File: Test3dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 43111ms, 85.51% of 50414ms total Dropped 825 nodes (cum <= 252.07ms) flat flat% sum% cum cum% 0 0% 0% 50374ms 99.92% __libc_start_call_main 0 0% 0% 50374ms 99.92% __libc_start_main_impl 0 0% 0% 50374ms 99.92% _start 0 0% 0% 50360ms 99.89% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 50360ms 99.89% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 50360ms 99.89% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 50360ms 99.89% main 0 0% 0% 50327ms 99.83% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 50327ms 99.83% CxxTest::TestRunner::runTest (inline) 0 0% 0% 50327ms 99.83% Test3dTissueRepresentativeSimulation::Test3DHoneycombMeshWithGhostNodes 1ms 0.002% 0.002% 50137ms 99.45% AbstractCellBasedSimulation::Solve 0 0% 0.002% 41794ms 82.90% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0.002% 41740ms 82.79% MeshBasedCellPopulation::Update 0 0% 0.002% 25408ms 50.40% MeshBasedCellPopulation::TessellateIfNeeded 0 0% 0.002% 25407ms 50.40% MeshBasedCellPopulation::CreateVoronoiTessellation (inline) 204ms 0.4% 0.41% 23043ms 45.71% VertexMesh::VertexMesh 0 0% 0.41% 12750ms 25.29% MutableMesh::ReMesh 456ms 0.9% 1.31% 11266ms 22.35% TetrahedralMesh::EdgeIterator::operator++ 0 0% 1.31% 9614ms 19.07% tetgen::tetrahedralize 0 0% 1.31% 9520ms 18.88% tetgen::tetgenmesh::delaunizevertices 7ms 0.014% 1.33% 9516ms 18.88% tetgen::tetgenmesh::incrflipdelaunay 37ms 0.073% 1.40% 9466ms 18.78% std::set::insert (inline) 122ms 0.24% 1.64% 8956ms 17.76% std::_Rb_tree::_M_insert_unique 3609ms 7.16% 8.80% 8891ms 17.64% std::_Rb_tree::_M_lower_bound (inline) 255ms 0.51% 9.30% 8846ms 17.55% VertexElement::AddFace 200ms 0.4% 9.70% 8523ms 16.91% std::_Rb_tree::find (inline) 396ms 0.79% 10.49% 8399ms 16.66% tetgen::tetgenmesh::lawson 0 0% 10.49% 7988ms 15.84% std::set::count (inline) 246ms 0.49% 10.98% 5982ms 11.87% std::_Rb_tree::_M_insert_ (inline) 182ms 0.36% 11.34% 5813ms 11.53% operator new 1883ms 3.74% 15.07% 5568ms 11.04% __GI___libc_malloc 82ms 0.16% 15.23% 5078ms 10.07% std::__new_allocator::allocate (inline) 0 0% 15.23% 5062ms 10.04% std::allocator_traits::allocate (inline) 0 0% 15.23% 4920ms 9.76% OffLatticeSimulation::UpdateCellLocationsAndTopology 1ms 0.002% 15.24% 4795ms 9.51% ForwardEulerNumericalMethod::UpdateAllNodePositions 4ms 0.0079% 15.24% 4775ms 9.47% AbstractNumericalMethod::ComputeForcesIncludingDamping 4669ms 9.26% 24.51% 4669ms 9.26% std::_Rb_tree_increment 4627ms 9.18% 33.68% 4627ms 9.18% std::operator< (inline) 64ms 0.13% 33.81% 4615ms 9.15% std::less::operator() (inline) 0 0% 33.81% 4179ms 8.29% std::_Rb_tree::_M_create_node (inline) 0 0% 33.81% 4165ms 8.26% std::_Rb_tree::_M_get_node (inline) 0 0% 33.81% 4137ms 8.21% std::_Rb_tree::_Alloc_node::operator() (inline) 4ms 0.0079% 33.82% 3892ms 7.72% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 3ms 0.006% 33.82% 3865ms 7.67% MeshBasedCellPopulation::UpdateNodePairs 17ms 0.034% 33.86% 3766ms 7.47% MeshBasedCellPopulation::SpringIterator::operator++ 3ms 0.006% 33.86% 3712ms 7.36% std::set_intersection (inline) 225ms 0.45% 34.31% 3709ms 7.36% std::__set_intersection 592ms 1.17% 35.48% 3655ms 7.25% __GI___libc_free 2774ms 5.50% 40.99% 3354ms 6.65% _int_malloc 66ms 0.13% 41.12% 3337ms 6.62% std::__new_allocator::deallocate (inline) 0 0% 41.12% 3318ms 6.58% std::allocator_traits::deallocate (inline) 0 0% 41.12% 3282ms 6.51% AbstractCellPopulation::WriteResultsToFiles 1079ms 2.14% 43.26% 3159ms 6.27% std::_Rb_tree::_M_get_insert_unique_pos 19ms 0.038% 43.30% 3085ms 6.12% std::_Rb_tree::~_Rb_tree (inline) 0 0% 43.30% 3055ms 6.06% std::set::~set (inline) 728ms 1.44% 44.74% 3050ms 6.05% std::_Rb_tree::_M_erase 1532ms 3.04% 47.78% 3042ms 6.03% _int_free 230ms 0.46% 48.23% 2954ms 5.86% std::_Rb_tree_const_iterator::operator++ (inline) 38ms 0.075% 48.31% 2928ms 5.81% Node::AddElement 2703ms 5.36% 53.67% 2703ms 5.36% std::_Rb_tree::_S_right (inline) 76ms 0.15% 53.82% 2577ms 5.11% tetgen::tetgenmesh::insphere_sos 2287ms 4.54% 58.36% 2479ms 4.92% tetgen::insphere 213ms 0.42% 58.78% 2430ms 4.82% std::_Rb_tree_iterator::operator++ (inline) 0 0% 58.78% 2414ms 4.79% VertexMesh::GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex 0 0% 58.78% 2380ms 4.72% VertexMesh::~VertexMesh 2ms 0.004% 58.79% 2355ms 4.67% TetrahedralMesh::ImportFromMesher 2ms 0.004% 58.79% 2342ms 4.65% MeshBasedCellPopulationWithGhostNodes::WriteVtkResultsToFile 46ms 0.091% 58.88% 2119ms 4.20% MutableElement::AddNode 222ms 0.44% 59.32% 2043ms 4.05% tetgen::tetgenmesh::flip23 0 0% 59.32% 1992ms 3.95% std::_Rb_tree::_M_drop_node (inline) 0 0% 59.32% 1973ms 3.91% std::_Rb_tree::_M_put_node (inline) 1790ms 3.55% 62.87% 1790ms 3.55% [libchaste_mesh.so] 1670ms 3.31% 66.18% 1670ms 3.31% std::_Rb_tree_insert_and_rebalance 3ms 0.006% 66.19% 1496ms 2.97% Element::Element 192ms 0.38% 66.57% 1373ms 2.72% tetgen::tetgenmesh::flip32 16ms 0.032% 66.60% 1361ms 2.70% std::_Vector_base::_M_deallocate (inline) 758ms 1.50% 68.11% 1325ms 2.63% malloc_consolidate 1279ms 2.54% 70.64% 1320ms 2.62% tetgen::orient3d 6ms 0.012% 70.65% 1307ms 2.59% VertexMesh::Clear 12ms 0.024% 70.68% 1285ms 2.55% Node::~Node 4ms 0.0079% 70.69% 1233ms 2.45% Element::RegisterWithNodes (inline) 0 0% 70.69% 1221ms 2.42% std::vector::~vector (inline) 0 0% 70.69% 1185ms 2.35% std::_Vector_base::~_Vector_base (inline) 7ms 0.014% 70.70% 1163ms 2.31% _int_free_maybe_consolidate 86ms 0.17% 70.87% 1049ms 2.08% std::map::operator[] 46ms 0.091% 70.96% 1035ms 2.05% std::vector::_M_realloc_insert 1022ms 2.03% 72.99% 1022ms 2.03% Node::GetIndex 27ms 0.054% 73.04% 921ms 1.83% tetgen::tetgenmesh::locate 172ms 0.34% 73.38% 915ms 1.81% tetgen::tetgenmesh::enqueueflipface 5ms 0.0099% 73.39% 902ms 1.79% std::_Vector_base::_M_allocate (inline) 1ms 0.002% 73.40% 884ms 1.75% VertexMesh::GenerateVerticesFromElementCircumcentres 0 0% 73.40% 871ms 1.73% std::_Rb_tree::lower_bound (inline) 0 0% 73.40% 871ms 1.73% std::map::lower_bound (inline) 869ms 1.72% 75.12% 869ms 1.72% unlink_chunk 66ms 0.13% 75.25% 863ms 1.71% tetgen::tetgenmesh::preciselocate 52ms 0.1% 75.35% 824ms 1.63% std::vector::push_back (inline) 1ms 0.002% 75.36% 769ms 1.53% TetrahedralMesh::RefreshJacobianCachedData 0 0% 75.36% 762ms 1.51% VoronoiDataWriter::Visit 2ms 0.004% 75.36% 702ms 1.39% AbstractTetrahedralElement::CalculateInverseJacobian 1ms 0.002% 75.36% 674ms 1.34% AbstractTwoBodyInteractionForce::AddForceContribution 366ms 0.73% 76.09% 657ms 1.30% AbstractElement::GetNodeGlobalIndex 9ms 0.018% 76.11% 647ms 1.28% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 6ms 0.012% 76.12% 570ms 1.13% AbstractTetrahedralElement::CalculateJacobian 2ms 0.004% 76.12% 550ms 1.09% TetrahedralMesh::Clear 4ms 0.0079% 76.13% 549ms 1.09% boost::numeric::ublas::vector_assign (inline) 0 0% 76.13% 531ms 1.05% std::set::find (inline) 529ms 1.05% 77.18% 529ms 1.05% Node::rGetLocation 6ms 0.012% 77.19% 516ms 1.02% boost::numeric::ublas::c_vector::c_vector (inline) 260ms 0.52% 77.71% 515ms 1.02% AbstractElement::GetNodeLocation 309ms 0.61% 78.32% 512ms 1.02% tetgen::tetgenmesh::sym 93ms 0.18% 78.50% 477ms 0.95% std::_Rb_tree_iterator::operator-- (inline) 0 0% 78.50% 474ms 0.94% std::insert_iterator::operator= (inline) 465ms 0.92% 79.43% 465ms 0.92% std::vector::size (inline) 18ms 0.036% 79.46% 462ms 0.92% __atan2 460ms 0.91% 80.37% 460ms 0.91% tetgen::tetgenmesh::oppo 399ms 0.79% 81.17% 441ms 0.87% __ieee754_atan2_fma 0 0% 81.17% 439ms 0.87% std::_Rb_tree::_M_insert_unique_ (inline) 18ms 0.036% 81.20% 419ms 0.83% AbstractTetrahedralElement::RefreshJacobian 2ms 0.004% 81.21% 415ms 0.82% Element::CalculateCircumsphere 1ms 0.002% 81.21% 376ms 0.75% Cell::GetCellId 5ms 0.0099% 81.22% 366ms 0.73% CellPropertyCollection::GetPropertiesType (inline) 364ms 0.72% 81.94% 364ms 0.72% std::_Rb_tree_decrement 0 0% 81.94% 353ms 0.7% boost::numeric::ublas::inner_prod (inline) 20ms 0.04% 81.98% 353ms 0.7% boost::numeric::ublas::vector_scalar_binary::evaluate 0 0% 81.98% 353ms 0.7% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 157ms 0.31% 82.29% 352ms 0.7% Inverse 328ms 0.65% 82.94% 328ms 0.65% boost::numeric::ublas::c_vector::operator() 14ms 0.028% 82.97% 324ms 0.64% std::vector::insert (inline) 86ms 0.17% 83.14% 320ms 0.63% __dynamic_cast 0 0% 83.14% 319ms 0.63% VertexMeshWriter::WriteVtkUsingMesh 26ms 0.052% 83.19% 306ms 0.61% tetgen::tetgenmesh::enext2fnext 87ms 0.17% 83.36% 299ms 0.59% boost::numeric::ublas::vector_inner_prod::apply (inline) 15ms 0.03% 83.39% 284ms 0.56% boost::numeric::ublas::vector_reference::operator() (inline) 8ms 0.016% 83.41% 279ms 0.55% AbstractCellProperty::IsSubType (inline) 238ms 0.47% 83.88% 279ms 0.55% tetgen::tetgenmesh::fnextself 160ms 0.32% 84.20% 278ms 0.55% tetgen::tetgenmesh::bond 20ms 0.04% 84.24% 268ms 0.53% tetgen::tetgenmesh::enextfnext 42ms 0.083% 84.32% 268ms 0.53% tetgen::tetgenmesh::queue::push 8ms 0.016% 84.34% 266ms 0.53% VertexMesh::CalculateUnitNormalToFaceWithArea 0 0% 84.34% 265ms 0.53% tcache_get (inline) 265ms 0.53% 84.86% 265ms 0.53% tcache_get_n (inline) 3ms 0.006% 84.87% 261ms 0.52% AbstractTetrahedralElement::AbstractTetrahedralElement 63ms 0.12% 84.99% 261ms 0.52% boost::numeric::ublas::indexing_vector_assign 5ms 0.0099% 85.00% 260ms 0.52% boost::numeric::ublas::c_vector::operator= (inline) 257ms 0.51% 85.51% 257ms 0.51% tetgen::tetgenmesh::triface::triface