File: Test3dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 61960ms, 87.74% of 70616ms total Dropped 893 nodes (cum <= 353.08ms) flat flat% sum% cum cum% 0 0% 0% 70560ms 99.92% __libc_start_call_main 0 0% 0% 70560ms 99.92% __libc_start_main_impl 0 0% 0% 70560ms 99.92% _start 0 0% 0% 70544ms 99.90% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 70544ms 99.90% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 70544ms 99.90% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 70544ms 99.90% main 0 0% 0% 70507ms 99.85% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 70507ms 99.85% CxxTest::TestRunner::runTest (inline) 0 0% 0% 70507ms 99.85% Test3dTissueRepresentativeSimulation::Test3DHoneycombMeshWithGhostNodes 0 0% 0% 70243ms 99.47% AbstractCellBasedSimulation::Solve 0 0% 0% 59245ms 83.90% AbstractCellBasedSimulation::UpdateCellPopulation 1ms 0.0014% 0.0014% 59185ms 83.81% MeshBasedCellPopulation::Update 0 0% 0.0014% 36557ms 51.77% MeshBasedCellPopulation::CreateVoronoiTessellation (inline) 0 0% 0.0014% 36557ms 51.77% MeshBasedCellPopulation::TessellateIfNeeded 283ms 0.4% 0.4% 31676ms 44.86% VertexMesh::VertexMesh 0 0% 0.4% 18113ms 25.65% MutableMesh::ReMesh 527ms 0.75% 1.15% 14039ms 19.88% TetrahedralMesh::EdgeIterator::operator++ 0 0% 1.15% 12865ms 18.22% tetgen::tetrahedralize 1ms 0.0014% 1.15% 12734ms 18.03% tetgen::tetgenmesh::delaunizevertices 8ms 0.011% 1.16% 12729ms 18.03% tetgen::tetgenmesh::incrflipdelaunay 32ms 0.045% 1.21% 12051ms 17.07% std::set::insert (inline) 215ms 0.3% 1.51% 11509ms 16.30% std::_Rb_tree::_M_insert_unique 569ms 0.81% 2.32% 11244ms 15.92% tetgen::tetgenmesh::lawson 3091ms 4.38% 6.69% 10826ms 15.33% std::_Rb_tree::_M_lower_bound (inline) 440ms 0.62% 7.32% 10686ms 15.13% VertexElement::AddFace 218ms 0.31% 7.63% 9928ms 14.06% std::_Rb_tree::find (inline) 0 0% 7.63% 9383ms 13.29% std::set::count (inline) 7900ms 11.19% 18.81% 7900ms 11.19% std::_Rb_tree_increment 128ms 0.18% 18.99% 7212ms 10.21% std::less::operator() (inline) 7144ms 10.12% 29.11% 7144ms 10.12% std::operator< (inline) 250ms 0.35% 29.46% 6638ms 9.40% std::_Rb_tree::_M_insert_ (inline) 184ms 0.26% 29.73% 6572ms 9.31% operator new 1150ms 1.63% 31.35% 6304ms 8.93% __GI___libc_malloc 0 0% 31.35% 6080ms 8.61% OffLatticeSimulation::UpdateCellLocationsAndTopology 1ms 0.0014% 31.36% 5905ms 8.36% ForwardEulerNumericalMethod::UpdateAllNodePositions 2ms 0.0028% 31.36% 5878ms 8.32% AbstractNumericalMethod::ComputeForcesIncludingDamping 3ms 0.0042% 31.36% 5688ms 8.05% std::set_intersection (inline) 307ms 0.43% 31.80% 5685ms 8.05% std::__set_intersection 54ms 0.076% 31.87% 5361ms 7.59% std::__new_allocator::allocate (inline) 0 0% 31.87% 5335ms 7.55% std::allocator_traits::allocate (inline) 34ms 0.048% 31.92% 5233ms 7.41% Node::AddElement 7ms 0.0099% 31.93% 5203ms 7.37% std::_Rb_tree::~_Rb_tree (inline) 2277ms 3.22% 35.16% 5194ms 7.36% std::_Rb_tree::_M_erase 0 0% 35.16% 5128ms 7.26% std::set::~set (inline) 1323ms 1.87% 37.03% 5004ms 7.09% std::_Rb_tree::_M_get_insert_unique_pos 0 0% 37.03% 4907ms 6.95% VertexMesh::~VertexMesh 5ms 0.0071% 37.04% 4892ms 