File: Test3dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 44244ms, 86.14% of 51360ms total Dropped 862 nodes (cum <= 256.80ms) flat flat% sum% cum cum% 0 0% 0% 51295ms 99.87% __libc_start_call_main 0 0% 0% 51295ms 99.87% __libc_start_main_impl 0 0% 0% 51295ms 99.87% _start 0 0% 0% 51280ms 99.84% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 51280ms 99.84% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 51280ms 99.84% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 51280ms 99.84% main 0 0% 0% 51244ms 99.77% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 51244ms 99.77% CxxTest::TestRunner::runTest (inline) 0 0% 0% 51244ms 99.77% Test3dTissueRepresentativeSimulation::Test3DHoneycombMeshWithGhostNodes 0 0% 0% 51000ms 99.30% AbstractCellBasedSimulation::Solve 0 0% 0% 42681ms 83.10% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 42642ms 83.03% MeshBasedCellPopulation::Update 0 0% 0% 23341ms 45.45% MeshBasedCellPopulation::TessellateIfNeeded 0 0% 0% 23339ms 45.44% MeshBasedCellPopulation::CreateVoronoiTessellation (inline) 152ms 0.3% 0.3% 21060ms 41.00% VertexMesh::VertexMesh 0 0% 0.3% 15777ms 30.72% MutableMesh::ReMesh 1ms 0.0019% 0.3% 12642ms 24.61% tetgen::tetrahedralize 0 0% 0.3% 12513ms 24.36% tetgen::tetgenmesh::delaunizevertices 9ms 0.018% 0.32% 12513ms 24.36% tetgen::tetgenmesh::incrflipdelaunay 535ms 1.04% 1.36% 11098ms 21.61% tetgen::tetgenmesh::lawson 604ms 1.18% 2.53% 10807ms 21.04% TetrahedralMesh::EdgeIterator::operator++ 3177ms 6.19% 8.72% 8537ms 16.62% std::_Rb_tree::_M_lower_bound (inline) 33ms 0.064% 8.78% 8519ms 16.59% std::set::insert (inline) 301ms 0.59% 9.37% 8382ms 16.32% VertexElement::AddFace 232ms 0.45% 9.82% 8074ms 15.72% std::_Rb_tree::find (inline) 164ms 0.32% 10.14% 7996ms 15.57% std::_Rb_tree::_M_insert_unique 0 0% 10.14% 7518ms 14.64% std::set::count (inline) 119ms 0.23% 10.37% 5288ms 10.30% std::less::operator() (inline) 5219ms 10.16% 20.53% 5219ms 10.16% std::operator< (inline) 1ms 0.0019% 20.54% 4873ms 9.49% OffLatticeSimulation::UpdateCellLocationsAndTopology 277ms 0.54% 21.07% 4838ms 9.42% std::_Rb_tree::_M_insert_ (inline) 1ms 0.0019% 21.08% 4760ms 9.27% ForwardEulerNumericalMethod::UpdateAllNodePositions 2ms 0.0039% 21.08% 4725ms 9.20% AbstractNumericalMethod::ComputeForcesIncludingDamping 4012ms 7.81% 28.89% 4012ms 7.81% std::_Rb_tree_increment 210ms 0.41% 29.30% 3969ms 7.73% operator new 4ms 0.0078% 29.31% 3889ms 7.57% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 2ms 0.0039% 29.31% 3864ms 7.52% MeshBasedCellPopulation::UpdateNodePairs 7ms 0.014% 29.33% 3756ms 7.31% MeshBasedCellPopulation::SpringIterator::operator++ 1016ms 1.98% 31.30% 3689ms 7.18% __GI___libc_malloc 50ms 0.097% 31.40% 3515ms 6.84% std::__new_allocator::allocate (inline) 0 0% 31.40% 3494ms 6.80% std::allocator_traits::allocate (inline) 104ms 0.2% 31.60% 3430ms 6.68% tetgen::tetgenmesh::insphere_sos 7ms 0.014% 31.62% 3366ms 6.55% std::_Rb_tree::~_Rb_tree (inline) 1092ms 2.13% 33.74% 3357ms 6.54% std::_Rb_tree::_M_erase 0 0% 33.74% 3326ms 6.48% std::set::~set (inline) 1214ms 2.36% 36.11% 3319ms 6.46% std::_Rb_tree::_M_get_insert_unique_pos 3036ms 5.91% 42.02% 3313ms 6.45% tetgen::insphere 0 0% 42.02% 3297ms 6.42% AbstractCellPopulation::WriteResultsToFiles 899ms 