File: Test3dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 49678ms, 87.28% of 56917ms total Dropped 858 nodes (cum <= 284.58ms) flat flat% sum% cum cum% 0 0% 0% 56858ms 99.90% __libc_start_call_main 0 0% 0% 56858ms 99.90% __libc_start_main_impl 0 0% 0% 56858ms 99.90% _start 0 0% 0% 56842ms 99.87% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 56842ms 99.87% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 56842ms 99.87% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 56842ms 99.87% main 0 0% 0% 56806ms 99.80% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 56806ms 99.80% CxxTest::TestRunner::runTest (inline) 0 0% 0% 56806ms 99.80% Test3dTissueRepresentativeSimulation::Test3DHoneycombMeshWithGhostNodes 0 0% 0% 56557ms 99.37% AbstractCellBasedSimulation::Solve 0 0% 0% 48059ms 84.44% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 48016ms 84.36% MeshBasedCellPopulation::Update 0 0% 0% 27470ms 48.26% MeshBasedCellPopulation::CreateVoronoiTessellation (inline) 0 0% 0% 27470ms 48.26% MeshBasedCellPopulation::TessellateIfNeeded 184ms 0.32% 0.32% 24249ms 42.60% VertexMesh::VertexMesh 1ms 0.0018% 0.33% 16836ms 29.58% MutableMesh::ReMesh 2ms 0.0035% 0.33% 12823ms 22.53% tetgen::tetrahedralize 1ms 0.0018% 0.33% 12683ms 22.28% tetgen::tetgenmesh::delaunizevertices 8ms 0.014% 0.34% 12678ms 22.27% tetgen::tetgenmesh::incrflipdelaunay 612ms 1.08% 1.42% 11345ms 19.93% TetrahedralMesh::EdgeIterator::operator++ 571ms 1.00% 2.42% 11234ms 19.74% tetgen::tetgenmesh::lawson 23ms 0.04% 2.46% 9881ms 17.36% std::set::insert (inline) 169ms 0.3% 2.76% 9430ms 16.57% std::_Rb_tree::_M_insert_unique 367ms 0.64% 3.40% 9078ms 15.95% VertexElement::AddFace 2928ms 5.14% 8.55% 8342ms 14.66% std::_Rb_tree::_M_lower_bound (inline) 207ms 0.36% 8.91% 7790ms 13.69% std::_Rb_tree::find (inline) 0 0% 8.91% 7253ms 12.74% std::set::count (inline) 257ms 0.45% 9.36% 5669ms 9.96% std::_Rb_tree::_M_insert_ (inline) 123ms 0.22% 9.58% 5288ms 9.29% std::less::operator() (inline) 5224ms 9.18% 18.76% 5224ms 9.18% std::operator< (inline) 0 0% 18.76% 5059ms 8.89% OffLatticeSimulation::UpdateCellLocationsAndTopology 232ms 0.41% 19.17% 4979ms 8.75% operator new 3ms 0.0053% 19.17% 4938ms 8.68% ForwardEulerNumericalMethod::UpdateAllNodePositions 1ms 0.0018% 19.17% 4907ms 8.62% AbstractNumericalMethod::ComputeForcesIncludingDamping 1070ms 1.88% 21.05% 4668ms 8.20% __GI___libc_malloc 4647ms 8.16% 29.22% 4647ms 8.16% std::_Rb_tree_increment 55ms 0.097% 29.31% 4276ms 7.51% std::__new_allocator::allocate (inline) 0 0% 29.31% 4246ms 7.46% std::allocator_traits::allocate (inline) 8ms 0.014% 29.33% 4213ms 7.40% std::_Rb_tree::~_Rb_tree (inline) 1607ms 2.82% 32.15% 4205ms 7.39% std::_Rb_tree::_M_erase 0 0% 32.15% 4163ms 7.31% std::set::~set (inline) 7ms 0.012% 32.16% 4053ms 7.12% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 2ms 0.0035% 32.17% 4052ms 7.12% MeshBasedCellPopulation::UpdateNodePairs 13ms 0.023% 32.19% 3904ms 6.86% MeshBasedCellPopulation::SpringIterator::operator++ 1219ms 2.14% 34.33% 3885ms 6.83% std::_Rb_tree::_M_get_insert_unique_pos 1146ms 2.01% 36.35% 3748ms 6.59% __GI___libc_free 2ms 0.0035% 36.35% 3623ms 6.37% std::set_intersection (inline) 242ms 0.43% 36.77% 3621ms 6.36% std::__set_intersection 33ms 0.058% 36.83% 3503ms 6.15% Node::AddElement 0 0% 36.83% 3463ms 6.08% std::_Rb_tree::_M_create_node (inline) 0 0% 36.83% 3430ms 6.03% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 36.83% 3420ms 6.01% std::_Rb_tree::_M_get_node (inline) 94ms 0.17% 37.00% 3409ms 5.99% tetgen::tetgenmesh::insphere_sos 140ms 0.25% 37.24% 3310ms 5.82% std::__new_allocator::deallocate (inline) 0 0% 37.24% 3296ms 5.79% std::allocator_traits::deallocate (inline) 0 0% 37.24% 3295ms 5.79% AbstractCellPopulation::WriteResultsToFiles 3002ms 5.27% 42.52% 3295ms 5.79% tetgen::insphere 2389ms 4.20% 46.72% 3263ms 5.73% _int_malloc 7ms 0.012% 46.73% 3257ms 5.72% TetrahedralMesh::ImportFromMesher 0 0% 46.73% 3239ms 5.69% VertexMesh::~VertexMesh 3174ms 5.58% 52.30% 3174ms 5.58% std::_Rb_tree::_S_right (inline) 164ms 0.29% 52.59% 2944ms 5.17% std::_Rb_tree_const_iterator::operator++ (inline) 80ms 0.14% 52.73% 2800ms 4.92% MutableElement::AddNode 188ms 0.33% 53.06% 2709ms 4.76% tetgen::tetgenmesh::flip23 1220ms 2.14% 55.21% 2600ms 4.57% _int_free 171ms 0.3% 55.51% 2386ms 4.19% Node::~Node 175ms 0.31% 55.81% 2171ms 3.81% VertexMesh::Clear 2ms 0.0035% 55.82% 2162ms 3.80% MeshBasedCellPopulationWithGhostNodes::WriteVtkResultsToFile 197ms 0.35% 56.16% 2132ms 3.75% VertexMesh::GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex 2056ms 3.61% 59.78% 2056ms 3.61% std::_Rb_tree_insert_and_rebalance 0 0% 59.78% 1963ms 3.45% std::_Rb_tree::_M_drop_node (inline) 0 0% 59.78% 1951ms 3.43% std::_Rb_tree::_M_put_node (inline) 0 0% 59.78% 1948ms 3.42% std::_Rb_tree_iterator::operator++ (inline) 167ms 0.29% 60.07% 1732ms 3.04% tetgen::tetgenmesh::flip32 5ms 0.0088% 60.08% 1481ms 2.60% Element::Element 1332ms 2.34% 62.42% 1427ms 2.51% tetgen::orient3d 213ms 0.37% 62.79% 1414ms 2.48% TetrahedralMesh::Clear 18ms 0.032% 62.82% 1362ms 2.39% std::_Vector_base::_M_deallocate (inline) 897ms 1.58% 64.40% 1344ms 2.36% malloc_consolidate 1305ms 2.29% 66.69% 1305ms 2.29% Node::GetIndex 0 0% 66.69% 1265ms 2.22% std::vector::~vector (inline) 216ms 0.38% 67.07% 1259ms 2.21% tetgen::tetgenmesh::enqueueflipface 5ms 0.0088% 67.08% 1206ms 2.12% Element::RegisterWithNodes (inline) 31ms 0.054% 67.14% 1200ms 2.11% tetgen::tetgenmesh::locate 0 0% 67.14% 1186ms 2.08% std::_Vector_base::~_Vector_base (inline) 9ms 0.016% 67.15% 1151ms 2.02% _int_free_maybe_consolidate 111ms 0.2% 67.35% 1120ms 1.97% tetgen::tetgenmesh::preciselocate 69ms 0.12% 67.47% 1092ms 1.92% std::map::operator[] 1057ms 1.86% 69.33% 1057ms 1.86% unlink_chunk 60ms 0.11% 69.43% 1052ms 1.85% std::vector::_M_realloc_insert 767ms 1.35% 70.78% 953ms 1.67% AbstractElement::GetNodeGlobalIndex 0 0% 70.78% 953ms 1.67% std::_Rb_tree::lower_bound (inline) 0 0% 70.78% 953ms 1.67% std::map::lower_bound (inline) 2ms 0.0035% 70.78% 939ms 1.65% VertexMesh::GenerateVerticesFromElementCircumcentres 0 0% 70.78% 896ms 1.57% VoronoiDataWriter::Visit 852ms 1.50% 72.28% 852ms 1.50% tetgen::tetgenmesh::triface::operator= 110ms 0.19% 72.47% 840ms 1.48% std::vector::push_back (inline) 9ms 0.016% 72.49% 835ms 1.47% std::_Vector_base::_M_allocate (inline) 2ms 0.0035% 72.49% 739ms 1.30% TetrahedralMesh::RefreshJacobianCachedData 1ms 0.0018% 72.49% 704ms 1.24% AbstractTwoBodyInteractionForce::AddForceContribution 11ms 0.019% 72.51% 701ms 1.23% boost::numeric::ublas::vector_assign (inline) 11ms 0.019% 72.53% 689ms 1.21% boost::numeric::ublas::c_vector::c_vector (inline) 