File: Test3dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 58113ms, 87.53% of 66391ms total Dropped 882 nodes (cum <= 331.95ms) flat flat% sum% cum cum% 0 0% 0% 66337ms 99.92% __libc_start_call_main 0 0% 0% 66337ms 99.92% __libc_start_main_impl 0 0% 0% 66337ms 99.92% _start 0 0% 0% 66320ms 99.89% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 66320ms 99.89% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 66320ms 99.89% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 66320ms 99.89% main 0 0% 0% 66284ms 99.84% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 66284ms 99.84% CxxTest::TestRunner::runTest (inline) 0 0% 0% 66284ms 99.84% Test3dTissueRepresentativeSimulation::Test3DHoneycombMeshWithGhostNodes 0 0% 0% 65990ms 99.40% AbstractCellBasedSimulation::Solve 0 0% 0% 55070ms 82.95% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 55025ms 82.88% MeshBasedCellPopulation::Update 0 0% 0% 32423ms 48.84% MeshBasedCellPopulation::TessellateIfNeeded 0 0% 0% 32422ms 48.83% MeshBasedCellPopulation::CreateVoronoiTessellation (inline) 214ms 0.32% 0.32% 28161ms 42.42% VertexMesh::VertexMesh 0 0% 0.32% 18146ms 27.33% MutableMesh::ReMesh 547ms 0.82% 1.15% 13606ms 20.49% TetrahedralMesh::EdgeIterator::operator++ 0 0% 1.15% 12779ms 19.25% tetgen::tetrahedralize 3ms 0.0045% 1.15% 12642ms 19.04% tetgen::tetgenmesh::delaunizevertices 8ms 0.012% 1.16% 12635ms 19.03% tetgen::tetgenmesh::incrflipdelaunay 26ms 0.039% 1.20% 11285ms 17.00% std::set::insert (inline) 560ms 0.84% 2.05% 11200ms 16.87% tetgen::tetgenmesh::lawson 187ms 0.28% 2.33% 10777ms 16.23% std::_Rb_tree::_M_insert_unique 3044ms 4.58% 6.91% 10598ms 15.96% std::_Rb_tree::_M_lower_bound (inline) 239ms 0.36% 7.27% 9872ms 14.87% std::_Rb_tree::find (inline) 388ms 0.58% 7.86% 9774ms 14.72% VertexElement::AddFace 0 0% 7.86% 9284ms 13.98% std::set::count (inline) 120ms 0.18% 8.04% 7217ms 10.87% std::less::operator() (inline) 7148ms 10.77% 18.80% 7148ms 10.77% std::operator< (inline) 6993ms 10.53% 29.34% 6993ms 10.53% std::_Rb_tree_increment 280ms 0.42% 29.76% 6246ms 9.41% std::_Rb_tree::_M_insert_ (inline) 217ms 0.33% 30.09% 5965ms 8.98% operator new 0 0% 30.09% 5920ms 8.92% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 30.09% 5749ms 8.66% ForwardEulerNumericalMethod::UpdateAllNodePositions 5ms 0.0075% 30.09% 5724ms 8.62% AbstractNumericalMethod::ComputeForcesIncludingDamping 1096ms 1.65% 31.74% 5686ms 8.56% __GI___libc_malloc 30ms 0.045% 31.79% 4978ms 7.50% std::__new_allocator::allocate (inline) 0 0% 31.79% 4958ms 7.47% std::allocator_traits::allocate (inline) 15ms 0.023% 31.81% 4940ms 7.44% std::_Rb_tree::~_Rb_tree (inline) 2147ms 3.23% 35.05% 4924ms 7.42% std::_Rb_tree::_M_erase 28ms 0.042% 35.09% 4864ms 7.33% Node::AddElement 0 0% 35.09% 4855ms 7.31% AbstractCellPopulation::WriteResultsToFiles 0 0% 35.09% 4854ms 7.31% std::set::~set (inline) 1ms 0.0015% 35.09% 4780ms 7.20% MeshBasedCellPopulation::UpdateNodePairs 8ms 0.012% 35.10% 4751ms 7.16% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 2ms 0.003% 35.10% 4681ms 7.05% std::set_intersection (inline) 289ms 0.44% 35.54% 4679ms 7.05% std::__set_intersection 1289ms 1.94% 37.48% 4675ms 