File: Test3dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 64656ms, 87.11% of 74223ms total Dropped 911 nodes (cum <= 371.12ms) flat flat% sum% cum cum% 0 0% 0% 74162ms 99.92% __libc_start_call_main 0 0% 0% 74162ms 99.92% __libc_start_main_impl 0 0% 0% 74162ms 99.92% _start 0 0% 0% 74144ms 99.89% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 74144ms 99.89% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 74144ms 99.89% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 74144ms 99.89% main 0 0% 0% 74102ms 99.84% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 74102ms 99.84% CxxTest::TestRunner::runTest (inline) 0 0% 0% 74102ms 99.84% Test3dTissueRepresentativeSimulation::Test3DHoneycombMeshWithGhostNodes 0 0% 0% 73806ms 99.44% AbstractCellBasedSimulation::Solve 0 0% 0% 64012ms 86.24% AbstractCellBasedSimulation::UpdateCellPopulation 1ms 0.0013% 0.0013% 63959ms 86.17% MeshBasedCellPopulation::Update 0 0% 0.0013% 37975ms 51.16% MeshBasedCellPopulation::CreateVoronoiTessellation (inline) 0 0% 0.0013% 37975ms 51.16% MeshBasedCellPopulation::TessellateIfNeeded 301ms 0.41% 0.41% 33081ms 44.57% VertexMesh::VertexMesh 0 0% 0.41% 21517ms 28.99% MutableMesh::ReMesh 2ms 0.0027% 0.41% 16550ms 22.30% tetgen::tetrahedralize 3ms 0.004% 0.41% 16396ms 22.09% tetgen::tetgenmesh::delaunizevertices 11ms 0.015% 0.43% 16389ms 22.08% tetgen::tetgenmesh::incrflipdelaunay 531ms 0.72% 1.14% 14670ms 19.76% tetgen::tetgenmesh::lawson 634ms 0.85% 2.00% 14093ms 18.99% TetrahedralMesh::EdgeIterator::operator++ 31ms 0.042% 2.04% 12425ms 16.74% std::set::insert (inline) 236ms 0.32% 2.36% 11998ms 16.16% std::_Rb_tree::_M_insert_unique 448ms 0.6% 2.96% 11207ms 15.10% VertexElement::AddFace 3192ms 4.30% 7.26% 9871ms 13.30% std::_Rb_tree::_M_lower_bound (inline) 253ms 0.34% 7.60% 9217ms 12.42% std::_Rb_tree::find (inline) 0 0% 7.60% 8694ms 11.71% std::set::count (inline) 7308ms 9.85% 17.45% 7308ms 9.85% std::_Rb_tree_increment 329ms 0.44% 17.89% 7104ms 9.57% std::_Rb_tree::_M_insert_ (inline) 187ms 0.25% 18.14% 6951ms 9.37% operator new 1260ms 1.70% 19.84% 6681ms 9.00% __GI___libc_malloc 106ms 0.14% 19.98% 6463ms 8.71% std::less::operator() (inline) 6413ms 8.64% 28.62% 6413ms 8.64% std::operator< (inline) 3ms 0.004% 28.63% 6379ms 8.59% std::set_intersection (inline) 384ms 0.52% 29.15% 6376ms 8.59% std::__set_intersection 0 0% 29.15% 5982ms 8.06% OffLatticeSimulation::UpdateCellLocationsAndTopology 1ms 0.0013% 29.15% 5840ms 7.87% ForwardEulerNumericalMethod::UpdateAllNodePositions 2ms 0.0027% 29.15% 5813ms 7.83% AbstractNumericalMethod::ComputeForcesIncludingDamping 35ms 0.047% 29.20% 5586ms 7.53% std::__new_allocator::allocate (inline) 0 0% 29.20% 5574ms 7.51% std::allocator_traits::allocate (inline) 218ms 0.29% 29.49% 5449ms 7.34% std::_Rb_tree_const_iterator::operator++ (inline) 44ms 0.059% 29.55% 5276ms 7.11% Node::AddElement 14ms 0.019% 29.57% 5105ms 6.88% std::_Rb_tree::~_Rb_tree (inline) 1875ms 2.53% 32.10% 5089ms 6.86% std::_Rb_tree::_M_erase 1359ms 1.83% 33.93% 5087ms 6.85% __GI___libc_free 3726ms 5.02% 38.95% 5067ms 6.83% _int_malloc 0 0% 38.95% 5042ms 6.79% std::set::~set (inline) 0 0% 38.95% 4929ms 6.64% VertexMesh::~VertexMesh 1358ms 1.83% 40.78% 4921ms 