File: Test3dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 57897ms, 86.75% of 66738ms total Dropped 873 nodes (cum <= 333.69ms) flat flat% sum% cum cum% 0 0% 0% 66681ms 99.91% __libc_start_call_main 0 0% 0% 66681ms 99.91% __libc_start_main_impl 0 0% 0% 66681ms 99.91% _start 0 0% 0% 66663ms 99.89% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 66663ms 99.89% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 66663ms 99.89% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 66663ms 99.89% main 0 0% 0% 66621ms 99.82% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 66621ms 99.82% CxxTest::TestRunner::runTest (inline) 0 0% 0% 66621ms 99.82% Test3dTissueRepresentativeSimulation::Test3DHoneycombMeshWithGhostNodes 0 0% 0% 66334ms 99.39% AbstractCellBasedSimulation::Solve 0 0% 0% 55840ms 83.67% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 55786ms 83.59% MeshBasedCellPopulation::Update 0 0% 0% 30981ms 46.42% MeshBasedCellPopulation::TessellateIfNeeded 0 0% 0% 30980ms 46.42% MeshBasedCellPopulation::CreateVoronoiTessellation (inline) 232ms 0.35% 0.35% 27629ms 41.40% VertexMesh::VertexMesh 0 0% 0.35% 20289ms 30.40% MutableMesh::ReMesh 0 0% 0.35% 15979ms 23.94% tetgen::tetrahedralize 3ms 0.0045% 0.35% 15826ms 23.71% tetgen::tetgenmesh::delaunizevertices 7ms 0.01% 0.36% 15816ms 23.70% tetgen::tetgenmesh::incrflipdelaunay 495ms 0.74% 1.10% 14237ms 21.33% tetgen::tetgenmesh::lawson 610ms 0.91% 2.02% 13832ms 20.73% TetrahedralMesh::EdgeIterator::operator++ 33ms 0.049% 2.07% 10538ms 15.79% std::set::insert (inline) 3119ms 4.67% 6.74% 10450ms 15.66% std::_Rb_tree::_M_lower_bound (inline) 390ms 0.58% 7.33% 10114ms 15.15% VertexElement::AddFace 260ms 0.39% 7.72% 10109ms 15.15% std::_Rb_tree::_M_insert_unique 241ms 0.36% 8.08% 9709ms 14.55% std::_Rb_tree::find (inline) 0 0% 8.08% 9164ms 13.73% std::set::count (inline) 120ms 0.18% 8.26% 7024ms 10.52% std::less::operator() (inline) 6968ms 10.44% 18.70% 6968ms 10.44% std::operator< (inline) 6272ms 9.40% 28.09% 6272ms 9.40% std::_Rb_tree_increment 0 0% 28.09% 6021ms 9.02% OffLatticeSimulation::UpdateCellLocationsAndTopology 311ms 0.47% 28.56% 5861ms 8.78% std::_Rb_tree::_M_insert_ (inline) 0 0% 28.56% 5858ms 8.78% ForwardEulerNumericalMethod::UpdateAllNodePositions 4ms 0.006% 28.57% 5836ms 8.74% AbstractNumericalMethod::ComputeForcesIncludingDamping 168ms 0.25% 28.82% 5432ms 8.14% operator new 1250ms 1.87% 30.69% 5186ms 7.77% __GI___libc_malloc 0 0% 30.69% 4890ms 7.33% MeshBasedCellPopulation::UpdateNodePairs 8ms 0.012% 30.70% 4869ms 7.30% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 15ms 0.022% 30.73% 4735ms 7.09% MeshBasedCellPopulation::SpringIterator::operator++ 33ms 0.049% 30.78% 4635ms 6.95% std::__new_allocator::allocate (inline) 0 0% 30.78% 4611ms 6.91% std::allocator_traits::allocate (inline) 5ms 0.0075% 30.78% 4417ms 6.62% std::_Rb_tree::~_Rb_tree (inline) 1649ms 2.47% 33.25% 4411ms 6.61% std::_Rb_tree::_M_erase 2ms 0.003% 33.26% 4411ms 6.61% std::set_intersection (inline) 280ms 0.42% 33.68% 4409ms 6.61% std::__set_intersection 0 0% 33.68% 4366ms 6.54% std::set::~set (inline) 0 0% 33.68% 4318ms 6.47% AbstractCellPopulation::WriteResultsToFiles 1352ms 2.03% 35.70% 4259ms 6.38% std::_Rb_tree::_M_get_insert_unique_pos 1199ms 1.80% 37.50% 4081ms 6.11% __GI___libc_free 136ms 0.2% 37.70% 3967ms 5.94% tetgen::tetgenmesh::insphere_sos 3489ms 5.23% 42.93% 3816ms 5.72% tetgen::insphere 38ms 0.057% 42.99% 3735ms 5.60% Node::AddElement 0 0% 42.99% 3727ms 5.58% std::_Rb_tree::_M_create_node (inline) 181ms 0.27% 43.26% 3695ms 5.54% std::_Rb_tree_const_iterator::operator++ (inline) 0 0% 43.26% 3690ms 5.53% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 43.26% 3682ms 5.52% std::_Rb_tree::_M_get_node (inline) 154ms 0.23% 43.49% 3636ms 5.45% std::__new_allocator::deallocate (inline) 0 0% 43.49% 3625ms 5.43% std::allocator_traits::deallocate (inline) 2522ms 3.78% 47.27% 3541ms 5.31% _int_malloc 110ms 0.16% 47.43% 3540ms 5.30% tetgen::tetgenmesh::flip23 3524ms 5.28% 52.71% 3524ms 5.28% std::_Rb_tree::_S_right (inline) 4ms 0.006% 52.72% 3473ms 5.20% TetrahedralMesh::ImportFromMesher 0 0% 52.72% 3378ms 5.06% VertexMesh::~VertexMesh 210ms 0.31% 53.03% 3092ms 4.63% VertexMesh::GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex 4ms 0.006% 53.04% 3015ms 4.52% MeshBasedCellPopulationWithGhostNodes::WriteVtkResultsToFile 0 0% 53.04% 2894ms 4.34% std::_Rb_tree_iterator::operator++ (inline) 1360ms 2.04% 55.08% 2880ms 4.32% _int_free 54ms 0.081% 55.16% 2811ms 4.21% MutableElement::AddNode 153ms 0.23% 55.39% 2539ms 3.80% tetgen::tetgenmesh::flip32 171ms 0.26% 55.64% 2473ms 3.71% Node::~Node 169ms 0.25% 55.90% 2210ms 3.31% VertexMesh::Clear 0 0% 55.90% 2162ms 3.24% std::_Rb_tree::_M_drop_node (inline) 0 0% 55.90% 2152ms 3.22% std::_Rb_tree::_M_put_node (inline) 1997ms 2.99% 58.89% 1997ms 2.99% Node::GetIndex 1948ms 2.92% 61.81% 1948ms 2.92% std::_Rb_tree_insert_and_rebalance 200ms 0.3% 62.11% 1788ms 2.68% tetgen::tetgenmesh::enqueueflipface 9ms 0.013% 62.12% 1730ms 2.59% Element::Element 1476ms 2.21% 64.33% 1549ms 2.32% tetgen::orient3d 926ms 1.39% 65.72% 1506ms 2.26% malloc_consolidate 28ms 0.042% 65.76% 1501ms 2.25% std::_Vector_base::_M_deallocate (inline) 99ms 0.15% 65.91% 1433ms 2.15% TetrahedralMesh::Clear 0 0% 65.91% 1424ms 2.13% std::vector::~vector (inline) 5ms 0.0075% 65.92% 1371ms 2.05% Element::RegisterWithNodes (inline) 95ms 0.14% 66.06% 1357ms 2.03% std::map::operator[] 0 0% 66.06% 1330ms 1.99% std::_Vector_base::~_Vector_base (inline) 42ms 0.063% 66.12% 1290ms 1.93% tetgen::tetgenmesh::locate 7ms 0.01% 66.13% 1273ms 1.91% _int_free_maybe_consolidate 1248ms 1.87% 68.00% 1248ms 1.87% unlink_chunk 73ms 0.11% 68.11% 1206ms 1.81% tetgen::tetgenmesh::preciselocate 0 0% 68.11% 1175ms 1.76% std::_Rb_tree::lower_bound (inline) 0 0% 68.11% 1175ms 1.76% std::map::lower_bound (inline) 56ms 0.084% 68.20% 1140ms 1.71% std::vector::_M_realloc_insert 1133ms 1.70% 69.90% 1133ms 1.70% tetgen::tetgenmesh::triface::triface 918ms 1.38% 71.27% 1128ms 1.69% AbstractElement::GetNodeGlobalIndex 2ms 0.003% 71.27% 1041ms 1.56% VoronoiDataWriter::Visit 973ms 1.46% 72.73% 973ms 1.46% tetgen::tetgenmesh::oppo 3ms 0.0045% 72.74% 971ms 1.45% VertexMesh::GenerateVerticesFromElementCircumcentres 135ms 0.2% 72.94% 959ms 1.44% std::vector::push_back (inline) 5ms 0.0075% 72.95% 934ms 1.40% std::_Vector_base::_M_allocate (inline) 0 0% 72.95% 824ms 1.23% TetrahedralMesh::RefreshJacobianCachedData 819ms 1.23% 74.17% 819ms 1.23% tetgen::tetgenmesh::triface::operator= 800ms 1.20% 75.37% 800ms 1.20% [libchaste_mesh.so] 319ms 0.48% 75.85% 795ms 