7.04% std::_Rb_tree::_M_get_insert_unique_pos 15ms 0.023% 37.50% 4600ms 6.93% MeshBasedCellPopulation::SpringIterator::operator++ 11ms 0.017% 37.52% 4445ms 6.70% TetrahedralMesh::ImportFromMesher 1275ms 1.92% 39.44% 4336ms 6.53% __GI___libc_free 0 0% 39.44% 4306ms 6.49% VertexMesh::~VertexMesh 4281ms 6.45% 45.89% 4281ms 6.45% std::_Rb_tree::_S_right (inline) 3094ms 4.66% 50.55% 4213ms 6.35% _int_malloc 0 0% 50.55% 3975ms 5.99% std::_Rb_tree::_M_create_node (inline) 0 0% 50.55% 3938ms 5.93% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 50.55% 3934ms 5.93% std::_Rb_tree::_M_get_node (inline) 167ms 0.25% 50.80% 3887ms 5.85% std::_Rb_tree_const_iterator::operator++ (inline) 123ms 0.19% 50.99% 3771ms 5.68% std::__new_allocator::deallocate (inline) 0 0% 50.99% 3748ms 5.65% std::allocator_traits::deallocate (inline) 265ms 0.4% 51.38% 3610ms 5.44% VertexMesh::GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex 102ms 0.15% 51.54% 3553ms 5.35% tetgen::tetgenmesh::insphere_sos 3131ms 4.72% 56.25% 3437ms 5.18% tetgen::insphere 2ms 0.003% 56.26% 3390ms 5.11% MeshBasedCellPopulationWithGhostNodes::WriteVtkResultsToFile 0 0% 56.26% 3367ms 5.07% std::_Rb_tree_iterator::operator++ (inline) 82ms 0.12% 56.38% 3362ms 5.06% MutableElement::AddNode 1115ms 1.68% 58.06% 3061ms 4.61% _int_free 192ms 0.29% 58.35% 3028ms 4.56% Node::~Node 253ms 0.38% 58.73% 2741ms 4.13% VertexMesh::Clear 217ms 0.33% 59.06% 2687ms 4.05% tetgen::tetgenmesh::flip23 1ms 0.0015% 59.06% 2382ms 3.59% Element::Element 2119ms 3.19% 62.25% 2119ms 3.19% std::_Rb_tree_insert_and_rebalance 7ms 0.011% 62.26% 2027ms 3.05% Element::RegisterWithNodes (inline) 2017ms 3.04% 65.30% 2017ms 3.04% Node::GetIndex 1272ms 1.92% 67.22% 1980ms 2.98% malloc_consolidate 0 0% 67.22% 1926ms 2.90% std::_Rb_tree::_M_drop_node (inline) 0 0% 67.22% 1914ms 2.88% std::_Rb_tree::_M_put_node (inline) 144ms 0.22% 67.43% 1861ms 2.80% tetgen::tetgenmesh::flip32 16ms 0.024% 67.46% 1850ms 2.79% std::_Vector_base::_M_deallocate (inline) 0 0% 67.46% 1751ms 2.64% std::vector::~vector (inline) 1ms 0.0015% 67.46% 1697ms 2.56% _int_free_maybe_consolidate 3ms 0.0045% 67.46% 1680ms 2.53% std::_Vector_base::~_Vector_base (inline) 238ms 0.36% 67.82% 1649ms 2.48% TetrahedralMesh::Clear 1444ms 2.17% 70.00% 1444ms 2.17% unlink_chunk 1353ms 2.04% 72.03% 1426ms 2.15% tetgen::orient3d 191ms 0.29% 72.32% 1348ms 2.03% tetgen::tetgenmesh::enqueueflipface 66ms 0.099% 72.42% 1295ms 1.95% std::map::operator[] 59ms 0.089% 72.51% 1239ms 1.87% std::vector::_M_realloc_insert 41ms 0.062% 72.57% 1213ms 1.83% tetgen::tetgenmesh::locate 0 0% 72.57% 1198ms 1.80% VoronoiDataWriter::Visit 5ms 0.0075% 72.58% 1153ms 1.74% VertexMesh::GenerateVerticesFromElementCircumcentres 0 0% 72.58% 1148ms 1.73% std::_Rb_tree::lower_bound (inline) 0 0% 72.58% 1148ms 1.73% std::map::lower_bound (inline) 78ms 0.12% 72.70% 1121ms 1.69% tetgen::tetgenmesh::preciselocate 6ms 0.009% 72.71% 1030ms 1.55% std::_Vector_base::_M_allocate (inline) 885ms 1.33% 74.04% 1027ms 1.55% AbstractElement::GetNodeGlobalIndex 116ms 0.17% 74.21% 1008ms 1.52% std::vector::push_back (inline) 1ms 0.0015% 74.21% 899ms 1.35% TetrahedralMesh::RefreshJacobianCachedData 880ms 1.33% 75.54% 880ms 