File: Test3dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 63920ms, 86.86% of 73587ms total Dropped 904 nodes (cum <= 367.94ms) flat flat% sum% cum cum% 0 0% 0% 73526ms 99.92% __libc_start_call_main 0 0% 0% 73526ms 99.92% __libc_start_main_impl 0 0% 0% 73526ms 99.92% _start 0 0% 0% 73507ms 99.89% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 73507ms 99.89% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 73507ms 99.89% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 73507ms 99.89% main 0 0% 0% 73465ms 99.83% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 73465ms 99.83% CxxTest::TestRunner::runTest (inline) 0 0% 0% 73465ms 99.83% Test3dTissueRepresentativeSimulation::Test3DHoneycombMeshWithGhostNodes 0 0% 0% 73160ms 99.42% AbstractCellBasedSimulation::Solve 0 0% 0% 62290ms 84.65% AbstractCellBasedSimulation::UpdateCellPopulation 1ms 0.0014% 0.0014% 62236ms 84.57% MeshBasedCellPopulation::Update 0 0% 0.0014% 36424ms 49.50% MeshBasedCellPopulation::TessellateIfNeeded 0 0% 0.0014% 36423ms 49.50% MeshBasedCellPopulation::CreateVoronoiTessellation (inline) 259ms 0.35% 0.35% 31643ms 43.00% VertexMesh::VertexMesh 0 0% 0.35% 21119ms 28.70% MutableMesh::ReMesh 0 0% 0.35% 16167ms 21.97% tetgen::tetrahedralize 1ms 0.0014% 0.35% 16007ms 21.75% tetgen::tetgenmesh::delaunizevertices 12ms 0.016% 0.37% 16000ms 21.74% tetgen::tetgenmesh::incrflipdelaunay 605ms 0.82% 1.19% 14706ms 19.98% TetrahedralMesh::EdgeIterator::operator++ 559ms 0.76% 1.95% 14287ms 19.42% tetgen::tetgenmesh::lawson 37ms 0.05% 2.00% 11960ms 16.25% std::set::insert (inline) 250ms 0.34% 2.34% 11490ms 15.61% std::_Rb_tree::_M_insert_unique 471ms 0.64% 2.98% 11070ms 15.04% VertexElement::AddFace 3243ms 4.41% 7.39% 10781ms 14.65% std::_Rb_tree::_M_lower_bound (inline) 282ms 0.38% 7.77% 10120ms 13.75% std::_Rb_tree::find (inline) 0 0% 7.77% 9517ms 12.93% std::set::count (inline) 7317ms 9.94% 17.72% 7317ms 9.94% std::_Rb_tree_increment 97ms 0.13% 17.85% 7211ms 9.80% std::less::operator() (inline) 7177ms 9.75% 27.60% 7177ms 9.75% std::operator< (inline) 297ms 0.4% 28.00% 6792ms 9.23% std::_Rb_tree::_M_insert_ (inline) 195ms 0.26% 28.27% 6601ms 8.97% operator new 1281ms 1.74% 30.01% 6334ms 8.61% __GI___libc_malloc 1ms 0.0014% 30.01% 6304ms 8.57% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 30.01% 6130ms 8.33% ForwardEulerNumericalMethod::UpdateAllNodePositions 7ms 0.0095% 30.02% 6106ms 8.30% AbstractNumericalMethod::ComputeForcesIncludingDamping 3ms 0.0041% 30.03% 5506ms 7.48% std::set_intersection (inline) 339ms 0.46% 30.49% 5503ms 7.48% std::__set_intersection 35ms 0.048% 30.53% 5456ms 7.41% std::__new_allocator::allocate (inline) 0 0% 30.53% 5440ms 7.39% std::allocator_traits::allocate (inline) 10ms 0.014% 30.55% 5196ms 7.06% std::_Rb_tree::~_Rb_tree (inline) 1985ms 2.70% 33.25% 5183ms 7.04% std::_Rb_tree::_M_erase 0 0% 33.25% 5132ms 6.97% std::set::~set (inline) 10ms 0.014% 33.26% 5092ms 6.92% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 0 0% 33.26% 5075ms 6.90% MeshBasedCellPopulation::UpdateNodePairs 1408ms 1.91% 35.17% 5059ms 6.87% __GI___libc_free 24ms 0.033% 35.20% 4890ms 6.65% MeshBasedCellPopulation::SpringIterator::operator++ 39ms 