File: Test3dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 67902ms, 86.75% of 78277ms total Dropped 855 nodes (cum <= 391.38ms) flat flat% sum% cum cum% 0 0% 0% 78218ms 99.92% __libc_start_call_main 0 0% 0% 78218ms 99.92% __libc_start_main_impl 0 0% 0% 78218ms 99.92% _start 0 0% 0% 78198ms 99.90% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 78198ms 99.90% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 78198ms 99.90% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 78198ms 99.90% main 0 0% 0% 78154ms 99.84% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 78154ms 99.84% CxxTest::TestRunner::runTest (inline) 0 0% 0% 78154ms 99.84% Test3dTissueRepresentativeSimulation::Test3DHoneycombMeshWithGhostNodes 0 0% 0% 77856ms 99.46% AbstractCellBasedSimulation::Solve 0 0% 0% 66722ms 85.24% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 66676ms 85.18% MeshBasedCellPopulation::Update 0 0% 0% 40272ms 51.45% MeshBasedCellPopulation::CreateVoronoiTessellation (inline) 0 0% 0% 40272ms 51.45% MeshBasedCellPopulation::TessellateIfNeeded 329ms 0.42% 0.42% 34793ms 44.45% VertexMesh::VertexMesh 0 0% 0.42% 21558ms 27.54% MutableMesh::ReMesh 0 0% 0.42% 16021ms 20.47% tetgen::tetrahedralize 0 0% 0.42% 15860ms 20.26% tetgen::tetgenmesh::delaunizevertices 13ms 0.017% 0.44% 15858ms 20.26% tetgen::tetgenmesh::incrflipdelaunay 646ms 0.83% 1.26% 15376ms 19.64% TetrahedralMesh::EdgeIterator::operator++ 526ms 0.67% 1.93% 14078ms 17.98% tetgen::tetgenmesh::lawson 36ms 0.046% 1.98% 12969ms 16.57% std::set::insert (inline) 205ms 0.26% 2.24% 12505ms 15.98% std::_Rb_tree::_M_insert_unique 472ms 0.6% 2.85% 11761ms 15.02% VertexElement::AddFace 3336ms 4.26% 7.11% 11402ms 14.57% std::_Rb_tree::_M_lower_bound (inline) 272ms 0.35% 7.45% 10521ms 13.44% std::_Rb_tree::find (inline) 0 0% 7.45% 9879ms 12.62% std::set::count (inline) 8250ms 10.54% 17.99% 8250ms 10.54% std::_Rb_tree_increment 127ms 0.16% 18.16% 7568ms 9.67% std::less::operator() (inline) 7502ms 9.58% 27.74% 7502ms 9.58% std::operator< (inline) 189ms 0.24% 27.98% 7388ms 9.44% operator new 335ms 0.43% 28.41% 7326ms 9.36% std::_Rb_tree::_M_insert_ (inline) 1290ms 1.65% 30.06% 7120ms 9.10% __GI___libc_malloc 0 0% 30.06% 6480ms 8.28% OffLatticeSimulation::UpdateCellLocationsAndTopology 1ms 0.0013% 30.06% 6480ms 8.28% std::set_intersection (inline) 341ms 0.44% 30.49% 6479ms 8.28% std::__set_intersection 0 0% 30.49% 6285ms 8.03% ForwardEulerNumericalMethod::UpdateAllNodePositions 8ms 0.01% 30.50% 6258ms 7.99% AbstractNumericalMethod::ComputeForcesIncludingDamping 47ms 0.06% 30.56% 5950ms 7.60% std::__new_allocator::allocate (inline) 0 0% 30.56% 5923ms 7.57% std::allocator_traits::allocate (inline) 187ms 0.24% 30.80% 5618ms 7.18% std::_Rb_tree_const_iterator::operator++ (inline) 51ms 0.065% 30.87% 5592ms 7.14% Node::AddElement 1423ms 1.82% 32.69% 5538ms 7.07% __GI___libc_free 0 0% 32.69% 5513ms 7.04% VertexMesh::~VertexMesh 5ms 0.0064% 32.69% 5467ms 6.98% std::_Rb_tree::~_Rb_tree (inline) 2143ms 2.74% 35.43% 5458ms 6.97% std::_Rb_tree::_M_erase 3884ms 4.96% 40.39% 5419ms 6.92% _int_malloc 0 0% 40.39% 5391ms 