File: Test3dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 45116ms, 86.59% of 52101ms total Dropped 844 nodes (cum <= 260.50ms) flat flat% sum% cum cum% 0 0% 0% 52055ms 99.91% __libc_start_call_main 0 0% 0% 52055ms 99.91% __libc_start_main_impl 0 0% 0% 52055ms 99.91% _start 0 0% 0% 52041ms 99.88% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 52041ms 99.88% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 52041ms 99.88% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 52041ms 99.88% main 0 0% 0% 52004ms 99.81% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 52004ms 99.81% CxxTest::TestRunner::runTest (inline) 0 0% 0% 52004ms 99.81% Test3dTissueRepresentativeSimulation::Test3DHoneycombMeshWithGhostNodes 0 0% 0% 51785ms 99.39% AbstractCellBasedSimulation::Solve 0 0% 0% 43609ms 83.70% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 43571ms 83.63% MeshBasedCellPopulation::Update 0 0% 0% 24276ms 46.59% MeshBasedCellPopulation::TessellateIfNeeded 0 0% 0% 24275ms 46.59% MeshBasedCellPopulation::CreateVoronoiTessellation (inline) 161ms 0.31% 0.31% 21429ms 41.13% VertexMesh::VertexMesh 0 0% 0.31% 15787ms 30.30% MutableMesh::ReMesh 0 0% 0.31% 12353ms 23.71% tetgen::tetrahedralize 0 0% 0.31% 12236ms 23.49% tetgen::tetgenmesh::delaunizevertices 0 0% 0.31% 12230ms 23.47% tetgen::tetgenmesh::incrflipdelaunay 425ms 0.82% 1.12% 10974ms 21.06% tetgen::tetgenmesh::lawson 470ms 0.9% 2.03% 10664ms 20.47% TetrahedralMesh::EdgeIterator::operator++ 22ms 0.042% 2.07% 8209ms 15.76% std::set::insert (inline) 2464ms 4.73% 6.80% 8129ms 15.60% std::_Rb_tree::_M_lower_bound (inline) 311ms 0.6% 7.40% 7993ms 15.34% VertexElement::AddFace 202ms 0.39% 7.78% 7864ms 15.09% std::_Rb_tree::_M_insert_unique 223ms 0.43% 8.21% 7607ms 14.60% std::_Rb_tree::find (inline) 0 0% 8.21% 7131ms 13.69% std::set::count (inline) 86ms 0.17% 8.38% 5417ms 10.40% std::less::operator() (inline) 5373ms 10.31% 18.69% 5373ms 10.31% std::operator< (inline) 4816ms 9.24% 27.93% 4816ms 9.24% std::_Rb_tree_increment 1ms 0.0019% 27.93% 4678ms 8.98% OffLatticeSimulation::UpdateCellLocationsAndTopology 240ms 0.46% 28.39% 4557ms 8.75% std::_Rb_tree::_M_insert_ (inline) 1ms 0.0019% 28.40% 4549ms 8.73% ForwardEulerNumericalMethod::UpdateAllNodePositions 0 0% 28.40% 4525ms 8.69% AbstractNumericalMethod::ComputeForcesIncludingDamping 134ms 0.26% 28.65% 4256ms 8.17% operator new 934ms 1.79% 30.45% 4069ms 7.81% __GI___libc_malloc 0 0% 30.45% 3797ms 7.29% MeshBasedCellPopulation::UpdateNodePairs 3ms 0.0058% 30.45% 3774ms 7.24% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 14ms 0.027% 30.48% 3671ms 7.05% MeshBasedCellPopulation::SpringIterator::operator++ 24ms 0.046% 30.53% 3655ms 7.02% std::__new_allocator::allocate (inline) 0 0% 30.53% 3644ms 6.99% std::allocator_traits::allocate (inline) 8ms 0.015% 30.54% 3602ms 6.91% std::_Rb_tree::~_Rb_tree (inline) 1354ms 2.60% 33.14% 3591ms 6.89% std::_Rb_tree::_M_erase 0 0% 33.14% 3558ms 6.83% std::set::~set (inline) 6ms 0.012% 33.15% 3391ms 6.51% std::set_intersection (inline) 216ms 0.41% 33.57% 3385ms 6.50% std::__set_intersection 0 0% 33.57% 3374ms 6.48% AbstractCellPopulation::WriteResultsToFiles 995ms 1.91% 35.48% 3332ms 6.40% __GI___libc_free 1018ms 1.95% 37.43% 3313ms 6.36% std::_Rb_tree::_M_get_insert_unique_pos 99ms 0.19% 