6.93% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 2ms 0.0028% 37.04% 4872ms 6.90% MeshBasedCellPopulation::UpdateNodePairs 179ms 0.25% 37.29% 4865ms 6.89% std::_Rb_tree_const_iterator::operator++ (inline) 4849ms 6.87% 44.16% 4849ms 6.87% std::_Rb_tree::_S_right (inline) 1345ms 1.90% 46.06% 4813ms 6.82% __GI___libc_free 3468ms 4.91% 50.98% 4780ms 6.77% _int_malloc 0 0% 50.98% 4753ms 6.73% AbstractCellPopulation::WriteResultsToFiles 10ms 0.014% 50.99% 4685ms 6.63% MeshBasedCellPopulation::SpringIterator::operator++ 0 0% 50.99% 4310ms 6.10% std::_Rb_tree::_M_create_node (inline) 0 0% 50.99% 4268ms 6.04% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 50.99% 4251ms 6.02% std::_Rb_tree::_M_get_node (inline) 11ms 0.016% 51.01% 4249ms 6.02% TetrahedralMesh::ImportFromMesher 133ms 0.19% 51.19% 4187ms 5.93% std::__new_allocator::deallocate (inline) 0 0% 51.19% 4168ms 5.90% std::allocator_traits::deallocate (inline) 60ms 0.085% 51.28% 3931ms 5.57% MutableElement::AddNode 124ms 0.18% 51.45% 3575ms 5.06% tetgen::tetgenmesh::insphere_sos 234ms 0.33% 51.79% 3513ms 4.97% VertexMesh::GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex 1197ms 1.70% 53.48% 3464ms 4.91% _int_free 3144ms 4.45% 57.93% 3437ms 4.87% tetgen::insphere 1ms 0.0014% 57.93% 3310ms 4.69% std::_Rb_tree_iterator::operator++ (inline) 3ms 0.0042% 57.94% 3307ms 4.68% MeshBasedCellPopulationWithGhostNodes::WriteVtkResultsToFile 176ms 0.25% 58.19% 3210ms 4.55% Node::~Node 262ms 0.37% 58.56% 2997ms 4.24% VertexMesh::Clear 202ms 0.29% 58.85% 2671ms 3.78% tetgen::tetgenmesh::flip23 2515ms 3.56% 62.41% 2515ms 3.56% Node::GetIndex 1533ms 2.17% 64.58% 2315ms 3.28% malloc_consolidate 2272ms 3.22% 67.79% 2272ms 3.22% std::_Rb_tree_insert_and_rebalance 16ms 0.023% 67.82% 2214ms 3.14% std::_Vector_base::_M_deallocate (inline) 9ms 0.013% 67.83% 2184ms 3.09% Element::Element 0 0% 67.83% 2058ms 2.91% std::vector::~vector (inline) 1ms 0.0014% 67.83% 2007ms 2.84% std::_Vector_base::~_Vector_base (inline) 3ms 0.0042% 67.84% 2005ms 2.84% _int_free_maybe_consolidate 0 0% 67.84% 1980ms 2.80% std::_Rb_tree::_M_drop_node (inline) 0 0% 67.84% 1969ms 2.79% std::_Rb_tree::_M_put_node (inline) 160ms 0.23% 68.06% 1845ms 2.61% tetgen::tetgenmesh::flip32 5ms 0.0071% 68.07% 1843ms 2.61% Element::RegisterWithNodes (inline) 1682ms 2.38% 70.45% 1682ms 2.38% unlink_chunk 236ms 0.33% 70.79% 1633ms 2.31% TetrahedralMesh::Clear 5ms 0.0071% 70.79% 1474ms 2.09% VertexMesh::GenerateVerticesFromElementCircumcentres 69ms 0.098% 70.89% 1474ms 2.09% std::map::operator[] 1339ms 1.90% 72.79% 1413ms 2.00% tetgen::orient3d 75ms 0.11% 72.89% 1345ms 1.90% std::vector::_M_realloc_insert 0 0% 72.89% 1300ms 1.84% std::_Rb_tree::lower_bound (inline) 0 0% 72.89% 1300ms 1.84% std::map::lower_bound (inline) 167ms 0.24% 73.13% 1298ms 1.84% tetgen::tetgenmesh::enqueueflipface 34ms 0.048% 73.18% 1247ms 1.77% tetgen::tetgenmesh::locate 0 0% 73.18% 1183ms 1.68% VoronoiDataWriter::Visit 93ms 0.13% 73.31% 1167ms 1.65% tetgen::tetgenmesh::preciselocate 143ms 0.2% 73.51% 1114ms 1.58% std::vector::push_back (inline) 1000ms 1.42% 74.93% 1102ms 