File: Test3dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 51951ms, 86.67% of 59943ms total Dropped 883 nodes (cum <= 299.71ms) flat flat% sum% cum cum% 0 0% 0% 59892ms 99.91% __libc_start_call_main 0 0% 0% 59892ms 99.91% __libc_start_main_impl 0 0% 0% 59892ms 99.91% _start 0 0% 0% 59874ms 99.88% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 59874ms 99.88% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 59874ms 99.88% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 59874ms 99.88% main 0 0% 0% 59837ms 99.82% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 59837ms 99.82% CxxTest::TestRunner::runTest (inline) 0 0% 0% 59837ms 99.82% Test3dTissueRepresentativeSimulation::Test3DHoneycombMeshWithGhostNodes 0 0% 0% 59569ms 99.38% AbstractCellBasedSimulation::Solve 0 0% 0% 50629ms 84.46% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 50578ms 84.38% MeshBasedCellPopulation::Update 0 0% 0% 26787ms 44.69% MeshBasedCellPopulation::TessellateIfNeeded 0 0% 0% 26786ms 44.69% MeshBasedCellPopulation::CreateVoronoiTessellation (inline) 200ms 0.33% 0.33% 24082ms 40.17% VertexMesh::VertexMesh 0 0% 0.33% 19832ms 33.08% MutableMesh::ReMesh 0 0% 0.33% 16208ms 27.04% tetgen::tetrahedralize 3ms 0.005% 0.34% 16062ms 26.80% tetgen::tetgenmesh::delaunizevertices 8ms 0.013% 0.35% 16053ms 26.78% tetgen::tetgenmesh::incrflipdelaunay 571ms 0.95% 1.30% 14369ms 23.97% tetgen::tetgenmesh::lawson 641ms 1.07% 2.37% 12065ms 20.13% TetrahedralMesh::EdgeIterator::operator++ 38ms 0.063% 2.44% 9553ms 15.94% std::set::insert (inline) 344ms 0.57% 3.01% 9384ms 15.65% VertexElement::AddFace 215ms 0.36% 3.37% 9063ms 15.12% std::_Rb_tree::_M_insert_unique 3133ms 5.23% 8.60% 8991ms 15.00% std::_Rb_tree::_M_lower_bound (inline) 241ms 0.4% 9.00% 8463ms 14.12% std::_Rb_tree::find (inline) 0 0% 9.00% 7940ms 13.25% std::set::count (inline) 108ms 0.18% 9.18% 5722ms 9.55% std::less::operator() (inline) 5685ms 9.48% 18.66% 5685ms 9.48% std::operator< (inline) 325ms 0.54% 19.20% 5428ms 9.06% std::_Rb_tree::_M_insert_ (inline) 1ms 0.0017% 19.21% 5300ms 8.84% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 19.21% 5190ms 8.66% ForwardEulerNumericalMethod::UpdateAllNodePositions 1ms 0.0017% 19.21% 5160ms 8.61% AbstractNumericalMethod::ComputeForcesIncludingDamping 4816ms 8.03% 27.24% 4816ms 8.03% std::_Rb_tree_increment 167ms 0.28% 27.52% 4639ms 7.74% operator new 1177ms 1.96% 29.48% 4419ms 7.37% __GI___libc_malloc 0 0% 29.48% 4320ms 7.21% MeshBasedCellPopulation::UpdateNodePairs 7ms 0.012% 29.50% 4268ms 7.12% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 10ms 0.017% 29.51% 4184ms 6.98% MeshBasedCellPopulation::SpringIterator::operator++ 47ms 0.078% 29.59% 4058ms 6.77% std::__new_allocator::allocate (inline) 0 0% 29.59% 4037ms 6.73% std::allocator_traits::allocate (inline) 7ms 0.012% 29.60% 3940ms 6.57% std::_Rb_tree::~_Rb_tree (inline) 1307ms 2.18% 31.78% 3931ms 6.56% std::_Rb_tree::_M_erase 0 0% 31.78% 3896ms 6.50% std::set::~set (inline) 113ms 0.19% 31.97% 3877ms 6.47% tetgen::tetgenmesh::insphere_sos 3437ms 5.73% 37.71% 3748ms 6.25% tetgen::insphere 1328ms 2.22% 39.92% 3718ms 6.20% std::_Rb_tree::_M_get_insert_unique_pos 1057ms 1.76% 41.68% 3693ms 6.16% __GI___libc_free 7ms 0.012% 41.70% 3626ms 6.05% std::set_intersection (inline) 244ms 0.41% 42.10% 3619ms 6.04% std::__set_intersection 