6.89% std::set::~set (inline) 9ms 0.011% 40.40% 5262ms 6.72% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 1425ms 1.82% 42.22% 5256ms 6.71% std::_Rb_tree::_M_get_insert_unique_pos 1ms 0.0013% 42.23% 5247ms 6.70% MeshBasedCellPopulation::UpdateNodePairs 18ms 0.023% 42.25% 5064ms 6.47% MeshBasedCellPopulation::SpringIterator::operator++ 4964ms 6.34% 48.59% 4964ms 6.34% std::_Rb_tree::_S_right (inline) 114ms 0.15% 48.74% 4821ms 6.16% std::__new_allocator::deallocate (inline) 0 0% 48.74% 4798ms 6.13% std::allocator_traits::deallocate (inline) 0 0% 48.74% 4753ms 6.07% std::_Rb_tree::_M_create_node (inline) 0 0% 48.74% 4703ms 6.01% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 48.74% 4702ms 6.01% std::_Rb_tree::_M_get_node (inline) 0 0% 48.74% 4460ms 5.70% AbstractCellPopulation::WriteResultsToFiles 9ms 0.011% 48.75% 4410ms 5.63% TetrahedralMesh::ImportFromMesher 69ms 0.088% 48.84% 4174ms 5.33% MutableElement::AddNode 1451ms 1.85% 50.69% 4108ms 5.25% _int_free 86ms 0.11% 50.80% 3743ms 4.78% tetgen::tetgenmesh::insphere_sos 3381ms 4.32% 55.12% 3643ms 4.65% tetgen::insphere 157ms 0.2% 55.32% 3616ms 4.62% tetgen::tetgenmesh::flip23 262ms 0.33% 55.65% 3521ms 4.50% Node::~Node 202ms 0.26% 55.91% 3288ms 4.20% VertexMesh::Clear 165ms 0.21% 56.12% 3124ms 3.99% VertexMesh::GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex 7ms 0.0089% 56.13% 3062ms 3.91% MeshBasedCellPopulationWithGhostNodes::WriteVtkResultsToFile 0 0% 56.13% 2980ms 3.81% std::_Rb_tree_iterator::operator++ (inline) 1843ms 2.35% 58.49% 2709ms 3.46% malloc_consolidate 2705ms 3.46% 61.94% 2705ms 3.46% Node::GetIndex 43ms 0.055% 62.00% 2537ms 3.24% std::_Vector_base::_M_deallocate (inline) 140ms 0.18% 62.18% 2482ms 3.17% tetgen::tetgenmesh::flip32 0 0% 62.18% 2439ms 3.12% std::vector::~vector (inline) 2ms 0.0026% 62.18% 2382ms 3.04% std::_Vector_base::~_Vector_base (inline) 2378ms 3.04% 65.22% 2378ms 3.04% std::_Rb_tree_insert_and_rebalance 9ms 0.011% 65.23% 2365ms 3.02% _int_free_maybe_consolidate 5ms 0.0064% 65.23% 2348ms 3.00% Element::Element 0 0% 65.23% 2316ms 2.96% std::_Rb_tree::_M_drop_node (inline) 0 0% 65.23% 2304ms 2.94% std::_Rb_tree::_M_put_node (inline) 1960ms 2.50% 67.74% 1960ms 2.50% unlink_chunk 224ms 0.29% 68.02% 1937ms 2.47% tetgen::tetgenmesh::enqueueflipface 6ms 0.0077% 68.03% 1919ms 2.45% Element::RegisterWithNodes (inline) 5ms 0.0064% 68.04% 1722ms 2.20% VertexMesh::GenerateVerticesFromElementCircumcentres 1587ms 2.03% 70.07% 1668ms 2.13% tetgen::orient3d 101ms 0.13% 70.19% 1608ms 2.05% TetrahedralMesh::Clear 68ms 0.087% 70.28% 1492ms 1.91% std::map::operator[] 1235ms 1.58% 71.86% 1466ms 1.87% AbstractElement::GetNodeGlobalIndex 43ms 0.055% 71.91% 1458ms 1.86% tetgen::tetgenmesh::locate 66ms 0.084% 72.00% 1369ms 1.75% std::vector::_M_realloc_insert 76ms 0.097% 72.10% 1359ms 1.74% tetgen::tetgenmesh::preciselocate 0 0% 72.10% 1317ms 1.68% std::_Rb_tree::lower_bound (inline) 0 0% 72.10% 1317ms 1.68% std::map::lower_bound (inline) 0 0% 72.10% 1221ms 1.56% std::_Vector_base::_M_allocate (inline) 142ms 0.18% 72.28% 1161ms 1.48% std::vector::push_back (inline) 0 0% 72.28% 1128ms 