File: Test3dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 59187ms, 85.52% of 69211ms total Dropped 887 nodes (cum <= 346.06ms) flat flat% sum% cum cum% 0 0% 0% 69160ms 99.93% __libc_start_call_main 0 0% 0% 69160ms 99.93% __libc_start_main_impl 0 0% 0% 69160ms 99.93% _start 0 0% 0% 69143ms 99.90% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 69143ms 99.90% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 69143ms 99.90% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 69143ms 99.90% main 0 0% 0% 69107ms 99.85% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 69107ms 99.85% CxxTest::TestRunner::runTest (inline) 0 0% 0% 69107ms 99.85% Test3dTissueRepresentativeSimulation::Test3DHoneycombMeshWithGhostNodes 0 0% 0% 68861ms 99.49% AbstractCellBasedSimulation::Solve 0 0% 0% 58898ms 85.10% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 58829ms 85.00% MeshBasedCellPopulation::Update 0 0% 0% 38144ms 55.11% MeshBasedCellPopulation::CreateVoronoiTessellation (inline) 0 0% 0% 38144ms 55.11% MeshBasedCellPopulation::TessellateIfNeeded 342ms 0.49% 0.49% 33760ms 48.78% VertexMesh::VertexMesh 1ms 0.0014% 0.5% 16260ms 23.49% MutableMesh::ReMesh 553ms 0.8% 1.29% 13931ms 20.13% TetrahedralMesh::EdgeIterator::operator++ 42ms 0.061% 1.36% 13532ms 19.55% std::set::insert (inline) 165ms 0.24% 1.59% 12940ms 18.70% std::_Rb_tree::_M_insert_unique 383ms 0.55% 2.15% 11771ms 17.01% VertexElement::AddFace 0 0% 2.15% 11354ms 16.40% tetgen::tetrahedralize 1ms 0.0014% 2.15% 11238ms 16.24% tetgen::tetgenmesh::delaunizevertices 11ms 0.016% 2.16% 11232ms 16.23% tetgen::tetgenmesh::incrflipdelaunay 4267ms 6.17% 8.33% 10288ms 14.86% std::_Rb_tree::_M_lower_bound (inline) 479ms 0.69% 9.02% 9914ms 14.32% tetgen::tetgenmesh::lawson 160ms 0.23% 9.25% 9807ms 14.17% std::_Rb_tree::find (inline) 232ms 0.34% 9.59% 9319ms 13.46% operator new 0 0% 9.59% 9243ms 13.35% std::set::count (inline) 3186ms 4.60% 14.19% 9008ms 13.02% __GI___libc_malloc 286ms 0.41% 14.60% 8732ms 12.62% std::_Rb_tree::_M_insert_ (inline) 78ms 0.11% 14.72% 7681ms 11.10% std::__new_allocator::allocate (inline) 0 0% 14.72% 7649ms 11.05% std::allocator_traits::allocate (inline) 6936ms 10.02% 24.74% 6936ms 10.02% std::_Rb_tree_increment 2ms 0.0029% 24.74% 6253ms 9.03% std::set_intersection (inline) 462ms 0.67% 25.41% 6251ms 9.03% std::__set_intersection 0 0% 25.41% 6241ms 9.02% std::_Rb_tree::_M_create_node (inline) 0 0% 25.41% 6197ms 8.95% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 25.41% 6193ms 8.95% std::_Rb_tree::_M_get_node (inline) 1ms 0.0014% 25.41% 5955ms 8.60% OffLatticeSimulation::UpdateCellLocationsAndTopology 2ms 0.0029% 25.41% 5785ms 8.36% ForwardEulerNumericalMethod::UpdateAllNodePositions 6ms 0.0087% 25.42% 5760ms 8.32% AbstractNumericalMethod::ComputeForcesIncludingDamping 990ms 1.43% 26.85% 5644ms 8.15% __GI___libc_free 4077ms 5.89% 32.74% 5359ms 7.74% _int_malloc 5267ms 7.61% 40.35% 5267ms 7.61% std::operator< (inline) 75ms 