1.56% AbstractElement::GetNodeGlobalIndex 8ms 0.011% 74.94% 1091ms 1.54% std::_Vector_base::_M_allocate (inline) 0 0% 74.94% 970ms 1.37% TetrahedralMesh::RefreshJacobianCachedData 431ms 0.61% 75.55% 896ms 1.27% AbstractElement::GetNodeLocation 882ms 1.25% 76.80% 882ms 1.25% tetgen::tetgenmesh::triface::triface 818ms 1.16% 77.96% 818ms 1.16% AbstractElement::IsDeleted 15ms 0.021% 77.98% 808ms 1.14% AbstractTetrahedralElement::CalculateInverseJacobian 771ms 1.09% 79.07% 771ms 1.09% Node::rGetLocation 14ms 0.02% 79.09% 761ms 1.08% AbstractTetrahedralElement::CalculateJacobian 451ms 0.64% 79.73% 758ms 1.07% tetgen::tetgenmesh::fnextself 2ms 0.0028% 79.73% 754ms 1.07% AbstractTwoBodyInteractionForce::AddForceContribution 736ms 1.04% 80.77% 736ms 1.04% tetgen::tetgenmesh::oppo 23ms 0.033% 80.81% 705ms 1% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 15ms 0.021% 80.83% 667ms 0.94% Element::CalculateCircumsphere 12ms 0.017% 80.84% 654ms 0.93% boost::numeric::ublas::vector_assign (inline) 649ms 0.92% 81.76% 649ms 0.92% [libchaste_mesh.so] 8ms 0.011% 81.77% 639ms 0.9% boost::numeric::ublas::c_vector::c_vector (inline) 43ms 0.061% 81.84% 634ms 0.9% __atan2 482ms 0.68% 82.52% 591ms 0.84% __ieee754_atan2_fma 585ms 0.83% 83.35% 585ms 0.83% tetgen::tetgenmesh::triface::operator= 40ms 0.057% 83.40% 580ms 0.82% AbstractTetrahedralElement::RefreshJacobian 0 0% 83.40% 540ms 0.76% std::insert_iterator::operator= (inline) 0 0% 83.40% 539ms 0.76% std::set::find (inline) 538ms 0.76% 84.17% 538ms 0.76% std::vector::size (inline) 0 0% 84.17% 493ms 0.7% boost::numeric::ublas::inner_prod (inline) 8ms 0.011% 84.18% 490ms 0.69% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 40ms 0.057% 84.23% 487ms 0.69% tetgen::tetgenmesh::enextfnext 0 0% 84.23% 484ms 0.69% std::_Rb_tree::_M_insert_unique_ (inline) 43ms 0.061% 84.29% 484ms 0.69% tetgen::tetgenmesh::enext2fnext 30ms 0.042% 84.34% 482ms 0.68% boost::numeric::ublas::vector_scalar_binary::evaluate 0 0% 84.34% 452ms 0.64% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 16ms 0.023% 84.36% 448ms 0.63% VertexMesh::CalculateUnitNormalToFaceWithArea 285ms 0.4% 84.76% 428ms 0.61% tetgen::tetgenmesh::sym 111ms 0.16% 84.92% 425ms 0.6% boost::numeric::ublas::indexing_vector_assign 424ms 0.6% 85.52% 424ms 0.6% boost::numeric::ublas::c_vector::operator() 27ms 0.038% 85.56% 423ms 0.6% std::_Rb_tree_iterator::operator-- (inline) 180ms 0.25% 85.81% 410ms 0.58% boost::numeric::ublas::vector_inner_prod::apply (inline) 18ms 0.025% 85.84% 407ms 0.58% std::vector::insert (inline) 243ms 0.34% 86.18% 403ms 0.57% AbstractTetrahedralMesh::GetElement 0 0% 86.18% 395ms 0.56% VertexMeshWriter::WriteVtkUsingMesh 2ms 0.0028% 86.19% 394ms 0.56% CellPropertyCollection::GetPropertiesType (inline) 4ms 0.0057% 86.19% 390ms 0.55% boost::numeric::ublas::c_vector::operator= (inline) 380ms 0.54% 86.73% 380ms 0.54% tetgen::tetgenmesh::org 29ms 0.041% 86.77% 376ms 0.53% tetgen::tetgenmesh::queue::push 105ms 0.15% 86.92% 374ms 0.53% __dynamic_cast 367ms 0.52% 87.44% 367ms 0.52% std::_Rb_tree_decrement 214ms 0.3% 87.74% 358ms 0.51% tetgen::tetgenmesh::bond