstractNumericalMethod::ComputeForcesIncludingDamping 3ms 0.0043% 31.43% 5494ms 7.84% std::set_intersection (inline) 309ms 0.44% 31.88% 5491ms 7.84% std::__set_intersection 38ms 0.054% 31.93% 5293ms 7.56% std::__new_allocator::allocate (inline) 0 0% 31.93% 5272ms 7.53% std::allocator_traits::allocate (inline) 5ms 0.0071% 31.94% 5165ms 7.37% std::_Rb_tree::~_Rb_tree (inline) 2199ms 3.14% 35.08% 5160ms 7.37% std::_Rb_tree::_M_erase 24ms 0.034% 35.11% 5156ms 7.36% Node::AddElement 0 0% 35.11% 5083ms 7.26% std::set::~set (inline) 1ms 0.0014% 35.11% 4964ms 7.09% AbstractCellPopulation::WriteResultsToFiles 0 0% 35.11% 4911ms 7.01% VertexMesh::~VertexMesh 2ms 0.0029% 35.11% 4895ms 6.99% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 1ms 0.0014% 35.12% 4883ms 6.97% MeshBasedCellPopulation::UpdateNodePairs 1266ms 1.81% 36.92% 4819ms 6.88% std::_Rb_tree::_M_get_insert_unique_pos 1358ms 1.94% 38.86% 4775ms 6.82% __GI___libc_free 3367ms 4.81% 43.67% 4719ms 6.74% _int_malloc 13ms 0.019% 43.69% 4716ms 6.73% MeshBasedCellPopulation::SpringIterator::operator++ 186ms 0.27% 43.95% 4691ms 6.70% std::_Rb_tree_const_iterator::operator++ (inline) 4679ms 6.68% 50.63% 4679ms 6.68% std::_Rb_tree::_S_right (inline) 0 0% 50.63% 4233ms 6.04% std::_Rb_tree::_M_create_node (inline) 115ms 0.16% 50.79% 4205ms 6.00% std::__new_allocator::deallocate (inline) 0 0% 50.79% 4195ms 5.99% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 50.79% 4184ms 5.97% std::allocator_traits::deallocate (inline) 0 0% 50.79% 4179ms 5.97% std::_Rb_tree::_M_get_node (inline) 9ms 0.013% 50.81% 4106ms 5.86% TetrahedralMesh::ImportFromMesher 78ms 0.11% 50.92% 3918ms 5.59% MutableElement::AddNode 265ms 0.38% 51.30% 3680ms 5.25% VertexMesh::GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex 112ms 0.16% 51.46% 3511ms 5.01% tetgen::tetgenmesh::insphere_sos 7ms 0.01% 51.47% 3465ms 4.95% MeshBasedCellPopulationWithGhostNodes::WriteVtkResultsToFile 1ms 0.0014% 51.47% 3439ms 4.91% std::_Rb_tree_iterator::operator++ (inline) 1189ms 1.70% 53.17% 3416ms 4.88% _int_free 3078ms 4.39% 57.56% 3389ms 4.84% tetgen::insphere 221ms 0.32% 57.87% 3246ms 4.63% Node::~Node 291ms 0.42% 58.29% 3024ms 4.32% VertexMesh::Clear 188ms 0.27% 58.56% 2690ms 3.84% tetgen::tetgenmesh::flip23 2376ms 3.39% 61.95% 2376ms 3.39% Node::GetIndex 2314ms 3.30% 65.25% 2314ms 3.30% std::_Rb_tree_insert_and_rebalance 1532ms 2.19% 67.44% 2281ms 3.26% malloc_consolidate 18ms 0.026% 67.47% 2189ms 3.12% std::_Vector_base::_M_deallocate (inline) 0 0% 67.47% 2134ms 3.05% Element::Element 0 0% 67.47% 2035ms 2.90% std::vector::~vector (inline) 0 0% 67.47% 2024ms 2.89% std::_Rb_tree::_M_drop_node (inline) 0 0% 67.47% 2012ms 2.87% std::_Rb_tree::_M_put_node (inline) 1ms 0.0014% 67.47% 1994ms 2.85% std::_Vector_base::~_Vector_base (inline) 6ms 0.0086% 67.48% 1980ms 2.83% _int_free_maybe_consolidate 164ms 0.23% 67.71% 1823ms 2.60% tetgen::tetgenmesh::flip32 4ms 0.0057% 67.71% 1779ms 2.54% Element::RegisterWithNodes (inline) 1691ms 2.41% 70.13% 1691ms 2.41% unlink_chunk 229ms 0.33% 70.46% 1599ms 2.28% TetrahedralMesh::Clear 7ms 0.01% 70.47% 1475ms 2.11% VertexMesh::GenerateVerticesFromElementCircumcentres 1383ms 1.97% 72.44% 1475ms 2.11% tetgen::orient3d 64ms 0.091% 72.53% 1426ms 2.04% std::map::operator[] 67ms 0.096% 72.63% 1325ms 1.89% std::vector::_M_realloc_insert 0 0% 72.63% 1279ms 1.83% std::_Rb_tree::lower_bound (inline) 0 0% 72.63% 1279ms 1.83% std::map::lower_bound (inline) 185ms 0.26% 72.89% 1243ms 1.77% tetgen::tetgenmesh::enqueueflipface 0 0% 72.89% 1241ms 1.77% VoronoiDataWriter::Visit 35ms 0.05% 72.94% 1221ms 1.74% tetgen::tetgenmesh::locate 1048ms 1.50% 74.44% 1189ms 1.70% AbstractElement::GetNodeGlobalIndex 92ms 0.13% 74.57% 1146ms 1.64% tetgen::tetgenmesh::preciselocate 139ms 0.2% 74.77% 1098ms 1.57% std::vector::push_back (inline) 3ms 0.0043% 74.77% 1096ms 1.56% std::_Vector_base::_M_allocate (inline) 1ms 0.0014% 74.77% 949ms 1.35% TetrahedralMesh::RefreshJacobianCachedData 402ms 0.57% 75.35% 931ms 1.33% AbstractElement::GetNodeLocation 879ms 1.25% 76.60% 879ms 1.25% Node::rGetLocation 849ms 1.21% 77.81% 849ms 1.21% tetgen::tetgenmesh::triface::triface 836ms 1.19% 79.01% 836ms 1.19% AbstractElement::IsDeleted 12ms 0.017% 79.02% 784ms 1.12% AbstractTetrahedralElement::CalculateInverseJacobian 11ms 0.016% 79.04% 773ms 1.10% AbstractTetrahedralElement::CalculateJacobian 438ms 0.63% 79.66% 758ms 1.08% tetgen::tetgenmesh::fnextself 3ms 0.0043% 79.67% 736ms 1.05% AbstractTwoBodyInteractionForce::AddForceContribution 729ms 1.04% 80.71% 729ms 1.04% tetgen::tetgenmesh::oppo 19ms 0.027% 80.74% 700ms 1% Element::CalculateCircumsphere 61ms 0.087% 80.82% 680ms 0.97% __atan2 13ms 0.019% 80.84% 679ms 0.97% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 11ms 0.016% 80.86% 649ms 0.93% boost::numeric::ublas::vector_assign (inline) 634ms 0.9% 81.76% 634ms 0.9% [libchaste_mesh.so] 11ms 0.016% 81.78% 629ms 0.9% boost::numeric::ublas::c_vector::c_vector (inline) 625ms 0.89% 82.67% 625ms 0.89% tetgen::tetgenmesh::triface::operator= 501ms 0.72% 83.38% 619ms 0.88% __ieee754_atan2_fma 604ms 0.86% 84.25% 604ms 0.86% std::vector::size (inline) 35ms 0.05% 84.30% 576ms 0.82% AbstractTetrahedralElement::RefreshJacobian 0 0% 84.30% 521ms 0.74% std::set::find (inline) 0 0% 84.30% 519ms 0.74% boost::numeric::ublas::inner_prod (inline) 6ms 0.0086% 84.31% 516ms 0.74% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 38ms 0.054% 84.36% 510ms 0.73% boost::numeric::ublas::vector_scalar_binary::evaluate 23ms 0.033% 84.39% 494ms 0.71% tetgen::tetgenmesh::enext2fnext 0 0% 84.39% 486ms 0.69% std::insert_iterator::operator= (inline) 26ms 0.037% 84.43% 464ms 0.66% VertexMesh::CalculateUnitNormalToFaceWithArea 38ms 0.054% 84.48% 457ms 0.65% tetgen::tetgenmesh::enextfnext 0 0% 84.48% 441ms 0.63% std::_Rb_tree::_M_insert_unique_ (inline) 0 0% 84.48% 435ms 0.62% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 124ms 0.18% 84.66% 435ms 0.62% boost::numeric::ublas::indexing_vector_assign 432ms 0.62% 85.28% 432ms 0.62% boost::numeric::ublas::c_vector::operator() 25ms 0.036% 85.31% 428ms 0.61% std::_Rb_tree_iterator::operator-- (inline) 188ms 0.27% 85.58% 423ms 0.6% boost::numeric::ublas::vector_inner_prod::apply (inline) 248ms 0.35% 85.94% 421ms 0.6% AbstractTetrahedralMesh::GetElement 290ms 0.41% 86.35% 411ms 0.59% tetgen::tetgenmesh::sym 309ms 0.44% 86.79% 405ms 0.58% tetgen::tetgenmesh::bond 3ms 0.0043% 86.80% 402ms 0.57% CellPropertyCollection::GetPropertiesType (inline) 0 0% 86.80% 395ms 0.56% VertexMeshWriter::WriteVtkUsingMesh 20ms 0.029% 86.82% 386ms 0.55% tetgen::tetgenmesh::queue::push 13ms 0.019% 86.84% 385ms 0.55% std::vector::insert (inline) 3ms 0.0043% 86.85% 382ms 0.55% boost::numeric::ublas::c_vector::operator= (inline) 382ms 0.55% 87.39% 382ms 0.55% std::_Rb_tree_decrement 88ms 0.13% 87.52% 376ms 0.54% __dynamic_cast 1ms 0.0014% 87.52% 370ms 0.53% Cell::GetCellId 258ms 0.37% 87.89% 363ms 0.52% tetgen::tetgenmesh::link::add 5ms 0.0071% 87.89% 355ms 0.51% AbstractTetrahedralElement::AbstractTetrahedralElement 354ms 0.51% 88.40% 354ms 0.51% tetgen::tetgenmesh::org 4ms 0.0057% 88.41% 352ms 0.5% VertexElement::~VertexElement