File: Test3dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 52129ms, 86.20% of 60472ms total Dropped 885 nodes (cum <= 302.36ms) flat flat% sum% cum cum% 0 0% 0% 60403ms 99.89% __libc_start_call_main 0 0% 0% 60403ms 99.89% __libc_start_main_impl 0 0% 0% 60403ms 99.89% _start 0 0% 0% 60387ms 99.86% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 60387ms 99.86% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 60387ms 99.86% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 60387ms 99.86% main 0 0% 0% 60347ms 99.79% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 60347ms 99.79% CxxTest::TestRunner::runTest (inline) 0 0% 0% 60347ms 99.79% Test3dTissueRepresentativeSimulation::Test3DHoneycombMeshWithGhostNodes 0 0% 0% 60077ms 99.35% AbstractCellBasedSimulation::Solve 0 0% 0% 51041ms 84.40% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 50995ms 84.33% MeshBasedCellPopulation::Update 0 0% 0% 27277ms 45.11% MeshBasedCellPopulation::TessellateIfNeeded 0 0% 0% 27276ms 45.11% MeshBasedCellPopulation::CreateVoronoiTessellation (inline) 214ms 0.35% 0.35% 24578ms 40.64% VertexMesh::VertexMesh 2ms 0.0033% 0.36% 19740ms 32.64% MutableMesh::ReMesh 0 0% 0.36% 16124ms 26.66% tetgen::tetrahedralize 2ms 0.0033% 0.36% 15960ms 26.39% tetgen::tetgenmesh::delaunizevertices 13ms 0.021% 0.38% 15952ms 26.38% tetgen::tetgenmesh::incrflipdelaunay 503ms 0.83% 1.21% 14278ms 23.61% tetgen::tetgenmesh::lawson 606ms 1.00% 2.22% 12183ms 20.15% TetrahedralMesh::EdgeIterator::operator++ 28ms 0.046% 2.26% 9691ms 16.03% std::set::insert (inline) 370ms 0.61% 2.87% 9659ms 15.97% VertexElement::AddFace 237ms 0.39% 3.27% 9278ms 15.34% std::_Rb_tree::_M_insert_unique 3189ms 5.27% 8.54% 9127ms 15.09% std::_Rb_tree::_M_lower_bound (inline) 252ms 0.42% 8.96% 8543ms 14.13% std::_Rb_tree::find (inline) 0 0% 8.96% 7953ms 13.15% std::set::count (inline) 123ms 0.2% 9.16% 5798ms 9.59% std::less::operator() (inline) 5742ms 9.50% 18.65% 5742ms 9.50% std::operator< (inline) 310ms 0.51% 19.17% 5389ms 8.91% std::_Rb_tree::_M_insert_ (inline) 0 0% 19.17% 5364ms 8.87% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 19.17% 5239ms 8.66% ForwardEulerNumericalMethod::UpdateAllNodePositions 1ms 0.0017% 19.17% 5211ms 8.62% AbstractNumericalMethod::ComputeForcesIncludingDamping 4794ms 7.93% 27.10% 4794ms 7.93% std::_Rb_tree_increment 170ms 0.28% 27.38% 4718ms 7.80% operator new 1123ms 1.86% 29.24% 4472ms 7.40% __GI___libc_malloc 1ms 0.0017% 29.24% 4348ms 7.19% MeshBasedCellPopulation::UpdateNodePairs 13ms 0.021% 29.26% 4308ms 7.12% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 12ms 0.02% 29.28% 4227ms 6.99% MeshBasedCellPopulation::SpringIterator::operator++ 32ms 0.053% 29.33% 4134ms 6.84% std::__new_allocator::allocate (inline) 0 0% 29.33% 4106ms 6.79% std::allocator_traits::allocate (inline) 7ms 0.012% 29.34% 3963ms 6.55% std::_Rb_tree::~_Rb_tree (inline) 1303ms 2.15% 31.50% 3955ms 6.54% std::_Rb_tree::_M_erase 0 0% 31.50% 3919ms 6.48% std::set::~set (inline) 1371ms 2.27% 33.76% 3900ms 6.45% std::_Rb_tree::_M_get_insert_unique_pos 125ms 0.21% 33.97% 3804ms 6.29% tetgen::tetgenmesh::insphere_sos 3392ms 5.61% 39.58% 3669ms 6.07% tetgen::insphere 1034ms 1.71% 41.29% 3640ms 6.02% __GI___libc_free 1ms 0.0017% 41.29% 3630ms 6.00% std::set_intersection (inline) 242ms 0.4% 41.69% 3629ms 6.00% std::__set_intersection 0 0% 41.69% 3515ms 5.81% AbstractCellPopulation::WriteResultsToFiles 130ms 0.21% 41.91% 3509ms 5.80% tetgen::tetgenmesh::flip23 0 0% 41.91% 3327ms 5.50% std::_Rb_tree::_M_create_node (inline) 0 0% 41.91% 3301ms 5.46% std::_Rb_tree::_Alloc_node::operator() (inline) 133ms 0.22% 42.13% 3294ms 5.45% std::__new_allocator::deallocate (inline) 0 0% 42.13% 3293ms 5.45% std::_Rb_tree::_M_get_node (inline) 0 0% 42.13% 3275ms 5.42% std::allocator_traits::deallocate (inline) 35ms 0.058% 42.18% 3012ms 4.98% Node::AddElement 2155ms 3.56% 45.75% 2972ms 4.91% _int_malloc 200ms 0.33% 46.08% 2955ms 4.89% std::_Rb_tree_const_iterator::operator++ (inline) 2945ms 4.87% 50.95% 2945ms 4.87% std::_Rb_tree::_S_right (inline) 8ms 0.013% 50.96% 2870ms 4.75% TetrahedralMesh::ImportFromMesher 0 0% 50.96% 2715ms 4.49% VertexMesh::~VertexMesh 1394ms 2.31% 53.27% 2604ms 4.31% _int_free 160ms 0.26% 53.53% 2538ms 4.20% tetgen::tetgenmesh::flip32 5ms 0.0083% 53.54% 2401ms 3.97% MeshBasedCellPopulationWithGhostNodes::WriteVtkResultsToFile 79ms 0.13% 53.67% 2395ms 3.96% MutableElement::AddNode 215ms 0.36% 54.03% 2387ms 3.95% VertexMesh::GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex 4ms 0.0066% 54.03% 2186ms 3.61% std::_Rb_tree_iterator::operator++ (inline) 0 0% 54.03% 2115ms 3.50% std::_Rb_tree::_M_drop_node (inline) 0 0% 54.03% 2105ms 3.48% std::_Rb_tree::_M_put_node (inline) 140ms 0.23% 54.26% 2014ms 3.33% Node::~Node 223ms 0.37% 54.63% 1950ms 3.22% tetgen::tetgenmesh::enqueueflipface 1836ms 3.04% 57.67% 1836ms 3.04% std::_Rb_tree_insert_and_rebalance 154ms 0.25% 57.92% 1803ms 2.98% VertexMesh::Clear 1581ms 2.61% 60.54% 1656ms 2.74% tetgen::orient3d 1589ms 2.63% 63.17% 1589ms 2.63% Node::GetIndex 6ms 0.0099% 63.18% 1396ms 2.31% Element::Element 45ms 0.074% 63.25% 1362ms 2.25% tetgen::tetgenmesh::locate 68ms 0.11% 63.36% 1267ms 2.10% tetgen::tetgenmesh::preciselocate 71ms 0.12% 63.48% 1203ms 1.99% TetrahedralMesh::Clear 19ms 0.031% 63.51% 1189ms 1.97% std::_Vector_base::_M_deallocate (inline) 784ms 1.30% 64.81% 1186ms 1.96% malloc_consolidate 64ms 0.11% 64.91% 1155ms 1.91% std::map::operator[] 0 0% 64.91% 1122ms 1.86% std::vector::~vector (inline) 4ms 0.0066% 64.92% 1102ms 1.82% Element::RegisterWithNodes (inline) 1083ms 1.79% 66.71% 1083ms 1.79% tetgen::tetgenmesh::oppo 57ms 0.094% 66.81% 1054ms 1.74% std::vector::_M_realloc_insert 0 0% 66.81% 1032ms 1.71% std::_Rb_tree::lower_bound (inline) 0 0% 66.81% 1032ms 1.71% std::map::lower_bound (inline) 3ms 0.005% 66.81% 1027ms 1.70% std::_Vector_base::~_Vector_base (inline) 8ms 0.013% 66.82% 999ms 1.65% _int_free_maybe_consolidate 939ms 1.55% 68.38% 939ms 1.55% unlink_chunk 910ms 1.50% 69.88% 910ms 1.50% tetgen::tetgenmesh::triface::triface 0 0% 69.88% 880ms 1.46% VoronoiDataWriter::Visit 135ms 0.22% 70.11% 870ms 1.44% std::vector::push_back (inline) 699ms 1.16% 71.26% 862ms 1.43% AbstractElement::GetNodeGlobalIndex 6ms 0.0099% 71.27% 819ms 1.35% std::_Vector_base::_M_allocate (inline) 799ms 1.32% 72.59% 799ms 1.32% [libchaste_mesh.so] 7ms 0.012% 72.60% 785ms 1.30% VertexMesh::GenerateVerticesFromElementCircumcentres 771ms 1.27% 73.88% 771ms 1.27% tetgen::tetgenmesh::triface::operator= 2ms 0.0033% 73.88% 744ms 