File: Test3dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 49822ms, 86.47% of 57615ms total Dropped 871 nodes (cum <= 288.07ms) flat flat% sum% cum cum% 0 0% 0% 57566ms 99.91% __libc_start_call_main 0 0% 0% 57566ms 99.91% __libc_start_main_impl 0 0% 0% 57566ms 99.91% _start 0 0% 0% 57552ms 99.89% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 57552ms 99.89% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 57552ms 99.89% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 57552ms 99.89% main 0 0% 0% 57511ms 99.82% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 57511ms 99.82% CxxTest::TestRunner::runTest (inline) 0 0% 0% 57511ms 99.82% Test3dTissueRepresentativeSimulation::Test3DHoneycombMeshWithGhostNodes 1ms 0.0017% 0.0017% 57243ms 99.35% AbstractCellBasedSimulation::Solve 0 0% 0.0017% 48706ms 84.54% AbstractCellBasedSimulation::UpdateCellPopulation 1ms 0.0017% 0.0035% 48659ms 84.46% MeshBasedCellPopulation::Update 0 0% 0.0035% 28039ms 48.67% MeshBasedCellPopulation::TessellateIfNeeded 0 0% 0.0035% 28038ms 48.66% MeshBasedCellPopulation::CreateVoronoiTessellation (inline) 199ms 0.35% 0.35% 24695ms 42.86% VertexMesh::VertexMesh 0 0% 0.35% 16847ms 29.24% MutableMesh::ReMesh 1ms 0.0017% 0.35% 12807ms 22.23% tetgen::tetrahedralize 2ms 0.0035% 0.35% 12664ms 21.98% tetgen::tetgenmesh::delaunizevertices 7ms 0.012% 0.37% 12659ms 21.97% tetgen::tetgenmesh::incrflipdelaunay 570ms 0.99% 1.36% 11575ms 20.09% TetrahedralMesh::EdgeIterator::operator++ 604ms 1.05% 2.40% 11213ms 19.46% tetgen::tetgenmesh::lawson 29ms 0.05% 2.45% 9899ms 17.18% std::set::insert (inline) 234ms 0.41% 2.86% 9413ms 16.34% std::_Rb_tree::_M_insert_unique 359ms 0.62% 3.48% 9228ms 16.02% VertexElement::AddFace 3049ms 5.29% 8.78% 8575ms 14.88% std::_Rb_tree::_M_lower_bound (inline) 236ms 0.41% 9.19% 8062ms 13.99% std::_Rb_tree::find (inline) 0 0% 9.19% 7472ms 12.97% std::set::count (inline) 275ms 0.48% 9.66% 5613ms 9.74% std::_Rb_tree::_M_insert_ (inline) 110ms 0.19% 9.85% 5383ms 9.34% std::less::operator() (inline) 5335ms 9.26% 19.11% 5335ms 9.26% std::operator< (inline) 0 0% 19.11% 5143ms 8.93% OffLatticeSimulation::UpdateCellLocationsAndTopology 223ms 0.39% 19.50% 5020ms 8.71% operator new 0 0% 19.50% 5016ms 8.71% ForwardEulerNumericalMethod::UpdateAllNodePositions 2ms 0.0035% 19.50% 4988ms 8.66% AbstractNumericalMethod::ComputeForcesIncludingDamping 1122ms 1.95% 21.45% 4711ms 8.18% __GI___libc_malloc 4575ms 7.94% 29.39% 4575ms 7.94% std::_Rb_tree_increment 10ms 0.017% 29.41% 4308ms 7.48% std::_Rb_tree::~_Rb_tree (inline) 1602ms 2.78% 32.19% 4297ms 7.46% std::_Rb_tree::_M_erase 47ms 0.082% 32.27% 4267ms 7.41% std::__new_allocator::allocate (inline) 0 0% 32.27% 4262ms 7.40% std::set::~set (inline) 0 0% 32.27% 4244ms 7.37% std::allocator_traits::allocate (inline) 1ms 0.0017% 32.27% 4119ms 7.15% MeshBasedCellPopulation::UpdateNodePairs 4ms 0.0069% 32.28% 4116ms 7.14% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 14ms 0.024% 32.30% 3969ms 6.89% MeshBasedCellPopulation::SpringIterator::operator++ 1286ms 2.23% 34.54% 3884ms 6.74% std::_Rb_tree::_M_get_insert_unique_pos 1232ms 2.14% 36.67% 3842ms 6.67% __GI___libc_free 3ms 0.0052% 36.68% 3663ms 6.36% std::set_intersection (inline) 266ms 0.46% 37.14% 3660ms 6.35% std::__set_intersection 107ms 0.19% 