File: Test3dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 50081ms, 87.39% of 57309ms total Dropped 874 nodes (cum <= 286.55ms) flat flat% sum% cum cum% 0 0% 0% 57234ms 99.87% __libc_start_call_main 0 0% 0% 57234ms 99.87% __libc_start_main_impl 0 0% 0% 57234ms 99.87% _start 0 0% 0% 57220ms 99.84% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 57220ms 99.84% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 57220ms 99.84% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 57220ms 99.84% main 0 0% 0% 57183ms 99.78% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 57183ms 99.78% CxxTest::TestRunner::runTest (inline) 0 0% 0% 57183ms 99.78% Test3dTissueRepresentativeSimulation::Test3DHoneycombMeshWithGhostNodes 0 0% 0% 56936ms 99.35% AbstractCellBasedSimulation::Solve 0 0% 0% 48306ms 84.29% AbstractCellBasedSimulation::UpdateCellPopulation 1ms 0.0017% 0.0017% 48255ms 84.20% MeshBasedCellPopulation::Update 0 0% 0.0017% 27606ms 48.17% MeshBasedCellPopulation::TessellateIfNeeded 0 0% 0.0017% 27605ms 48.17% MeshBasedCellPopulation::CreateVoronoiTessellation (inline) 206ms 0.36% 0.36% 24368ms 42.52% VertexMesh::VertexMesh 0 0% 0.36% 16893ms 29.48% MutableMesh::ReMesh 0 0% 0.36% 12756ms 22.26% tetgen::tetrahedralize 1ms 0.0017% 0.36% 12622ms 22.02% tetgen::tetgenmesh::delaunizevertices 6ms 0.01% 0.37% 12620ms 22.02% tetgen::tetgenmesh::incrflipdelaunay 571ms 1% 1.37% 11490ms 20.05% TetrahedralMesh::EdgeIterator::operator++ 530ms 0.92% 2.29% 11239ms 19.61% tetgen::tetgenmesh::lawson 34ms 0.059% 2.35% 10016ms 17.48% std::set::insert (inline) 225ms 0.39% 2.75% 9482ms 16.55% std::_Rb_tree::_M_insert_unique 359ms 0.63% 3.37% 9251ms 16.14% VertexElement::AddFace 3009ms 5.25% 8.62% 8637ms 15.07% std::_Rb_tree::_M_lower_bound (inline) 235ms 0.41% 9.03% 8119ms 14.17% std::_Rb_tree::find (inline) 0 0% 9.03% 7581ms 13.23% std::set::count (inline) 257ms 0.45% 9.48% 5746ms 10.03% std::_Rb_tree::_M_insert_ (inline) 114ms 0.2% 9.68% 5549ms 9.68% std::less::operator() (inline) 5510ms 9.61% 19.30% 5510ms 9.61% std::operator< (inline) 232ms 0.4% 19.70% 5103ms 8.90% operator new 1ms 0.0017% 19.70% 5078ms 8.86% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 19.70% 4972ms 8.68% ForwardEulerNumericalMethod::UpdateAllNodePositions 0 0% 19.70% 4944ms 8.63% AbstractNumericalMethod::ComputeForcesIncludingDamping 1164ms 2.03% 21.73% 4808ms 8.39% __GI___libc_malloc 4574ms 7.98% 29.71% 4574ms 7.98% std::_Rb_tree_increment 38ms 0.066% 29.78% 4359ms 7.61% std::__new_allocator::allocate (inline) 0 0% 29.78% 4337ms 7.57% std::allocator_traits::allocate (inline) 7ms 0.012% 29.79% 4212ms 7.35% std::_Rb_tree::~_Rb_tree (inline) 1568ms 2.74% 32.53% 4203ms 7.33% std::_Rb_tree::_M_erase 0 0% 32.53% 4159ms 7.26% std::set::~set (inline) 4ms 0.007% 32.54% 4098ms 7.15% MeshBasedCellPopulation::UpdateNodePairs 5ms 0.0087% 32.54% 4060ms 7.08% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 13ms 0.023% 32.57% 3955ms 6.90% MeshBasedCellPopulation::SpringIterator::operator++ 1188ms 2.07% 34.64% 3866ms 6.75% std::_Rb_tree::_M_get_insert_unique_pos 1160ms 2.02% 36.66% 3833ms 6.69% __GI___libc_free 271ms 0.47% 37.14% 3635ms 6.34% std::__set_intersection 0 0% 37.14% 3635ms 6.34% std::set_intersection (inline) 0 0% 37.14% 3597ms 6.28% std::_Rb_tree::_M_create_node (inline) 115ms 0.2% 37.34% 3572ms 6.23% tetgen::tetgenmesh::insphere_sos 28ms 0.049% 37.39% 3567ms 6.22% Node::AddElement 0 0% 37.39% 3562ms 6.22% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 37.39% 3562ms 6.22% std::_Rb_tree::_M_get_node (inline) 138ms 0.24% 37.63% 3484ms 6.08% std::__new_allocator::deallocate (inline) 0 0% 37.63% 3471ms 6.06% std::allocator_traits::deallocate (inline) 3155ms 5.51% 43.13% 3446ms 6.01% tetgen::insphere 0 0% 43.13% 3396ms 5.93% AbstractCellPopulation::WriteResultsToFiles 11ms 0.019% 43.15% 3349ms 5.84% TetrahedralMesh::ImportFromMesher 2459ms 4.29% 47.44% 3254ms 5.68% _int_malloc 0 0% 47.44% 3253ms 5.68% VertexMesh::~VertexMesh 3120ms 5.44% 52.89% 3120ms 5.44% std::_Rb_tree::_S_right (inline) 198ms 0.35% 53.23% 2875ms 5.02% std::_Rb_tree_const_iterator::operator++ (inline) 216ms 0.38% 53.61% 2772ms 4.84% tetgen::tetgenmesh::flip23 70ms 0.12% 53.73% 2724ms 4.75% MutableElement::AddNode 1232ms 2.15% 55.88% 2672ms 4.66% _int_free 182ms 0.32% 56.20% 2342ms 4.09% Node::~Node 3ms 0.0052% 56.20% 2248ms 3.92% MeshBasedCellPopulationWithGhostNodes::WriteVtkResultsToFile 233ms 0.41% 56.61% 2225ms 3.88% VertexMesh::GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex 179ms 0.31% 56.92% 2091ms 3.65% VertexMesh::Clear 0 0% 56.92% 2017ms 3.52% std::_Rb_tree::_M_drop_node (inline) 0 0% 56.92% 2008ms 3.50% std::_Rb_tree::_M_put_node (inline) 3ms 0.0052% 56.93% 2003ms 3.50% std::_Rb_tree_iterator::operator++ (inline) 1984ms 3.46% 60.39% 1984ms 3.46% std::_Rb_tree_insert_and_rebalance 160ms 0.28% 60.67% 1820ms 3.18% tetgen::tetgenmesh::flip32 4ms 0.007% 60.68% 1650ms 2.88% Element::Element 19ms 0.033% 60.71% 1482ms 2.59% std::_Vector_base::_M_deallocate (inline) 1448ms 2.53% 63.24% 1448ms 2.53% Node::GetIndex 977ms 1.70% 64.94% 1447ms 2.52% malloc_consolidate 0 0% 64.94% 1360ms 2.37% std::vector::~vector (inline) 215ms 0.38% 65.32% 1356ms 2.37% TetrahedralMesh::Clear 1262ms 2.20% 67.52% 1346ms 2.35% tetgen::orient3d 2ms 0.0035% 67.52% 1323ms 2.31% Element::RegisterWithNodes (inline) 181ms 0.32% 67.84% 1291ms 2.25% tetgen::tetgenmesh::enqueueflipface 0 0% 67.84% 1277ms 2.23% std::_Vector_base::~_Vector_base (inline) 3ms 0.0052% 67.84% 1244ms 2.17% _int_free_maybe_consolidate 38ms 0.066% 67.91% 1160ms 2.02% tetgen::tetgenmesh::locate 91ms 0.16% 68.07% 1077ms 1.88% tetgen::tetgenmesh::preciselocate 69ms 0.12% 68.19% 1060ms 1.85% std::map::operator[] 53ms 0.092% 68.28% 1051ms 1.83% std::vector::_M_realloc_insert 989ms 1.73% 70.01% 989ms 1.73% unlink_chunk 6ms 0.01% 70.02% 933ms 1.63% VertexMesh::GenerateVerticesFromElementCircumcentres 0 0% 70.02% 923ms 1.61% std::_Rb_tree::lower_bound (inline) 0 0% 70.02% 923ms 1.61% std::map::lower_bound (inline) 0 0% 70.02% 914ms 1.59% VoronoiDataWriter::Visit 893ms 1.56% 71.58% 893ms 1.56% tetgen::tetgenmesh::triface::triface 710ms 1.24% 72.81% 862ms 1.50% AbstractElement::GetNodeGlobalIndex 82ms 0.14% 72.96% 818ms 1.43% std::vector::push_back (inline) 3ms 0.0052% 72.96% 778ms 1.36% std::_Vector_base::_M_allocate (inline) 2ms 0.0035% 72.97% 763ms 1.33% TetrahedralMesh::RefreshJacobianCachedData 395ms 0.69% 73.66% 753ms 1.31% tetgen::tetgenmesh::fnextself 1ms 0.0017% 73.66% 721ms 1.26% AbstractTwoBodyInteractionForce::AddForceContribution 682ms 1.19% 74.85% 682ms 1.19% tetgen::tetgenmesh::oppo 14ms 0.024% 74.87% 679ms 1.18% AbstractTetrahedralElement::CalculateInverseJacobian 16ms 0.028% 74.90% 674ms 1.18% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 17ms 0.03% 74.93% 665ms 1.16% boost::numeric::ublas::vector_assign (inline) 9ms 0.016% 74.94% 633ms 1.10% boost::numeric::ublas::c_vector::c_vector (inline) 280ms 0.49% 75.43% 631ms 1.10% AbstractElement::GetNodeLocation 10ms 0.017% 75.45% 623ms 1.09% AbstractTetrahedralElement::CalculateJacobian 613ms 1.07% 76.52% 613ms 1.07% [libchaste_mesh.so] 46ms 0.08% 76.60% 597ms 1.04% __atan2 552ms 0.96% 77.56% 552ms 0.96% tetgen::tetgenmesh::triface::operator= 438ms 0.76% 78.33% 551ms 0.96% __ieee754_atan2_fma 0 0% 78.33% 532ms 0.93% std::set::find (inline) 0 0% 78.33% 515ms 0.9% std::insert_iterator::operator= (inline) 497ms 0.87% 79.20% 497ms 0.87% Node::rGetLocation 41ms 0.072% 79.27% 495ms 0.86% tetgen::tetgenmesh::enextfnext 494ms 0.86% 80.13% 494ms 0.86% std::vector::size (inline) 44ms 0.077% 80.21% 491ms 0.86% tetgen::tetgenmesh::enext2fnext 0 0% 80.21% 488ms 0.85% boost::numeric::ublas::inner_prod (inline) 7ms 0.012% 80.22% 487ms 0.85% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 486ms 0.85% 81.07% 486ms 0.85% AbstractElement::IsDeleted 35ms 0.061% 81.13% 481ms 0.84% AbstractTetrahedralElement::RefreshJacobian 28ms 0.049% 81.18% 480ms 0.84% boost::numeric::ublas::vector_scalar_binary::evaluate 1ms 0.0017% 81.18% 474ms 0.83% std::_Rb_tree::_M_insert_unique_ (inline) 20ms 0.035% 81.21% 466ms 0.81% Element::CalculateCircumsphere 120ms 0.21% 81.42% 440ms 0.77% boost::numeric::ublas::indexing_vector_assign 17ms 0.03% 81.45% 417ms 0.73% VertexMesh::CalculateUnitNormalToFaceWithArea 279ms 0.49% 81.94% 411ms 0.72% tetgen::tetgenmesh::sym 23ms 0.04% 81.98% 410ms 0.72% tetgen::tetgenmesh::queue::push 403ms 0.7% 82.68% 403ms 0.7% boost::numeric::ublas::c_vector::operator() 3ms 0.0052% 82.69% 402ms 0.7% CellPropertyCollection::GetPropertiesType (inline) 0 0% 82.69% 401ms 0.7% VertexMeshWriter::WriteVtkUsingMesh 190ms 0.33% 83.02% 400ms 0.7% boost::numeric::ublas::vector_inner_prod::apply (inline) 4ms 0.007% 83.03% 391ms 0.68% boost::numeric::ublas::c_vector::operator= (inline) 219ms 0.38% 83.41% 387ms 0.68% AbstractTetrahedralMesh::GetElement 98ms 0.17% 83.58% 387ms 0.68% __dynamic_cast 21ms 0.037% 83.62% 385ms 0.67% std::_Rb_tree_iterator::operator-- (inline) 262ms 0.46% 84.07% 383ms 0.67% tetgen::tetgenmesh::link::add 284ms 0.5% 84.57% 382ms 0.67% tetgen::tetgenmesh::bond 1ms 0.0017% 84.57% 371ms 0.65% Cell::GetCellId 365ms 0.64% 85.21% 365ms 0.64% tetgen::tetgenmesh::org 14ms 0.024% 85.23% 349ms 0.61% std::vector::insert (inline) 0 0% 85.23% 348ms 0.61% tcache_get (inline) 348ms 0.61% 85.84% 348ms 0.61% tcache_get_n (inline) 341ms 0.6% 86.43% 341ms 0.6% std::_Rb_tree_decrement 4ms 0.007% 86.44% 324ms 0.57% AbstractCellProperty::IsSubType (inline) 4ms 0.007% 86.45% 324ms 0.57% AbstractTetrahedralElement::AbstractTetrahedralElement 49ms 0.086% 86.53% 312ms 0.54% boost::numeric::ublas::vector_reference::operator() (inline) 143ms 0.25% 86.78% 310ms 0.54% Inverse 9ms 0.016% 86.80% 304ms 0.53% VertexElement::~VertexElement 0 0% 86.80% 300ms 0.52% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 6ms 0.01% 86.81% 295ms 0.51% VertexMesh::GetVolumeOfElement 44ms 0.077% 86.89% 291ms 0.51% tetgen::insphereadapt 288ms 0.5% 87.39% 288ms 0.5% tetgen::tetgenmesh::pointmark