File: Test3dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 53522ms, 87.69% of 61036ms total Dropped 871 nodes (cum <= 305.18ms) flat flat% sum% cum cum% 0 0% 0% 60972ms 99.90% __libc_start_call_main 0 0% 0% 60972ms 99.90% __libc_start_main_impl 0 0% 0% 60972ms 99.90% _start 0 0% 0% 60952ms 99.86% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 60952ms 99.86% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 60952ms 99.86% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 60952ms 99.86% main 0 0% 0% 60914ms 99.80% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 60914ms 99.80% CxxTest::TestRunner::runTest (inline) 0 0% 0% 60914ms 99.80% Test3dTissueRepresentativeSimulation::Test3DHoneycombMeshWithGhostNodes 1ms 0.0016% 0.0016% 60641ms 99.35% AbstractCellBasedSimulation::Solve 0 0% 0.0016% 51637ms 84.60% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0.0016% 51594ms 84.53% MeshBasedCellPopulation::Update 0 0% 0.0016% 27595ms 45.21% MeshBasedCellPopulation::TessellateIfNeeded 0 0% 0.0016% 27594ms 45.21% MeshBasedCellPopulation::CreateVoronoiTessellation (inline) 208ms 0.34% 0.34% 24788ms 40.61% VertexMesh::VertexMesh 0 0% 0.34% 20036ms 32.83% MutableMesh::ReMesh 0 0% 0.34% 16336ms 26.76% tetgen::tetrahedralize 2ms 0.0033% 0.35% 16189ms 26.52% tetgen::tetgenmesh::delaunizevertices 14ms 0.023% 0.37% 16184ms 26.52% tetgen::tetgenmesh::incrflipdelaunay 499ms 0.82% 1.19% 14547ms 23.83% tetgen::tetgenmesh::lawson 598ms 0.98% 2.17% 12121ms 19.86% TetrahedralMesh::EdgeIterator::operator++ 31ms 0.051% 2.22% 9793ms 16.04% std::set::insert (inline) 347ms 0.57% 2.79% 9791ms 16.04% VertexElement::AddFace 227ms 0.37% 3.16% 9352ms 15.32% std::_Rb_tree::_M_insert_unique 3266ms 5.35% 8.51% 9182ms 15.04% std::_Rb_tree::_M_lower_bound (inline) 243ms 0.4% 8.91% 8607ms 14.10% std::_Rb_tree::find (inline) 0 0% 8.91% 8035ms 13.16% std::set::count (inline) 120ms 0.2% 9.10% 5772ms 9.46% std::less::operator() (inline) 5701ms 9.34% 18.44% 5701ms 9.34% std::operator< (inline) 298ms 0.49% 18.93% 5638ms 9.24% std::_Rb_tree::_M_insert_ (inline) 1ms 0.0016% 18.93% 5314ms 8.71% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 18.93% 5180ms 8.49% ForwardEulerNumericalMethod::UpdateAllNodePositions 0 0% 18.93% 5158ms 8.45% AbstractNumericalMethod::ComputeForcesIncludingDamping 4935ms 8.09% 27.02% 4935ms 8.09% std::_Rb_tree_increment 187ms 0.31% 27.32% 4871ms 7.98% operator new 1178ms 1.93% 29.25% 4588ms 7.52% __GI___libc_malloc 0 0% 29.25% 4349ms 7.13% MeshBasedCellPopulation::UpdateNodePairs 4ms 0.0066% 29.26% 4263ms 6.98% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 28ms 0.046% 29.31% 4261ms 6.98% std::__new_allocator::allocate (inline) 0 0% 29.31% 4240ms 6.95% std::allocator_traits::allocate (inline) 14ms 0.023% 29.33% 4199ms 6.88% MeshBasedCellPopulation::SpringIterator::operator++ 7ms 0.011% 29.34% 3950ms 6.47% std::_Rb_tree::~_Rb_tree (inline) 1276ms 2.09% 31.43% 3941ms 6.46% std::_Rb_tree::_M_erase 0 0% 31.43% 3910ms 6.41% std::set::~set (inline) 88ms 0.14% 31.58% 3848ms 6.30% tetgen::tetgenmesh::insphere_sos 2ms 0.0033% 31.58% 3797ms 6.22% std::set_intersection (inline) 235ms 0.39% 31.96% 3795ms 6.22% std::__set_intersection 1329ms 2.18% 34.14% 3765ms 6.17% std::_Rb_tree::_M_get_insert_unique_pos 1058ms 1.73% 35.88% 3752ms 6.15% __GI___libc_free 3452ms 5.66% 41.53% 3746ms 6.14% tetgen::insphere 0 0% 41.53% 3516ms 5.76% AbstractCellPopulation::WriteResultsToFiles 