37.33% 3518ms 6.11% tetgen::tetgenmesh::insphere_sos 23ms 0.04% 37.37% 3508ms 6.09% Node::AddElement 0 0% 37.37% 3482ms 6.04% std::_Rb_tree::_M_create_node (inline) 0 0% 37.37% 3452ms 5.99% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 37.37% 3442ms 5.97% std::_Rb_tree::_M_get_node (inline) 136ms 0.24% 37.60% 3413ms 5.92% std::__new_allocator::deallocate (inline) 3100ms 5.38% 42.98% 3399ms 5.90% tetgen::insphere 0 0% 42.98% 3393ms 5.89% std::allocator_traits::deallocate (inline) 0 0% 42.98% 3376ms 5.86% VertexMesh::~VertexMesh 2389ms 4.15% 47.13% 3274ms 5.68% _int_malloc 4ms 0.0069% 47.14% 3254ms 5.65% TetrahedralMesh::ImportFromMesher 0 0% 47.14% 3241ms 5.63% AbstractCellPopulation::WriteResultsToFiles 3146ms 5.46% 52.60% 3146ms 5.46% std::_Rb_tree::_S_right (inline) 205ms 0.36% 52.95% 2950ms 5.12% std::_Rb_tree_const_iterator::operator++ (inline) 91ms 0.16% 53.11% 2832ms 4.92% MutableElement::AddNode 190ms 0.33% 53.44% 2675ms 4.64% tetgen::tetgenmesh::flip23 1195ms 2.07% 55.52% 2608ms 4.53% _int_free 190ms 0.33% 55.84% 2467ms 4.28% Node::~Node 216ms 0.37% 56.22% 2253ms 3.91% VertexMesh::Clear 1ms 0.0017% 56.22% 2134ms 3.70% MeshBasedCellPopulationWithGhostNodes::WriteVtkResultsToFile 200ms 0.35% 56.57% 2119ms 3.68% VertexMesh::GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex 0 0% 56.57% 2006ms 3.48% std::_Rb_tree::_M_drop_node (inline) 0 0% 56.57% 1993ms 3.46% std::_Rb_tree::_M_put_node (inline) 1972ms 3.42% 59.99% 1972ms 3.42% std::_Rb_tree_insert_and_rebalance 0 0% 59.99% 1927ms 3.34% std::_Rb_tree_iterator::operator++ (inline) 141ms 0.24% 60.24% 1806ms 3.13% tetgen::tetgenmesh::flip32 5ms 0.0087% 60.24% 1486ms 2.58% Element::Element 212ms 0.37% 60.61% 1425ms 2.47% TetrahedralMesh::Clear 14ms 0.024% 60.64% 1414ms 2.45% std::_Vector_base::_M_deallocate (inline) 1319ms 2.29% 62.93% 1406ms 2.44% tetgen::orient3d 1390ms 2.41% 65.34% 1390ms 2.41% Node::GetIndex 940ms 1.63% 66.97% 1389ms 2.41% malloc_consolidate 0 0% 66.97% 1320ms 2.29% std::vector::~vector (inline) 175ms 0.3% 67.27% 1284ms 2.23% tetgen::tetgenmesh::enqueueflipface 0 0% 67.27% 1257ms 2.18% std::_Vector_base::~_Vector_base (inline) 30ms 0.052% 67.33% 1227ms 2.13% tetgen::tetgenmesh::locate 10ms 0.017% 67.34% 1196ms 2.08% _int_free_maybe_consolidate 2ms 0.0035% 67.35% 1176ms 2.04% Element::RegisterWithNodes (inline) 109ms 0.19% 67.54% 1150ms 2.00% tetgen::tetgenmesh::preciselocate 1074ms 1.86% 69.40% 1074ms 1.86% unlink_chunk 62ms 0.11% 69.51% 1046ms 1.82% std::vector::_M_realloc_insert 62ms 0.11% 69.62% 1045ms 1.81% std::map::operator[] 965ms 1.67% 71.29% 965ms 1.67% tetgen::tetgenmesh::triface::triface 765ms 1.33% 72.62% 929ms 1.61% AbstractElement::GetNodeGlobalIndex 3ms 0.0052% 72.62% 924ms 1.60% VertexMesh::GenerateVerticesFromElementCircumcentres 0 0% 72.62% 912ms 1.58% std::_Rb_tree::lower_bound (inline) 0 0% 72.62% 912ms 1.58% std::map::lower_bound (inline) 0 0% 72.62% 870ms 1.51% VoronoiDataWriter::Visit 111ms 0.19% 72.82% 852ms 1.48% std::vector::push_back (inline) 9ms 0.016% 72.83% 811ms 1.41% std::_Vector_base::_M_allocate (inline) 1ms 0.0017% 72.83% 767ms 1.33% TetrahedralMesh::RefreshJacobianCachedData 0 0% 72.83% 714ms 1.24% AbstractTwoBodyInteractionForce::AddForceContribution 703ms 1.22% 74.05% 703ms 1.22% [libchaste_mesh.so] 357ms 0.62% 