1.44% VoronoiDataWriter::Visit 1103ms 1.41% 73.69% 1103ms 1.41% tetgen::tetgenmesh::oppo 0 0% 73.69% 1079ms 1.38% TetrahedralMesh::RefreshJacobianCachedData 1073ms 1.37% 75.06% 1073ms 1.37% Node::rGetLocation 1041ms 1.33% 76.39% 1041ms 1.33% AbstractElement::IsDeleted 459ms 0.59% 76.97% 1034ms 1.32% AbstractElement::GetNodeLocation 958ms 1.22% 78.20% 958ms 1.22% tetgen::tetgenmesh::triface::triface 16ms 0.02% 78.22% 897ms 1.15% AbstractTetrahedralElement::CalculateInverseJacobian 18ms 0.023% 78.24% 880ms 1.12% AbstractTetrahedralElement::CalculateJacobian 840ms 1.07% 79.31% 840ms 1.07% [libchaste_mesh.so] 302ms 0.39% 79.70% 828ms 1.06% tetgen::tetgenmesh::sym 790ms 1.01% 80.71% 790ms 1.01% std::vector::size (inline) 0 0% 80.71% 757ms 0.97% AbstractTwoBodyInteractionForce::AddForceContribution 24ms 0.031% 80.74% 751ms 0.96% Element::CalculateCircumsphere 10ms 0.013% 80.75% 703ms 0.9% AbstractVariableSizeTwoBodyInteractionForce::CalculateForceBetweenNodes 16ms 0.02% 80.77% 693ms 0.89% boost::numeric::ublas::vector_assign (inline) 683ms 0.87% 81.64% 683ms 0.87% tetgen::tetgenmesh::triface::operator= 53ms 0.068% 81.71% 682ms 0.87% AbstractTetrahedralElement::RefreshJacobian 15ms 0.019% 81.73% 659ms 0.84% boost::numeric::ublas::c_vector::c_vector (inline) 227ms 0.29% 82.02% 648ms 0.83% tetgen::tetgenmesh::bond 60ms 0.077% 82.10% 645ms 0.82% __atan2 431ms 0.55% 82.65% 639ms 0.82% tetgen::tetgenmesh::fnextself 0 0% 82.65% 635ms 0.81% std::set::find (inline) 66ms 0.084% 82.73% 630ms 0.8% tetgen::tetgenmesh::enext2fnext 34ms 0.043% 82.78% 593ms 0.76% tetgen::tetgenmesh::queue::push 460ms 0.59% 83.36% 581ms 0.74% __ieee754_atan2_fma 358ms 0.46% 83.82% 559ms 0.71% tetgen::tetgenmesh::link::add 51ms 0.065% 83.89% 539ms 0.69% tetgen::tetgenmesh::enextfnext 535ms 0.68% 84.57% 535ms 0.68% tetgen::tetgenmesh::decode 0 0% 84.57% 502ms 0.64% boost::numeric::ublas::inner_prod (inline) 3ms 0.0038% 84.57% 502ms 0.64% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 39ms 0.05% 84.62% 499ms 0.64% boost::numeric::ublas::vector_scalar_binary::evaluate 0 0% 84.62% 491ms 0.63% std::insert_iterator::operator= (inline) 16ms 0.02% 84.64% 487ms 0.62% VertexMesh::CalculateUnitNormalToFaceWithArea 10ms 0.013% 84.66% 463ms 0.59% VertexElement::~VertexElement 456ms 0.58% 85.24% 456ms 0.58% tetgen::tetgenmesh::org 21ms 0.027% 85.27% 452ms 0.58% std::_Rb_tree_iterator::operator-- (inline) 218ms 0.28% 85.54% 450ms 0.57% AbstractTetrahedralMesh::GetElement 5ms 0.0064% 85.55% 450ms 0.57% CellPropertyCollection::GetPropertiesType (inline) 0 0% 85.55% 444ms 0.57% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 0 0% 85.55% 425ms 0.54% std::_Rb_tree::_M_insert_unique_ (inline) 4ms 0.0051% 85.56% 424ms 0.54% AbstractTetrahedralElement::AbstractTetrahedralElement 1ms 0.0013% 85.56% 410ms 0.52% Cell::GetCellId 6ms 0.0077% 85.57% 410ms 0.52% boost::numeric::ublas::c_vector::operator= (inline) 409ms 0.52% 86.09% 409ms 0.52% tetgen::tetgenmesh::encode 108ms 0.14% 86.23% 408ms 0.52% __dynamic_cast 407ms 0.52% 86.75% 407ms 0.52% std::_Rb_tree_decrement 0 0% 86.75% 402ms 0.51% VertexMeshWriter::WriteVtkUsingMesh