0 0% 42.10% 3489ms 5.82% AbstractCellPopulation::WriteResultsToFiles 133ms 0.22% 42.33% 3462ms 5.78% tetgen::tetgenmesh::flip23 0 0% 42.33% 3346ms 5.58% std::_Rb_tree::_M_create_node (inline) 0 0% 42.33% 3323ms 5.54% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 42.33% 3317ms 5.53% std::_Rb_tree::_M_get_node (inline) 125ms 0.21% 42.53% 3314ms 5.53% std::__new_allocator::deallocate (inline) 0 0% 42.53% 3296ms 5.50% std::allocator_traits::deallocate (inline) 36ms 0.06% 42.59% 2961ms 4.94% Node::AddElement 2161ms 3.61% 46.20% 2897ms 4.83% _int_malloc 193ms 0.32% 46.52% 2895ms 4.83% std::_Rb_tree_const_iterator::operator++ (inline) 7ms 0.012% 46.53% 2885ms 4.81% TetrahedralMesh::ImportFromMesher 2734ms 4.56% 51.09% 2734ms 4.56% std::_Rb_tree::_S_right (inline) 0 0% 51.09% 2721ms 4.54% VertexMesh::~VertexMesh 1393ms 2.32% 53.42% 2631ms 4.39% _int_free 142ms 0.24% 53.65% 2543ms 4.24% tetgen::tetgenmesh::flip32 181ms 0.3% 53.96% 2411ms 4.02% VertexMesh::GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex 3ms 0.005% 53.96% 2398ms 4.00% MeshBasedCellPopulationWithGhostNodes::WriteVtkResultsToFile 66ms 0.11% 54.07% 2349ms 3.92% MutableElement::AddNode 3ms 0.005% 54.08% 2242ms 3.74% std::_Rb_tree_iterator::operator++ (inline) 0 0% 54.08% 2102ms 3.51% std::_Rb_tree::_M_drop_node (inline) 0 0% 54.08% 2093ms 3.49% std::_Rb_tree::_M_put_node (inline) 113ms 0.19% 54.26% 1985ms 3.31% Node::~Node 222ms 0.37% 54.64% 1867ms 3.11% tetgen::tetgenmesh::enqueueflipface 1815ms 3.03% 57.66% 1815ms 3.03% std::_Rb_tree_insert_and_rebalance 166ms 0.28% 57.94% 1797ms 3.00% VertexMesh::Clear 1519ms 2.53% 60.47% 1611ms 2.69% tetgen::orient3d 1533ms 2.56% 63.03% 1533ms 2.56% Node::GetIndex 8ms 0.013% 63.04% 1397ms 2.33% Element::Element 41ms 0.068% 63.11% 1373ms 2.29% tetgen::tetgenmesh::locate 89ms 0.15% 63.26% 1286ms 2.15% tetgen::tetgenmesh::preciselocate 14ms 0.023% 63.29% 1217ms 2.03% std::_Vector_base::_M_deallocate (inline) 99ms 0.17% 63.45% 1204ms 2.01% TetrahedralMesh::Clear 779ms 1.30% 64.75% 1198ms 2.00% malloc_consolidate 0 0% 64.75% 1126ms 1.88% std::vector::~vector (inline) 79ms 0.13% 64.88% 1083ms 1.81% std::map::operator[] 6ms 0.01% 64.89% 1059ms 1.77% Element::RegisterWithNodes (inline) 0 0% 64.89% 1036ms 1.73% std::_Vector_base::~_Vector_base (inline) 10ms 0.017% 64.91% 1025ms 1.71% _int_free_maybe_consolidate 992ms 1.65% 66.56% 992ms 1.65% tetgen::tetgenmesh::oppo 61ms 0.1% 66.66% 987ms 1.65% std::vector::_M_realloc_insert 947ms 1.58% 68.24% 947ms 1.58% tetgen::tetgenmesh::triface::triface 0 0% 68.24% 944ms 1.57% std::_Rb_tree::lower_bound (inline) 0 0% 68.24% 944ms 1.57% std::map::lower_bound (inline) 880ms 1.47% 69.71% 880ms 1.47% unlink_chunk 0 0% 69.71% 862ms 1.44% VoronoiDataWriter::Visit 677ms 1.13% 70.84% 848ms 1.41% AbstractElement::GetNodeGlobalIndex 848ms 1.41% 72.26% 848ms 1.41% [libchaste_mesh.so] 817ms 1.36% 73.62% 817ms 1.36% tetgen::tetgenmesh::triface::operator= 111ms 0.19% 73.81% 806ms 1.34% std::vector::push_back (inline) 6ms 0.01% 73.82% 796ms 1.33% VertexMesh::GenerateVerticesFromElementCircumcentres 280ms 0.47% 74.28% 765ms 1.28% tetgen::tetgenmesh::sym 0 0% 74.28% 725ms 1.21% AbstractTwoBodyInteractionForce::AddForceContribution 3ms 0.005% 74.29% 723ms 1.21% std::_Vector_base::_M_allocate (inline) 0 0% 74.29% 720ms 