1.33% tetgen::tetgenmesh::triface::triface 353ms 0.53% 76.07% 853ms 1.28% AbstractElement::GetNodeLocation 8ms 0.012% 76.08% 772ms 1.16% AbstractTetrahedralElement::CalculateInverseJacobian 12ms 0.018% 76.10% 767ms 1.16% AbstractTetrahedralElement::CalculateJacobian 2ms 0.003% 76.11% 746ms 1.12% AbstractTwoBodyInteractionForce::AddForceContribution 741ms 1.12% 77.22% 741ms 1.12% Node::rGetLocation 378ms 0.57% 77.79% 706ms 1.06% tetgen::tetgenmesh::fnextself 15ms 0.023% 77.81% 694ms 1.05% AbstractVariableSizeTwoBodyInteractionForce::CalculateForceBetweenNodes 15ms 0.023% 77.84% 662ms 1% boost::numeric::ublas::vector_assign (inline) 662ms 1% 78.83% 662ms 1% tetgen::tetgenmesh::oppo 641ms 0.97% 79.80% 641ms 0.97% [libchaste_mesh.so] 8ms 0.012% 79.81% 637ms 0.96% boost::numeric::ublas::c_vector::c_vector (inline) 635ms 0.96% 80.77% 635ms 0.96% AbstractElement::IsDeleted 50ms 0.075% 80.84% 617ms 0.93% __atan2 39ms 0.059% 80.90% 613ms 0.92% AbstractTetrahedralElement::RefreshJacobian 18ms 0.027% 80.93% 592ms 0.89% Element::CalculateCircumsphere 0 0% 80.93% 581ms 0.88% std::set::find (inline) 467ms 0.7% 81.63% 566ms 0.85% __ieee754_atan2_fma 557ms 0.84% 82.47% 557ms 0.84% tetgen::tetgenmesh::triface::operator= 539ms 0.81% 83.28% 539ms 0.81% std::vector::size (inline) 0 0% 83.28% 513ms 0.77% std::insert_iterator::operator= (inline) 0 0% 83.28% 493ms 0.74% boost::numeric::ublas::inner_prod (inline) 7ms 0.011% 83.29% 491ms 0.74% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 35ms 0.053% 83.35% 484ms 0.73% boost::numeric::ublas::vector_scalar_binary::evaluate 41ms 0.062% 83.41% 475ms 0.72% tetgen::tetgenmesh::enextfnext 317ms 0.48% 83.88% 473ms 0.71% tetgen::tetgenmesh::sym 0 0% 83.88% 458ms 0.69% std::_Rb_tree::_M_insert_unique_ (inline) 45ms 0.068% 83.95% 456ms 0.69% tetgen::tetgenmesh::enext2fnext 3ms 0.0045% 83.96% 433ms 0.65% CellPropertyCollection::GetPropertiesType (inline) 14ms 0.021% 83.98% 431ms 0.65% VertexMesh::CalculateUnitNormalToFaceWithArea 23ms 0.035% 84.01% 421ms 0.63% std::_Rb_tree_iterator::operator-- (inline) 131ms 0.2% 84.21% 418ms 0.63% boost::numeric::ublas::indexing_vector_assign 107ms 0.16% 84.37% 405ms 0.61% __dynamic_cast 0 0% 84.37% 402ms 0.61% VertexMeshWriter::WriteVtkUsingMesh 1ms 0.0015% 84.37% 401ms 0.6% Cell::GetCellId 0 0% 84.37% 400ms 0.6% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 397ms 0.6% 84.97% 397ms 0.6% boost::numeric::ublas::c_vector::operator() 188ms 0.28% 85.25% 396ms 0.6% boost::numeric::ublas::vector_inner_prod::apply (inline) 212ms 0.32% 85.57% 391ms 0.59% AbstractTetrahedralMesh::GetElement 5ms 0.0075% 85.58% 387ms 0.58% boost::numeric::ublas::c_vector::operator= (inline) 38ms 0.057% 85.64% 385ms 0.58% tetgen::tetgenmesh::queue::push 380ms 0.57% 86.21% 380ms 0.57% std::_Rb_tree_decrement 15ms 0.023% 86.23% 376ms 0.57% std::vector::insert (inline) 266ms 0.4% 86.63% 361ms 0.54% tetgen::tetgenmesh::bond 1ms 0.0015% 86.64% 356ms 0.54% AbstractTetrahedralElement::AbstractTetrahedralElement 2ms 0.003% 86.64% 352ms 0.53% AbstractCellProperty::IsSubType (inline) 248ms 0.37% 87.01% 345ms 0.52% tetgen::tetgenmesh::link::add 345ms 0.52% 87.53% 345ms 0.52% tetgen::tetgenmesh::org