File: Test3dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 60987ms, 86.74% of 70313ms total Dropped 848 nodes (cum <= 351.56ms) flat flat% sum% cum cum% 0 0% 0% 70271ms 99.94% __libc_start_call_main 0 0% 0% 70271ms 99.94% __libc_start_main_impl 0 0% 0% 70271ms 99.94% _start 0 0% 0% 70257ms 99.92% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 70257ms 99.92% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 70257ms 99.92% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 70257ms 99.92% main 0 0% 0% 70222ms 99.87% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 70222ms 99.87% CxxTest::TestRunner::runTest (inline) 0 0% 0% 70222ms 99.87% Test3dTissueRepresentativeSimulation::Test3DHoneycombMeshWithGhostNodes 0 0% 0% 69958ms 99.50% AbstractCellBasedSimulation::Solve 0 0% 0% 60336ms 85.81% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 60268ms 85.71% MeshBasedCellPopulation::Update 0 0% 0% 38349ms 54.54% MeshBasedCellPopulation::CreateVoronoiTessellation (inline) 0 0% 0% 38349ms 54.54% MeshBasedCellPopulation::TessellateIfNeeded 468ms 0.67% 0.67% 33659ms 47.87% VertexMesh::VertexMesh 0 0% 0.67% 17697ms 25.17% MutableMesh::ReMesh 601ms 0.85% 1.52% 13391ms 19.04% TetrahedralMesh::EdgeIterator::operator++ 33ms 0.047% 1.57% 13259ms 18.86% std::set::insert (inline) 198ms 0.28% 1.85% 12728ms 18.10% std::_Rb_tree::_M_insert_unique 0 0% 1.85% 12659ms 18.00% tetgen::tetrahedralize 5ms 0.0071% 1.86% 12498ms 17.77% tetgen::tetgenmesh::delaunizevertices 7ms 0.01% 1.87% 12489ms 17.76% tetgen::tetgenmesh::incrflipdelaunay 405ms 0.58% 2.44% 11616ms 16.52% VertexElement::AddFace 617ms 0.88% 3.32% 11068ms 15.74% tetgen::tetgenmesh::lawson 2761ms 3.93% 7.25% 9506ms 13.52% std::_Rb_tree::_M_lower_bound (inline) 219ms 0.31% 7.56% 9361ms 13.31% operator new 3161ms 4.50% 12.05% 9024ms 12.83% __GI___libc_malloc 241ms 0.34% 12.40% 9022ms 12.83% std::_Rb_tree::find (inline) 0 0% 12.40% 8575ms 12.20% std::set::count (inline) 315ms 0.45% 12.84% 8486ms 12.07% std::_Rb_tree::_M_insert_ (inline) 90ms 0.13% 12.97% 7562ms 10.75% std::__new_allocator::allocate (inline) 0 0% 12.97% 7530ms 10.71% std::allocator_traits::allocate (inline) 6789ms 9.66% 22.63% 6789ms 9.66% std::_Rb_tree_increment 451ms 0.64% 23.27% 6258ms 8.90% std::__set_intersection 0 0% 23.27% 6258ms 8.90% std::set_intersection (inline) 0 0% 23.27% 6056ms 8.61% std::_Rb_tree::_M_create_node (inline) 0 0% 23.27% 6034ms 8.58% std::_Rb_tree::_M_get_node (inline) 0 0% 23.27% 6001ms 8.53% std::_Rb_tree::_Alloc_node::operator() (inline) 1077ms 1.53% 24.80% 5985ms 8.51% __GI___libc_free 0 0% 24.80% 5886ms 8.37% OffLatticeSimulation::UpdateCellLocationsAndTopology 1ms 0.0014% 24.80% 5734ms 8.15% ForwardEulerNumericalMethod::UpdateAllNodePositions 0 0% 24.80% 5710ms 8.12% AbstractNumericalMethod::ComputeForcesIncludingDamping 5649ms 8.03% 32.84% 5649ms 8.03% std::operator< (inline) 18ms 0.026% 32.86% 5625ms 8.00% std::less::operator() (inline) 4119ms 5.86% 38.72% 5451ms 7.75% _int_malloc 249ms 0.35% 39.07% 5260ms 7.48% std::_Rb_tree_const_iterator::operator++ (inline) 35ms 0.05% 39.12% 5222ms 7.43% Node::AddElement 99ms 0.14% 39.26% 5056ms 