File: Test3dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 57869ms, 87.80% of 65909ms total Dropped 881 nodes (cum <= 329.55ms) flat flat% sum% cum cum% 0 0% 0% 65853ms 99.92% __libc_start_call_main 0 0% 0% 65853ms 99.92% __libc_start_main_impl 0 0% 0% 65853ms 99.92% _start 0 0% 0% 65837ms 99.89% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 65837ms 99.89% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 65837ms 99.89% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 65837ms 99.89% main 0 0% 0% 65801ms 99.84% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 65801ms 99.84% CxxTest::TestRunner::runTest (inline) 0 0% 0% 65801ms 99.84% Test3dTissueRepresentativeSimulation::Test3DHoneycombMeshWithGhostNodes 0 0% 0% 65528ms 99.42% AbstractCellBasedSimulation::Solve 0 0% 0% 54568ms 82.79% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 54518ms 82.72% MeshBasedCellPopulation::Update 0 0% 0% 32613ms 49.48% MeshBasedCellPopulation::CreateVoronoiTessellation (inline) 0 0% 0% 32613ms 49.48% MeshBasedCellPopulation::TessellateIfNeeded 228ms 0.35% 0.35% 28467ms 43.19% VertexMesh::VertexMesh 0 0% 0.35% 17522ms 26.59% MutableMesh::ReMesh 536ms 0.81% 1.16% 13511ms 20.50% TetrahedralMesh::EdgeIterator::operator++ 1ms 0.0015% 1.16% 12803ms 19.43% tetgen::tetrahedralize 3ms 0.0046% 1.17% 12662ms 19.21% tetgen::tetgenmesh::delaunizevertices 11ms 0.017% 1.18% 12657ms 19.20% tetgen::tetgenmesh::incrflipdelaunay 505ms 0.77% 1.95% 11262ms 17.09% tetgen::tetgenmesh::lawson 35ms 0.053% 2.00% 10942ms 16.60% std::set::insert (inline) 3140ms 4.76% 6.77% 10504ms 15.94% std::_Rb_tree::_M_lower_bound (inline) 174ms 0.26% 7.03% 10430ms 15.82% std::_Rb_tree::_M_insert_unique 451ms 0.68% 7.71% 9914ms 15.04% VertexElement::AddFace 243ms 0.37% 8.08% 9671ms 14.67% std::_Rb_tree::find (inline) 0 0% 8.08% 9131ms 13.85% std::set::count (inline) 7071ms 10.73% 18.81% 7071ms 10.73% std::_Rb_tree_increment 116ms 0.18% 18.99% 6907ms 10.48% std::less::operator() (inline) 6845ms 10.39% 29.37% 6845ms 10.39% std::operator< (inline) 269ms 0.41% 29.78% 6052ms 9.18% std::_Rb_tree::_M_insert_ (inline) 0 0% 29.78% 5841ms 8.86% OffLatticeSimulation::UpdateCellLocationsAndTopology 235ms 0.36% 30.14% 5775ms 8.76% operator new 1ms 0.0015% 30.14% 5697ms 8.64% ForwardEulerNumericalMethod::UpdateAllNodePositions 2ms 0.003% 30.14% 5664ms 8.59% AbstractNumericalMethod::ComputeForcesIncludingDamping 1055ms 1.60% 31.74% 5472ms 8.30% __GI___libc_malloc 0 0% 31.74% 4978ms 7.55% AbstractCellPopulation::WriteResultsToFiles 42ms 0.064% 31.81% 4818ms 7.31% std::__new_allocator::allocate (inline) 8ms 0.012% 31.82% 4808ms 7.29% std::_Rb_tree::~_Rb_tree (inline) 2009ms 3.05% 34.87% 4800ms 7.28% std::_Rb_tree::_M_erase 0 0% 34.87% 4795ms 7.28% std::allocator_traits::allocate (inline) 0 0% 34.87% 4738ms 7.19% std::set::~set (inline) 0 0% 34.87% 4717ms 7.16% MeshBasedCellPopulation::UpdateNodePairs 5ms 0.0076% 34.87% 4702ms 7.13% std::set_intersection (inline) 269ms 0.41% 35.28% 4697ms 7.13% std::__set_intersection 4ms 0.0061% 35.29% 4688ms 7.11% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 17ms 0.026% 35.31% 4559ms 6.92% MeshBasedCellPopulation::SpringIterator::operator++ 1246ms 1.89% 37.20% 4516ms 