74.67% 701ms 1.22% tetgen::tetgenmesh::fnextself 10ms 0.017% 74.69% 699ms 1.21% AbstractTetrahedralElement::CalculateInverseJacobian 17ms 0.03% 74.72% 693ms 1.20% boost::numeric::ublas::vector_assign (inline) 10ms 0.017% 74.74% 685ms 1.19% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 679ms 1.18% 75.92% 679ms 1.18% tetgen::tetgenmesh::oppo 11ms 0.019% 75.94% 653ms 1.13% boost::numeric::ublas::c_vector::c_vector (inline) 11ms 0.019% 75.95% 642ms 1.11% AbstractTetrahedralElement::CalculateJacobian 273ms 0.47% 76.43% 624ms 1.08% AbstractElement::GetNodeLocation 0 0% 76.43% 587ms 1.02% std::set::find (inline) 45ms 0.078% 76.51% 582ms 1.01% __atan2 572ms 0.99% 77.50% 572ms 0.99% tetgen::tetgenmesh::triface::operator= 565ms 0.98% 78.48% 565ms 0.98% Node::rGetLocation 550ms 0.95% 79.43% 550ms 0.95% AbstractElement::IsDeleted 421ms 0.73% 80.16% 536ms 0.93% __ieee754_atan2_fma 531ms 0.92% 81.09% 531ms 0.92% std::vector::size (inline) 57ms 0.099% 81.19% 496ms 0.86% AbstractTetrahedralElement::RefreshJacobian 0 0% 81.19% 493ms 0.86% std::insert_iterator::operator= (inline) 16ms 0.028% 81.21% 492ms 0.85% Element::CalculateCircumsphere 49ms 0.085% 81.30% 476ms 0.83% tetgen::tetgenmesh::enextfnext 286ms 0.5% 81.79% 450ms 0.78% tetgen::tetgenmesh::sym 119ms 0.21% 82.00% 444ms 0.77% boost::numeric::ublas::indexing_vector_assign 0 0% 82.00% 438ms 0.76% boost::numeric::ublas::inner_prod (inline) 7ms 0.012% 82.01% 433ms 0.75% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 0 0% 82.01% 433ms 0.75% std::_Rb_tree::_M_insert_unique_ (inline) 25ms 0.043% 82.06% 430ms 0.75% tetgen::tetgenmesh::enext2fnext 236ms 0.41% 82.47% 428ms 0.74% AbstractTetrahedralMesh::GetElement 428ms 0.74% 83.21% 428ms 0.74% boost::numeric::ublas::c_vector::operator() 18ms 0.031% 83.24% 426ms 0.74% boost::numeric::ublas::vector_scalar_binary::evaluate 400ms 0.69% 83.93% 400ms 0.69% tetgen::tetgenmesh::org 4ms 0.0069% 83.94% 399ms 0.69% CellPropertyCollection::GetPropertiesType (inline) 5ms 0.0087% 83.95% 390ms 0.68% boost::numeric::ublas::c_vector::operator= (inline) 84ms 0.15% 84.10% 389ms 0.68% __dynamic_cast 4ms 0.0069% 84.10% 386ms 0.67% Cell::GetCellId 30ms 0.052% 84.16% 386ms 0.67% std::_Rb_tree_iterator::operator-- (inline) 0 0% 84.16% 385ms 0.67% VertexMeshWriter::WriteVtkUsingMesh 20ms 0.035% 84.19% 382ms 0.66% tetgen::tetgenmesh::queue::push 16ms 0.028% 84.22% 379ms 0.66% VertexMesh::CalculateUnitNormalToFaceWithArea 142ms 0.25% 84.46% 364ms 0.63% boost::numeric::ublas::vector_inner_prod::apply (inline) 252ms 0.44% 84.90% 360ms 0.62% tetgen::tetgenmesh::link::add 253ms 0.44% 85.34% 339ms 0.59% tetgen::tetgenmesh::bond 338ms 0.59% 85.93% 338ms 0.59% std::_Rb_tree_decrement 16ms 0.028% 85.96% 331ms 0.57% std::vector::insert (inline) 0 0% 85.96% 327ms 0.57% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 72ms 0.12% 86.08% 322ms 0.56% tetgen::tetgenmesh::queue::pop 4ms 0.0069% 86.09% 317ms 0.55% AbstractCellProperty::IsSubType (inline) 54ms 0.094% 86.18% 317ms 0.55% boost::numeric::ublas::vector_reference::operator() (inline) 8ms 0.014% 86.19% 311ms 0.54% VertexElement::~VertexElement 119ms 0.21% 86.40% 310ms 0.54% Inverse 5ms 0.0087% 86.41% 304ms 0.53% AbstractTetrahedralElement::AbstractTetrahedralElement 37ms 0.064% 86.47% 298ms 0.52% tetgen::insphereadapt