File: Test3dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 52916ms, 87.51% of 60467ms total Dropped 882 nodes (cum <= 302.33ms) flat flat% sum% cum cum% 0 0% 0% 60396ms 99.88% __libc_start_call_main 0 0% 0% 60396ms 99.88% __libc_start_main_impl 0 0% 0% 60396ms 99.88% _start 0 0% 0% 60379ms 99.85% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 60379ms 99.85% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 60379ms 99.85% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 60379ms 99.85% main 0 0% 0% 60346ms 99.80% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 60346ms 99.80% CxxTest::TestRunner::runTest (inline) 0 0% 0% 60346ms 99.80% Test3dTissueRepresentativeSimulation::Test3DHoneycombMeshWithGhostNodes 0 0% 0% 60084ms 99.37% AbstractCellBasedSimulation::Solve 0 0% 0% 49726ms 82.24% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 49678ms 82.16% MeshBasedCellPopulation::Update 0 0% 0% 28460ms 47.07% MeshBasedCellPopulation::CreateVoronoiTessellation (inline) 0 0% 0% 28460ms 47.07% MeshBasedCellPopulation::TessellateIfNeeded 196ms 0.32% 0.32% 25086ms 41.49% VertexMesh::VertexMesh 0 0% 0.32% 17151ms 28.36% MutableMesh::ReMesh 0 0% 0.32% 12810ms 21.19% tetgen::tetrahedralize 1ms 0.0017% 0.33% 12676ms 20.96% tetgen::tetgenmesh::delaunizevertices 10ms 0.017% 0.34% 12672ms 20.96% tetgen::tetgenmesh::incrflipdelaunay 493ms 0.82% 1.16% 12473ms 20.63% TetrahedralMesh::EdgeIterator::operator++ 536ms 0.89% 2.04% 11285ms 18.66% tetgen::tetgenmesh::lawson 3014ms 4.98% 7.03% 9923ms 16.41% std::_Rb_tree::_M_lower_bound (inline) 35ms 0.058% 7.09% 9859ms 16.30% std::set::insert (inline) 200ms 0.33% 7.42% 9343ms 15.45% std::_Rb_tree::_M_insert_unique 368ms 0.61% 8.03% 9179ms 15.18% VertexElement::AddFace 228ms 0.38% 8.40% 9135ms 15.11% std::_Rb_tree::find (inline) 0 0% 8.40% 8564ms 14.16% std::set::count (inline) 111ms 0.18% 8.59% 6565ms 10.86% std::less::operator() (inline) 6502ms 10.75% 19.34% 6502ms 10.75% std::operator< (inline) 6139ms 10.15% 29.49% 6139ms 10.15% std::_Rb_tree_increment 249ms 0.41% 29.90% 5505ms 9.10% std::_Rb_tree::_M_insert_ (inline) 1ms 0.0017% 29.91% 5474ms 9.05% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 29.91% 5329ms 8.81% ForwardEulerNumericalMethod::UpdateAllNodePositions 4ms 0.0066% 29.91% 5304ms 8.77% AbstractNumericalMethod::ComputeForcesIncludingDamping 213ms 0.35% 30.26% 5170ms 8.55% operator new 1051ms 1.74% 32.00% 4893ms 8.09% __GI___libc_malloc 0 0% 32.00% 4743ms 7.84% AbstractCellPopulation::WriteResultsToFiles 2ms 0.0033% 32.01% 4397ms 7.27% MeshBasedCellPopulation::UpdateNodePairs 49ms 0.081% 32.09% 4397ms 7.27% std::__new_allocator::allocate (inline) 5ms 0.0083% 32.10% 4389ms 7.26% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 0 0% 32.10% 4379ms 7.24% std::allocator_traits::allocate (inline) 8ms 0.013% 32.11% 4321ms 7.15% std::_Rb_tree::~_Rb_tree (inline) 1726ms 2.85% 34.96% 4312ms 7.13% std::_Rb_tree::_M_erase 0 0% 34.96% 4262ms 7.05% std::set::~set (inline) 7ms 0.012% 34.97% 4247ms 7.02% MeshBasedCellPopulation::SpringIterator::operator++ 1177ms 1.95% 36.92% 3951ms 6.53% std::_Rb_tree::_M_get_insert_unique_pos 1089ms 1.80% 38.72% 3808ms 6.30% __GI___libc_free 2ms 0.0033% 38.73% 3789ms 6.27% std::set_intersection (inline) 230ms 0.38% 39.11% 3787ms 6.26% std::__set_intersection 138ms 0.23% 39.33% 3594ms 5.94% tetgen::tetgenmesh::insphere_sos 29ms 0.048% 39.38% 3581ms 5.92% Node::AddElement 226ms 0.37% 39.76% 3551ms 5.87% VertexMesh::GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex 20ms 0.033% 39.79% 3541ms 5.86% TetrahedralMesh::ImportFromMesher 3530ms 5.84% 45.63% 3530ms 5.84% std::_Rb_tree::_S_right (inline) 0 0% 45.63% 3480ms 5.76% std::_Rb_tree::_M_create_node (inline) 0 0% 45.63% 3448ms 5.70% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 45.63% 3447ms 5.70% std::_Rb_tree::_M_get_node (inline) 3160ms 5.23% 50.85% 3445ms 5.70% tetgen::insphere 2571ms 4.25% 55.10% 3418ms 5.65% _int_malloc 1ms 0.0017% 55.11% 3399ms 5.62% VertexMesh::~VertexMesh 8ms 0.013% 55.12% 3337ms 5.52% MeshBasedCellPopulationWithGhostNodes::WriteVtkResultsToFile 0 0% 55.12% 3337ms 5.52% std::_Rb_tree_iterator::operator++ (inline) 112ms 0.19% 55.30% 3313ms 5.48% std::__new_allocator::deallocate (inline) 0 0% 55.30% 3287ms 5.44% std::allocator_traits::deallocate (inline) 163ms 0.27% 55.57% 3067ms 5.07% std::_Rb_tree_const_iterator::operator++ (inline) 184ms 0.3% 55.88% 2793ms 4.62% tetgen::tetgenmesh::flip23 1216ms 2.01% 57.89% 2714ms 4.49% _int_free 73ms 0.12% 58.01% 2601ms 4.30% MutableElement::AddNode 167ms 0.28% 58.29% 2435ms 4.03% Node::~Node 188ms 0.31% 58.60% 2240ms 3.70% VertexMesh::Clear 1902ms 3.15% 61.74% 1902ms 3.15% std::_Rb_tree_insert_and_rebalance 0 0% 61.74% 1880ms 3.11% std::_Rb_tree::_M_drop_node (inline) 0 0% 61.74% 1868ms 3.09% std::_Rb_tree::_M_put_node (inline) 159ms 0.26% 62.01% 1829ms 3.02% tetgen::tetgenmesh::flip32 2ms 0.0033% 62.01% 1795ms 2.97% Element::Element 1534ms 2.54% 64.55% 1534ms 2.54% Node::GetIndex 5ms 0.0083% 64.55% 1465ms 2.42% Element::RegisterWithNodes (inline) 896ms 1.48% 66.04% 1457ms 2.41% malloc_consolidate 13ms 0.021% 66.06% 1432ms 2.37% std::_Vector_base::_M_deallocate (inline) 210ms 0.35% 66.40% 1393ms 2.30% TetrahedralMesh::Clear 1294ms 2.14% 68.54% 1377ms 2.28% tetgen::orient3d 0 0% 68.54% 1350ms 2.23% std::vector::~vector (inline) 61ms 0.1% 68.65% 1291ms 2.14% std::map::operator[] 2ms 0.0033% 68.65% 1269ms 2.10% std::_Vector_base::~_Vector_base (inline) 10ms 0.017% 68.67% 1261ms 2.09% _int_free_maybe_consolidate 163ms 0.27% 68.94% 1209ms 2.00% tetgen::tetgenmesh::enqueueflipface 0 0% 68.94% 1152ms 1.91% std::_Rb_tree::lower_bound (inline) 0 0% 68.94% 1152ms 1.91% std::map::lower_bound (inline) 0 0% 68.94% 1150ms 1.90% VoronoiDataWriter::Visit 37ms 0.061% 69.00% 1130ms 1.87% tetgen::tetgenmesh::locate 55ms 0.091% 69.09% 1127ms 1.86% std::vector::_M_realloc_insert 1091ms 1.80% 70.89% 1091ms 1.80% unlink_chunk 82ms 0.14% 71.03% 1047ms 1.73% tetgen::tetgenmesh::preciselocate 6ms 0.0099% 71.04% 1016ms 1.68% VertexMesh::GenerateVerticesFromElementCircumcentres 616ms 1.02% 72.06% 947ms 1.57% tetgen::tetgenmesh::fnextself 10ms 0.017% 72.07% 942ms 1.56% std::_Vector_base::_M_allocate (inline) 114ms 0.19% 72.26% 922ms 1.52% std::vector::push_back (inline) 662ms 1.09% 73.36% 844ms 1.40% AbstractElement::GetNodeGlobalIndex 818ms 1.35% 74.71% 818ms 1.35% tetgen::tetgenmesh::triface::triface 1ms 0.0017% 74.71% 772ms 1.28% TetrahedralMesh::RefreshJacobianCachedData 1ms 0.0017% 74.71% 727ms 1.20% AbstractTwoBodyInteractionForce::AddForceContribution 10ms 