0.053% 35.26% 4828ms 6.56% Node::AddElement 0 0% 35.26% 4823ms 6.55% VertexMesh::~VertexMesh 1353ms 1.84% 37.10% 4739ms 6.44% std::_Rb_tree::_M_get_insert_unique_pos 178ms 0.24% 37.34% 4672ms 6.35% std::_Rb_tree_const_iterator::operator++ (inline) 3352ms 4.56% 41.89% 4657ms 6.33% _int_malloc 153ms 0.21% 42.10% 4428ms 6.02% std::__new_allocator::deallocate (inline) 0 0% 42.10% 4410ms 5.99% std::allocator_traits::deallocate (inline) 0 0% 42.10% 4398ms 5.98% AbstractCellPopulation::WriteResultsToFiles 0 0% 42.10% 4396ms 5.97% std::_Rb_tree::_M_create_node (inline) 0 0% 42.10% 4358ms 5.92% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 42.10% 4358ms 5.92% std::_Rb_tree::_M_get_node (inline) 4296ms 5.84% 47.94% 4296ms 5.84% std::_Rb_tree::_S_right (inline) 11ms 0.015% 47.95% 4000ms 5.44% TetrahedralMesh::ImportFromMesher 116ms 0.16% 48.11% 3910ms 5.31% tetgen::tetgenmesh::insphere_sos 3480ms 4.73% 52.84% 3778ms 5.13% tetgen::insphere 78ms 0.11% 52.95% 3663ms 4.98% MutableElement::AddNode 1409ms 1.91% 54.86% 3645ms 4.95% _int_free 136ms 0.18% 55.05% 3541ms 4.81% tetgen::tetgenmesh::flip23 250ms 0.34% 55.39% 3219ms 4.37% Node::~Node 158ms 0.21% 55.60% 3102ms 4.22% VertexMesh::GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex 5ms 0.0068% 55.61% 3031ms 4.12% MeshBasedCellPopulationWithGhostNodes::WriteVtkResultsToFile 203ms 0.28% 55.88% 3015ms 4.10% VertexMesh::Clear 1ms 0.0014% 55.88% 2969ms 4.03% std::_Rb_tree_iterator::operator++ (inline) 158ms 0.21% 56.10% 2542ms 3.45% tetgen::tetgenmesh::flip32 2426ms 3.30% 59.40% 2426ms 3.30% Node::GetIndex 0 0% 59.40% 2334ms 3.17% std::_Rb_tree::_M_drop_node (inline) 0 0% 59.40% 2325ms 3.16% std::_Rb_tree::_M_put_node (inline) 1500ms 2.04% 61.43% 2224ms 3.02% malloc_consolidate 2211ms 3.00% 64.44% 2211ms 3.00% std::_Rb_tree_insert_and_rebalance 45ms 0.061% 64.50% 2130ms 2.89% std::_Vector_base::_M_deallocate (inline) 8ms 0.011% 64.51% 2066ms 2.81% Element::Element 0 0% 64.51% 2052ms 2.79% std::vector::~vector (inline) 0 0% 64.51% 1969ms 2.68% std::_Vector_base::~_Vector_base (inline) 195ms 0.26% 64.78% 1942ms 2.64% tetgen::tetgenmesh::enqueueflipface 8ms 0.011% 64.79% 1937ms 2.63% _int_free_maybe_consolidate 3ms 0.0041% 64.79% 1704ms 2.32% Element::RegisterWithNodes (inline) 1623ms 2.21% 67.00% 1623ms 2.21% unlink_chunk 1522ms 2.07% 69.07% 1596ms 2.17% tetgen::orient3d 97ms 0.13% 69.20% 1556ms 2.11% TetrahedralMesh::Clear 42ms 0.057% 69.25% 1372ms 1.86% tetgen::tetgenmesh::locate 7ms 0.0095% 69.26% 1346ms 1.83% VertexMesh::GenerateVerticesFromElementCircumcentres 1104ms 1.50% 70.76% 1333ms 1.81% AbstractElement::GetNodeGlobalIndex 71ms 0.096% 70.86% 1310ms 1.78% std::map::operator[] 56ms 0.076% 70.94% 1268ms 1.72% std::vector::_M_realloc_insert 76ms 0.1% 71.04% 1267ms 1.72% tetgen::tetgenmesh::preciselocate 0 0% 71.04% 1156ms 1.57% std::_Rb_tree::lower_bound (inline) 0 0% 71.04% 1156ms 1.57% std::map::lower_bound (inline) 1119ms 1.52% 72.56% 1119ms 1.52% tetgen::tetgenmesh::oppo 0 0% 72.56% 1092ms 1.48% VoronoiDataWriter::Visit 5ms 0.0068% 72.57% 1087ms 1.48% std::_Vector_base::_M_allocate (inline) 160ms 0.22% 72.78% 1041ms 1.41% std::vector::push_back (inline) 1014ms 1.38% 74.16% 1014ms 