1.75% 43.77% 3084ms 6.00% __GI___libc_free 7ms 0.014% 43.78% 2869ms 5.59% std::set_intersection (inline) 0 0% 43.78% 2862ms 5.57% std::_Rb_tree::_M_create_node (inline) 206ms 0.4% 44.18% 2862ms 5.57% std::__set_intersection 119ms 0.23% 44.42% 2858ms 5.56% std::__new_allocator::deallocate (inline) 0 0% 44.42% 2839ms 5.53% std::_Rb_tree::_M_get_node (inline) 0 0% 44.42% 2832ms 5.51% std::allocator_traits::deallocate (inline) 0 0% 44.42% 2831ms 5.51% std::_Rb_tree::_Alloc_node::operator() (inline) 196ms 0.38% 44.80% 2714ms 5.28% tetgen::tetgenmesh::flip23 22ms 0.043% 44.84% 2500ms 4.87% Node::AddElement 10ms 0.019% 44.86% 2426ms 4.72% TetrahedralMesh::ImportFromMesher 2379ms 4.63% 49.49% 2379ms 4.63% std::_Rb_tree::_S_right (inline) 1834ms 3.57% 53.06% 2363ms 4.60% _int_malloc 0 0% 53.06% 2293ms 4.46% VertexMesh::~VertexMesh 203ms 0.4% 53.46% 2273ms 4.43% VertexMesh::GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex 3ms 0.0058% 53.46% 2244ms 4.37% MeshBasedCellPopulationWithGhostNodes::WriteVtkResultsToFile 184ms 0.36% 53.82% 2223ms 4.33% std::_Rb_tree_const_iterator::operator++ (inline) 1149ms 2.24% 56.06% 2182ms 4.25% _int_free 1ms 0.0019% 56.06% 2080ms 4.05% std::_Rb_tree_iterator::operator++ (inline) 166ms 0.32% 56.38% 1901ms 3.70% tetgen::tetgenmesh::flip32 87ms 0.17% 56.55% 1871ms 3.64% MutableElement::AddNode 0 0% 56.55% 1819ms 3.54% std::_Rb_tree::_M_drop_node (inline) 0 0% 56.55% 1809ms 3.52% std::_Rb_tree::_M_put_node (inline) 1771ms 3.45% 60.00% 1771ms 3.45% std::_Rb_tree_insert_and_rebalance 61ms 0.12% 60.12% 1552ms 3.02% Node::~Node 110ms 0.21% 60.33% 1522ms 2.96% VertexMesh::Clear 1303ms 2.54% 62.87% 1396ms 2.72% tetgen::orient3d 5ms 0.0097% 62.88% 1377ms 2.68% Element::Element 174ms 0.34% 63.22% 1307ms 2.54% tetgen::tetgenmesh::enqueueflipface 52ms 0.1% 63.32% 1189ms 2.32% tetgen::tetgenmesh::locate 1177ms 2.29% 65.61% 1177ms 2.29% Node::GetIndex 71ms 0.14% 65.75% 1091ms 2.12% tetgen::tetgenmesh::preciselocate 1ms 0.0019% 65.75% 1044ms 2.03% Element::RegisterWithNodes (inline) 10ms 0.019% 65.77% 1033ms 2.01% std::_Vector_base::_M_deallocate (inline) 54ms 0.11% 65.88% 1004ms 1.95% std::map::operator[] 595ms 1.16% 67.04% 982ms 1.91% malloc_consolidate 0 0% 67.04% 965ms 1.88% std::vector::~vector (inline) 962ms 1.87% 68.91% 962ms 1.87% tetgen::tetgenmesh::triface::triface 0 0% 68.91% 876ms 1.71% std::_Rb_tree::lower_bound (inline) 0 0% 68.91% 876ms 1.71% std::_Vector_base::~_Vector_base (inline) 0 0% 68.91% 876ms 1.71% std::map::lower_bound (inline) 52ms 0.1% 69.01% 859ms 1.67% std::vector::_M_realloc_insert 6ms 0.012% 69.02% 849ms 1.65% _int_free_maybe_consolidate 0 0% 69.02% 840ms 1.64% VoronoiDataWriter::Visit 75ms 0.15% 69.17% 794ms 1.55% TetrahedralMesh::Clear 430ms 0.84% 70.01% 792ms 1.54% tetgen::tetgenmesh::fnextself 5ms 0.0097% 70.02% 734ms 1.43% VertexMesh::GenerateVerticesFromElementCircumcentres 99ms 0.19% 70.21% 725ms 1.41% std::vector::push_back (inline) 707ms 1.38% 71.58% 707ms 1.38% tetgen::tetgenmesh::oppo 1ms 0.0019% 71.59% 702ms 1.37% AbstractTwoBodyInteractionForce::AddForceContribution 694ms 1.35% 72.94% 694ms 1.35% [libchaste_mesh.so] 0 0% 72.94% 687ms 1.34% TetrahedralMesh::RefreshJacobianCachedData 682ms 1.33% 74.27% 682ms 1.33% unlink_chunk 8ms 0.016% 74.28% 663ms 