File: Test3dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 58975ms, 86.73% of 67999ms total Dropped 902 nodes (cum <= 340ms) flat flat% sum% cum cum% 0 0% 0% 67946ms 99.92% __libc_start_call_main 0 0% 0% 67946ms 99.92% __libc_start_main_impl 0 0% 0% 67946ms 99.92% _start 0 0% 0% 67928ms 99.90% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 67928ms 99.90% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 67928ms 99.90% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 67928ms 99.90% main 0 0% 0% 67887ms 99.84% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 67887ms 99.84% CxxTest::TestRunner::runTest (inline) 0 0% 0% 67887ms 99.84% Test3dTissueRepresentativeSimulation::Test3DHoneycombMeshWithGhostNodes 0 0% 0% 67602ms 99.42% AbstractCellBasedSimulation::Solve 0 0% 0% 57039ms 83.88% AbstractCellBasedSimulation::UpdateCellPopulation 1ms 0.0015% 0.0015% 56989ms 83.81% MeshBasedCellPopulation::Update 0 0% 0.0015% 31787ms 46.75% MeshBasedCellPopulation::TessellateIfNeeded 0 0% 0.0015% 31785ms 46.74% MeshBasedCellPopulation::CreateVoronoiTessellation (inline) 254ms 0.37% 0.38% 28221ms 41.50% VertexMesh::VertexMesh 0 0% 0.38% 20688ms 30.42% MutableMesh::ReMesh 0 0% 0.38% 16315ms 23.99% tetgen::tetrahedralize 2ms 0.0029% 0.38% 16168ms 23.78% tetgen::tetgenmesh::delaunizevertices 4ms 0.0059% 0.38% 16154ms 23.76% tetgen::tetgenmesh::incrflipdelaunay 503ms 0.74% 1.12% 14474ms 21.29% tetgen::tetgenmesh::lawson 552ms 0.81% 1.94% 13943ms 20.50% TetrahedralMesh::EdgeIterator::operator++ 29ms 0.043% 1.98% 10730ms 15.78% std::set::insert (inline) 3270ms 4.81% 6.79% 10633ms 15.64% std::_Rb_tree::_M_lower_bound (inline) 264ms 0.39% 7.18% 10292ms 15.14% std::_Rb_tree::_M_insert_unique 365ms 0.54% 7.71% 10256ms 15.08% VertexElement::AddFace 252ms 0.37% 8.08% 9913ms 14.58% std::_Rb_tree::find (inline) 0 0% 8.08% 9331ms 13.72% std::set::count (inline) 109ms 0.16% 8.24% 7064ms 10.39% std::less::operator() (inline) 7023ms 10.33% 18.57% 7023ms 10.33% std::operator< (inline) 6424ms 9.45% 28.02% 6424ms 9.45% std::_Rb_tree_increment 0 0% 28.02% 6045ms 8.89% OffLatticeSimulation::UpdateCellLocationsAndTopology 332ms 0.49% 28.51% 5976ms 8.79% std::_Rb_tree::_M_insert_ (inline) 0 0% 28.51% 5892ms 8.66% ForwardEulerNumericalMethod::UpdateAllNodePositions 1ms 0.0015% 28.51% 5857ms 8.61% AbstractNumericalMethod::ComputeForcesIncludingDamping 162ms 0.24% 28.75% 5627ms 8.28% operator new 1205ms 1.77% 30.52% 5382ms 7.91% __GI___libc_malloc 0 0% 30.52% 4907ms 7.22% MeshBasedCellPopulation::UpdateNodePairs 4ms 0.0059% 30.52% 4896ms 7.20% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 27ms 0.04% 30.56% 4747ms 6.98% std::__new_allocator::allocate (inline) 14ms 0.021% 30.58% 4735ms 6.96% MeshBasedCellPopulation::SpringIterator::operator++ 0 0% 30.58% 4717ms 6.94% std::allocator_traits::allocate (inline) 5ms 0.0074% 30.59% 4578ms 6.73% std::set_intersection (inline) 279ms 0.41% 31.00% 4573ms 6.73% std::__set_intersection 10ms 0.015% 31.02% 4475ms 6.58% std::_Rb_tree::~_Rb_tree (inline) 1635ms 2.40% 33.42% 4462ms 6.56% std::_Rb_tree::_M_erase 0 0% 33.42% 4422ms 6.50% std::set::~set (inline) 0 0% 33.42% 4341ms 6.38% AbstractCellPopulation::WriteResultsToFiles 1298ms 1.91% 35.33% 4316ms 6.35% std::_Rb_tree::_M_get_insert_unique_pos 1235ms 1.82% 37.15% 4298ms 