134ms 0.22% 41.75% 3505ms 5.74% tetgen::tetgenmesh::flip23 0 0% 41.75% 3469ms 5.68% std::_Rb_tree::_M_create_node (inline) 0 0% 41.75% 3441ms 5.64% std::_Rb_tree::_M_get_node (inline) 0 0% 41.75% 3432ms 5.62% std::_Rb_tree::_Alloc_node::operator() (inline) 131ms 0.21% 41.97% 3337ms 5.47% std::__new_allocator::deallocate (inline) 0 0% 41.97% 3323ms 5.44% std::allocator_traits::deallocate (inline) 201ms 0.33% 42.29% 3087ms 5.06% std::_Rb_tree_const_iterator::operator++ (inline) 43ms 0.07% 42.37% 3075ms 5.04% Node::AddElement 2300ms 3.77% 46.13% 3054ms 5.00% _int_malloc 17ms 0.028% 46.16% 2937ms 4.81% TetrahedralMesh::ImportFromMesher 0 0% 46.16% 2823ms 4.63% VertexMesh::~VertexMesh 2796ms 4.58% 50.74% 2796ms 4.58% std::_Rb_tree::_S_right (inline) 1394ms 2.28% 53.03% 2687ms 4.40% _int_free 150ms 0.25% 53.27% 2647ms 4.34% tetgen::tetgenmesh::flip32 3ms 0.0049% 53.28% 2396ms 3.93% MeshBasedCellPopulationWithGhostNodes::WriteVtkResultsToFile 60ms 0.098% 53.38% 2393ms 3.92% MutableElement::AddNode 200ms 0.33% 53.70% 2367ms 3.88% VertexMesh::GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex 0 0% 53.70% 2183ms 3.58% std::_Rb_tree_iterator::operator++ (inline) 0 0% 53.70% 2134ms 3.50% std::_Rb_tree::_M_drop_node (inline) 0 0% 53.70% 2118ms 3.47% std::_Rb_tree::_M_put_node (inline) 133ms 0.22% 53.92% 2053ms 3.36% Node::~Node 1950ms 3.19% 57.12% 1950ms 3.19% std::_Rb_tree_insert_and_rebalance 211ms 0.35% 57.46% 1894ms 3.10% tetgen::tetgenmesh::enqueueflipface 121ms 0.2% 57.66% 1877ms 3.08% VertexMesh::Clear 1576ms 2.58% 60.24% 1576ms 2.58% Node::GetIndex 1451ms 2.38% 62.62% 1532ms 2.51% tetgen::orient3d 13ms 0.021% 62.64% 1463ms 2.40% Element::Element 36ms 0.059% 62.70% 1324ms 2.17% tetgen::tetgenmesh::locate 814ms 1.33% 64.03% 1256ms 2.06% malloc_consolidate 81ms 0.13% 64.17% 1245ms 2.04% tetgen::tetgenmesh::preciselocate 26ms 0.043% 64.21% 1231ms 2.02% std::_Vector_base::_M_deallocate (inline) 85ms 0.14% 64.35% 1187ms 1.94% TetrahedralMesh::Clear 0 0% 64.35% 1158ms 1.90% std::vector::~vector (inline) 5ms 0.0082% 64.36% 1143ms 1.87% Element::RegisterWithNodes (inline) 68ms 0.11% 64.47% 1100ms 1.80% std::map::operator[] 8ms 0.013% 64.48% 1074ms 1.76% _int_free_maybe_consolidate 2ms 0.0033% 64.48% 1062ms 1.74% std::_Vector_base::~_Vector_base (inline) 1031ms 1.69% 66.17% 1031ms 1.69% tetgen::tetgenmesh::triface::triface 1012ms 1.66% 67.83% 1012ms 1.66% tetgen::tetgenmesh::oppo 59ms 0.097% 67.93% 1007ms 1.65% std::vector::_M_realloc_insert 0 0% 67.93% 964ms 1.58% std::_Rb_tree::lower_bound (inline) 0 0% 67.93% 964ms 1.58% std::map::lower_bound (inline) 739ms 1.21% 69.14% 942ms 1.54% AbstractElement::GetNodeGlobalIndex 940ms 1.54% 70.68% 940ms 1.54% unlink_chunk 1ms 0.0016% 70.68% 893ms 1.46% VoronoiDataWriter::Visit 131ms 0.21% 70.89% 848ms 1.39% std::vector::push_back (inline) 842ms 1.38% 72.27% 842ms 1.38% tetgen::tetgenmesh::triface::operator= 4ms 0.0066% 72.28% 803ms 1.32% std::_Vector_base::_M_allocate (inline) 4ms 0.0066% 72.29% 801ms 1.31% VertexMesh::GenerateVerticesFromElementCircumcentres 288ms 0.47% 72.76% 800ms 1.31% tetgen::tetgenmesh::sym 785ms 1.29% 74.04% 785ms 1.29% [libchaste_mesh.so] 0 0% 74.04% 738ms 1.21% TetrahedralMesh::RefreshJacobianCachedData 2ms 0.0033% 74.05% 731ms 1.20% AbstractTwoBodyInteractionForce::AddForceContribution 16ms 0.026% 74.07% 699ms 1.15% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 7ms 0.011% 74.09% 667ms 