File: Test3dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 47229ms, 86.49% of 54607ms total Dropped 869 nodes (cum <= 273.04ms) flat flat% sum% cum cum% 0 0% 0% 54543ms 99.88% __libc_start_call_main 0 0% 0% 54543ms 99.88% __libc_start_main_impl 0 0% 0% 54543ms 99.88% _start 0 0% 0% 54529ms 99.86% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 54529ms 99.86% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 54529ms 99.86% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 54529ms 99.86% main 0 0% 0% 54494ms 99.79% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 54494ms 99.79% CxxTest::TestRunner::runTest (inline) 0 0% 0% 54494ms 99.79% Test3dTissueRepresentativeSimulation::Test3DHoneycombMeshWithGhostNodes 0 0% 0% 54241ms 99.33% AbstractCellBasedSimulation::Solve 0 0% 0% 45885ms 84.03% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 45849ms 83.96% MeshBasedCellPopulation::Update 0 0% 0% 25605ms 46.89% MeshBasedCellPopulation::CreateVoronoiTessellation (inline) 0 0% 0% 25605ms 46.89% MeshBasedCellPopulation::TessellateIfNeeded 167ms 0.31% 0.31% 22746ms 41.65% VertexMesh::VertexMesh 0 0% 0.31% 16633ms 30.46% MutableMesh::ReMesh 0 0% 0.31% 12766ms 23.38% tetgen::tetrahedralize 4ms 0.0073% 0.31% 12632ms 23.13% tetgen::tetgenmesh::delaunizevertices 9ms 0.016% 0.33% 12622ms 23.11% tetgen::tetgenmesh::incrflipdelaunay 568ms 1.04% 1.37% 11210ms 20.53% tetgen::tetgenmesh::lawson 556ms 1.02% 2.39% 11090ms 20.31% TetrahedralMesh::EdgeIterator::operator++ 31ms 0.057% 2.44% 9281ms 17.00% std::set::insert (inline) 205ms 0.38% 2.82% 8798ms 16.11% std::_Rb_tree::_M_insert_unique 361ms 0.66% 3.48% 8786ms 16.09% VertexElement::AddFace 3013ms 5.52% 9.00% 8393ms 15.37% std::_Rb_tree::_M_lower_bound (inline) 243ms 0.44% 9.44% 7901ms 14.47% std::_Rb_tree::find (inline) 0 0% 9.44% 7318ms 13.40% std::set::count (inline) 276ms 0.51% 9.95% 5343ms 9.78% std::_Rb_tree::_M_insert_ (inline) 116ms 0.21% 10.16% 5235ms 9.59% std::less::operator() (inline) 5176ms 9.48% 19.64% 5176ms 9.48% std::operator< (inline) 0 0% 19.64% 4948ms 9.06% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 19.64% 4829ms 8.84% ForwardEulerNumericalMethod::UpdateAllNodePositions 1ms 0.0018% 19.64% 4800ms 8.79% AbstractNumericalMethod::ComputeForcesIncludingDamping 179ms 0.33% 19.97% 4580ms 8.39% operator new 1037ms 1.90% 21.87% 4306ms 7.89% __GI___libc_malloc 4203ms 7.70% 29.57% 4203ms 7.70% std::_Rb_tree_increment 3ms 0.0055% 29.57% 3954ms 7.24% MeshBasedCellPopulation::UpdateNodePairs 37ms 0.068% 29.64% 3954ms 7.24% std::__new_allocator::allocate (inline) 5ms 0.0092% 29.65% 3939ms 7.21% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 0 0% 29.65% 3935ms 7.21% std::allocator_traits::allocate (inline) 6ms 0.011% 29.66% 3934ms 7.20% std::_Rb_tree::~_Rb_tree (inline) 1488ms 2.72% 32.38% 3928ms 7.19% std::_Rb_tree::_M_erase 0 0% 32.38% 3869ms 7.09% std::set::~set (inline) 11ms 0.02% 32.40% 3828ms 7.01% MeshBasedCellPopulation::SpringIterator::operator++ 1212ms 2.22% 34.62% 3545ms 6.49% std::_Rb_tree::_M_get_insert_unique_pos 113ms 0.21% 34.83% 3523ms 6.45% tetgen::tetgenmesh::insphere_sos 1122ms 2.05% 36.89% 3509ms 6.43% __GI___libc_free 3101ms 5.68% 42.56% 3391ms 6.21% tetgen::insphere 0 0% 42.56% 3260ms 5.97% AbstractCellPopulation::WriteResultsToFiles 