1.23% AbstractTwoBodyInteractionForce::AddForceContribution 0 0% 73.88% 724ms 1.20% TetrahedralMesh::RefreshJacobianCachedData 297ms 0.49% 74.37% 719ms 1.19% tetgen::tetgenmesh::sym 24ms 0.04% 74.41% 695ms 1.15% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 227ms 0.38% 74.79% 677ms 1.12% tetgen::tetgenmesh::bond 5ms 0.0083% 74.80% 666ms 1.10% AbstractTetrahedralElement::CalculateInverseJacobian 41ms 0.068% 74.86% 627ms 1.04% tetgen::tetgenmesh::queue::push 57ms 0.094% 74.96% 610ms 1.01% __atan2 340ms 0.56% 75.52% 609ms 1.01% tetgen::tetgenmesh::fnextself 14ms 0.023% 75.54% 597ms 0.99% boost::numeric::ublas::vector_assign (inline) 0 0% 75.54% 586ms 0.97% std::set::find (inline) 368ms 0.61% 76.15% 586ms 0.97% tetgen::tetgenmesh::link::add 62ms 0.1% 76.26% 575ms 0.95% tetgen::tetgenmesh::enext2fnext 22ms 0.036% 76.29% 573ms 0.95% AbstractTetrahedralElement::CalculateJacobian 46ms 0.076% 76.37% 567ms 0.94% tetgen::tetgenmesh::enextfnext 11ms 0.018% 76.39% 560ms 0.93% boost::numeric::ublas::c_vector::c_vector (inline) 425ms 0.7% 77.09% 550ms 0.91% __ieee754_atan2_fma 532ms 0.88% 77.97% 532ms 0.88% tetgen::tetgenmesh::org 503ms 0.83% 78.80% 503ms 0.83% Node::rGetLocation 218ms 0.36% 79.16% 498ms 0.82% AbstractElement::GetNodeLocation 0 0% 79.16% 497ms 0.82% boost::numeric::ublas::inner_prod (inline) 3ms 0.005% 79.17% 495ms 0.82% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 51ms 0.084% 79.25% 492ms 0.81% boost::numeric::ublas::vector_scalar_binary::evaluate 474ms 0.78% 80.03% 474ms 0.78% std::vector::size (inline) 468ms 0.77% 80.81% 468ms 0.77% tetgen::tetgenmesh::pointmark 459ms 0.76% 81.57% 459ms 0.76% AbstractElement::IsDeleted 0 0% 81.57% 453ms 0.75% std::insert_iterator::operator= (inline) 432ms 0.71% 82.28% 432ms 0.71% tetgen::tetgenmesh::encode 427ms 0.71% 82.99% 427ms 0.71% tetgen::tetgenmesh::decode 199ms 0.33% 83.32% 420ms 0.69% AbstractTetrahedralMesh::GetElement 17ms 0.028% 83.34% 411ms 0.68% Element::CalculateCircumsphere 42ms 0.069% 83.41% 400ms 0.66% AbstractTetrahedralElement::RefreshJacobian 24ms 0.04% 83.45% 398ms 0.66% std::_Rb_tree_iterator::operator-- (inline) 393ms 0.65% 84.10% 393ms 0.65% boost::numeric::ublas::c_vector::operator() 19ms 0.031% 84.13% 391ms 0.65% VertexMesh::CalculateUnitNormalToFaceWithArea 6ms 0.0099% 84.14% 388ms 0.64% boost::numeric::ublas::c_vector::operator= (inline) 0 0% 84.14% 386ms 0.64% VertexMeshWriter::WriteVtkUsingMesh 156ms 0.26% 84.40% 386ms 0.64% boost::numeric::ublas::vector_inner_prod::apply (inline) 106ms 0.18% 84.58% 385ms 0.64% __dynamic_cast 0 0% 84.58% 382ms 0.63% std::_Rb_tree::_M_insert_unique_ (inline) 1ms 0.0017% 84.58% 380ms 0.63% CellPropertyCollection::GetPropertiesType (inline) 4ms 0.0066% 84.59% 377ms 0.62% Cell::GetCellId 72ms 0.12% 84.71% 356ms 0.59% boost::numeric::ublas::indexing_vector_assign 347ms 0.57% 85.28% 347ms 0.57% std::_Rb_tree_decrement 16ms 0.026% 85.31% 343ms 0.57% std::vector::insert (inline) 114ms 0.19% 85.49% 329ms 0.54% Inverse 0 0% 85.49% 329ms 0.54% tcache_get (inline) 329ms 0.54% 86.04% 329ms 0.54% tcache_get_n (inline) 90ms 0.15% 86.19% 326ms 0.54% tetgen::tetgenmesh::queue::pop 6ms 0.0099% 86.20% 321ms 0.53% AbstractCellProperty::IsSubType (inline) 4ms 0.0066% 86.20% 308ms 0.51% VertexElement::~VertexElement