1.09% AbstractTetrahedralElement::CalculateInverseJacobian 400ms 0.66% 74.74% 666ms 1.09% tetgen::tetgenmesh::fnextself 10ms 0.016% 74.76% 661ms 1.08% boost::numeric::ublas::vector_assign (inline) 16ms 0.026% 74.78% 642ms 1.05% boost::numeric::ublas::c_vector::c_vector (inline) 222ms 0.36% 75.15% 641ms 1.05% tetgen::tetgenmesh::bond 66ms 0.11% 75.26% 639ms 1.05% tetgen::tetgenmesh::enextfnext 74ms 0.12% 75.38% 624ms 1.02% tetgen::tetgenmesh::enext2fnext 48ms 0.079% 75.46% 600ms 0.98% __atan2 22ms 0.036% 75.49% 583ms 0.96% AbstractTetrahedralElement::CalculateJacobian 25ms 0.041% 75.53% 581ms 0.95% tetgen::tetgenmesh::queue::push 0 0% 75.53% 569ms 0.93% std::set::find (inline) 385ms 0.63% 76.16% 555ms 0.91% tetgen::tetgenmesh::link::add 549ms 0.9% 77.06% 549ms 0.9% std::vector::size (inline) 434ms 0.71% 77.77% 544ms 0.89% __ieee754_atan2_fma 522ms 0.86% 78.63% 522ms 0.86% tetgen::tetgenmesh::decode 521ms 0.85% 79.48% 521ms 0.85% Node::rGetLocation 223ms 0.37% 79.85% 516ms 0.85% AbstractElement::GetNodeLocation 0 0% 79.85% 506ms 0.83% boost::numeric::ublas::inner_prod (inline) 1ms 0.0016% 79.85% 504ms 0.83% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 35ms 0.057% 79.91% 503ms 0.82% boost::numeric::ublas::vector_scalar_binary::evaluate 496ms 0.81% 80.72% 496ms 0.81% tetgen::tetgenmesh::org 0 0% 80.72% 471ms 0.77% std::insert_iterator::operator= (inline) 450ms 0.74% 81.46% 450ms 0.74% AbstractElement::IsDeleted 446ms 0.73% 82.19% 446ms 0.73% tetgen::tetgenmesh::pointmark 14ms 0.023% 82.21% 432ms 0.71% Element::CalculateCircumsphere 221ms 0.36% 82.57% 431ms 0.71% AbstractTetrahedralMesh::GetElement 109ms 0.18% 82.75% 424ms 0.69% boost::numeric::ublas::indexing_vector_assign 4ms 0.0066% 82.76% 420ms 0.69% boost::numeric::ublas::c_vector::operator= (inline) 186ms 0.3% 83.06% 420ms 0.69% boost::numeric::ublas::vector_inner_prod::apply (inline) 412ms 0.68% 83.74% 412ms 0.68% boost::numeric::ublas::c_vector::operator() 42ms 0.069% 83.81% 408ms 0.67% AbstractTetrahedralElement::RefreshJacobian 2ms 0.0033% 83.81% 407ms 0.67% std::_Rb_tree::_M_insert_unique_ (inline) 18ms 0.029% 83.84% 404ms 0.66% VertexMesh::CalculateUnitNormalToFaceWithArea 404ms 0.66% 84.50% 404ms 0.66% tetgen::tetgenmesh::encode 24ms 0.039% 84.54% 402ms 0.66% std::_Rb_tree_iterator::operator-- (inline) 50ms 0.082% 84.62% 401ms 0.66% tetgen::tetgenmesh::queue::pop 111ms 0.18% 84.80% 395ms 0.65% __dynamic_cast 2ms 0.0033% 84.81% 383ms 0.63% CellPropertyCollection::GetPropertiesType (inline) 0 0% 84.81% 382ms 0.63% VertexMeshWriter::WriteVtkUsingMesh 2ms 0.0033% 84.81% 378ms 0.62% Cell::GetCellId 351ms 0.58% 85.39% 351ms 0.58% std::_Rb_tree_decrement 348ms 0.57% 85.96% 348ms 0.57% tetgen::tetgenmesh::dest 215ms 0.35% 86.31% 342ms 0.56% tetgen::tetgenmesh::link::deletenode 8ms 0.013% 86.32% 332ms 0.54% VertexElement::~VertexElement 19ms 0.031% 86.35% 327ms 0.54% std::vector::insert (inline) 325ms 0.53% 86.88% 325ms 0.53% tetgen::tetgenmesh::face::face 44ms 0.072% 86.96% 324ms 0.53% boost::numeric::ublas::vector_reference::operator() (inline) 2ms 0.0033% 86.96% 323ms 0.53% AbstractCellProperty::IsSubType (inline) 123ms 0.2% 87.16% 321ms 0.53% Inverse 1ms 0.0016% 87.16% 320ms 0.52% tcache_get (inline) 319ms 0.52% 87.69% 319ms 0.52% tcache_get_n (inline) 2ms 0.0033% 87.69% 308ms 0.5% AbstractTetrahedralElement::AbstractTetrahedralElement 0 0% 87.69% 308ms 0.5% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline)