File: Test3dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 52962ms, 86.55% of 61192ms total Dropped 870 nodes (cum <= 305.96ms) flat flat% sum% cum cum% 0 0% 0% 61134ms 99.91% __libc_start_call_main 0 0% 0% 61134ms 99.91% __libc_start_main_impl 0 0% 0% 61134ms 99.91% _start 0 0% 0% 61116ms 99.88% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 61116ms 99.88% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 61116ms 99.88% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 61116ms 99.88% main 0 0% 0% 61074ms 99.81% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 61074ms 99.81% CxxTest::TestRunner::runTest (inline) 0 0% 0% 61074ms 99.81% Test3dTissueRepresentativeSimulation::Test3DHoneycombMeshWithGhostNodes 0 0% 0% 60798ms 99.36% AbstractCellBasedSimulation::Solve 0 0% 0% 51768ms 84.60% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 51714ms 84.51% MeshBasedCellPopulation::Update 0 0% 0% 27850ms 45.51% MeshBasedCellPopulation::CreateVoronoiTessellation (inline) 0 0% 0% 27850ms 45.51% MeshBasedCellPopulation::TessellateIfNeeded 211ms 0.34% 0.34% 24866ms 40.64% VertexMesh::VertexMesh 0 0% 0.34% 19846ms 32.43% MutableMesh::ReMesh 0 0% 0.34% 16066ms 26.26% tetgen::tetrahedralize 2ms 0.0033% 0.35% 15920ms 26.02% tetgen::tetgenmesh::delaunizevertices 8ms 0.013% 0.36% 15915ms 26.01% tetgen::tetgenmesh::incrflipdelaunay 540ms 0.88% 1.24% 14267ms 23.32% tetgen::tetgenmesh::lawson 647ms 1.06% 2.30% 12241ms 20.00% TetrahedralMesh::EdgeIterator::operator++ 37ms 0.06% 2.36% 9967ms 16.29% std::set::insert (inline) 371ms 0.61% 2.97% 9736ms 15.91% VertexElement::AddFace 238ms 0.39% 3.36% 9521ms 15.56% std::_Rb_tree::_M_insert_unique 3202ms 5.23% 8.59% 8995ms 14.70% std::_Rb_tree::_M_lower_bound (inline) 279ms 0.46% 9.05% 8531ms 13.94% std::_Rb_tree::find (inline) 0 0% 9.05% 7908ms 12.92% std::set::count (inline) 117ms 0.19% 9.24% 5688ms 9.30% std::less::operator() (inline) 324ms 0.53% 9.77% 5679ms 9.28% std::_Rb_tree::_M_insert_ (inline) 5633ms 9.21% 18.97% 5633ms 9.21% std::operator< (inline) 0 0% 18.97% 5385ms 8.80% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 18.97% 5255ms 8.59% ForwardEulerNumericalMethod::UpdateAllNodePositions 4ms 0.0065% 18.98% 5230ms 8.55% AbstractNumericalMethod::ComputeForcesIncludingDamping 217ms 0.35% 19.33% 4880ms 7.97% operator new 4838ms 7.91% 27.24% 4838ms 7.91% std::_Rb_tree_increment 1195ms 1.95% 29.19% 4603ms 7.52% __GI___libc_malloc 0 0% 29.19% 4385ms 7.17% MeshBasedCellPopulation::UpdateNodePairs 12ms 0.02% 29.21% 4340ms 7.09% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 49ms 0.08% 29.29% 4271ms 6.98% std::__new_allocator::allocate (inline) 0 0% 29.29% 4243ms 6.93% std::allocator_traits::allocate (inline) 11ms 0.018% 29.31% 4242ms 6.93% MeshBasedCellPopulation::SpringIterator::operator++ 5ms 0.0082% 29.32% 4125ms 6.74% std::_Rb_tree::~_Rb_tree (inline) 1383ms 2.26% 31.58% 4114ms 6.72% std::_Rb_tree::_M_erase 0 0% 31.58% 4082ms 6.67% std::set::~set (inline) 1347ms 2.20% 33.78% 3887ms 6.35% std::_Rb_tree::_M_get_insert_unique_pos 1119ms 1.83% 35.61% 3846ms 6.29% __GI___libc_free 125ms 0.2% 35.81% 3812ms 6.23% tetgen::tetgenmesh::insphere_sos 1ms 0.0016% 35.81% 3722ms 6.08% std::set_intersection (inline) 247ms 0.4% 36.22% 3721ms 6.08% std::__set_intersection 3375ms 5.52% 41.73% 3672ms 6.00% tetgen::insphere 137ms 0.22% 