0 0% 42.56% 3231ms 5.92% std::_Rb_tree::_M_create_node (inline) 0 0% 42.56% 3204ms 5.87% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 42.56% 3201ms 5.86% std::_Rb_tree::_M_get_node (inline) 215ms 0.39% 42.96% 3196ms 5.85% std::__set_intersection 0 0% 42.96% 3196ms 5.85% std::set_intersection (inline) 13ms 0.024% 42.98% 3110ms 5.70% TetrahedralMesh::ImportFromMesher 125ms 0.23% 43.21% 3099ms 5.68% std::__new_allocator::deallocate (inline) 33ms 0.06% 43.27% 3096ms 5.67% Node::AddElement 0 0% 43.27% 3081ms 5.64% std::allocator_traits::deallocate (inline) 2211ms 4.05% 47.32% 2933ms 5.37% _int_malloc 0 0% 47.32% 2880ms 5.27% VertexMesh::~VertexMesh 2797ms 5.12% 52.44% 2797ms 5.12% std::_Rb_tree::_S_right (inline) 190ms 0.35% 52.79% 2738ms 5.01% tetgen::tetgenmesh::flip23 174ms 0.32% 53.11% 2564ms 4.70% std::_Rb_tree_const_iterator::operator++ (inline) 79ms 0.14% 53.25% 2425ms 4.44% MutableElement::AddNode 1150ms 2.11% 55.36% 2381ms 4.36% _int_free 0 0% 55.36% 2153ms 3.94% MeshBasedCellPopulationWithGhostNodes::WriteVtkResultsToFile 148ms 0.27% 55.63% 2145ms 3.93% Node::~Node 199ms 0.36% 55.99% 2127ms 3.90% VertexMesh::GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex 149ms 0.27% 56.27% 1941ms 3.55% VertexMesh::Clear 1ms 0.0018% 56.27% 1935ms 3.54% std::_Rb_tree_iterator::operator++ (inline) 1922ms 3.52% 59.79% 1922ms 3.52% std::_Rb_tree_insert_and_rebalance 0 0% 59.79% 1866ms 3.42% std::_Rb_tree::_M_drop_node (inline) 0 0% 59.79% 1856ms 3.40% std::_Rb_tree::_M_put_node (inline) 142ms 0.26% 60.05% 1808ms 3.31% tetgen::tetgenmesh::flip32 4ms 0.0073% 60.06% 1466ms 2.68% Element::Element 1389ms 2.54% 62.60% 1463ms 2.68% tetgen::orient3d 188ms 0.34% 62.94% 1328ms 2.43% TetrahedralMesh::Clear 165ms 0.3% 63.25% 1272ms 2.33% tetgen::tetgenmesh::enqueueflipface 15ms 0.027% 63.27% 1240ms 2.27% std::_Vector_base::_M_deallocate (inline) 37ms 0.068% 63.34% 1200ms 2.20% tetgen::tetgenmesh::locate 772ms 1.41% 64.76% 1176ms 2.15% malloc_consolidate 1ms 0.0018% 64.76% 1166ms 2.14% std::vector::~vector (inline) 1165ms 2.13% 66.89% 1165ms 2.13% Node::GetIndex 1ms 0.0018% 66.89% 1147ms 2.10% Element::RegisterWithNodes (inline) 90ms 0.16% 67.06% 1125ms 2.06% tetgen::tetgenmesh::preciselocate 1ms 0.0018% 67.06% 1042ms 1.91% std::_Vector_base::~_Vector_base (inline) 57ms 0.1% 67.16% 1030ms 1.89% std::map::operator[] 10ms 0.018% 67.18% 1026ms 1.88% _int_free_maybe_consolidate 52ms 0.095% 67.28% 1003ms 1.84% std::vector::_M_realloc_insert 934ms 1.71% 68.99% 934ms 1.71% tetgen::tetgenmesh::triface::triface 0 0% 68.99% 915ms 1.68% std::_Rb_tree::lower_bound (inline) 0 0% 68.99% 915ms 1.68% std::map::lower_bound (inline) 902ms 1.65% 70.64% 902ms 1.65% unlink_chunk 1ms 0.0018% 70.64% 877ms 1.61% VoronoiDataWriter::Visit 127ms 0.23% 70.87% 829ms 1.52% std::vector::push_back (inline) 5ms 0.0092% 70.88% 823ms 1.51% VertexMesh::GenerateVerticesFromElementCircumcentres 633ms 1.16% 72.04% 775ms 1.42% AbstractElement::GetNodeGlobalIndex 387ms 0.71% 72.75% 754ms 1.38% tetgen::tetgenmesh::fnextself 2ms 0.0037% 72.75% 736ms 1.35% std::_Vector_base::_M_allocate (inline) 0 0% 72.75% 730ms 1.34% TetrahedralMesh::RefreshJacobianCachedData 0 0% 72.75% 716ms 1.31% AbstractTwoBodyInteractionForce::AddForceContribution 13ms 0.024% 72.78% 677ms 1.24% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 12ms 0.022% 72.80% 674ms 1.23% AbstractTetrahedralElement::CalculateInverseJacobian 665ms 1.22% 74.02% 665ms 1.22% [libchaste_mesh.so] 639ms 1.17% 75.19% 639ms 1.17% tetgen::tetgenmesh::oppo 64ms 0.12% 75.31% 638ms 1.17% __atan2 20ms 0.037% 75.34% 630ms 1.15% AbstractTetrahedralElement::CalculateJacobian 13ms 0.024% 75.37% 613ms 1.12% boost::numeric::ublas::vector_assign (inline) 17ms 0.031% 75.40% 594ms 1.09% boost::numeric::ublas::c_vector::c_vector (inline) 0 0% 75.40% 579ms 1.06% std::set::find (inline) 462ms 0.85% 76.24% 574ms 1.05% __ieee754_atan2_fma 230ms 0.42% 76.66% 549ms 1.01% AbstractElement::GetNodeLocation 519ms 0.95% 77.61% 519ms 0.95% tetgen::tetgenmesh::triface::operator= 57ms 0.1% 77.72% 497ms 0.91% tetgen::tetgenmesh::enext2fnext 0 0% 77.72% 490ms 0.9% std::insert_iterator::operator= (inline) 0 0% 77.72% 489ms 0.9% boost::numeric::ublas::inner_prod (inline) 45ms 0.082% 77.80% 489ms 0.9% tetgen::tetgenmesh::enextfnext 4ms 0.0073% 77.81% 483ms 0.88% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 33ms 0.06% 77.87% 479ms 0.88% boost::numeric::ublas::vector_scalar_binary::evaluate 477ms 0.87% 78.74% 477ms 0.87% std::vector::size (inline) 457ms 0.84% 79.58% 457ms 0.84% Node::rGetLocation 22ms 0.04% 79.62% 451ms 0.83% tetgen::tetgenmesh::queue::push 17ms 0.031% 79.65% 446ms 0.82% Element::CalculateCircumsphere 47ms 0.086% 79.74% 445ms 0.81% AbstractTetrahedralElement::RefreshJacobian 436ms 0.8% 80.54% 436ms 0.8% AbstractElement::IsDeleted 322ms 0.59% 81.13% 426ms 0.78% tetgen::tetgenmesh::link::add 0 0% 81.13% 420ms 0.77% std::_Rb_tree::_M_insert_unique_ (inline) 239ms 0.44% 81.56% 418ms 0.77% AbstractTetrahedralMesh::GetElement 283ms 0.52% 82.08% 415ms 0.76% tetgen::tetgenmesh::sym 412ms 0.75% 82.84% 412ms 0.75% boost::numeric::ublas::c_vector::operator() (partial-inline) 5ms 0.0092% 82.84% 397ms 0.73% CellPropertyCollection::GetPropertiesType (inline) 171ms 0.31% 83.16% 394ms 0.72% boost::numeric::ublas::vector_inner_prod::apply (inline) 0 0% 83.16% 391ms 0.72% VertexMeshWriter::WriteVtkUsingMesh 102ms 0.19% 83.34% 391ms 0.72% boost::numeric::ublas::indexing_vector_assign 81ms 0.15% 83.49% 389ms 0.71% __dynamic_cast 3ms 0.0055% 83.50% 386ms 0.71% Cell::GetCellId 24ms 0.044% 83.54% 381ms 0.7% VertexMesh::CalculateUnitNormalToFaceWithArea 5ms 0.0092% 83.55% 372ms 0.68% boost::numeric::ublas::c_vector::operator= (inline) 276ms 0.51% 84.06% 372ms 0.68% tetgen::tetgenmesh::bond 370ms 0.68% 84.73% 370ms 0.68% tetgen::tetgenmesh::org 20ms 0.037% 84.77% 359ms 0.66% std::_Rb_tree_iterator::operator-- (inline) 1ms 0.0018% 84.77% 331ms 0.61% VertexElement::~VertexElement 15ms 0.027% 84.80% 327ms 0.6% std::vector::insert (inline) 324ms 0.59% 85.39% 324ms 0.59% std::_Rb_tree_decrement 6ms 0.011% 85.40% 322ms 0.59% AbstractCellProperty::IsSubType (inline) 4ms 0.0073% 85.41% 315ms 0.58% AbstractTetrahedralElement::AbstractTetrahedralElement 53ms 0.097% 85.51% 306ms 0.56% boost::numeric::ublas::vector_reference::operator() (inline) 139ms 0.25% 85.76% 302ms 0.55% Inverse 1ms 0.0018% 85.77% 298ms 0.55% tcache_get (inline) 297ms 0.54% 86.31% 297ms 0.54% tcache_get_n (inline) 63ms 0.12% 86.42% 297ms 0.54% tetgen::tetgenmesh::queue::pop 35ms 0.064% 86.49% 290ms 0.53% tetgen::insphereadapt