0.017% 74.73% 696ms 1.15% AbstractTetrahedralElement::CalculateInverseJacobian 17ms 0.028% 74.76% 688ms 1.14% boost::numeric::ublas::vector_assign (inline) 18ms 0.03% 74.79% 682ms 1.13% AbstractVariableSizeTwoBodyInteractionForce::CalculateForceBetweenNodes 275ms 0.45% 75.24% 661ms 1.09% AbstractElement::GetNodeLocation 661ms 1.09% 76.33% 661ms 1.09% [libchaste_mesh.so] 9ms 0.015% 76.35% 657ms 1.09% AbstractTetrahedralElement::CalculateJacobian 10ms 0.017% 76.37% 654ms 1.08% boost::numeric::ublas::c_vector::c_vector (inline) 653ms 1.08% 77.45% 653ms 1.08% tetgen::tetgenmesh::oppo 46ms 0.076% 77.52% 645ms 1.07% __atan2 46ms 0.076% 77.60% 628ms 1.04% tetgen::tetgenmesh::enextfnext 628ms 1.04% 78.64% 628ms 1.04% tetgen::tetgenmesh::triface::operator= 465ms 0.77% 79.41% 598ms 0.99% __ieee754_atan2_fma 583ms 0.96% 80.37% 583ms 0.96% Node::rGetLocation 0 0% 80.37% 564ms 0.93% std::set::find (inline) 527ms 0.87% 81.24% 527ms 0.87% std::vector::size (inline) 16ms 0.026% 81.27% 516ms 0.85% Element::CalculateCircumsphere 29ms 0.048% 81.32% 516ms 0.85% tetgen::tetgenmesh::enext2fnext 0 0% 81.32% 509ms 0.84% std::insert_iterator::operator= (inline) 0 0% 81.32% 505ms 0.84% boost::numeric::ublas::inner_prod (inline) 5ms 0.0083% 81.32% 501ms 0.83% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 43ms 0.071% 81.39% 496ms 0.82% AbstractTetrahedralElement::RefreshJacobian 26ms 0.043% 81.44% 496ms 0.82% boost::numeric::ublas::vector_scalar_binary::evaluate 480ms 0.79% 82.23% 480ms 0.79% AbstractElement::IsDeleted 0 0% 82.23% 457ms 0.76% std::_Rb_tree::_M_insert_unique_ (inline) 138ms 0.23% 82.46% 439ms 0.73% boost::numeric::ublas::indexing_vector_assign 232ms 0.38% 82.84% 430ms 0.71% AbstractTetrahedralMesh::GetElement 18ms 0.03% 82.87% 426ms 0.7% tetgen::tetgenmesh::queue::push 408ms 0.67% 83.55% 408ms 0.67% boost::numeric::ublas::c_vector::operator() 13ms 0.021% 83.57% 407ms 0.67% VertexMesh::CalculateUnitNormalToFaceWithArea 269ms 0.44% 84.01% 405ms 0.67% tetgen::tetgenmesh::link::add 191ms 0.32% 84.33% 404ms 0.67% boost::numeric::ublas::vector_inner_prod::apply (inline) 0 0% 84.33% 393ms 0.65% VertexMeshWriter::WriteVtkUsingMesh 262ms 0.43% 84.76% 393ms 0.65% tetgen::tetgenmesh::sym 0 0% 84.76% 391ms 0.65% tcache_get (inline) 391ms 0.65% 85.41% 391ms 0.65% tcache_get_n (inline) 8ms 0.013% 85.42% 387ms 0.64% CellPropertyCollection::GetPropertiesType (inline) 4ms 0.0066% 85.43% 384ms 0.64% Cell::GetCellId 17ms 0.028% 85.46% 381ms 0.63% std::_Rb_tree_iterator::operator-- (inline) 369ms 0.61% 86.07% 369ms 0.61% tetgen::tetgenmesh::org 5ms 0.0083% 86.08% 368ms 0.61% boost::numeric::ublas::c_vector::operator= (inline) 243ms 0.4% 86.48% 352ms 0.58% tetgen::tetgenmesh::bond 70ms 0.12% 86.59% 348ms 0.58% __dynamic_cast 20ms 0.033% 86.63% 346ms 0.57% std::vector::insert (inline) 9ms 0.015% 86.64% 344ms 0.57% VertexElement::~VertexElement 337ms 0.56% 87.20% 337ms 0.56% std::_Rb_tree_decrement 8ms 0.013% 87.21% 330ms 0.55% AbstractTetrahedralElement::AbstractTetrahedralElement 0 0% 87.21% 327ms 0.54% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 129ms 0.21% 87.43% 313ms 0.52% Inverse 1ms 0.0017% 87.43% 307ms 0.51% AbstractCellProperty::IsSubType (inline) 51ms 0.084% 87.51% 306ms 0.51% boost::numeric::ublas::vector_reference::operator() (inline)