41.96% 3568ms 5.83% tetgen::tetgenmesh::flip23 0 0% 41.96% 3496ms 5.71% std::_Rb_tree::_M_create_node (inline) 0 0% 41.96% 3490ms 5.70% AbstractCellPopulation::WriteResultsToFiles 0 0% 41.96% 3464ms 5.66% std::_Rb_tree::_M_get_node (inline) 0 0% 41.96% 3458ms 5.65% std::_Rb_tree::_Alloc_node::operator() (inline) 132ms 0.22% 42.17% 3445ms 5.63% std::__new_allocator::deallocate (inline) 0 0% 42.17% 3429ms 5.60% std::allocator_traits::deallocate (inline) 37ms 0.06% 42.23% 3238ms 5.29% Node::AddElement 2298ms 3.76% 45.99% 3065ms 5.01% _int_malloc 211ms 0.34% 46.33% 3017ms 4.93% std::_Rb_tree_const_iterator::operator++ (inline) 17ms 0.028% 46.36% 3013ms 4.92% TetrahedralMesh::ImportFromMesher 0 0% 46.36% 3006ms 4.91% VertexMesh::~VertexMesh 2931ms 4.79% 51.15% 2931ms 4.79% std::_Rb_tree::_S_right (inline) 1411ms 2.31% 53.46% 2723ms 4.45% _int_free 144ms 0.24% 53.69% 2599ms 4.25% tetgen::tetgenmesh::flip32 68ms 0.11% 53.80% 2585ms 4.22% MutableElement::AddNode 1ms 0.0016% 53.80% 2383ms 3.89% MeshBasedCellPopulationWithGhostNodes::WriteVtkResultsToFile 186ms 0.3% 54.11% 2341ms 3.83% VertexMesh::GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex 142ms 0.23% 54.34% 2186ms 3.57% Node::~Node 0 0% 54.34% 2168ms 3.54% std::_Rb_tree::_M_drop_node (inline) 1ms 0.0016% 54.34% 2163ms 3.53% std::_Rb_tree_iterator::operator++ (inline) 0 0% 54.34% 2155ms 3.52% std::_Rb_tree::_M_put_node (inline) 141ms 0.23% 54.57% 1987ms 3.25% VertexMesh::Clear 240ms 0.39% 54.96% 1986ms 3.25% tetgen::tetgenmesh::enqueueflipface 1955ms 3.19% 58.16% 1955ms 3.19% std::_Rb_tree_insert_and_rebalance 1584ms 2.59% 60.75% 1584ms 2.59% Node::GetIndex 1471ms 2.40% 63.15% 1550ms 2.53% tetgen::orient3d 9ms 0.015% 63.17% 1472ms 2.41% Element::Element 42ms 0.069% 63.24% 1325ms 2.17% tetgen::tetgenmesh::locate 25ms 0.041% 63.28% 1299ms 2.12% std::_Vector_base::_M_deallocate (inline) 841ms 1.37% 64.65% 1287ms 2.10% malloc_consolidate 84ms 0.14% 64.79% 1233ms 2.01% tetgen::tetgenmesh::preciselocate 83ms 0.14% 64.92% 1217ms 1.99% TetrahedralMesh::Clear 0 0% 64.92% 1217ms 1.99% std::vector::~vector (inline) 6ms 0.0098% 64.93% 1141ms 1.86% Element::RegisterWithNodes (inline) 2ms 0.0033% 64.94% 1134ms 1.85% std::_Vector_base::~_Vector_base (inline) 5ms 0.0082% 64.94% 1103ms 1.80% _int_free_maybe_consolidate 73ms 0.12% 65.06% 1102ms 1.80% std::map::operator[] 1044ms 1.71% 66.77% 1044ms 1.71% tetgen::tetgenmesh::oppo 1030ms 1.68% 68.45% 1030ms 1.68% tetgen::tetgenmesh::triface::triface 60ms 0.098% 68.55% 1029ms 1.68% std::vector::_M_realloc_insert 800ms 1.31% 69.86% 998ms 1.63% AbstractElement::GetNodeGlobalIndex 964ms 1.58% 71.43% 964ms 1.58% unlink_chunk 0 0% 71.43% 942ms 1.54% std::_Rb_tree::lower_bound (inline) 0 0% 71.43% 942ms 1.54% std::map::lower_bound (inline) 0 0% 71.43% 873ms 1.43% VoronoiDataWriter::Visit 112ms 0.18% 71.62% 829ms 1.35% std::vector::push_back (inline) 9ms 0.015% 71.63% 818ms 1.34% VertexMesh::GenerateVerticesFromElementCircumcentres 7ms 0.011% 71.64% 786ms 1.28% std::_Vector_base::_M_allocate (inline) 768ms 1.26% 72.90% 768ms 1.26% [libchaste_mesh.so] 294ms 0.48% 73.38% 749ms 1.22% tetgen::tetgenmesh::sym 0 0% 73.38% 746ms 1.22% TetrahedralMesh::RefreshJacobianCachedData 723ms 1.18% 74.56% 723ms 1.18% tetgen::tetgenmesh::triface::operator= 0 0% 74.56% 722ms 1.18% AbstractTwoBodyInteractionForce::AddForceContribution 