0.11% 40.46% 5261ms 7.60% std::less::operator() (inline) 282ms 0.41% 40.87% 5106ms 7.38% std::_Rb_tree_const_iterator::operator++ (inline) 105ms 0.15% 41.02% 5055ms 7.30% Node::AddElement 12ms 0.017% 41.04% 4836ms 6.99% std::_Rb_tree::~_Rb_tree (inline) 74ms 0.11% 41.15% 4813ms 6.95% std::__new_allocator::deallocate (inline) 1437ms 2.08% 43.22% 4812ms 6.95% std::_Rb_tree::_M_erase 0 0% 43.22% 4803ms 6.94% std::allocator_traits::deallocate (inline) 0 0% 43.22% 4790ms 6.92% std::set::~set (inline) 1ms 0.0014% 43.22% 4782ms 6.91% MeshBasedCellPopulation::UpdateNodePairs 6ms 0.0087% 43.23% 4692ms 6.78% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 2112ms 3.05% 46.28% 4638ms 6.70% _int_free 18ms 0.026% 46.31% 4620ms 6.68% MeshBasedCellPopulation::SpringIterator::operator++ 0 0% 46.31% 4416ms 6.38% VertexMesh::~VertexMesh 1452ms 2.10% 48.41% 4397ms 6.35% std::_Rb_tree::_M_get_insert_unique_pos 4019ms 5.81% 54.21% 4019ms 5.81% std::_Rb_tree::_S_right (inline) 46ms 0.066% 54.28% 3909ms 5.65% MutableElement::AddNode 3ms 0.0043% 54.28% 3856ms 5.57% TetrahedralMesh::ImportFromMesher 0 0% 54.28% 3821ms 5.52% AbstractCellPopulation::WriteResultsToFiles 102ms 0.15% 54.43% 3031ms 4.38% tetgen::tetgenmesh::insphere_sos 2673ms 3.86% 58.29% 2896ms 4.18% tetgen::insphere 0 0% 58.29% 2712ms 3.92% std::_Rb_tree::_M_drop_node (inline) 265ms 0.38% 58.68% 2695ms 3.89% std::_Rb_tree_iterator::operator++ (inline) 0 0% 58.68% 2686ms 3.88% std::_Rb_tree::_M_put_node (inline) 3ms 0.0043% 58.68% 2672ms 3.86% VertexMesh::GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex 33ms 0.048% 58.73% 2661ms 3.84% Node::~Node 4ms 0.0058% 58.73% 2649ms 3.83% VertexMesh::Clear 4ms 0.0058% 58.74% 2637ms 3.81% MeshBasedCellPopulationWithGhostNodes::WriteVtkResultsToFile 222ms 0.32% 59.06% 2378ms 3.44% tetgen::tetgenmesh::flip23 2312ms 3.34% 62.40% 2312ms 3.34% std::_Rb_tree_insert_and_rebalance 1610ms 2.33% 64.73% 2217ms 3.20% malloc_consolidate 1ms 0.0014% 64.73% 2200ms 3.18% Element::Element 2182ms 3.15% 67.88% 2182ms 3.15% [libchaste_mesh.so] 31ms 0.045% 67.93% 2148ms 3.10% std::_Vector_base::_M_deallocate (inline) 0 0% 67.93% 1988ms 2.87% std::vector::~vector (inline) 4ms 0.0058% 67.93% 1933ms 2.79% std::_Vector_base::~_Vector_base (inline) 7ms 0.01% 67.94% 1920ms 2.77% _int_free_maybe_consolidate 6ms 0.0087% 67.95% 1808ms 2.61% Element::RegisterWithNodes (inline) 61ms 0.088% 68.04% 1677ms 2.42% std::vector::_M_realloc_insert 5ms 0.0072% 68.05% 1639ms 2.37% VertexMesh::GenerateVerticesFromElementCircumcentres 1572ms 2.27% 70.32% 1625ms 2.35% tetgen::orient3d 203ms 0.29% 70.61% 1556ms 2.25% tetgen::tetgenmesh::flip32 1542ms 2.23% 72.84% 1542ms 2.23% Node::GetIndex 1480ms 2.14% 74.98% 1480ms 2.14% unlink_chunk 3ms 0.0043% 74.98% 1459ms 2.11% std::_Vector_base::_M_allocate (inline) 67ms 0.097% 75.08% 1233ms 1.78% std::vector::push_back (inline) 96ms 0.14% 75.22% 1199ms 1.73% std::map::operator[] 811ms 1.17% 76.39% 1127ms 