7.19% std::__new_allocator::deallocate (inline) 0 0% 39.26% 5040ms 7.17% std::allocator_traits::deallocate (inline) 2188ms 3.11% 42.38% 4851ms 6.90% _int_free 0 0% 42.38% 4730ms 6.73% VertexMesh::~VertexMesh 14ms 0.02% 42.40% 4679ms 6.65% std::_Rb_tree::~_Rb_tree (inline) 1267ms 1.80% 44.20% 4647ms 6.61% std::_Rb_tree::_M_erase 0 0% 44.20% 4628ms 6.58% std::set::~set (inline) 8ms 0.011% 44.21% 4610ms 6.56% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 0 0% 44.21% 4579ms 6.51% MeshBasedCellPopulation::UpdateNodePairs 4577ms 6.51% 50.72% 4577ms 6.51% std::_Rb_tree::_S_right (inline) 8ms 0.011% 50.73% 4409ms 6.27% MeshBasedCellPopulation::SpringIterator::operator++ 1140ms 1.62% 52.35% 4380ms 6.23% std::_Rb_tree::_M_get_insert_unique_pos 9ms 0.013% 52.36% 4021ms 5.72% TetrahedralMesh::ImportFromMesher 54ms 0.077% 52.44% 3920ms 5.58% MutableElement::AddNode 0 0% 52.44% 3543ms 5.04% AbstractCellPopulation::WriteResultsToFiles 111ms 0.16% 52.60% 2899ms 4.12% tetgen::tetgenmesh::insphere_sos 243ms 0.35% 52.94% 2882ms 4.10% tetgen::tetgenmesh::flip23 2547ms 3.62% 56.57% 2768ms 3.94% tetgen::insphere 0 0% 56.57% 2694ms 3.83% std::_Rb_tree::_M_drop_node (inline) 0 0% 56.57% 2666ms 3.79% std::_Rb_tree::_M_put_node (inline) 46ms 0.065% 56.63% 2650ms 3.77% VertexMesh::Clear 31ms 0.044% 56.68% 2550ms 3.63% Node::~Node 1835ms 2.61% 59.29% 2547ms 3.62% malloc_consolidate 17ms 0.024% 59.31% 2391ms 3.40% std::_Vector_base::_M_deallocate (inline) 3ms 0.0043% 59.31% 2358ms 3.35% Element::Element 5ms 0.0071% 59.32% 2339ms 3.33% MeshBasedCellPopulationWithGhostNodes::WriteVtkResultsToFile 67ms 0.095% 59.42% 2275ms 3.24% VertexMesh::GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex 2252ms 3.20% 62.62% 2252ms 3.20% std::_Rb_tree_insert_and_rebalance 227ms 0.32% 62.94% 2240ms 3.19% std::_Rb_tree_iterator::operator++ (inline) 9ms 0.013% 62.96% 2225ms 3.16% _int_free_maybe_consolidate 0 0% 62.96% 2219ms 3.16% std::vector::~vector (inline) 5ms 0.0071% 62.96% 2200ms 3.13% std::_Vector_base::~_Vector_base (inline) 2108ms 3.00% 65.96% 2108ms 3.00% Node::GetIndex 193ms 0.27% 66.24% 1961ms 2.79% tetgen::tetgenmesh::flip32 1944ms 2.76% 69.00% 1944ms 2.76% [libchaste_mesh.so] 5ms 0.0071% 69.01% 1922ms 2.73% Element::RegisterWithNodes (inline) 5ms 0.0071% 69.01% 1856ms 2.64% VertexMesh::GenerateVerticesFromElementCircumcentres 1634ms 2.32% 71.34% 1634ms 2.32% unlink_chunk 56ms 0.08% 71.42% 1608ms 2.29% std::vector::_M_realloc_insert 1505ms 2.14% 73.56% 1568ms 2.23% tetgen::orient3d 3ms 0.0043% 73.56% 1499ms 2.13% std::_Vector_base::_M_allocate (inline) 170ms 0.24% 73.80% 1438ms 2.05% tetgen::tetgenmesh::enqueueflipface 81ms 0.12% 73.92% 1247ms 1.77% std::vector::push_back (inline) 25ms 0.036% 73.96% 1189ms 1.69% tetgen::tetgenmesh::locate 64ms 0.091% 74.05% 1159ms 1.65% std::map::operator[] 58ms 0.082% 74.13% 1146ms 1.63% TetrahedralMesh::Clear 910ms 1.29% 75.42% 1143ms 1.63% AbstractElement::GetNodeGlobalIndex 101ms 0.14% 75.57% 1105ms 1.57% tetgen::tetgenmesh::preciselocate 1026ms 1.46% 77.03% 1026ms 1.46% Node::rGetLocation 0 0% 77.03% 992ms 1.41% TetrahedralMesh::RefreshJacobianCachedData 0 0% 77.03% 