1.29% std::_Vector_base::_M_allocate (inline) 10ms 0.019% 74.30% 659ms 1.28% AbstractVariableSizeTwoBodyInteractionForce::CalculateForceBetweenNodes 10ms 0.019% 74.32% 657ms 1.28% boost::numeric::ublas::vector_assign (inline) 12ms 0.023% 74.34% 645ms 1.26% AbstractTetrahedralElement::CalculateInverseJacobian 13ms 0.025% 74.37% 614ms 1.20% boost::numeric::ublas::c_vector::c_vector (inline) 55ms 0.11% 74.48% 607ms 1.18% __atan2 14ms 0.027% 74.50% 602ms 1.17% AbstractTetrahedralElement::CalculateJacobian 0 0% 74.50% 553ms 1.08% std::set::find (inline) 439ms 0.85% 75.36% 552ms 1.07% __ieee754_atan2_fma 542ms 1.06% 76.41% 542ms 1.06% tetgen::tetgenmesh::triface::operator= 0 0% 76.41% 514ms 1.00% std::insert_iterator::operator= (inline) 414ms 0.81% 77.22% 513ms 1% AbstractElement::GetNodeGlobalIndex 42ms 0.082% 77.30% 505ms 0.98% tetgen::tetgenmesh::enextfnext 205ms 0.4% 77.70% 499ms 0.97% AbstractElement::GetNodeLocation 0 0% 77.70% 497ms 0.97% boost::numeric::ublas::inner_prod (inline) 4ms 0.0078% 77.71% 496ms 0.97% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 33ms 0.064% 77.77% 492ms 0.96% boost::numeric::ublas::vector_scalar_binary::evaluate 41ms 0.08% 77.85% 482ms 0.94% tetgen::tetgenmesh::enext2fnext 0 0% 77.85% 460ms 0.9% std::_Rb_tree::_M_insert_unique_ (inline) 23ms 0.045% 77.90% 434ms 0.85% Element::CalculateCircumsphere 49ms 0.095% 77.99% 433ms 0.84% AbstractTetrahedralElement::RefreshJacobian 266ms 0.52% 78.51% 416ms 0.81% tetgen::tetgenmesh::sym 30ms 0.058% 78.57% 414ms 0.81% tetgen::tetgenmesh::queue::push 112ms 0.22% 78.79% 413ms 0.8% boost::numeric::ublas::indexing_vector_assign 6ms 0.012% 78.80% 402ms 0.78% CellPropertyCollection::GetPropertiesType (inline) 2ms 0.0039% 78.80% 400ms 0.78% Cell::GetCellId 400ms 0.78% 79.58% 400ms 0.78% boost::numeric::ublas::c_vector::operator() 188ms 0.37% 79.95% 400ms 0.78% boost::numeric::ublas::vector_inner_prod::apply (inline) 239ms 0.47% 80.41% 389ms 0.76% AbstractTetrahedralMesh::GetElement 388ms 0.76% 81.17% 388ms 0.76% Node::rGetLocation 270ms 0.53% 81.69% 384ms 0.75% tetgen::tetgenmesh::link::add 377ms 0.73% 82.43% 377ms 0.73% std::vector::size (inline) 22ms 0.043% 82.47% 376ms 0.73% std::_Rb_tree_iterator::operator-- (inline) 85ms 0.17% 82.64% 372ms 0.72% __dynamic_cast 276ms 0.54% 83.17% 372ms 0.72% tetgen::tetgenmesh::bond 0 0% 83.17% 367ms 0.71% VertexMeshWriter::WriteVtkUsingMesh 362ms 0.7% 83.88% 362ms 0.7% tetgen::tetgenmesh::org 5ms 0.0097% 83.89% 355ms 0.69% boost::numeric::ublas::c_vector::operator= (inline) 18ms 0.035% 83.92% 348ms 0.68% VertexMesh::CalculateUnitNormalToFaceWithArea 3ms 0.0058% 83.93% 328ms 0.64% AbstractTetrahedralElement::AbstractTetrahedralElement 148ms 0.29% 84.22% 327ms 0.64% Inverse 6ms 0.012% 84.23% 322ms 0.63% AbstractCellProperty::IsSubType (inline) 321ms 0.62% 84.85% 321ms 0.62% std::_Rb_tree_decrement 62ms 0.12% 84.97% 320ms 0.62% boost::numeric::ublas::vector_reference::operator() (inline) 280ms 0.55% 85.52% 280ms 0.55% tetgen::tetgenmesh::pointmark 0 0% 85.52% 277ms 0.54% tcache_get (inline) 277ms 0.54% 86.06% 277ms 0.54% tcache_get_n (inline) 26ms 0.051% 86.11% 277ms 0.54% tetgen::insphereadapt 4ms 0.0078% 86.12% 262ms 0.51% VertexElement::~VertexElement 14ms 0.027% 86.14% 262ms 0.51% std::vector::insert (inline)