6.63% std::_Rb_tree::_M_get_insert_unique_pos 1ms 0.0013% 40.78% 4887ms 6.58% MeshBasedCellPopulation::UpdateNodePairs 3ms 0.004% 40.78% 4845ms 6.53% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 12ms 0.016% 40.80% 4709ms 6.34% MeshBasedCellPopulation::SpringIterator::operator++ 136ms 0.18% 40.98% 4622ms 6.23% std::__new_allocator::deallocate (inline) 0 0% 40.98% 4606ms 6.21% std::allocator_traits::deallocate (inline) 0 0% 40.98% 4554ms 6.14% std::_Rb_tree::_M_create_node (inline) 0 0% 40.98% 4524ms 6.10% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 40.98% 4499ms 6.06% std::_Rb_tree::_M_get_node (inline) 4329ms 5.83% 46.81% 4329ms 5.83% std::_Rb_tree::_S_right (inline) 77ms 0.1% 46.92% 4092ms 5.51% MutableElement::AddNode 118ms 0.16% 47.08% 3959ms 5.33% tetgen::tetgenmesh::insphere_sos 13ms 0.018% 47.09% 3949ms 5.32% TetrahedralMesh::ImportFromMesher 3526ms 4.75% 51.84% 3827ms 5.16% tetgen::insphere 1398ms 1.88% 53.73% 3724ms 5.02% _int_free 135ms 0.18% 53.91% 3647ms 4.91% tetgen::tetgenmesh::flip23 0 0% 53.91% 3604ms 4.86% AbstractCellPopulation::WriteResultsToFiles 256ms 0.34% 54.25% 3167ms 4.27% Node::~Node 222ms 0.3% 54.55% 2935ms 3.95% VertexMesh::Clear 145ms 0.2% 54.75% 2679ms 3.61% tetgen::tetgenmesh::flip32 2545ms 3.43% 58.18% 2545ms 3.43% Node::GetIndex 1ms 0.0013% 58.18% 2406ms 3.24% MeshBasedCellPopulationWithGhostNodes::WriteVtkResultsToFile 1663ms 2.24% 60.42% 2385ms 3.21% malloc_consolidate 212ms 0.29% 60.70% 2372ms 3.20% VertexMesh::GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex 0 0% 60.70% 2351ms 3.17% std::_Rb_tree::_M_drop_node (inline) 2335ms 3.15% 63.85% 2335ms 3.15% std::_Rb_tree_insert_and_rebalance 0 0% 63.85% 2330ms 3.14% std::_Rb_tree::_M_put_node (inline) 54ms 0.073% 63.92% 2330ms 3.14% std::_Vector_base::_M_deallocate (inline) 1ms 0.0013% 63.92% 2200ms 2.96% std::_Rb_tree_iterator::operator++ (inline) 0 0% 63.92% 2200ms 2.96% std::vector::~vector (inline) 0 0% 63.92% 2147ms 2.89% std::_Vector_base::~_Vector_base (inline) 6ms 0.0081% 63.93% 2077ms 2.80% _int_free_maybe_consolidate 5ms 0.0067% 63.94% 2074ms 2.79% Element::Element 215ms 0.29% 64.23% 1865ms 2.51% tetgen::tetgenmesh::enqueueflipface 6ms 0.0081% 64.24% 1724ms 2.32% Element::RegisterWithNodes (inline) 1687ms 2.27% 66.51% 1687ms 2.27% unlink_chunk 1519ms 2.05% 68.56% 1606ms 2.16% tetgen::orient3d 7ms 0.0094% 68.57% 1570ms 2.12% VertexMesh::GenerateVerticesFromElementCircumcentres 1249ms 1.68% 70.25% 1490ms 2.01% AbstractElement::GetNodeGlobalIndex 81ms 0.11% 70.36% 1442ms 1.94% TetrahedralMesh::Clear 36ms 0.049% 70.41% 1412ms 1.90% tetgen::tetgenmesh::locate 74ms 0.1% 70.51% 1326ms 1.79% tetgen::tetgenmesh::preciselocate 65ms 0.088% 70.59% 1287ms 1.73% std::vector::_M_realloc_insert 1222ms 1.65% 72.24% 1222ms 1.65% tetgen::tetgenmesh::triface::triface 54ms 0.073% 72.31% 1218ms 1.64% std::map::operator[] 0 0% 72.31% 1078ms 1.45% std::_Rb_tree::lower_bound (inline) 0 0% 72.31% 1078ms 1.45% std::map::lower_bound (inline) 1ms 0.0013% 72.31% 1076ms 1.45% std::_Vector_base::_M_allocate (inline) 118ms 0.16% 72.47% 1031ms 1.39% std::vector::push_back (inline) 0 0% 72.47% 997ms 1.34% TetrahedralMesh::RefreshJacobianCachedData 983ms 1.32% 73.80% 983ms 