983ms 1.40% std::_Rb_tree::lower_bound (inline) 0 0% 77.03% 983ms 1.40% std::map::lower_bound (inline) 1ms 0.0014% 77.03% 976ms 1.39% VoronoiDataWriter::Visit 205ms 0.29% 77.32% 956ms 1.36% boost::numeric::ublas::vector_assign (inline) 553ms 0.79% 78.11% 940ms 1.34% AbstractElement::GetNodeLocation 9ms 0.013% 78.12% 916ms 1.30% Element::CalculateCircumsphere 547ms 0.78% 78.90% 916ms 1.30% tetgen::tetgenmesh::sym 5ms 0.0071% 78.90% 902ms 1.28% boost::numeric::ublas::c_vector::c_vector (inline) 19ms 0.027% 78.93% 857ms 1.22% AbstractTetrahedralElement::CalculateJacobian 4ms 0.0057% 78.94% 850ms 1.21% AbstractTwoBodyInteractionForce::AddForceContribution 9ms 0.013% 78.95% 805ms 1.14% AbstractTetrahedralElement::CalculateInverseJacobian 12ms 0.017% 78.97% 796ms 1.13% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 790ms 1.12% 80.09% 790ms 1.12% AbstractElement::IsDeleted 66ms 0.094% 80.18% 654ms 0.93% AbstractTetrahedralElement::RefreshJacobian 611ms 0.87% 81.05% 611ms 0.87% tetgen::tetgenmesh::oppo 585ms 0.83% 81.88% 585ms 0.83% std::vector::size (inline) 550ms 0.78% 82.67% 550ms 0.78% tetgen::tetgenmesh::triface::triface 31ms 0.044% 82.71% 518ms 0.74% __atan2 37ms 0.053% 82.76% 509ms 0.72% tetgen::tetgenmesh::enext2fnext 0 0% 82.76% 507ms 0.72% std::insert_iterator::operator= (inline) 125ms 0.18% 82.94% 506ms 0.72% std::_Rb_tree_iterator::operator-- (inline) 23ms 0.033% 82.97% 500ms 0.71% std::vector::insert (inline) 404ms 0.57% 83.55% 494ms 0.7% tetgen::tetgenmesh::fnextself 26ms 0.037% 83.58% 490ms 0.7% VertexMesh::CalculateUnitNormalToFaceWithArea 5ms 0.0071% 83.59% 489ms 0.7% CellPropertyCollection::GetPropertiesType (inline) 441ms 0.63% 84.22% 485ms 0.69% __ieee754_atan2_fma 66ms 0.094% 84.31% 483ms 0.69% tetgen::tetgenmesh::enextfnext 0 0% 84.31% 471ms 0.67% std::_Rb_tree::_M_insert_unique_ (inline) 3ms 0.0043% 84.32% 467ms 0.66% Cell::GetCellId 101ms 0.14% 84.46% 461ms 0.66% boost::numeric::ublas::indexing_vector_assign 0 0% 84.46% 443ms 0.63% std::set::find (inline) 1ms 0.0014% 84.46% 435ms 0.62% AbstractTetrahedralElement::AbstractTetrahedralElement 0 0% 84.46% 431ms 0.61% boost::numeric::ublas::inner_prod (inline) 2ms 0.0028% 84.47% 427ms 0.61% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 26ms 0.037% 84.50% 425ms 0.6% boost::numeric::ublas::vector_scalar_binary::evaluate 85ms 0.12% 84.62% 408ms 0.58% tetgen::tetgenmesh::queue::pop 17ms 0.024% 84.65% 407ms 0.58% tetgen::tetgenmesh::queue::push 0 0% 84.65% 404ms 0.57% VertexMeshWriter::WriteVtkUsingMesh 107ms 0.15% 84.80% 402ms 0.57% __dynamic_cast 8ms 0.011% 84.81% 400ms 0.57% boost::numeric::ublas::c_vector::operator= (inline) 211ms 0.3% 85.11% 384ms 0.55% tetgen::tetgenmesh::bond 0 0% 85.11% 383ms 0.54% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 135ms 0.19% 85.30% 376ms 0.53% boost::numeric::ublas::vector_inner_prod::apply (inline) 276ms 0.39% 85.70% 375ms 0.53% tetgen::tetgenmesh::link::add 2ms 0.0028% 85.70% 368ms 0.52% VertexElement::~VertexElement 366ms 0.52% 86.22% 366ms 0.52% std::_Rb_tree_decrement 1ms 0.0014% 86.22% 364ms 0.52% tcache_get (inline) 363ms 0.52% 86.74% 363ms 0.52% tcache_get_n (inline)