6.85% std::_Rb_tree::_M_get_insert_unique_pos 1279ms 1.94% 39.14% 4476ms 6.79% __GI___libc_free 32ms 0.049% 39.19% 4432ms 6.72% Node::AddElement 0 0% 39.19% 4183ms 6.35% VertexMesh::~VertexMesh 4160ms 6.31% 45.51% 4160ms 6.31% std::_Rb_tree::_S_right (inline) 2899ms 4.40% 49.90% 4054ms 6.15% _int_malloc 191ms 0.29% 50.19% 3939ms 5.98% std::_Rb_tree_const_iterator::operator++ (inline) 105ms 0.16% 50.35% 3880ms 5.89% std::__new_allocator::deallocate (inline) 0 0% 50.35% 3866ms 5.87% std::_Rb_tree::_M_create_node (inline) 0 0% 50.35% 3852ms 5.84% std::allocator_traits::deallocate (inline) 0 0% 50.35% 3827ms 5.81% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 50.35% 3811ms 5.78% std::_Rb_tree::_M_get_node (inline) 14ms 0.021% 50.37% 3808ms 5.78% TetrahedralMesh::ImportFromMesher 244ms 0.37% 50.74% 3658ms 5.55% VertexMesh::GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex 99ms 0.15% 50.89% 3496ms 5.30% tetgen::tetgenmesh::insphere_sos 5ms 0.0076% 50.90% 3448ms 5.23% MeshBasedCellPopulationWithGhostNodes::WriteVtkResultsToFile 2ms 0.003% 50.91% 3433ms 5.21% std::_Rb_tree_iterator::operator++ (inline) 103ms 0.16% 51.06% 3428ms 5.20% MutableElement::AddNode 3087ms 4.68% 55.75% 3382ms 5.13% tetgen::insphere 1307ms 1.98% 57.73% 3193ms 4.84% _int_free 194ms 0.29% 58.02% 2880ms 4.37% Node::~Node 201ms 0.3% 58.33% 2732ms 4.15% tetgen::tetgenmesh::flip23 220ms 0.33% 58.66% 2658ms 4.03% VertexMesh::Clear 0 0% 58.66% 2070ms 3.14% std::_Rb_tree::_M_drop_node (inline) 0 0% 58.66% 2060ms 3.13% std::_Rb_tree::_M_put_node (inline) 2060ms 3.13% 61.79% 2060ms 3.13% std::_Rb_tree_insert_and_rebalance 1994ms 3.03% 64.81% 1994ms 3.03% Node::GetIndex 1275ms 1.93% 66.75% 1905ms 2.89% malloc_consolidate 4ms 0.0061% 66.75% 1901ms 2.88% Element::Element 162ms 0.25% 67.00% 1880ms 2.85% tetgen::tetgenmesh::flip32 24ms 0.036% 67.03% 1816ms 2.76% std::_Vector_base::_M_deallocate (inline) 0 0% 67.03% 1695ms 2.57% std::vector::~vector (inline) 0 0% 67.03% 1639ms 2.49% std::_Vector_base::~_Vector_base (inline) 2ms 0.003% 67.04% 1634ms 2.48% _int_free_maybe_consolidate 6ms 0.0091% 67.05% 1561ms 2.37% Element::RegisterWithNodes (inline) 224ms 0.34% 67.39% 1547ms 2.35% TetrahedralMesh::Clear 1399ms 2.12% 69.51% 1399ms 2.12% unlink_chunk 59ms 0.09% 69.60% 1398ms 2.12% std::map::operator[] 1300ms 1.97% 71.57% 1380ms 2.09% tetgen::orient3d 169ms 0.26% 71.83% 1321ms 2.00% tetgen::tetgenmesh::enqueueflipface 2ms 0.003% 71.83% 1259ms 1.91% VoronoiDataWriter::Visit 0 0% 71.83% 1253ms 1.90% std::_Rb_tree::lower_bound (inline) 0 0% 71.83% 1253ms 1.90% std::map::lower_bound (inline) 6ms 0.0091% 71.84% 1243ms 1.89% VertexMesh::GenerateVerticesFromElementCircumcentres 33ms 0.05% 71.89% 1196ms 1.81% tetgen::tetgenmesh::locate 69ms 0.1% 71.99% 1181ms 1.79% std::vector::_M_realloc_insert 99ms 0.15% 72.14% 1113ms 1.69% tetgen::tetgenmesh::preciselocate 835ms 1.27% 73.41% 1007ms 1.53% AbstractElement::GetNodeGlobalIndex 7ms 0.011% 73.42% 991ms 1.50% std::_Vector_base::_M_allocate (inline) 131ms 0.2% 73.62% 964ms 1.46% std::vector::push_back (inline) 1ms 0.0015% 73.62% 880ms 1.34% TetrahedralMesh::RefreshJacobianCachedData 831ms 1.26% 74.88% 831ms 1.26% tetgen::tetgenmesh::triface::triface 469ms 0.71% 75.60% 799ms 