1.20% TetrahedralMesh::RefreshJacobianCachedData 11ms 0.018% 74.31% 676ms 1.13% AbstractTetrahedralElement::CalculateInverseJacobian 9ms 0.015% 74.32% 675ms 1.13% AbstractVariableSizeTwoBodyInteractionForce::CalculateForceBetweenNodes 367ms 0.61% 74.93% 628ms 1.05% tetgen::tetgenmesh::fnextself 45ms 0.075% 75.01% 623ms 1.04% __atan2 214ms 0.36% 75.36% 618ms 1.03% tetgen::tetgenmesh::bond 20ms 0.033% 75.40% 615ms 1.03% AbstractTetrahedralElement::CalculateJacobian 37ms 0.062% 75.46% 612ms 1.02% tetgen::tetgenmesh::queue::push 15ms 0.025% 75.49% 607ms 1.01% boost::numeric::ublas::vector_assign (inline) 56ms 0.093% 75.58% 600ms 1.00% tetgen::tetgenmesh::enext2fnext 13ms 0.022% 75.60% 582ms 0.97% boost::numeric::ublas::c_vector::c_vector (inline) 359ms 0.6% 76.20% 574ms 0.96% tetgen::tetgenmesh::link::add 443ms 0.74% 76.94% 573ms 0.96% __ieee754_atan2_fma 60ms 0.1% 77.04% 573ms 0.96% tetgen::tetgenmesh::enextfnext 203ms 0.34% 77.38% 533ms 0.89% AbstractElement::GetNodeLocation 523ms 0.87% 78.25% 523ms 0.87% Node::rGetLocation 0 0% 78.25% 519ms 0.87% std::insert_iterator::operator= (inline) 0 0% 78.25% 519ms 0.87% std::set::find (inline) 518ms 0.86% 79.11% 518ms 0.86% tetgen::tetgenmesh::org 512ms 0.85% 79.97% 512ms 0.85% tetgen::tetgenmesh::decode 494ms 0.82% 80.79% 494ms 0.82% std::vector::size (inline) 0 0% 80.79% 464ms 0.77% boost::numeric::ublas::inner_prod (inline) 3ms 0.005% 80.80% 461ms 0.77% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 33ms 0.055% 80.85% 458ms 0.76% boost::numeric::ublas::vector_scalar_binary::evaluate 0 0% 80.85% 449ms 0.75% std::_Rb_tree::_M_insert_unique_ (inline) 447ms 0.75% 81.60% 447ms 0.75% tetgen::tetgenmesh::pointmark 19ms 0.032% 81.63% 441ms 0.74% Element::CalculateCircumsphere 38ms 0.063% 81.69% 419ms 0.7% AbstractTetrahedralElement::RefreshJacobian 37ms 0.062% 81.75% 408ms 0.68% std::_Rb_tree_iterator::operator-- (inline) 186ms 0.31% 82.06% 405ms 0.68% AbstractTetrahedralMesh::GetElement 94ms 0.16% 82.22% 398ms 0.66% __dynamic_cast 397ms 0.66% 82.88% 397ms 0.66% tetgen::tetgenmesh::encode 395ms 0.66% 83.54% 395ms 0.66% AbstractElement::IsDeleted 1ms 0.0017% 83.54% 385ms 0.64% CellPropertyCollection::GetPropertiesType (inline) 0 0% 83.54% 385ms 0.64% VertexMeshWriter::WriteVtkUsingMesh 7ms 0.012% 83.56% 373ms 0.62% Cell::GetCellId 9ms 0.015% 83.57% 366ms 0.61% boost::numeric::ublas::c_vector::operator= (inline) 95ms 0.16% 83.73% 365ms 0.61% boost::numeric::ublas::indexing_vector_assign 30ms 0.05% 83.78% 361ms 0.6% VertexMesh::CalculateUnitNormalToFaceWithArea 160ms 0.27% 84.05% 356ms 0.59% boost::numeric::ublas::vector_inner_prod::apply (inline) 348ms 0.58% 84.63% 348ms 0.58% boost::numeric::ublas::c_vector::operator() 348ms 0.58% 85.21% 348ms 0.58% std::_Rb_tree_decrement 73ms 0.12% 85.33% 339ms 0.57% tetgen::tetgenmesh::queue::pop 111ms 0.19% 85.51% 333ms 0.56% Inverse 5ms 0.0083% 85.52% 332ms 0.55% AbstractTetrahedralElement::AbstractTetrahedralElement 1ms 0.0017% 85.52% 320ms 0.53% AbstractCellProperty::IsSubType (inline) 15ms 0.025% 85.55% 313ms 0.52% std::vector::insert (inline) 7ms 0.012% 85.56% 312ms 0.52% VertexElement::~VertexElement 43ms 0.072% 85.63% 311ms 0.52% tetgen::insphereadapt 311ms 0.52% 86.15% 311ms 0.52% tetgen::tetgenmesh::face::face 0 0% 86.15% 309ms 0.52% tcache_get (inline) 309ms 0.52% 86.67% 309ms 0.52% tcache_get_n (inline)