9ms 0.015% 74.58% 698ms 1.14% AbstractTetrahedralElement::CalculateInverseJacobian 15ms 0.025% 74.60% 686ms 1.12% AbstractVariableSizeTwoBodyInteractionForce::CalculateForceBetweenNodes 16ms 0.026% 74.63% 646ms 1.06% boost::numeric::ublas::vector_assign (inline) 20ms 0.033% 74.66% 630ms 1.03% AbstractTetrahedralElement::CalculateJacobian 384ms 0.63% 75.29% 630ms 1.03% tetgen::tetgenmesh::fnextself 42ms 0.069% 75.35% 629ms 1.03% tetgen::tetgenmesh::queue::push 0 0% 75.35% 620ms 1.01% std::set::find (inline) 13ms 0.021% 75.38% 616ms 1.01% boost::numeric::ublas::c_vector::c_vector (inline) 218ms 0.36% 75.73% 612ms 1.00% tetgen::tetgenmesh::bond 51ms 0.083% 75.82% 606ms 0.99% __atan2 67ms 0.11% 75.92% 597ms 0.98% tetgen::tetgenmesh::enext2fnext 364ms 0.59% 76.52% 587ms 0.96% tetgen::tetgenmesh::link::add 0 0% 76.52% 567ms 0.93% boost::numeric::ublas::inner_prod (inline) 1ms 0.0016% 76.52% 561ms 0.92% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 54ms 0.088% 76.61% 560ms 0.92% boost::numeric::ublas::vector_scalar_binary::evaluate 248ms 0.41% 77.01% 550ms 0.9% AbstractElement::GetNodeLocation 432ms 0.71% 77.72% 549ms 0.9% __ieee754_atan2_fma 44ms 0.072% 77.79% 532ms 0.87% tetgen::tetgenmesh::enextfnext 504ms 0.82% 78.62% 504ms 0.82% AbstractElement::IsDeleted 496ms 0.81% 79.43% 496ms 0.81% tetgen::tetgenmesh::org 481ms 0.79% 80.21% 481ms 0.79% Node::rGetLocation 481ms 0.79% 81.00% 481ms 0.79% std::vector::size (inline) 479ms 0.78% 81.78% 479ms 0.78% tetgen::tetgenmesh::decode 0 0% 81.78% 463ms 0.76% std::insert_iterator::operator= (inline) 457ms 0.75% 82.53% 457ms 0.75% tetgen::tetgenmesh::pointmark 196ms 0.32% 82.85% 446ms 0.73% boost::numeric::ublas::vector_inner_prod::apply (inline) 47ms 0.077% 82.93% 444ms 0.73% AbstractTetrahedralElement::RefreshJacobian 15ms 0.025% 82.95% 431ms 0.7% Element::CalculateCircumsphere 18ms 0.029% 82.98% 410ms 0.67% std::_Rb_tree_iterator::operator-- (inline) 0 0% 82.98% 408ms 0.67% std::_Rb_tree::_M_insert_unique_ (inline) 22ms 0.036% 83.02% 406ms 0.66% VertexMesh::CalculateUnitNormalToFaceWithArea 403ms 0.66% 83.67% 403ms 0.66% boost::numeric::ublas::c_vector::operator() 99ms 0.16% 83.84% 402ms 0.66% boost::numeric::ublas::indexing_vector_assign 3ms 0.0049% 83.84% 398ms 0.65% CellPropertyCollection::GetPropertiesType (inline) 5ms 0.0082% 83.85% 394ms 0.64% boost::numeric::ublas::c_vector::operator= (inline) 100ms 0.16% 84.01% 393ms 0.64% __dynamic_cast 202ms 0.33% 84.34% 389ms 0.64% AbstractTetrahedralMesh::GetElement 0 0% 84.34% 383ms 0.63% VertexMeshWriter::WriteVtkUsingMesh 1ms 0.0016% 84.34% 381ms 0.62% Cell::GetCellId 379ms 0.62% 84.96% 379ms 0.62% tetgen::tetgenmesh::encode 356ms 0.58% 85.55% 356ms 0.58% std::_Rb_tree_decrement 16ms 0.026% 85.57% 340ms 0.56% std::vector::insert (inline) 8ms 0.013% 85.58% 338ms 0.55% VertexElement::~VertexElement 80ms 0.13% 85.72% 338ms 0.55% tetgen::tetgenmesh::queue::pop 131ms 0.21% 85.93% 333ms 0.54% Inverse 50ms 0.082% 86.01% 329ms 0.54% boost::numeric::ublas::vector_reference::operator() (inline) 325ms 0.53% 86.54% 325ms 0.53% tetgen::tetgenmesh::face::face 1ms 0.0016% 86.54% 324ms 0.53% AbstractCellProperty::IsSubType (inline) 4ms 0.0065% 86.55% 323ms 0.53% AbstractTetrahedralElement::AbstractTetrahedralElement 0 0% 86.55% 320ms 0.52% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline)