File: Test3dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 58164ms, 86.63% of 67138ms total Dropped 881 nodes (cum <= 335.69ms) flat flat% sum% cum cum% 0 0% 0% 67087ms 99.92% __libc_start_call_main 0 0% 0% 67087ms 99.92% __libc_start_main_impl 0 0% 0% 67087ms 99.92% _start 0 0% 0% 67071ms 99.90% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 67071ms 99.90% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 67071ms 99.90% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 67071ms 99.90% main 0 0% 0% 67034ms 99.85% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 67034ms 99.85% CxxTest::TestRunner::runTest (inline) 0 0% 0% 67034ms 99.85% Test3dTissueRepresentativeSimulation::Test3DHoneycombMeshWithGhostNodes 0 0% 0% 66751ms 99.42% AbstractCellBasedSimulation::Solve 0 0% 0% 57399ms 85.49% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 57346ms 85.42% MeshBasedCellPopulation::Update 0 0% 0% 32762ms 48.80% MeshBasedCellPopulation::TessellateIfNeeded 0 0% 0% 32759ms 48.79% MeshBasedCellPopulation::CreateVoronoiTessellation (inline) 196ms 0.29% 0.29% 28829ms 42.94% VertexMesh::VertexMesh 1ms 0.0015% 0.29% 20429ms 30.43% MutableMesh::ReMesh 0 0% 0.29% 15884ms 23.66% tetgen::tetrahedralize 2ms 0.003% 0.3% 15729ms 23.43% tetgen::tetgenmesh::delaunizevertices 13ms 0.019% 0.32% 15725ms 23.42% tetgen::tetgenmesh::incrflipdelaunay 529ms 0.79% 1.10% 14002ms 20.86% tetgen::tetgenmesh::lawson 596ms 0.89% 1.99% 13168ms 19.61% TetrahedralMesh::EdgeIterator::operator++ 40ms 0.06% 2.05% 11513ms 17.15% std::set::insert (inline) 258ms 0.38% 2.44% 11065ms 16.48% std::_Rb_tree::_M_insert_unique 423ms 0.63% 3.07% 10382ms 15.46% VertexElement::AddFace 3252ms 4.84% 7.91% 9344ms 13.92% std::_Rb_tree::_M_lower_bound (inline) 263ms 0.39% 8.30% 8830ms 13.15% std::_Rb_tree::find (inline) 0 0% 8.30% 8280ms 12.33% std::set::count (inline) 306ms 0.46% 8.76% 6572ms 9.79% std::_Rb_tree::_M_insert_ (inline) 148ms 0.22% 8.98% 6105ms 9.09% operator new 116ms 0.17% 9.15% 5986ms 8.92% std::less::operator() (inline) 5967ms 8.89% 18.04% 5967ms 8.89% std::_Rb_tree_increment 5926ms 8.83% 26.86% 5926ms 8.83% std::operator< (inline) 1232ms 1.84% 28.70% 5879ms 8.76% __GI___libc_malloc 0 0% 28.70% 5617ms 8.37% OffLatticeSimulation::UpdateCellLocationsAndTopology 1ms 0.0015% 28.70% 5486ms 8.17% ForwardEulerNumericalMethod::UpdateAllNodePositions 1ms 0.0015% 28.70% 5459ms 8.13% AbstractNumericalMethod::ComputeForcesIncludingDamping 33ms 0.049% 28.75% 5152ms 7.67% std::__new_allocator::allocate (inline) 0 0% 28.75% 5138ms 7.65% std::allocator_traits::allocate (inline) 3ms 0.0045% 28.76% 4930ms 7.34% std::set_intersection (inline) 312ms 0.46% 29.22% 4927ms 7.34% std::__set_intersection 12ms 0.018% 29.24% 4604ms 6.86% std::_Rb_tree::~_Rb_tree (inline) 1676ms 2.50% 31.73% 4589ms 6.84% std::_Rb_tree::_M_erase 0 0% 31.73% 4570ms 6.81% MeshBasedCellPopulation::UpdateNodePairs 11ms 0.016% 31.75% 4557ms 6.79% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 0 0% 31.75% 4533ms 6.75% std::set::~set (inline) 1387ms 2.07% 33.82% 4503ms 6.71% std::_Rb_tree::_M_get_insert_unique_pos 1285ms 1.91% 35.73% 4453ms 6.63% __GI___libc_free 42ms 0.063% 35.79% 4410ms 6.57% Node::AddElement 13ms 0.019% 35.81% 4405ms 6.56% MeshBasedCellPopulation::SpringIterator::operator++ 3120ms 4.65% 40.46% 4280ms 6.37% _int_malloc 0 0% 40.46% 4261ms 6.35% std::_Rb_tree::_M_create_node (inline) 0 0% 40.46% 4235ms 6.31% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 40.46% 4224ms 6.29% std::_Rb_tree::_M_get_node (inline) 198ms 0.29% 40.75% 4147ms 6.18% std::_Rb_tree_const_iterator::operator++ (inline) 127ms 0.19% 40.94% 3955ms 5.89% std::__new_allocator::deallocate (inline) 0 0% 40.94% 3954ms 5.89% VertexMesh::~VertexMesh 0 0% 40.94% 3939ms 5.87% std::allocator_traits::deallocate (inline) 113ms 0.17% 41.11% 3910ms 5.82% tetgen::tetgenmesh::insphere_sos 3487ms 5.19% 46.31% 3786ms 5.64% tetgen::insphere 9ms 0.013% 46.32% 3623ms 5.40% TetrahedralMesh::ImportFromMesher 3589ms 5.35% 51.67% 3589ms 5.35% std::_Rb_tree::_S_right (inline) 0 0% 51.67% 3533ms 5.26% AbstractCellPopulation::WriteResultsToFiles 135ms 0.2% 51.87% 3437ms 5.12% tetgen::tetgenmesh::flip23 62ms 0.092% 51.96% 3333ms 4.96% MutableElement::AddNode 1365ms 2.03% 53.99% 3164ms 4.71% _int_free 197ms 0.29% 54.29% 2708ms 4.03% Node::~Node 162ms 0.24% 54.53% 2494ms 3.71% VertexMesh::Clear 133ms 0.2% 54.72% 2454ms 3.66% tetgen::tetgenmesh::flip32 7ms 0.01% 54.74% 2360ms 3.52% MeshBasedCellPopulationWithGhostNodes::WriteVtkResultsToFile 192ms 0.29% 55.02% 2323ms 3.46% VertexMesh::GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex 0 0% 55.02% 2210ms 3.29% std::_Rb_tree::_M_drop_node (inline) 0 0% 55.02% 2201ms 3.28% std::_Rb_tree::_M_put_node (inline) 1ms 0.0015% 55.02% 2147ms 3.20% std::_Rb_tree_iterator::operator++ (inline) 2101ms 3.13% 58.15% 2101ms 3.13% std::_Rb_tree_insert_and_rebalance 1974ms 2.94% 61.09% 1974ms 2.94% Node::GetIndex 3ms 0.0045% 61.10% 1896ms 2.82% Element::Element 214ms 0.32% 61.42% 1843ms 2.75% tetgen::tetgenmesh::enqueueflipface 1263ms 1.88% 63.30% 1790ms 2.67% malloc_consolidate 31ms 0.046% 63.34% 1768ms 2.63% std::_Vector_base::_M_deallocate (inline) 1606ms 2.39% 65.73% 1696ms 2.53% tetgen::orient3d 0 0% 65.73% 1682ms 2.51% std::vector::~vector (inline) 1ms 0.0015% 65.74% 1615ms 2.41% std::_Vector_base::~_Vector_base (inline) 3ms 0.0045% 65.74% 1557ms 2.32% Element::RegisterWithNodes (inline) 4ms 0.006% 65.75% 1544ms 2.30% _int_free_maybe_consolidate 42ms 0.063% 65.81% 1427ms 2.13% tetgen::tetgenmesh::locate 85ms 0.13% 65.94% 1356ms 2.02% TetrahedralMesh::Clear 1356ms 2.02% 67.96% 1356ms 2.02% unlink_chunk 72ms 0.11% 68.06% 1333ms 1.99% tetgen::tetgenmesh::preciselocate 967ms 1.44% 69.50% 1155ms 1.72% AbstractElement::GetNodeGlobalIndex 54ms 0.08% 69.58% 1152ms 1.72% std::vector::_M_realloc_insert 5ms 0.0074% 69.59% 1112ms 1.66% VertexMesh::GenerateVerticesFromElementCircumcentres 61ms 0.091% 69.68% 1101ms 1.64% std::map::operator[] 1054ms 1.57% 71.25% 1054ms 1.57% tetgen::tetgenmesh::oppo 989ms 1.47% 72.72% 989ms 1.47% tetgen::tetgenmesh::triface::triface 159ms 0.24% 72.96% 983ms 1.46% std::vector::push_back (inline) 0 0% 72.96% 964ms 1.44% std::_Rb_tree::lower_bound (inline) 0 0% 72.96% 964ms 1.44% std::map::lower_bound (inline) 0 0% 72.96% 927ms 1.38% VoronoiDataWriter::Visit 3ms 0.0045% 72.97% 917ms 1.37% std::_Vector_base::_M_allocate (inline) 0 0% 72.97% 901ms 1.34% TetrahedralMesh::RefreshJacobianCachedData 