1.32% tetgen::tetgenmesh::oppo 979ms 1.32% 75.12% 979ms 1.32% AbstractElement::IsDeleted 1ms 0.0013% 75.12% 947ms 1.28% VoronoiDataWriter::Visit 450ms 0.61% 75.72% 942ms 1.27% AbstractElement::GetNodeLocation 925ms 1.25% 76.97% 925ms 1.25% Node::rGetLocation 338ms 0.46% 77.43% 887ms 1.20% tetgen::tetgenmesh::sym 847ms 1.14% 78.57% 847ms 1.14% tetgen::tetgenmesh::triface::operator= 9ms 0.012% 78.58% 822ms 1.11% AbstractTetrahedralElement::CalculateInverseJacobian 803ms 1.08% 79.66% 803ms 1.08% [libchaste_mesh.so] 12ms 0.016% 79.68% 777ms 1.05% AbstractTetrahedralElement::CalculateJacobian 1ms 0.0013% 79.68% 776ms 1.05% AbstractTwoBodyInteractionForce::AddForceContribution 749ms 1.01% 80.69% 749ms 1.01% std::vector::size (inline) 20ms 0.027% 80.71% 734ms 0.99% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 403ms 0.54% 81.26% 708ms 0.95% tetgen::tetgenmesh::fnextself 18ms 0.024% 81.28% 679ms 0.91% Element::CalculateCircumsphere 73ms 0.098% 81.38% 669ms 0.9% tetgen::tetgenmesh::enext2fnext 17ms 0.023% 81.40% 621ms 0.84% boost::numeric::ublas::vector_assign (inline) 7ms 0.0094% 81.41% 620ms 0.84% boost::numeric::ublas::c_vector::c_vector (inline) 207ms 0.28% 81.69% 612ms 0.82% tetgen::tetgenmesh::bond 35ms 0.047% 81.74% 600ms 0.81% tetgen::tetgenmesh::queue::push 50ms 0.067% 81.81% 595ms 0.8% AbstractTetrahedralElement::RefreshJacobian 58ms 0.078% 81.88% 589ms 0.79% tetgen::tetgenmesh::enextfnext 38ms 0.051% 81.94% 588ms 0.79% __atan2 582ms 0.78% 82.72% 582ms 0.78% tetgen::tetgenmesh::decode 394ms 0.53% 83.25% 564ms 0.76% tetgen::tetgenmesh::link::add 434ms 0.58% 83.84% 548ms 0.74% __ieee754_atan2_fma 0 0% 83.84% 519ms 0.7% boost::numeric::ublas::inner_prod (inline) 0 0% 83.84% 519ms 0.7% std::set::find (inline) 3ms 0.004% 83.84% 514ms 0.69% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 40ms 0.054% 83.89% 511ms 0.69% boost::numeric::ublas::vector_scalar_binary::evaluate 478ms 0.64% 84.54% 478ms 0.64% tetgen::tetgenmesh::org 13ms 0.018% 84.55% 459ms 0.62% VertexMesh::CalculateUnitNormalToFaceWithArea 0 0% 84.55% 455ms 0.61% std::insert_iterator::operator= (inline) 5ms 0.0067% 84.56% 452ms 0.61% CellPropertyCollection::GetPropertiesType (inline) 26ms 0.035% 84.60% 441ms 0.59% std::_Rb_tree_iterator::operator-- (inline) 3ms 0.004% 84.60% 436ms 0.59% Cell::GetCellId 111ms 0.15% 84.75% 432ms 0.58% __dynamic_cast 0 0% 84.75% 426ms 0.57% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 46ms 0.062% 84.81% 409ms 0.55% tetgen::tetgenmesh::queue::pop 225ms 0.3% 85.12% 406ms 0.55% AbstractTetrahedralMesh::GetElement 6ms 0.0081% 85.12% 405ms 0.55% boost::numeric::ublas::c_vector::operator= (inline) 18ms 0.024% 85.15% 398ms 0.54% std::vector::insert (inline) 188ms 0.25% 85.40% 397ms 0.53% boost::numeric::ublas::vector_inner_prod::apply (inline) 397ms 0.53% 85.94% 397ms 0.53% tetgen::tetgenmesh::encode 100ms 0.13% 86.07% 395ms 0.53% boost::numeric::ublas::indexing_vector_assign 0 0% 86.07% 394ms 0.53% VertexMeshWriter::WriteVtkUsingMesh 390ms 0.53% 86.60% 390ms 0.53% std::_Rb_tree_decrement 0 0% 86.60% 389ms 0.52% std::_Rb_tree::_M_insert_unique_ (inline) 9ms 0.012% 86.61% 385ms 0.52% VertexElement::~VertexElement 373ms 0.5% 87.11% 373ms 0.5% tetgen::tetgenmesh::pointmark