1.63% AbstractElement::GetNodeGlobalIndex 4ms 0.0058% 76.40% 1116ms 1.61% TetrahedralMesh::Clear 211ms 0.3% 76.70% 1111ms 1.61% tetgen::tetgenmesh::enqueueflipface 24ms 0.035% 76.73% 1101ms 1.59% tetgen::tetgenmesh::locate 98ms 0.14% 76.88% 1046ms 1.51% tetgen::tetgenmesh::preciselocate 1027ms 1.48% 78.36% 1027ms 1.48% Node::rGetLocation 1ms 0.0014% 78.36% 1025ms 1.48% TetrahedralMesh::RefreshJacobianCachedData 0 0% 78.36% 1001ms 1.45% std::_Rb_tree::lower_bound (inline) 0 0% 78.36% 1001ms 1.45% std::map::lower_bound (inline) 0 0% 78.36% 955ms 1.38% VoronoiDataWriter::Visit 8ms 0.012% 78.37% 874ms 1.26% boost::numeric::ublas::c_vector::c_vector (inline) 13ms 0.019% 78.39% 859ms 1.24% Element::CalculateCircumsphere 6ms 0.0087% 78.40% 857ms 1.24% boost::numeric::ublas::vector_assign (inline) 3ms 0.0043% 78.41% 842ms 1.22% AbstractTetrahedralElement::CalculateInverseJacobian 443ms 0.64% 79.05% 821ms 1.19% AbstractElement::GetNodeLocation 3ms 0.0043% 79.05% 811ms 1.17% AbstractTwoBodyInteractionForce::AddForceContribution 10ms 0.014% 79.06% 779ms 1.13% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 11ms 0.016% 79.08% 730ms 1.05% AbstractTetrahedralElement::CalculateJacobian 615ms 0.89% 79.97% 615ms 0.89% std::vector::size (inline) 357ms 0.52% 80.48% 594ms 0.86% tetgen::tetgenmesh::sym 36ms 0.052% 80.54% 581ms 0.84% __atan2 580ms 0.84% 81.37% 580ms 0.84% tetgen::tetgenmesh::oppo 52ms 0.075% 81.45% 577ms 0.83% AbstractTetrahedralElement::RefreshJacobian 0 0% 81.45% 575ms 0.83% std::insert_iterator::operator= (inline) 0 0% 81.45% 559ms 0.81% std::set::find (inline) 8ms 0.012% 81.46% 555ms 0.8% std::vector::insert (inline) 492ms 0.71% 82.17% 541ms 0.78% __ieee754_atan2_fma 532ms 0.77% 82.94% 532ms 0.77% AbstractElement::IsDeleted 0 0% 82.94% 515ms 0.74% std::_Rb_tree::_M_insert_unique_ (inline) 94ms 0.14% 83.08% 498ms 0.72% std::_Rb_tree_iterator::operator-- (inline) 10ms 0.014% 83.09% 464ms 0.67% CellPropertyCollection::GetPropertiesType (inline) 1ms 0.0014% 83.09% 452ms 0.65% Cell::GetCellId 179ms 0.26% 83.35% 432ms 0.62% Inverse 132ms 0.19% 83.54% 429ms 0.62% _int_free_merge_chunk 105ms 0.15% 83.69% 412ms 0.6% __dynamic_cast 13ms 0.019% 83.71% 407ms 0.59% VertexMesh::CalculateUnitNormalToFaceWithArea 4ms 0.0058% 83.72% 391ms 0.56% AbstractTetrahedralElement::AbstractTetrahedralElement 386ms 0.56% 84.28% 386ms 0.56% std::_Rb_tree_decrement 385ms 0.56% 84.83% 385ms 0.56% boost::numeric::ublas::c_vector::operator() 0 0% 84.83% 383ms 0.55% VertexMeshWriter::WriteVtkUsingMesh 0 0% 84.83% 374ms 0.54% boost::numeric::ublas::inner_prod (inline) 23ms 0.033% 84.87% 372ms 0.54% boost::numeric::ublas::vector_scalar_binary::evaluate 0 0% 84.87% 372ms 0.54% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 39ms 0.056% 84.92% 358ms 0.52% tetgen::tetgenmesh::enext2fnext 0 0% 84.92% 352ms 0.51% tcache_get (inline) 352ms 0.51% 85.43% 352ms 0.51% tcache_get_n (inline) 60ms 0.087% 85.52% 347ms 0.5% tetgen::tetgenmesh::queue::push