318ms 0.47% 73.44% 829ms 1.23% tetgen::tetgenmesh::sym 820ms 1.22% 74.66% 820ms 1.22% AbstractElement::IsDeleted 790ms 1.18% 75.84% 790ms 1.18% [libchaste_mesh.so] 373ms 0.56% 76.39% 782ms 1.16% AbstractElement::GetNodeLocation 5ms 0.0074% 76.40% 768ms 1.14% AbstractTetrahedralElement::CalculateInverseJacobian 1ms 0.0015% 76.40% 729ms 1.09% AbstractTwoBodyInteractionForce::AddForceContribution 16ms 0.024% 76.43% 721ms 1.07% AbstractTetrahedralElement::CalculateJacobian 18ms 0.027% 76.45% 688ms 1.02% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 681ms 1.01% 77.47% 681ms 1.01% Node::rGetLocation 671ms 1% 78.47% 671ms 1% tetgen::tetgenmesh::triface::operator= 203ms 0.3% 78.77% 630ms 0.94% tetgen::tetgenmesh::bond 621ms 0.92% 79.69% 621ms 0.92% std::vector::size (inline) 368ms 0.55% 80.24% 609ms 0.91% tetgen::tetgenmesh::fnextself 48ms 0.071% 80.31% 602ms 0.9% __atan2 20ms 0.03% 80.34% 591ms 0.88% boost::numeric::ublas::vector_assign (inline) 19ms 0.028% 80.37% 588ms 0.88% boost::numeric::ublas::c_vector::c_vector (inline) 46ms 0.069% 80.44% 580ms 0.86% tetgen::tetgenmesh::enextfnext 29ms 0.043% 80.48% 571ms 0.85% tetgen::tetgenmesh::queue::push 61ms 0.091% 80.57% 565ms 0.84% tetgen::tetgenmesh::enext2fnext 47ms 0.07% 80.64% 550ms 0.82% AbstractTetrahedralElement::RefreshJacobian 0 0% 80.64% 547ms 0.81% std::set::find (inline) 428ms 0.64% 81.28% 546ms 0.81% __ieee754_atan2_fma 311ms 0.46% 81.75% 542ms 0.81% tetgen::tetgenmesh::link::add 24ms 0.036% 81.78% 536ms 0.8% Element::CalculateCircumsphere 0 0% 81.78% 529ms 0.79% boost::numeric::ublas::inner_prod (inline) 2ms 0.003% 81.78% 526ms 0.78% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 49ms 0.073% 81.86% 524ms 0.78% boost::numeric::ublas::vector_scalar_binary::evaluate 519ms 0.77% 82.63% 519ms 0.77% tetgen::tetgenmesh::decode 0 0% 82.63% 468ms 0.7% std::insert_iterator::operator= (inline) 28ms 0.042% 82.67% 443ms 0.66% std::_Rb_tree_iterator::operator-- (inline) 435ms 0.65% 83.32% 435ms 0.65% tetgen::tetgenmesh::org 13ms 0.019% 83.34% 434ms 0.65% VertexMesh::CalculateUnitNormalToFaceWithArea 217ms 0.32% 83.66% 427ms 0.64% AbstractTetrahedralMesh::GetElement 196ms 0.29% 83.95% 423ms 0.63% boost::numeric::ublas::vector_inner_prod::apply (inline) 6ms 0.0089% 83.96% 417ms 0.62% boost::numeric::ublas::c_vector::operator= (inline) 414ms 0.62% 84.58% 414ms 0.62% boost::numeric::ublas::c_vector::operator() 410ms 0.61% 85.19% 410ms 0.61% tetgen::tetgenmesh::encode 0 0% 85.19% 408ms 0.61% std::_Rb_tree::_M_insert_unique_ (inline) 3ms 0.0045% 85.19% 395ms 0.59% CellPropertyCollection::GetPropertiesType (inline) 0 0% 85.19% 394ms 0.59% VertexMeshWriter::WriteVtkUsingMesh 117ms 0.17% 85.37% 393ms 0.59% __dynamic_cast 390ms 0.58% 85.95% 390ms 0.58% std::_Rb_tree_decrement 1ms 0.0015% 85.95% 384ms 0.57% Cell::GetCellId 97ms 0.14% 86.10% 376ms 0.56% boost::numeric::ublas::indexing_vector_assign 6ms 0.0089% 86.10% 368ms 0.55% VertexElement::~VertexElement 0 0% 86.10% 364ms 0.54% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 12ms 0.018% 86.12% 350ms 0.52% std::vector::insert (inline) 4ms 0.006% 86.13% 339ms 0.5% AbstractTetrahedralElement::AbstractTetrahedralElement 339ms 0.5% 86.63% 339ms 0.5% tetgen::tetgenmesh::pointmark