37.62% 3002ms 5.76% tetgen::tetgenmesh::insphere_sos 0 0% 37.62% 2932ms 5.63% std::_Rb_tree::_M_create_node (inline) 36ms 0.069% 37.69% 2928ms 5.62% Node::AddElement 2907ms 5.58% 43.27% 2907ms 5.58% std::_Rb_tree::_S_right (inline) 0 0% 43.27% 2903ms 5.57% std::_Rb_tree::_M_get_node (inline) 0 0% 43.27% 2898ms 5.56% std::_Rb_tree::_Alloc_node::operator() (inline) 122ms 0.23% 43.50% 2897ms 5.56% std::__new_allocator::deallocate (inline) 2660ms 5.11% 48.61% 2891ms 5.55% tetgen::insphere 0 0% 48.61% 2886ms 5.54% std::allocator_traits::deallocate (inline) 0 0% 48.61% 2866ms 5.50% VertexMesh::~VertexMesh 2037ms 3.91% 52.52% 2843ms 5.46% _int_malloc 145ms 0.28% 52.80% 2814ms 5.40% std::_Rb_tree_const_iterator::operator++ (inline) 6ms 0.012% 52.81% 2794ms 5.36% TetrahedralMesh::ImportFromMesher 114ms 0.22% 53.03% 2734ms 5.25% tetgen::tetgenmesh::flip23 164ms 0.31% 53.34% 2424ms 4.65% VertexMesh::GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex 3ms 0.0058% 53.35% 2351ms 4.51% MeshBasedCellPopulationWithGhostNodes::WriteVtkResultsToFile 1056ms 2.03% 55.37% 2336ms 4.48% _int_free 1ms 0.0019% 55.38% 2272ms 4.36% std::_Rb_tree_iterator::operator++ (inline) 52ms 0.1% 55.47% 2255ms 4.33% MutableElement::AddNode 148ms 0.28% 55.76% 2089ms 4.01% Node::~Node 139ms 0.27% 56.03% 1854ms 3.56% VertexMesh::Clear 89ms 0.17% 56.20% 1852ms 3.55% tetgen::tetgenmesh::flip32 0 0% 56.20% 1680ms 3.22% std::_Rb_tree::_M_drop_node (inline) 0 0% 56.20% 1677ms 3.22% std::_Rb_tree::_M_put_node (inline) 1504ms 2.89% 59.08% 1504ms 2.89% Node::GetIndex 1473ms 2.83% 61.91% 1473ms 2.83% std::_Rb_tree_insert_and_rebalance 168ms 0.32% 62.23% 1425ms 2.74% tetgen::tetgenmesh::enqueueflipface 2ms 0.0038% 62.24% 1308ms 2.51% Element::Element 827ms 1.59% 63.82% 1283ms 2.46% malloc_consolidate 1194ms 2.29% 66.12% 1265ms 2.43% tetgen::orient3d 76ms 0.15% 66.26% 1236ms 2.37% TetrahedralMesh::Clear 0 0% 66.26% 1235ms 2.37% std::vector::~vector (inline) 21ms 0.04% 66.30% 1230ms 2.36% std::_Vector_base::_M_deallocate (inline) 2ms 0.0038% 66.31% 1116ms 2.14% std::_Vector_base::~_Vector_base (inline) 8ms 0.015% 66.32% 1102ms 2.12% _int_free_maybe_consolidate 5ms 0.0096% 66.33% 1045ms 2.01% Element::RegisterWithNodes (inline) 49ms 0.094% 66.42% 1036ms 1.99% std::map::operator[] 17ms 0.033% 66.46% 1029ms 1.98% tetgen::tetgenmesh::locate 982ms 1.88% 68.34% 982ms 1.88% unlink_chunk 61ms 0.12% 68.46% 978ms 1.88% tetgen::tetgenmesh::preciselocate 0 0% 68.46% 912ms 1.75% std::_Rb_tree::lower_bound (inline) 0 0% 68.46% 912ms 1.75% std::map::lower_bound (inline) 52ms 0.1% 68.56% 899ms 1.73% std::vector::_M_realloc_insert 834ms 1.60% 70.16% 834ms 1.60% tetgen::tetgenmesh::oppo 692ms 1.33% 71.49% 815ms 1.56% AbstractElement::GetNodeGlobalIndex 0 0% 71.49% 814ms 1.56% VoronoiDataWriter::Visit 1ms 0.0019% 71.49% 788ms 1.51% VertexMesh::GenerateVerticesFromElementCircumcentres 788ms 1.51% 73.00% 788ms 1.51% tetgen::tetgenmesh::triface::triface 114ms 0.22% 73.22% 760ms 1.46% std::vector::push_back (inline) 1ms 0.0019% 73.22% 742ms 1.42% std::_Vector_base::_M_allocate (inline) 648ms 1.24% 74.47% 648ms 1.24% [libchaste_mesh.so] 1ms 0.0019% 74.47% 616ms 1.18% TetrahedralMesh::RefreshJacobianCachedData 216ms 0.41% 74.88% 614ms 1.18% tetgen::tetgenmesh::sym 0 0% 74.88% 591ms 