1.38% tetgen::tetgenmesh::triface::triface 0 0% 74.16% 928ms 1.26% TetrahedralMesh::RefreshJacobianCachedData 394ms 0.54% 74.70% 880ms 1.20% AbstractElement::GetNodeLocation 858ms 1.17% 75.86% 858ms 1.17% Node::rGetLocation 857ms 1.16% 77.03% 857ms 1.16% AbstractElement::IsDeleted 328ms 0.45% 77.47% 854ms 1.16% tetgen::tetgenmesh::sym 822ms 1.12% 78.59% 822ms 1.12% [libchaste_mesh.so] 11ms 0.015% 78.61% 804ms 1.09% AbstractTetrahedralElement::CalculateInverseJacobian 2ms 0.0027% 78.61% 785ms 1.07% AbstractTwoBodyInteractionForce::AddForceContribution 758ms 1.03% 79.64% 758ms 1.03% tetgen::tetgenmesh::triface::operator= 15ms 0.02% 79.66% 750ms 1.02% AbstractTetrahedralElement::CalculateJacobian 15ms 0.02% 79.68% 747ms 1.02% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 385ms 0.52% 80.20% 678ms 0.92% tetgen::tetgenmesh::fnextself 659ms 0.9% 81.10% 659ms 0.9% std::vector::size (inline) 45ms 0.061% 81.16% 632ms 0.86% __atan2 10ms 0.014% 81.17% 625ms 0.85% boost::numeric::ublas::vector_assign (inline) 9ms 0.012% 81.19% 622ms 0.85% boost::numeric::ublas::c_vector::c_vector (inline) 16ms 0.022% 81.21% 613ms 0.83% Element::CalculateCircumsphere 38ms 0.052% 81.26% 611ms 0.83% tetgen::tetgenmesh::queue::push 58ms 0.079% 81.34% 606ms 0.82% tetgen::tetgenmesh::enext2fnext 0 0% 81.34% 600ms 0.82% std::set::find (inline) 210ms 0.29% 81.62% 599ms 0.81% tetgen::tetgenmesh::bond 59ms 0.08% 81.70% 590ms 0.8% tetgen::tetgenmesh::enextfnext 461ms 0.63% 82.33% 584ms 0.79% __ieee754_atan2_fma 348ms 0.47% 82.80% 573ms 0.78% tetgen::tetgenmesh::link::add 40ms 0.054% 82.86% 568ms 0.77% AbstractTetrahedralElement::RefreshJacobian 543ms 0.74% 83.59% 543ms 0.74% tetgen::tetgenmesh::decode 537ms 0.73% 84.32% 537ms 0.73% tetgen::tetgenmesh::org 0 0% 84.32% 515ms 0.7% boost::numeric::ublas::inner_prod (inline) 36ms 0.049% 84.37% 512ms 0.7% boost::numeric::ublas::vector_scalar_binary::evaluate 0 0% 84.37% 512ms 0.7% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 0 0% 84.37% 487ms 0.66% std::insert_iterator::operator= (inline) 19ms 0.026% 84.40% 476ms 0.65% VertexMesh::CalculateUnitNormalToFaceWithArea 4ms 0.0054% 84.40% 450ms 0.61% CellPropertyCollection::GetPropertiesType (inline) 27ms 0.037% 84.44% 436ms 0.59% std::_Rb_tree_iterator::operator-- (inline) 7ms 0.0095% 84.45% 435ms 0.59% VertexElement::~VertexElement 202ms 0.27% 84.73% 432ms 0.59% AbstractTetrahedralMesh::GetElement 0 0% 84.73% 429ms 0.58% std::_Rb_tree::_M_insert_unique_ (inline) 427ms 0.58% 85.31% 427ms 0.58% boost::numeric::ublas::c_vector::operator() 0 0% 85.31% 425ms 0.58% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 7ms 0.0095% 85.32% 415ms 0.56% Cell::GetCellId 119ms 0.16% 85.48% 414ms 0.56% __dynamic_cast 157ms 0.21% 85.69% 412ms 0.56% boost::numeric::ublas::vector_inner_prod::apply (inline) 12ms 0.016% 85.71% 406ms 0.55% std::vector::insert (inline) 0 0% 85.71% 398ms 0.54% VertexMeshWriter::WriteVtkUsingMesh 97ms 0.13% 85.84% 390ms 0.53% boost::numeric::ublas::indexing_vector_assign 7ms 0.0095% 85.85% 387ms 0.53% boost::numeric::ublas::c_vector::operator= (inline) 377ms 0.51% 86.36% 377ms 0.51% std::_Rb_tree_decrement 370ms 0.5% 86.86% 370ms 0.5% tetgen::tetgenmesh::encode