File: Test3dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 50100ms, 85.46% of 58622ms total Dropped 855 nodes (cum <= 293.11ms) flat flat% sum% cum cum% 0 0% 0% 58571ms 99.91% __libc_start_call_main 0 0% 0% 58571ms 99.91% __libc_start_main_impl 0 0% 0% 58571ms 99.91% _start 0 0% 0% 58554ms 99.88% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 58554ms 99.88% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 58554ms 99.88% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 58554ms 99.88% main 0 0% 0% 58519ms 99.82% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 58519ms 99.82% CxxTest::TestRunner::runTest (inline) 0 0% 0% 58519ms 99.82% Test3dTissueRepresentativeSimulation::Test3DHoneycombMeshWithGhostNodes 0 0% 0% 58295ms 99.44% AbstractCellBasedSimulation::Solve 0 0% 0% 48908ms 83.43% AbstractCellBasedSimulation::UpdateCellPopulation 1ms 0.0017% 0.0017% 48844ms 83.32% MeshBasedCellPopulation::Update 0 0% 0.0017% 29555ms 50.42% MeshBasedCellPopulation::CreateVoronoiTessellation (inline) 0 0% 0.0017% 29555ms 50.42% MeshBasedCellPopulation::TessellateIfNeeded 235ms 0.4% 0.4% 26563ms 45.31% VertexMesh::VertexMesh 1ms 0.0017% 0.4% 15173ms 25.88% MutableMesh::ReMesh 554ms 0.95% 1.35% 12675ms 21.62% TetrahedralMesh::EdgeIterator::operator++ 41ms 0.07% 1.42% 11289ms 19.26% std::set::insert (inline) 0 0% 1.42% 11214ms 19.13% tetgen::tetrahedralize 1ms 0.0017% 1.42% 11098ms 18.93% tetgen::tetgenmesh::delaunizevertices 5ms 0.0085% 1.43% 11096ms 18.93% tetgen::tetgenmesh::incrflipdelaunay 160ms 0.27% 1.70% 10708ms 18.27% std::_Rb_tree::_M_insert_unique 261ms 0.45% 2.15% 10358ms 17.67% VertexElement::AddFace 514ms 0.88% 3.02% 9792ms 16.70% tetgen::tetgenmesh::lawson 4179ms 7.13% 10.15% 9788ms 16.70% std::_Rb_tree::_M_lower_bound (inline) 185ms 0.32% 10.47% 9376ms 15.99% std::_Rb_tree::find (inline) 0 0% 10.47% 8791ms 15.00% std::set::count (inline) 327ms 0.56% 11.03% 7252ms 12.37% std::_Rb_tree::_M_insert_ (inline) 192ms 0.33% 11.35% 7198ms 12.28% operator new 2586ms 4.41% 15.77% 6930ms 11.82% __GI___libc_malloc 75ms 0.13% 15.89% 6235ms 10.64% std::__new_allocator::allocate (inline) 0 0% 15.89% 6208ms 10.59% std::allocator_traits::allocate (inline) 0 0% 15.89% 5554ms 9.47% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 15.89% 5419ms 9.24% ForwardEulerNumericalMethod::UpdateAllNodePositions 6ms 0.01% 15.90% 5397ms 9.21% AbstractNumericalMethod::ComputeForcesIncludingDamping 0 0% 15.90% 5091ms 8.68% std::_Rb_tree::_M_create_node (inline) 0 0% 15.90% 5071ms 8.65% std::_Rb_tree::_M_get_node (inline) 0 0% 15.90% 5045ms 8.61% std::_Rb_tree::_Alloc_node::operator() (inline) 4966ms 8.47% 24.37% 4966ms 8.47% std::_Rb_tree_increment 84ms 0.14% 24.52% 4843ms 8.26% std::less::operator() (inline) 4816ms 8.22% 32.73% 4816ms 8.22% std::operator< (inline) 815ms 1.39% 34.12% 4528ms 7.72% __GI___libc_free 1ms 0.0017% 34.13% 4448ms 7.59% MeshBasedCellPopulation::UpdateNodePairs 3ms 0.0051% 34.13% 4375ms 7.46% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 25ms 0.043% 34.17% 4323ms 7.37% MeshBasedCellPopulation::SpringIterator::operator++ 14ms 0.024% 34.20% 4062ms 6.93% std::_Rb_tree::~_Rb_tree (inline) 1088ms 1.86% 36.05% 4038ms 6.89% std::_Rb_tree::_M_erase 0 0% 36.05% 4012ms 6.84% std::set::~set (inline) 78ms 0.13% 36.19% 3968ms 6.77% std::__new_allocator::deallocate (inline) 240ms 0.41% 36.60% 3963ms 6.76% std::__set_intersection 0 0% 36.60% 3963ms 6.76% std::set_intersection (inline) 0 0% 36.60% 3950ms 6.74% std::allocator_traits::deallocate (inline) 3154ms 5.38% 41.98% 3894ms 6.64% _int_malloc 2023ms 3.45% 45.43% 3692ms 6.30% _int_free 0 0% 45.43% 3663ms 6.25% AbstractCellPopulation::WriteResultsToFiles 1331ms 2.27% 47.70% 3636ms 6.20% std::_Rb_tree::_M_get_insert_unique_pos 74ms 0.13% 47.82% 3517ms 6.00% Node::AddElement 3213ms 5.48% 53.30% 3213ms 5.48% std::_Rb_tree::_S_right (inline) 278ms 0.47% 53.78% 3174ms 5.41% std::_Rb_tree_const_iterator::operator++ (inline) 2ms 0.0034% 53.78% 3080ms 5.25% TetrahedralMesh::ImportFromMesher 0 0% 53.78% 3013ms 5.14% VertexMesh::~VertexMesh 107ms 0.18% 53.96% 2974ms 5.07% tetgen::tetgenmesh::insphere_sos 2621ms 4.47% 58.44% 2841ms 4.85% tetgen::insphere 39ms 0.067% 58.50% 2646ms 4.51% MutableElement::AddNode 288ms 0.49% 58.99% 2643ms 4.51% std::_Rb_tree_iterator::operator++ (inline) 7ms 0.012% 59.01% 2631ms 4.49% VertexMesh::GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex 2ms 0.0034% 59.01% 2576ms 4.39% MeshBasedCellPopulationWithGhostNodes::WriteVtkResultsToFile 0 0% 59.01% 2526ms 4.31% std::_Rb_tree::_M_drop_node (inline) 0 0% 59.01% 2506ms 4.27% std::_Rb_tree::_M_put_node (inline) 234ms 0.4% 59.41% 2313ms 3.95% tetgen::tetgenmesh::flip23 2129ms 3.63% 63.04% 2129ms 3.63% [libchaste_mesh.so] 52ms 0.089% 63.13% 2012ms 3.43% Node::~Node 1924ms 3.28% 66.41% 1924ms 3.28% std::_Rb_tree_insert_and_rebalance 5ms 0.0085% 66.42% 1898ms 3.24% VertexMesh::Clear 2ms 0.0034% 66.42% 1737ms 2.96% Element::Element 202ms 0.34% 66.77% 1607ms 2.74% tetgen::tetgenmesh::flip32 1530ms 2.61% 69.38% 1585ms 2.70% tetgen::orient3d 33ms 0.056% 69.43% 1477ms 2.52% std::_Vector_base::_M_deallocate (inline) 3ms 0.0051% 69.44% 1416ms 2.42% Element::RegisterWithNodes (inline) 873ms 1.49% 70.93% 1412ms 2.41% malloc_consolidate 0 0% 70.93% 1346ms 2.30% std::vector::~vector (inline) 52ms 0.089% 71.02% 1332ms 2.27% std::vector::_M_realloc_insert 4ms 0.0068% 71.02% 1270ms 2.17% std::_Vector_base::~_Vector_base (inline) 7ms 0.012% 71.03% 1225ms 2.09% _int_free_maybe_consolidate 0 0% 71.03% 1137ms 1.94% std::_Vector_base::_M_allocate (inline) 99ms 0.17% 71.20% 1131ms 1.93% std::map::operator[] 33ms 0.056% 71.26% 1090ms 1.86% tetgen::tetgenmesh::locate 230ms 0.39% 71.65% 1076ms 1.84% tetgen::tetgenmesh::enqueueflipface 1060ms 1.81% 73.46% 1060ms 1.81% Node::GetIndex 90ms 0.15% 73.61% 1030ms 1.76% tetgen::tetgenmesh::preciselocate 58ms 0.099% 73.71% 978ms 1.67% std::vector::push_back (inline) 974ms 1.66% 75.37% 974ms 1.66% unlink_chunk 5ms 0.0085% 75.38% 969ms 1.65% TetrahedralMesh::Clear 2ms 0.0034% 75.39% 969ms 1.65% VertexMesh::GenerateVerticesFromElementCircumcentres 0 0% 75.39% 953ms 1.63% std::_Rb_tree::lower_bound (inline) 0 0% 75.39% 953ms 1.63% std::map::lower_bound (inline) 0 0% 75.39% 877ms 1.50% VoronoiDataWriter::Visit 1ms 0.0017% 75.39% 856ms 1.46% TetrahedralMesh::RefreshJacobianCachedData 491ms 0.84% 76.23% 817ms 1.39% AbstractElement::GetNodeGlobalIndex 3ms 0.0051% 76.23% 780ms 1.33% AbstractTwoBodyInteractionForce::AddForceContribution 3ms 0.0051% 76.24% 771ms 1.32% AbstractTetrahedralElement::CalculateInverseJacobian 19ms 0.032% 76.27% 757ms 1.29% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 9ms 0.015% 76.28% 671ms 1.14% AbstractTetrahedralElement::CalculateJacobian 10ms 0.017% 76.30% 664ms 1.13% boost::numeric::ublas::vector_assign (inline) 8ms 0.014% 76.31% 640ms 1.09% boost::numeric::ublas::c_vector::c_vector (inline) 364ms 0.62% 76.94% 612ms 1.04% tetgen::tetgenmesh::sym 44ms 0.075% 77.01% 608ms 1.04% __atan2 0 0% 77.01% 582ms 0.99% std::set::find (inline) 580ms 0.99% 78.00% 580ms 0.99% Node::rGetLocation 0 0% 78.00% 579ms 0.99% std::insert_iterator::operator= (inline) 510ms 0.87% 78.87% 559ms 0.95% __ieee754_atan2_fma 304ms 0.52% 79.39% 549ms 0.94% AbstractElement::GetNodeLocation 541ms 0.92% 80.31% 541ms 0.92% tetgen::tetgenmesh::oppo 521ms 0.89% 81.20% 521ms 0.89% std::vector::size (inline) 0 0% 81.20% 503ms 0.86% std::_Rb_tree::_M_insert_unique_ (inline) 46ms 0.078% 81.28% 498ms 0.85% AbstractTetrahedralElement::RefreshJacobian 9ms 0.015% 81.29% 481ms 0.82% Element::CalculateCircumsphere 20ms 0.034% 81.33% 467ms 0.8% std::vector::insert (inline) 7ms 0.012% 81.34% 464ms 0.79% CellPropertyCollection::GetPropertiesType (inline) 3ms 0.0051% 81.34% 445ms 0.76% Cell::GetCellId 55ms 0.094% 81.44% 425ms 0.72% std::_Rb_tree_iterator::operator-- (inline) 0 0% 81.44% 379ms 0.65% boost::numeric::ublas::inner_prod (inline) 378ms 0.64% 82.08% 378ms 0.64% boost::numeric::ublas::c_vector::operator() 22ms 0.038% 82.12% 377ms 0.64% boost::numeric::ublas::vector_scalar_binary::evaluate 0 0% 82.12% 377ms 0.64% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 0 0% 82.12% 372ms 0.63% VertexMeshWriter::WriteVtkUsingMesh 138ms 0.24% 82.36% 369ms 0.63% Inverse 87ms 0.15% 82.50% 365ms 0.62% __dynamic_cast 20ms 0.034% 82.54% 355ms 0.61% VertexMesh::CalculateUnitNormalToFaceWithArea 0 0% 82.54% 355ms 0.61% tcache_get (inline) 355ms 0.61% 83.14% 355ms 0.61% tcache_get_n (inline) 25ms 0.043% 83.19% 354ms 0.6% tetgen::tetgenmesh::enext2fnext 336ms 0.57% 83.76% 336ms 0.57% std::_Rb_tree_decrement 270ms 0.46% 84.22% 336ms 0.57% tetgen::tetgenmesh::fnextself 97ms 0.17% 84.39% 326ms 0.56% boost::numeric::ublas::vector_inner_prod::apply (inline) 6ms 0.01% 84.40% 320ms 0.55% AbstractTetrahedralElement::AbstractTetrahedralElement 23ms 0.039% 84.44% 320ms 0.55% boost::numeric::ublas::vector_reference::operator() (inline) 44ms 0.075% 84.51% 320ms 0.55% tetgen::tetgenmesh::queue::push 3ms 0.0051% 84.52% 315ms 0.54% AbstractCellProperty::IsSubType (inline) 4ms 0.0068% 84.52% 315ms 0.54% boost::numeric::ublas::c_vector::operator= (inline) 92ms 0.16% 84.68% 304ms 0.52% tetgen::tetgenmesh::queue::pop 201ms 0.34% 85.02% 301ms 0.51% AbstractTetrahedralMesh::GetElement 159ms 0.27% 85.29% 301ms 0.51% tetgen::tetgenmesh::bond 66ms 0.11% 85.41% 296ms 0.5% boost::numeric::ublas::indexing_vector_assign 33ms 0.056% 85.46% 295ms 0.5% tetgen::tetgenmesh::enextfnext