File: Test3dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 61790ms, 88.24% of 70022ms total Dropped 882 nodes (cum <= 350.11ms) flat flat% sum% cum cum% 0 0% 0% 69961ms 99.91% __libc_start_call_main 0 0% 0% 69961ms 99.91% __libc_start_main_impl 0 0% 0% 69961ms 99.91% _start 0 0% 0% 69944ms 99.89% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 69944ms 99.89% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 69944ms 99.89% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 69944ms 99.89% main 0 0% 0% 69903ms 99.83% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 69903ms 99.83% CxxTest::TestRunner::runTest (inline) 0 0% 0% 69903ms 99.83% Test3dTissueRepresentativeSimulation::Test3DHoneycombMeshWithGhostNodes 0 0% 0% 69621ms 99.43% AbstractCellBasedSimulation::Solve 0 0% 0% 58597ms 83.68% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 58541ms 83.60% MeshBasedCellPopulation::Update 0 0% 0% 35913ms 51.29% MeshBasedCellPopulation::CreateVoronoiTessellation (inline) 0 0% 0% 35913ms 51.29% MeshBasedCellPopulation::TessellateIfNeeded 286ms 0.41% 0.41% 31081ms 44.39% VertexMesh::VertexMesh 1ms 0.0014% 0.41% 18196ms 25.99% MutableMesh::ReMesh 586ms 0.84% 1.25% 13824ms 19.74% TetrahedralMesh::EdgeIterator::operator++ 0 0% 1.25% 13027ms 18.60% tetgen::tetrahedralize 3ms 0.0043% 1.25% 12893ms 18.41% tetgen::tetgenmesh::delaunizevertices 13ms 0.019% 1.27% 12888ms 18.41% tetgen::tetgenmesh::incrflipdelaunay 27ms 0.039% 1.31% 11949ms 17.06% std::set::insert (inline) 208ms 0.3% 1.61% 11437ms 16.33% std::_Rb_tree::_M_insert_unique 537ms 0.77% 2.37% 11413ms 16.30% tetgen::tetgenmesh::lawson 470ms 0.67% 3.04% 10431ms 14.90% VertexElement::AddFace 2952ms 4.22% 7.26% 10412ms 14.87% std::_Rb_tree::_M_lower_bound (inline) 246ms 0.35% 7.61% 9607ms 13.72% std::_Rb_tree::find (inline) 0 0% 7.61% 9124ms 13.03% std::set::count (inline) 7768ms 11.09% 18.70% 7768ms 11.09% std::_Rb_tree_increment 131ms 0.19% 18.89% 7065ms 10.09% std::less::operator() (inline) 6995ms 9.99% 28.88% 6995ms 9.99% std::operator< (inline) 250ms 0.36% 29.24% 6600ms 9.43% std::_Rb_tree::_M_insert_ (inline) 221ms 0.32% 29.55% 6346ms 9.06% operator new 1002ms 1.43% 30.98% 6059ms 8.65% __GI___libc_malloc 0 0% 30.98% 5964ms 8.52% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 30.98% 5795ms 8.28% ForwardEulerNumericalMethod::UpdateAllNodePositions 4ms 0.0057% 30.99% 5761ms 8.23% AbstractNumericalMethod::ComputeForcesIncludingDamping 4ms 0.0057% 31.00% 5572ms 7.96% std::set_intersection (inline) 344ms 0.49% 31.49% 5568ms 7.95% std::__set_intersection 31ms 0.044% 31.53% 5254ms 7.50% Node::AddElement 56ms 0.08% 31.61% 5192ms 7.41% std::__new_allocator::allocate (inline) 0 0% 31.61% 5174ms 7.39% std::allocator_traits::allocate (inline) 6ms 0.0086% 31.62% 5061ms 7.23% std::_Rb_tree::~_Rb_tree (inline) 2135ms 3.05% 34.67% 5053ms 7.22% std::_Rb_tree::_M_erase 0 0% 34.67% 4991ms 7.13% std::set::~set (inline) 1244ms 1.78% 36.45% 4940ms 7.05% std::_Rb_tree::_M_get_insert_unique_pos 0 0% 36.45% 4886ms 6.98% AbstractCellPopulation::WriteResultsToFiles 0 0% 36.45% 4870ms 6.95% VertexMesh::~VertexMesh 4ms 0.0057% 36.45% 4801ms 6.86% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 0 0% 36.45% 4798ms 6.85% MeshBasedCellPopulation::UpdateNodePairs 1358ms 1.94% 38.39% 4737ms 6.77% __GI___libc_free 179ms 0.26% 38.65% 4701ms 6.71% std::_Rb_tree_const_iterator::operator++ (inline) 3308ms 4.72% 43.37% 4679ms 6.68% _int_malloc 4654ms 6.65% 50.02% 4654ms 6.65% std::_Rb_tree::_S_right (inline) 14ms 0.02% 50.04% 4634ms 6.62% MeshBasedCellPopulation::SpringIterator::operator++ 2ms 0.0029% 50.04% 4190ms 5.98% TetrahedralMesh::ImportFromMesher 113ms 0.16% 50.20% 4175ms 5.96% std::__new_allocator::deallocate (inline) 0 0% 50.20% 4156ms 5.94% std::allocator_traits::deallocate (inline) 0 0% 50.20% 4146ms 5.92% std::_Rb_tree::_M_create_node (inline) 0 0% 50.20% 4108ms 5.87% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 50.20% 4093ms 5.85% std::_Rb_tree::_M_get_node (inline) 69ms 0.099% 50.30% 3891ms 5.56% MutableElement::AddNode 239ms 0.34% 50.64% 3573ms 5.10% VertexMesh::GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex 96ms 0.14% 50.78% 3471ms 4.96% tetgen::tetgenmesh::insphere_sos 7ms 0.01% 50.79% 3393ms 4.85% MeshBasedCellPopulationWithGhostNodes::WriteVtkResultsToFile 1163ms 1.66% 52.45% 3376ms 4.82% _int_free 1ms 0.0014% 52.45% 3361ms 4.80% std::_Rb_tree_iterator::operator++ (inline) 3083ms 4.40% 56.85% 3359ms 4.80% tetgen::insphere 235ms 0.34% 57.19% 3213ms 4.59% Node::~Node 262ms 0.37% 57.56% 2980ms 4.26% VertexMesh::Clear 220ms 0.31% 57.88% 2713ms 3.87% tetgen::tetgenmesh::flip23 2413ms 3.45% 61.32% 2413ms 3.45% Node::GetIndex 2355ms 3.36% 64.69% 2355ms 3.36% std::_Rb_tree_insert_and_rebalance 1569ms 2.24% 66.93% 2305ms 3.29% malloc_consolidate 3ms 0.0043% 66.93% 2193ms 3.13% Element::Element 19ms 0.027% 66.96% 2174ms 3.10% std::_Vector_base::_M_deallocate (inline) 0 0% 66.96% 2043ms 2.92% std::vector::~vector (inline) 0 0% 66.96% 2012ms 2.87% std::_Rb_tree::_M_drop_node (inline) 0 0% 66.96% 2001ms 2.86% std::_Rb_tree::_M_put_node (inline) 0 0% 66.96% 1996ms 2.85% std::_Vector_base::~_Vector_base (inline) 4ms 0.0057% 66.96% 1984ms 2.83% _int_free_maybe_consolidate 5ms 0.0071% 66.97% 1837ms 2.62% Element::RegisterWithNodes (inline) 142ms 0.2% 67.17% 1756ms 2.51% tetgen::tetgenmesh::flip32 1666ms 2.38% 69.55% 1666ms 2.38% unlink_chunk 243ms 0.35% 69.90% 1617ms 2.31% TetrahedralMesh::Clear 1355ms 1.94% 71.84% 1447ms 2.07% tetgen::orient3d 10ms 0.014% 71.85% 1423ms 2.03% VertexMesh::GenerateVerticesFromElementCircumcentres 55ms 0.079% 71.93% 1356ms 1.94% std::map::operator[] 177ms 0.25% 72.18% 1323ms 1.89% tetgen::tetgenmesh::enqueueflipface 57ms 0.081% 72.26% 1260ms 1.80% std::vector::_M_realloc_insert 37ms 0.053% 72.32% 1237ms 1.77% tetgen::tetgenmesh::locate 0 0% 72.32% 1229ms 1.76% VoronoiDataWriter::Visit 0 0% 72.32% 1215ms 1.74% std::_Rb_tree::lower_bound (inline) 0 0% 72.32% 1215ms 1.74% std::map::lower_bound (inline) 983ms 1.40% 73.72% 1178ms 1.68% AbstractElement::GetNodeGlobalIndex 106ms 0.15% 73.87% 1136ms 1.62% tetgen::tetgenmesh::preciselocate 1ms 0.0014% 73.87% 1082ms 1.55% std::_Vector_base::_M_allocate (inline) 118ms 0.17% 74.04% 1055ms 1.51% std::vector::push_back (inline) 0 0% 74.04% 960ms 1.37% TetrahedralMesh::RefreshJacobianCachedData 399ms 0.57% 74.61% 914ms 1.31% AbstractElement::GetNodeLocation 901ms 1.29% 75.90% 901ms 1.29% Node::rGetLocation 852ms 1.22% 77.11% 852ms 1.22% tetgen::tetgenmesh::triface::operator= 15ms 0.021% 77.14% 807ms 1.15% AbstractTetrahedralElement::CalculateInverseJacobian 797ms 1.14% 78.27% 797ms 1.14% AbstractElement::IsDeleted 16ms 0.023% 78.30% 785ms 1.12% AbstractTetrahedralElement::CalculateJacobian 2ms 0.0029% 78.30% 743ms 1.06% AbstractTwoBodyInteractionForce::AddForceContribution 17ms 0.024% 78.32% 690ms 0.99% Element::CalculateCircumsphere 7ms 0.01% 78.33% 686ms 0.98% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 19ms 0.027% 78.36% 678ms 0.97% boost::numeric::ublas::vector_assign (inline) 655ms 0.94% 79.30% 655ms 0.94% [libchaste_mesh.so] 13ms 0.019% 79.32% 646ms 0.92% boost::numeric::ublas::c_vector::c_vector (inline) 512ms 0.73% 80.05% 644ms 0.92% tetgen::tetgenmesh::fnextself 56ms 0.08% 80.13% 640ms 0.91% __atan2 636ms 0.91% 81.03% 636ms 0.91% tetgen::tetgenmesh::oppo 632ms 0.9% 81.94% 632ms 0.9% std::vector::size (inline) 41ms 0.059% 82.00% 595ms 0.85% AbstractTetrahedralElement::RefreshJacobian 479ms 0.68% 82.68% 584ms 0.83% __ieee754_atan2_fma 0 0% 82.68% 525ms 0.75% boost::numeric::ublas::inner_prod (inline) 2ms 0.0029% 82.68% 519ms 0.74% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 33ms 0.047% 82.73% 517ms 0.74% boost::numeric::ublas::vector_scalar_binary::evaluate 0 0% 82.73% 505ms 0.72% std::insert_iterator::operator= (inline) 503ms 0.72% 83.45% 503ms 0.72% tetgen::tetgenmesh::triface::triface 19ms 0.027% 83.48% 486ms 0.69% VertexMesh::CalculateUnitNormalToFaceWithArea 0 0% 83.48% 481ms 0.69% std::set::find (inline) 457ms 0.65% 84.13% 457ms 0.65% boost::numeric::ublas::c_vector::operator() 286ms 0.41% 84.54% 451ms 0.64% tetgen::tetgenmesh::sym 0 0% 84.54% 449ms 0.64% std::_Rb_tree::_M_insert_unique_ (inline) 19ms 0.027% 84.56% 444ms 0.63% tetgen::tetgenmesh::queue::push 30ms 0.043% 84.61% 437ms 0.62% tetgen::tetgenmesh::enext2fnext 8ms 0.011% 84.62% 430ms 0.61% CellPropertyCollection::GetPropertiesType (inline) 358ms 0.51% 85.13% 425ms 0.61% tetgen::tetgenmesh::link::add 14ms 0.02% 85.15% 424ms 0.61% std::_Rb_tree_iterator::operator-- (inline) 54ms 0.077% 85.23% 424ms 0.61% tetgen::tetgenmesh::enextfnext 238ms 0.34% 85.57% 423ms 0.6% AbstractTetrahedralMesh::GetElement 423ms 0.6% 86.17% 423ms 0.6% tetgen::tetgenmesh::pointmark 184ms 0.26% 86.43% 422ms 0.6% boost::numeric::ublas::vector_inner_prod::apply (inline) 0 0% 86.43% 421ms 0.6% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 1ms 0.0014% 86.43% 405ms 0.58% Cell::GetCellId 98ms 0.14% 86.57% 405ms 0.58% __dynamic_cast 0 0% 86.57% 403ms 0.58% VertexMeshWriter::WriteVtkUsingMesh 126ms 0.18% 86.75% 403ms 0.58% boost::numeric::ublas::indexing_vector_assign 394ms 0.56% 87.32% 394ms 0.56% std::_Rb_tree_decrement 365ms 0.52% 87.84% 365ms 0.52% tetgen::tetgenmesh::org 11ms 0.016% 87.85% 360ms 0.51% VertexElement::~VertexElement 262ms 0.37% 88.23% 355ms 0.51% tetgen::tetgenmesh::bond 4ms 0.0057% 88.23% 353ms 0.5% AbstractTetrahedralElement::AbstractTetrahedralElement 7ms 0.01% 88.24% 351ms 0.5% VertexMesh::GetVolumeOfElement