1.13% AbstractTwoBodyInteractionForce::AddForceContribution 579ms 1.11% 75.99% 579ms 1.11% Node::rGetLocation 15ms 0.029% 76.02% 564ms 1.08% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 213ms 0.41% 76.43% 556ms 1.07% AbstractElement::GetNodeLocation 6ms 0.012% 76.44% 547ms 1.05% AbstractTetrahedralElement::CalculateInverseJacobian 526ms 1.01% 77.45% 526ms 1.01% tetgen::tetgenmesh::triface::operator= 11ms 0.021% 77.47% 519ms 1% AbstractTetrahedralElement::CalculateJacobian 500ms 0.96% 78.43% 500ms 0.96% AbstractElement::IsDeleted 304ms 0.58% 79.02% 492ms 0.94% tetgen::tetgenmesh::fnextself 37ms 0.071% 79.09% 481ms 0.92% __atan2 15ms 0.029% 79.12% 476ms 0.91% boost::numeric::ublas::vector_assign (inline) 0 0% 79.12% 475ms 0.91% std::set::find (inline) 23ms 0.044% 79.16% 474ms 0.91% tetgen::tetgenmesh::queue::push 11ms 0.021% 79.18% 467ms 0.9% boost::numeric::ublas::c_vector::c_vector (inline) 41ms 0.079% 79.26% 457ms 0.88% tetgen::tetgenmesh::enext2fnext 302ms 0.58% 79.84% 451ms 0.87% tetgen::tetgenmesh::link::add 337ms 0.65% 80.49% 441ms 0.85% __ieee754_atan2_fma 33ms 0.063% 80.55% 432ms 0.83% tetgen::tetgenmesh::enextfnext 420ms 0.81% 81.36% 420ms 0.81% std::vector::size (inline) 174ms 0.33% 81.69% 418ms 0.8% tetgen::tetgenmesh::bond 416ms 0.8% 82.49% 416ms 0.8% tetgen::tetgenmesh::decode 13ms 0.025% 82.51% 411ms 0.79% Element::CalculateCircumsphere 0 0% 82.51% 386ms 0.74% boost::numeric::ublas::inner_prod (inline) 19ms 0.036% 82.55% 384ms 0.74% boost::numeric::ublas::vector_scalar_binary::evaluate 0 0% 82.55% 384ms 0.74% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 32ms 0.061% 82.61% 380ms 0.73% AbstractTetrahedralElement::RefreshJacobian 0 0% 82.61% 372ms 0.71% std::insert_iterator::operator= (inline) 350ms 0.67% 83.28% 350ms 0.67% tetgen::tetgenmesh::pointmark 2ms 0.0038% 83.29% 344ms 0.66% CellPropertyCollection::GetPropertiesType (inline) 340ms 0.65% 83.94% 340ms 0.65% tetgen::tetgenmesh::org 9ms 0.017% 83.96% 337ms 0.65% VertexElement::~VertexElement 166ms 0.32% 84.28% 331ms 0.64% AbstractTetrahedralMesh::GetElement 0 0% 84.28% 322ms 0.62% std::_Rb_tree::_M_insert_unique_ (inline) 2ms 0.0038% 84.28% 319ms 0.61% Cell::GetCellId 0 0% 84.28% 317ms 0.61% VertexMeshWriter::WriteVtkUsingMesh 97ms 0.19% 84.47% 316ms 0.61% __dynamic_cast 13ms 0.025% 84.49% 314ms 0.6% VertexMesh::CalculateUnitNormalToFaceWithArea 22ms 0.042% 84.53% 311ms 0.6% std::_Rb_tree_iterator::operator-- (inline) 122ms 0.23% 84.77% 307ms 0.59% boost::numeric::ublas::vector_inner_prod::apply (inline) 3ms 0.0058% 84.77% 306ms 0.59% boost::numeric::ublas::c_vector::operator= (inline) 75ms 0.14% 84.92% 293ms 0.56% boost::numeric::ublas::indexing_vector_assign 290ms 0.56% 85.47% 290ms 0.56% boost::numeric::ublas::c_vector::operator() 285ms 0.55% 86.02% 285ms 0.55% tetgen::tetgenmesh::face::face 0 0% 86.02% 282ms 0.54% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 2ms 0.0038% 86.03% 277ms 0.53% Element::~Element 0 0% 86.03% 275ms 0.53% AbstractTetrahedralElement::~AbstractTetrahedralElement (inline) 275ms 0.53% 86.55% 275ms 0.53% std::_Rb_tree_decrement 13ms 0.025% 86.58% 273ms 0.52% std::vector::insert (inline) 3ms 0.0058% 86.58% 270ms 0.52% AbstractCellProperty::IsSubType (inline) 5ms 0.0096% 86.59% 262ms 0.5% AbstractTetrahedralElement::AbstractTetrahedralElement