10ms 0.018% 72.55% 684ms 1.20% AbstractTetrahedralElement::CalculateInverseJacobian 524ms 0.92% 73.47% 672ms 1.18% tetgen::tetgenmesh::fnextself 16ms 0.028% 73.50% 671ms 1.18% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 625ms 1.10% 74.60% 625ms 1.10% [libchaste_mesh.so] 19ms 0.033% 74.63% 595ms 1.05% AbstractTetrahedralElement::CalculateJacobian 246ms 0.43% 75.06% 593ms 1.04% AbstractElement::GetNodeLocation 45ms 0.079% 75.14% 569ms 1% __atan2 542ms 0.95% 76.09% 542ms 0.95% std::vector::size (inline) 538ms 0.95% 77.04% 538ms 0.95% tetgen::tetgenmesh::oppo 536ms 0.94% 77.98% 536ms 0.94% tetgen::tetgenmesh::triface::triface 0 0% 77.98% 535ms 0.94% std::set::find (inline) 533ms 0.94% 78.92% 533ms 0.94% Node::rGetLocation 20ms 0.035% 78.95% 530ms 0.93% Element::CalculateCircumsphere 417ms 0.73% 79.68% 523ms 0.92% __ieee754_atan2_fma 509ms 0.89% 80.58% 509ms 0.89% AbstractElement::IsDeleted 0 0% 80.58% 487ms 0.86% boost::numeric::ublas::inner_prod (inline) 6ms 0.011% 80.59% 485ms 0.85% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 31ms 0.054% 80.64% 479ms 0.84% boost::numeric::ublas::vector_scalar_binary::evaluate 43ms 0.076% 80.72% 473ms 0.83% tetgen::tetgenmesh::enext2fnext 315ms 0.55% 81.27% 464ms 0.82% tetgen::tetgenmesh::sym 0 0% 81.27% 454ms 0.8% std::insert_iterator::operator= (inline) 140ms 0.25% 81.52% 453ms 0.8% boost::numeric::ublas::indexing_vector_assign 38ms 0.067% 81.59% 425ms 0.75% AbstractTetrahedralElement::RefreshJacobian 7ms 0.012% 81.60% 421ms 0.74% CellPropertyCollection::GetPropertiesType (inline) 16ms 0.028% 81.63% 420ms 0.74% VertexMesh::CalculateUnitNormalToFaceWithArea 28ms 0.049% 81.68% 418ms 0.73% tetgen::tetgenmesh::queue::push 1ms 0.0018% 81.68% 409ms 0.72% std::_Rb_tree::_M_insert_unique_ (inline) 2ms 0.0035% 81.68% 406ms 0.71% Cell::GetCellId 399ms 0.7% 82.38% 399ms 0.7% boost::numeric::ublas::c_vector::operator() 205ms 0.36% 82.74% 394ms 0.69% AbstractTetrahedralMesh::GetElement 0 0% 82.74% 393ms 0.69% VertexMeshWriter::WriteVtkUsingMesh 39ms 0.069% 82.81% 389ms 0.68% tetgen::tetgenmesh::enextfnext 322ms 0.57% 83.38% 389ms 0.68% tetgen::tetgenmesh::link::add 15ms 0.026% 83.40% 387ms 0.68% std::_Rb_tree_iterator::operator-- (inline) 86ms 0.15% 83.55% 384ms 0.67% __dynamic_cast 9ms 0.016% 83.57% 384ms 0.67% boost::numeric::ublas::c_vector::operator= (inline) 162ms 0.28% 83.85% 379ms 0.67% boost::numeric::ublas::vector_inner_prod::apply (inline) 285ms 0.5% 84.35% 371ms 0.65% tetgen::tetgenmesh::bond 359ms 0.63% 84.99% 359ms 0.63% std::_Rb_tree_decrement 358ms 0.63% 85.61% 358ms 0.63% tetgen::tetgenmesh::org 352ms 0.62% 86.23% 352ms 0.62% tetgen::tetgenmesh::pointmark 65ms 0.11% 86.35% 349ms 0.61% tetgen::tetgenmesh::queue::pop 13ms 0.023% 86.37% 344ms 0.6% std::vector::insert (inline) 5ms 0.0088% 86.38% 334ms 0.59% VertexElement::~VertexElement 6ms 0.011% 86.39% 330ms 0.58% AbstractCellProperty::IsSubType (inline) 0 0% 86.39% 304ms 0.53% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 54ms 0.095% 86.48% 301ms 0.53% boost::numeric::ublas::vector_reference::operator() (inline) 122ms 0.21% 86.70% 298ms 0.52% Inverse 5ms 0.0088% 86.71% 296ms 0.52% VertexMesh::GetVolumeOfElement 37ms 0.065% 86.77% 293ms 0.51% tetgen::insphereadapt 0 0% 86.77% 290ms 0.51% tcache_get (inline) 290ms 0.51% 87.28% 290ms 0.51% tcache_get_n (inline)