6.32% __GI___libc_free 55ms 0.081% 37.23% 3894ms 5.73% Node::AddElement 124ms 0.18% 37.41% 3881ms 5.71% tetgen::tetgenmesh::insphere_sos 181ms 0.27% 37.68% 3821ms 5.62% std::_Rb_tree_const_iterator::operator++ (inline) 2736ms 4.02% 41.70% 3790ms 5.57% _int_malloc 0 0% 41.70% 3785ms 5.57% std::_Rb_tree::_M_create_node (inline) 129ms 0.19% 41.89% 3745ms 5.51% std::__new_allocator::deallocate (inline) 0 0% 41.89% 3744ms 5.51% std::_Rb_tree::_M_get_node (inline) 0 0% 41.89% 3742ms 5.50% std::_Rb_tree::_Alloc_node::operator() (inline) 3453ms 5.08% 46.97% 3740ms 5.50% tetgen::insphere 0 0% 46.97% 3731ms 5.49% std::allocator_traits::deallocate (inline) 3659ms 5.38% 52.35% 3659ms 5.38% std::_Rb_tree::_S_right (inline) 0 0% 52.35% 3589ms 5.28% VertexMesh::~VertexMesh 143ms 0.21% 52.56% 3525ms 5.18% tetgen::tetgenmesh::flip23 9ms 0.013% 52.57% 3521ms 5.18% TetrahedralMesh::ImportFromMesher 222ms 0.33% 52.90% 3099ms 4.56% VertexMesh::GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex 1396ms 2.05% 54.95% 3059ms 4.50% _int_free 1ms 0.0015% 54.95% 3021ms 4.44% MeshBasedCellPopulationWithGhostNodes::WriteVtkResultsToFile 70ms 0.1% 55.06% 3020ms 4.44% MutableElement::AddNode 1ms 0.0015% 55.06% 2894ms 4.26% std::_Rb_tree_iterator::operator++ (inline) 142ms 0.21% 55.27% 2624ms 3.86% tetgen::tetgenmesh::flip32 173ms 0.25% 55.52% 2550ms 3.75% Node::~Node 175ms 0.26% 55.78% 2312ms 3.40% VertexMesh::Clear 0 0% 55.78% 2175ms 3.20% std::_Rb_tree::_M_drop_node (inline) 0 0% 55.78% 2165ms 3.18% std::_Rb_tree::_M_put_node (inline) 1972ms 2.90% 58.68% 1972ms 2.90% Node::GetIndex 1967ms 2.89% 61.57% 1967ms 2.89% std::_Rb_tree_insert_and_rebalance 6ms 0.0088% 61.58% 1732ms 2.55% Element::Element 218ms 0.32% 61.90% 1710ms 2.51% tetgen::tetgenmesh::enqueueflipface 1049ms 1.54% 63.44% 1666ms 2.45% malloc_consolidate 1533ms 2.25% 65.70% 1628ms 2.39% tetgen::orient3d 24ms 0.035% 65.73% 1590ms 2.34% std::_Vector_base::_M_deallocate (inline) 0 0% 65.73% 1507ms 2.22% std::vector::~vector (inline) 86ms 0.13% 65.86% 1442ms 2.12% TetrahedralMesh::Clear 2ms 0.0029% 65.86% 1415ms 2.08% std::_Vector_base::~_Vector_base (inline) 5ms 0.0074% 65.87% 1409ms 2.07% _int_free_maybe_consolidate 4ms 0.0059% 65.87% 1371ms 2.02% Element::RegisterWithNodes (inline) 47ms 0.069% 65.94% 1367ms 2.01% tetgen::tetgenmesh::locate 60ms 0.088% 66.03% 1312ms 1.93% std::map::operator[] 79ms 0.12% 66.15% 1274ms 1.87% tetgen::tetgenmesh::preciselocate 1266ms 1.86% 68.01% 1266ms 1.86% unlink_chunk 61ms 0.09% 68.10% 1223ms 1.80% std::vector::_M_realloc_insert 1206ms 1.77% 69.87% 1206ms 1.77% tetgen::tetgenmesh::triface::triface 0 0% 69.87% 1160ms 1.71% std::_Rb_tree::lower_bound (inline) 0 0% 69.87% 1160ms 1.71% std::map::lower_bound (inline) 924ms 1.36% 71.23% 1158ms 1.70% AbstractElement::GetNodeGlobalIndex 0 0% 71.23% 1056ms 1.55% VoronoiDataWriter::Visit 2ms 0.0029% 71.23% 1054ms 1.55% VertexMesh::GenerateVerticesFromElementCircumcentres 142ms 0.21% 71.44% 1021ms 1.50% std::vector::push_back (inline) 9ms 0.013% 71.46% 982ms 1.44% std::_Vector_base::_M_allocate (inline) 861ms 1.27% 72.72% 861ms 1.27% tetgen::tetgenmesh::oppo 0 0% 72.72% 828ms 1.22% TetrahedralMesh::RefreshJacobianCachedData 805ms 1.18% 73.91% 805ms 1.18% tetgen::tetgenmesh::triface::operator= 804ms 1.18% 75.09% 804ms 1.18% [libchaste_mesh.so] 