1.19% tetgen::tetgenmesh::sym 0 0% 75.85% 759ms 1.14% AbstractTwoBodyInteractionForce::AddForceContribution 11ms 0.016% 75.87% 746ms 1.12% AbstractTetrahedralElement::CalculateInverseJacobian 11ms 0.016% 75.88% 723ms 1.08% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 299ms 0.45% 76.33% 690ms 1.03% AbstractElement::GetNodeLocation 677ms 1.01% 77.35% 677ms 1.01% Node::rGetLocation 57ms 0.085% 77.43% 676ms 1.01% tetgen::tetgenmesh::enext2fnext 29ms 0.043% 77.47% 673ms 1.01% AbstractTetrahedralElement::CalculateJacobian 404ms 0.61% 78.08% 673ms 1.01% tetgen::tetgenmesh::fnextself 42ms 0.063% 78.14% 667ms 1% __atan2 641ms 0.96% 79.10% 641ms 0.96% AbstractElement::IsDeleted 14ms 0.021% 79.12% 631ms 0.95% boost::numeric::ublas::vector_assign (inline) 492ms 0.74% 79.86% 618ms 0.93% __ieee754_atan2_fma 8ms 0.012% 79.87% 600ms 0.9% boost::numeric::ublas::c_vector::c_vector (inline) 595ms 0.89% 80.77% 595ms 0.89% std::vector::size (inline) 48ms 0.072% 80.84% 583ms 0.87% tetgen::tetgenmesh::queue::push 77ms 0.12% 80.95% 575ms 0.86% tetgen::tetgenmesh::enextfnext 0 0% 80.95% 540ms 0.81% std::set::find (inline) 357ms 0.53% 81.49% 535ms 0.8% tetgen::tetgenmesh::link::add 241ms 0.36% 81.85% 529ms 0.79% tetgen::tetgenmesh::bond 18ms 0.027% 81.88% 506ms 0.76% Element::CalculateCircumsphere 0 0% 81.88% 503ms 0.75% boost::numeric::ublas::inner_prod (inline) 55ms 0.082% 81.96% 499ms 0.75% boost::numeric::ublas::vector_scalar_binary::evaluate 0 0% 81.96% 499ms 0.75% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 497ms 0.74% 82.70% 497ms 0.74% tetgen::tetgenmesh::decode 40ms 0.06% 82.76% 485ms 0.73% AbstractTetrahedralElement::RefreshJacobian 482ms 0.72% 83.48% 482ms 0.72% tetgen::tetgenmesh::org 0 0% 83.48% 454ms 0.68% std::insert_iterator::operator= (inline) 21ms 0.031% 83.52% 439ms 0.66% VertexMesh::CalculateUnitNormalToFaceWithArea 5ms 0.0075% 83.52% 425ms 0.64% CellPropertyCollection::GetPropertiesType (inline) 195ms 0.29% 83.82% 424ms 0.64% AbstractTetrahedralMesh::GetElement 109ms 0.16% 83.98% 421ms 0.63% __dynamic_cast 8ms 0.012% 83.99% 421ms 0.63% boost::numeric::ublas::c_vector::operator= (inline) 25ms 0.037% 84.03% 418ms 0.63% std::_Rb_tree_iterator::operator-- (inline) 74ms 0.11% 84.14% 418ms 0.63% tetgen::tetgenmesh::queue::pop 105ms 0.16% 84.30% 410ms 0.61% boost::numeric::ublas::indexing_vector_assign 402ms 0.6% 84.90% 402ms 0.6% boost::numeric::ublas::c_vector::operator() 2ms 0.003% 84.90% 401ms 0.6% Cell::GetCellId 0 0% 84.90% 396ms 0.59% std::_Rb_tree::_M_insert_unique_ (inline) 0 0% 84.90% 395ms 0.59% VertexMeshWriter::WriteVtkUsingMesh 9ms 0.013% 84.92% 384ms 0.58% VertexElement::~VertexElement 176ms 0.26% 85.18% 379ms 0.57% boost::numeric::ublas::vector_inner_prod::apply (inline) 0 0% 85.18% 366ms 0.55% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 366ms 0.55% 85.73% 366ms 0.55% std::_Rb_tree_decrement 5ms 0.0075% 85.74% 351ms 0.53% AbstractTetrahedralElement::AbstractTetrahedralElement 1ms 0.0015% 85.74% 351ms 0.53% tcache_get (inline) 350ms 0.52% 86.26% 350ms 0.52% tcache_get_n (inline) 136ms 0.2% 86.46% 342ms 0.51% Inverse 0 0% 86.46% 341ms 0.51% AbstractCellProperty::IsSubType (inline) 11ms 0.016% 86.48% 338ms 0.51% std::vector::insert (inline) 181ms 0.27% 86.75% 336ms 0.5% tetgen::tetgenmesh::link::deletenode