File: Test3dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 55778ms, 87.09% of 64044ms total Dropped 850 nodes (cum <= 320.22ms) flat flat% sum% cum cum% 0 0% 0% 63976ms 99.89% __libc_start_call_main 0 0% 0% 63976ms 99.89% __libc_start_main_impl 0 0% 0% 63976ms 99.89% _start 0 0% 0% 63960ms 99.87% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 63960ms 99.87% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 63960ms 99.87% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 63960ms 99.87% main 0 0% 0% 63923ms 99.81% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 63923ms 99.81% CxxTest::TestRunner::runTest (inline) 0 0% 0% 63923ms 99.81% Test3dTissueRepresentativeSimulation::Test3DHoneycombMeshWithGhostNodes 2ms 0.0031% 0.0031% 63658ms 99.40% AbstractCellBasedSimulation::Solve 0 0% 0.0031% 54579ms 85.22% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0.0031% 54540ms 85.16% MeshBasedCellPopulation::Update 0 0% 0.0031% 32961ms 51.47% MeshBasedCellPopulation::CreateVoronoiTessellation (inline) 0 0% 0.0031% 32961ms 51.47% MeshBasedCellPopulation::TessellateIfNeeded 267ms 0.42% 0.42% 28676ms 44.78% VertexMesh::VertexMesh 0 0% 0.42% 17516ms 27.35% MutableMesh::ReMesh 0 0% 0.42% 12826ms 20.03% tetgen::tetrahedralize 1ms 0.0016% 0.42% 12690ms 19.81% tetgen::tetgenmesh::delaunizevertices 8ms 0.012% 0.43% 12687ms 19.81% tetgen::tetgenmesh::incrflipdelaunay 557ms 0.87% 1.30% 12530ms 19.56% TetrahedralMesh::EdgeIterator::operator++ 579ms 0.9% 2.21% 11277ms 17.61% tetgen::tetgenmesh::lawson 32ms 0.05% 2.26% 11094ms 17.32% std::set::insert (inline) 193ms 0.3% 2.56% 10613ms 16.57% std::_Rb_tree::_M_insert_unique 396ms 0.62% 3.18% 9884ms 15.43% VertexElement::AddFace 3123ms 4.88% 8.05% 9169ms 14.32% std::_Rb_tree::_M_lower_bound (inline) 243ms 0.38% 8.43% 8554ms 13.36% std::_Rb_tree::find (inline) 0 0% 8.43% 7975ms 12.45% std::set::count (inline) 236ms 0.37% 8.80% 6229ms 9.73% std::_Rb_tree::_M_insert_ (inline) 6060ms 9.46% 18.26% 6060ms 9.46% std::_Rb_tree_increment 196ms 0.31% 18.57% 5997ms 9.36% operator new 113ms 0.18% 18.75% 5855ms 9.14% std::less::operator() (inline) 5814ms 9.08% 27.82% 5814ms 9.08% std::operator< (inline) 1130ms 1.76% 29.59% 5733ms 8.95% __GI___libc_malloc 0 0% 29.59% 5435ms 8.49% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 29.59% 5295ms 8.27% ForwardEulerNumericalMethod::UpdateAllNodePositions 1ms 0.0016% 29.59% 5271ms 8.23% AbstractNumericalMethod::ComputeForcesIncludingDamping 1ms 0.0016% 29.59% 4984ms 7.78% std::set_intersection (inline) 269ms 0.42% 30.01% 4983ms 7.78% std::__set_intersection 44ms 0.069% 30.08% 4931ms 7.70% std::__new_allocator::allocate (inline) 0 0% 30.08% 4915ms 7.67% std::allocator_traits::allocate (inline) 5ms 0.0078% 30.09% 4733ms 7.39% std::_Rb_tree::~_Rb_tree (inline) 1928ms 3.01% 33.10% 4726ms 7.38% std::_Rb_tree::_M_erase 0 0% 33.10% 4671ms 7.29% std::set::~set (inline) 30ms 0.047% 33.15% 4646ms 7.25% Node::AddElement 1249ms 1.95% 35.10% 4491ms 7.01% std::_Rb_tree::_M_get_insert_unique_pos 1272ms 1.99% 37.08% 4421ms 6.90% __GI___libc_free 1ms 0.0016% 37.08% 4404ms 6.88% MeshBasedCellPopulation::UpdateNodePairs 1ms 0.0016% 37.09% 4389ms 6.85% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 0 0% 37.09% 4312ms 6.73% VertexMesh::~VertexMesh 3143ms 4.91% 41.99% 4284ms 6.69% _int_malloc 12ms 0.019% 42.01% 4245ms 6.63% MeshBasedCellPopulation::SpringIterator::operator++ 173ms 0.27% 42.28% 4213ms 6.58% std::_Rb_tree_const_iterator::operator++ (inline) 4022ms 6.28% 48.56% 4022ms 6.28% std::_Rb_tree::_S_right (inline) 0 0% 48.56% 3954ms 6.17% std::_Rb_tree::_M_create_node (inline) 0 0% 48.56% 3926ms 6.13% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 48.56% 3901ms 6.09% std::_Rb_tree::_M_get_node (inline) 112ms 0.17% 48.74% 3867ms 6.04% std::__new_allocator::deallocate (inline) 0 0% 48.74% 3846ms 6.01% std::allocator_traits::deallocate (inline) 7ms 0.011% 48.75% 3744ms 5.85% TetrahedralMesh::ImportFromMesher 92ms 0.14% 48.89% 3558ms 5.56% MutableElement::AddNode 0 0% 48.89% 3488ms 5.45% AbstractCellPopulation::WriteResultsToFiles 116ms 0.18% 49.07% 3453ms 5.39% tetgen::tetgenmesh::insphere_sos 3029ms 4.73% 53.80% 3324ms 5.19% tetgen::insphere 1177ms 1.84% 55.64% 3144ms 4.91% _int_free 184ms 0.29% 55.93% 2871ms 4.48% Node::~Node 220ms 0.34% 56.27% 2738ms 4.28% tetgen::tetgenmesh::flip23 216ms 0.34% 56.61% 2682ms 4.19% VertexMesh::Clear 2ms 0.0031% 56.61% 2307ms 3.60% MeshBasedCellPopulationWithGhostNodes::WriteVtkResultsToFile 209ms 0.33% 56.94% 2297ms 3.59% VertexMesh::GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex 2151ms 3.36% 60.30% 2151ms 3.36% std::_Rb_tree_insert_and_rebalance 0 0% 60.30% 2111ms 3.30% std::_Rb_tree_iterator::operator++ (inline) 2041ms 3.19% 63.48% 2041ms 3.19% Node::GetIndex 1338ms 2.09% 65.57% 1974ms 3.08% malloc_consolidate 0 0% 65.57% 1941ms 3.03% std::_Rb_tree::_M_drop_node (inline) 0 0% 65.57% 1933ms 3.02% std::_Rb_tree::_M_put_node (inline) 16ms 0.025% 65.60% 1929ms 3.01% std::_Vector_base::_M_deallocate (inline) 2ms 0.0031% 65.60% 1909ms 2.98% Element::Element 152ms 0.24% 65.84% 1857ms 2.90% tetgen::tetgenmesh::flip32 0 0% 65.84% 1787ms 2.79% std::vector::~vector (inline) 0 0% 65.84% 1750ms 2.73% std::_Vector_base::~_Vector_base (inline) 7ms 0.011% 65.85% 1717ms 2.68% _int_free_maybe_consolidate 3ms 0.0047% 65.85% 1592ms 2.49% Element::RegisterWithNodes (inline) 1471ms 2.30% 68.15% 1471ms 2.30% unlink_chunk 222ms 0.35% 68.50% 1466ms 2.29% TetrahedralMesh::Clear 1280ms 2.00% 70.50% 1371ms 2.14% tetgen::orient3d 183ms 0.29% 70.78% 1329ms 2.08% tetgen::tetgenmesh::enqueueflipface 6ms 0.0094% 70.79% 1310ms 2.05% VertexMesh::GenerateVerticesFromElementCircumcentres 62ms 0.097% 70.89% 1194ms 1.86% std::vector::_M_realloc_insert 37ms 0.058% 70.94% 1192ms 1.86% tetgen::tetgenmesh::locate 57ms 0.089% 71.03% 1158ms 1.81% std::map::operator[] 1002ms 1.56% 72.60% 1140ms 1.78% AbstractElement::GetNodeGlobalIndex 73ms 0.11% 72.71% 1115ms 1.74% tetgen::tetgenmesh::preciselocate 0 0% 72.71% 1033ms 1.61% std::_Rb_tree::lower_bound (inline) 0 0% 72.71% 1033ms 1.61% std::map::lower_bound (inline) 0 0% 72.71% 1014ms 1.58% std::_Vector_base::_M_allocate (inline) 94ms 0.15% 72.86% 950ms 1.48% std::vector::push_back (inline) 0 0% 72.86% 937ms 1.46% VoronoiDataWriter::Visit 1ms 0.0016% 72.86% 923ms 1.44% TetrahedralMesh::RefreshJacobianCachedData 825ms 