311ms 0.46% 75.55% 753ms 1.11% tetgen::tetgenmesh::sym 12ms 0.018% 75.56% 751ms 1.10% AbstractTetrahedralElement::CalculateInverseJacobian 1ms 0.0015% 75.57% 748ms 1.10% AbstractTwoBodyInteractionForce::AddForceContribution 408ms 0.6% 76.17% 712ms 1.05% tetgen::tetgenmesh::fnextself 12ms 0.018% 76.18% 704ms 1.04% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 689ms 1.01% 77.20% 689ms 1.01% Node::rGetLocation 273ms 0.4% 77.60% 677ms 1% AbstractElement::GetNodeLocation 17ms 0.025% 77.62% 669ms 0.98% AbstractTetrahedralElement::CalculateJacobian 45ms 0.066% 77.69% 661ms 0.97% tetgen::tetgenmesh::enextfnext 13ms 0.019% 77.71% 659ms 0.97% boost::numeric::ublas::vector_assign (inline) 62ms 0.091% 77.80% 650ms 0.96% tetgen::tetgenmesh::enext2fnext 39ms 0.057% 77.86% 643ms 0.95% __atan2 11ms 0.016% 77.87% 637ms 0.94% boost::numeric::ublas::c_vector::c_vector (inline) 623ms 0.92% 78.79% 623ms 0.92% AbstractElement::IsDeleted 238ms 0.35% 79.14% 614ms 0.9% tetgen::tetgenmesh::bond 31ms 0.046% 79.18% 605ms 0.89% tetgen::tetgenmesh::queue::push 476ms 0.7% 79.88% 601ms 0.88% __ieee754_atan2_fma 598ms 0.88% 80.76% 598ms 0.88% std::vector::size (inline) 0 0% 80.76% 580ms 0.85% std::set::find (inline) 358ms 0.53% 81.29% 574ms 0.84% tetgen::tetgenmesh::link::add 13ms 0.019% 81.31% 531ms 0.78% Element::CalculateCircumsphere 0 0% 81.31% 516ms 0.76% boost::numeric::ublas::inner_prod (inline) 1ms 0.0015% 81.31% 514ms 0.76% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 49ms 0.072% 81.38% 513ms 0.75% boost::numeric::ublas::vector_scalar_binary::evaluate 39ms 0.057% 81.44% 480ms 0.71% AbstractTetrahedralElement::RefreshJacobian 0 0% 81.44% 465ms 0.68% std::insert_iterator::operator= (inline) 458ms 0.67% 82.11% 458ms 0.67% tetgen::tetgenmesh::decode 250ms 0.37% 82.48% 454ms 0.67% AbstractTetrahedralMesh::GetElement 21ms 0.031% 82.51% 445ms 0.65% VertexMesh::CalculateUnitNormalToFaceWithArea 439ms 0.65% 83.16% 439ms 0.65% tetgen::tetgenmesh::org 434ms 0.64% 83.80% 434ms 0.64% tetgen::tetgenmesh::pointmark 27ms 0.04% 83.84% 433ms 0.64% std::_Rb_tree_iterator::operator-- (inline) 79ms 0.12% 83.95% 428ms 0.63% tetgen::tetgenmesh::queue::pop 187ms 0.28% 84.23% 403ms 0.59% boost::numeric::ublas::vector_inner_prod::apply (inline) 0 0% 84.23% 403ms 0.59% std::_Rb_tree::_M_insert_unique_ (inline) 105ms 0.15% 84.38% 399ms 0.59% __dynamic_cast 120ms 0.18% 84.56% 397ms 0.58% boost::numeric::ublas::indexing_vector_assign 0 0% 84.56% 396ms 0.58% VertexMeshWriter::WriteVtkUsingMesh 3ms 0.0044% 84.56% 388ms 0.57% CellPropertyCollection::GetPropertiesType (inline) 3ms 0.0044% 84.57% 388ms 0.57% boost::numeric::ublas::c_vector::operator= (inline) 8ms 0.012% 84.58% 384ms 0.56% VertexElement::~VertexElement 384ms 0.56% 85.14% 384ms 0.56% std::_Rb_tree_decrement 2ms 0.0029% 85.15% 379ms 0.56% Cell::GetCellId 0 0% 85.15% 375ms 0.55% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 375ms 0.55% 85.70% 375ms 0.55% boost::numeric::ublas::c_vector::operator() 11ms 0.016% 85.71% 365ms 0.54% std::vector::insert (inline) 364ms 0.54% 86.25% 364ms 0.54% tetgen::tetgenmesh::encode 10ms 0.015% 86.26% 358ms 0.53% AbstractTetrahedralElement::AbstractTetrahedralElement 128ms 0.19% 86.45% 354ms 0.52% Inverse 188ms 0.28% 86.73% 343ms 0.5% tetgen::tetgenmesh::link::deletenode