1.21% tetgen::tetgenmesh::fnextself 316ms 0.48% 76.07% 780ms 1.18% AbstractElement::GetNodeLocation 10ms 0.015% 76.09% 768ms 1.17% AbstractTetrahedralElement::CalculateInverseJacobian 0 0% 76.09% 758ms 1.15% AbstractTwoBodyInteractionForce::AddForceContribution 723ms 1.10% 77.19% 723ms 1.10% tetgen::tetgenmesh::oppo 716ms 1.09% 78.27% 716ms 1.09% Node::rGetLocation 14ms 0.021% 78.29% 705ms 1.07% AbstractTetrahedralElement::CalculateJacobian 16ms 0.024% 78.32% 704ms 1.07% boost::numeric::ublas::vector_assign (inline) 18ms 0.027% 78.35% 703ms 1.07% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 693ms 1.05% 79.40% 693ms 1.05% AbstractElement::IsDeleted 7ms 0.011% 79.41% 669ms 1.02% boost::numeric::ublas::c_vector::c_vector (inline) 654ms 0.99% 80.40% 654ms 0.99% [libchaste_mesh.so] 49ms 0.074% 80.47% 631ms 0.96% __atan2 616ms 0.93% 81.41% 616ms 0.93% tetgen::tetgenmesh::triface::operator= 22ms 0.033% 81.44% 606ms 0.92% Element::CalculateCircumsphere 469ms 0.71% 82.15% 582ms 0.88% __ieee754_atan2_fma 564ms 0.86% 83.01% 564ms 0.86% std::vector::size (inline) 0 0% 83.01% 538ms 0.82% std::set::find (inline) 43ms 0.065% 83.08% 524ms 0.8% AbstractTetrahedralElement::RefreshJacobian 22ms 0.033% 83.11% 508ms 0.77% VertexMesh::CalculateUnitNormalToFaceWithArea 0 0% 83.11% 508ms 0.77% boost::numeric::ublas::inner_prod (inline) 0 0% 83.11% 506ms 0.77% std::insert_iterator::operator= (inline) 4ms 0.0061% 83.11% 504ms 0.76% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 34ms 0.052% 83.17% 500ms 0.76% boost::numeric::ublas::vector_scalar_binary::evaluate 48ms 0.073% 83.24% 494ms 0.75% tetgen::tetgenmesh::enextfnext 36ms 0.055% 83.29% 482ms 0.73% tetgen::tetgenmesh::enext2fnext 130ms 0.2% 83.49% 459ms 0.7% boost::numeric::ublas::indexing_vector_assign 451ms 0.68% 84.18% 451ms 0.68% boost::numeric::ublas::c_vector::operator() 1ms 0.0015% 84.18% 448ms 0.68% std::_Rb_tree::_M_insert_unique_ (inline) 32ms 0.049% 84.23% 437ms 0.66% tetgen::tetgenmesh::queue::push 291ms 0.44% 84.67% 437ms 0.66% tetgen::tetgenmesh::sym 186ms 0.28% 84.95% 416ms 0.63% boost::numeric::ublas::vector_inner_prod::apply (inline) 234ms 0.36% 85.30% 411ms 0.62% AbstractTetrahedralMesh::GetElement 5ms 0.0076% 85.31% 411ms 0.62% boost::numeric::ublas::c_vector::operator= (inline) 25ms 0.038% 85.35% 402ms 0.61% std::_Rb_tree_iterator::operator-- (inline) 289ms 0.44% 85.79% 402ms 0.61% tetgen::tetgenmesh::link::add 0 0% 85.79% 397ms 0.6% VertexMeshWriter::WriteVtkUsingMesh 5ms 0.0076% 85.80% 394ms 0.6% CellPropertyCollection::GetPropertiesType (inline) 1ms 0.0015% 85.80% 383ms 0.58% Cell::GetCellId 0 0% 85.80% 377ms 0.57% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 19ms 0.029% 85.83% 377ms 0.57% std::vector::insert (inline) 88ms 0.13% 85.96% 363ms 0.55% __dynamic_cast 11ms 0.017% 85.98% 362ms 0.55% VertexElement::~VertexElement 275ms 0.42% 86.39% 362ms 0.55% tetgen::tetgenmesh::bond 355ms 0.54% 86.93% 355ms 0.54% std::_Rb_tree_decrement 349ms 0.53% 87.46% 349ms 0.53% tetgen::tetgenmesh::org 160ms 0.24% 87.70% 340ms 0.52% Inverse 9ms 0.014% 87.72% 338ms 0.51% AbstractTetrahedralElement::AbstractTetrahedralElement 55ms 0.083% 87.80% 337ms 0.51% boost::numeric::ublas::vector_reference::operator() (inline)