1.29% 74.15% 825ms 1.29% tetgen::tetgenmesh::triface::triface 389ms 0.61% 74.76% 807ms 1.26% AbstractElement::GetNodeLocation 793ms 1.24% 75.99% 793ms 1.24% AbstractElement::IsDeleted 782ms 1.22% 77.22% 782ms 1.22% Node::rGetLocation 13ms 0.02% 77.24% 770ms 1.20% AbstractTetrahedralElement::CalculateInverseJacobian 1ms 0.0016% 77.24% 710ms 1.11% AbstractTwoBodyInteractionForce::AddForceContribution 15ms 0.023% 77.26% 703ms 1.10% AbstractTetrahedralElement::CalculateJacobian 402ms 0.63% 77.89% 687ms 1.07% tetgen::tetgenmesh::fnextself 687ms 1.07% 78.96% 687ms 1.07% tetgen::tetgenmesh::triface::operator= 18ms 0.028% 78.99% 680ms 1.06% boost::numeric::ublas::vector_assign (inline) 672ms 1.05% 80.04% 672ms 1.05% tetgen::tetgenmesh::oppo 8ms 0.012% 80.05% 662ms 1.03% AbstractVariableSizeTwoBodyInteractionForce::CalculateForceBetweenNodes 9ms 0.014% 80.07% 644ms 1.01% boost::numeric::ublas::c_vector::c_vector (inline) 637ms 0.99% 81.06% 637ms 0.99% [libchaste_mesh.so] 18ms 0.028% 81.09% 621ms 0.97% Element::CalculateCircumsphere 42ms 0.066% 81.15% 588ms 0.92% __atan2 0 0% 81.15% 577ms 0.9% std::set::find (inline) 417ms 0.65% 81.80% 546ms 0.85% __ieee754_atan2_fma 49ms 0.077% 81.88% 533ms 0.83% AbstractTetrahedralElement::RefreshJacobian 533ms 0.83% 82.71% 533ms 0.83% std::vector::size (inline) 0 0% 82.71% 493ms 0.77% std::insert_iterator::operator= (inline) 0 0% 82.71% 482ms 0.75% boost::numeric::ublas::inner_prod (inline) 4ms 0.0062% 82.72% 480ms 0.75% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 27ms 0.042% 82.76% 476ms 0.74% boost::numeric::ublas::vector_scalar_binary::evaluate 317ms 0.49% 83.26% 458ms 0.72% tetgen::tetgenmesh::sym 39ms 0.061% 83.32% 455ms 0.71% tetgen::tetgenmesh::enextfnext 37ms 0.058% 83.38% 448ms 0.7% tetgen::tetgenmesh::enext2fnext 0 0% 83.38% 432ms 0.67% std::_Rb_tree::_M_insert_unique_ (inline) 120ms 0.19% 83.56% 429ms 0.67% boost::numeric::ublas::indexing_vector_assign 429ms 0.67% 84.23% 429ms 0.67% tetgen::tetgenmesh::org 23ms 0.036% 84.27% 417ms 0.65% tetgen::tetgenmesh::queue::push 10ms 0.016% 84.28% 408ms 0.64% CellPropertyCollection::GetPropertiesType (inline) 14ms 0.022% 84.31% 407ms 0.64% VertexMesh::CalculateUnitNormalToFaceWithArea 232ms 0.36% 84.67% 405ms 0.63% AbstractTetrahedralMesh::GetElement 1ms 0.0016% 84.67% 398ms 0.62% VertexMeshWriter::WriteVtkUsingMesh 286ms 0.45% 85.12% 398ms 0.62% tetgen::tetgenmesh::bond 83ms 0.13% 85.25% 396ms 0.62% __dynamic_cast 0 0% 85.25% 392ms 0.61% Cell::GetCellId 261ms 0.41% 85.65% 392ms 0.61% tetgen::tetgenmesh::link::add 0 0% 85.65% 391ms 0.61% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 171ms 0.27% 85.92% 391ms 0.61% boost::numeric::ublas::vector_inner_prod::apply (inline) 20ms 0.031% 85.95% 383ms 0.6% std::_Rb_tree_iterator::operator-- (inline) 0 0% 85.95% 377ms 0.59% boost::numeric::ublas::c_vector::operator= (inline) 365ms 0.57% 86.52% 365ms 0.57% boost::numeric::ublas::c_vector::operator() 9ms 0.014% 86.54% 356ms 0.56% std::vector::insert (inline) 344ms 0.54% 87.07% 344ms 0.54% std::_Rb_tree_decrement 11ms 0.017% 87.09% 337ms 0.53% VertexElement::~VertexElement 2ms 0.0031% 87.09% 335ms 0.52% AbstractCellProperty::IsSubType (inline)