File: Test3dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 56676ms, 86.34% of 65646ms total Dropped 867 nodes (cum <= 328.23ms) flat flat% sum% cum cum% 0 0% 0% 65584ms 99.91% __libc_start_call_main 0 0% 0% 65584ms 99.91% __libc_start_main_impl 0 0% 0% 65584ms 99.91% _start 0 0% 0% 65566ms 99.88% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 65566ms 99.88% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 65566ms 99.88% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 65566ms 99.88% main 0 0% 0% 65525ms 99.82% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 65525ms 99.82% CxxTest::TestRunner::runTest (inline) 0 0% 0% 65525ms 99.82% Test3dTissueRepresentativeSimulation::Test3DHoneycombMeshWithGhostNodes 0 0% 0% 65246ms 99.39% AbstractCellBasedSimulation::Solve 0 0% 0% 54854ms 83.56% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 54806ms 83.49% MeshBasedCellPopulation::Update 0 0% 0% 30110ms 45.87% MeshBasedCellPopulation::TessellateIfNeeded 0 0% 0% 30109ms 45.87% MeshBasedCellPopulation::CreateVoronoiTessellation (inline) 204ms 0.31% 0.31% 26939ms 41.04% VertexMesh::VertexMesh 0 0% 0.31% 20236ms 30.83% MutableMesh::ReMesh 0 0% 0.31% 16136ms 24.58% tetgen::tetrahedralize 2ms 0.003% 0.31% 15988ms 24.35% tetgen::tetgenmesh::delaunizevertices 11ms 0.017% 0.33% 15982ms 24.35% tetgen::tetgenmesh::incrflipdelaunay 500ms 0.76% 1.09% 14256ms 21.72% tetgen::tetgenmesh::lawson 620ms 0.94% 2.04% 13635ms 20.77% TetrahedralMesh::EdgeIterator::operator++ 3182ms 4.85% 6.88% 10401ms 15.84% std::_Rb_tree::_M_lower_bound (inline) 34ms 0.052% 6.94% 10222ms 15.57% std::set::insert (inline) 386ms 0.59% 7.52% 10015ms 15.26% VertexElement::AddFace 237ms 0.36% 7.88% 9784ms 14.90% std::_Rb_tree::_M_insert_unique 262ms 0.4% 8.28% 9659ms 14.71% std::_Rb_tree::find (inline) 0 0% 8.28% 9063ms 13.81% std::set::count (inline) 116ms 0.18% 8.46% 6872ms 10.47% std::less::operator() (inline) 6818ms 10.39% 18.85% 6818ms 10.39% std::operator< (inline) 6143ms 9.36% 28.20% 6143ms 9.36% std::_Rb_tree_increment 0 0% 28.20% 5933ms 9.04% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 28.20% 5780ms 8.80% ForwardEulerNumericalMethod::UpdateAllNodePositions 2ms 0.003% 28.21% 5759ms 8.77% AbstractNumericalMethod::ComputeForcesIncludingDamping 292ms 0.44% 28.65% 5744ms 8.75% std::_Rb_tree::_M_insert_ (inline) 191ms 0.29% 28.94% 5345ms 8.14% operator new 1164ms 1.77% 30.72% 5029ms 7.66% __GI___libc_malloc 1ms 0.0015% 30.72% 4822ms 7.35% MeshBasedCellPopulation::UpdateNodePairs 8ms 0.012% 30.73% 4793ms 7.30% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 16ms 0.024% 30.75% 4667ms 7.11% MeshBasedCellPopulation::SpringIterator::operator++ 24ms 0.037% 30.79% 4565ms 6.95% std::__new_allocator::allocate (inline) 0 0% 30.79% 4542ms 6.92% std::allocator_traits::allocate (inline) 0 0% 30.79% 4301ms 6.55% AbstractCellPopulation::WriteResultsToFiles 6ms 0.0091% 30.80% 4260ms 6.49% std::set_intersection (inline) 269ms 0.41% 31.21% 4254ms 6.48% std::__set_intersection 7ms 0.011% 31.22% 4211ms 6.41% std::_Rb_tree::~_Rb_tree (inline) 1538ms 2.34% 33.56% 4203ms 6.40% std::_Rb_tree::_M_erase 0 0% 33.56% 4157ms 6.33% std::set::~set (inline) 1267ms 1.93% 35.49% 4082ms 6.22% std::_Rb_tree::_M_get_insert_unique_pos 1102ms 1.68% 37.17% 3859ms 5.88% __GI___libc_free 113ms 0.17% 37.34% 3815ms 5.81% tetgen::tetgenmesh::insphere_sos 3408ms 5.19% 42.54% 3690ms 5.62% tetgen::insphere 0 0% 42.54% 3663ms 5.58% std::_Rb_tree::_M_create_node (inline) 0 0% 42.54% 3625ms 5.52% std::_Rb_tree::_M_get_node (inline) 0 0% 42.54% 3623ms 5.52% std::_Rb_tree::_Alloc_node::operator() (inline) 189ms 0.29% 42.82% 3541ms 5.39% std::_Rb_tree_const_iterator::operator++ (inline) 43ms 0.066% 42.89% 3538ms 5.39% Node::AddElement 2461ms 3.75% 46.64% 3485ms 5.31% _int_malloc 121ms 0.18% 46.82% 3464ms 5.28% tetgen::tetgenmesh::flip23 3459ms 5.27% 52.09% 3459ms 5.27% std::_Rb_tree::_S_right (inline) 117ms 0.18% 52.27% 3424ms 5.22% std::__new_allocator::deallocate (inline) 0 0% 52.27% 3405ms 5.19% std::allocator_traits::deallocate (inline) 6ms 0.0091% 52.28% 3293ms 5.02% TetrahedralMesh::ImportFromMesher 0 0% 52.28% 3193ms 4.86% VertexMesh::~VertexMesh 216ms 0.33% 52.61% 3117ms 4.75% VertexMesh::GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex 3ms 0.0046% 52.61% 3014ms 4.59% MeshBasedCellPopulationWithGhostNodes::WriteVtkResultsToFile 2ms 0.003% 52.62% 2924ms 4.45% std::_Rb_tree_iterator::operator++ (inline) 1321ms 2.01% 54.63% 2756ms 4.20% _int_free 61ms 0.093% 54.72% 2712ms 4.13% MutableElement::AddNode 138ms 0.21% 54.93% 2633ms 4.01% tetgen::tetgenmesh::flip32 155ms 0.24% 55.17% 2315ms 3.53% Node::~Node 170ms 0.26% 55.43% 2065ms 3.15% VertexMesh::Clear 0 0% 55.43% 2032ms 3.10% std::_Rb_tree::_M_drop_node (inline) 0 0% 55.43% 2019ms 3.08% std::_Rb_tree::_M_put_node (inline) 2003ms 3.05% 58.48% 2003ms 3.05% Node::GetIndex 219ms 0.33% 58.81% 1948ms 2.97% tetgen::tetgenmesh::enqueueflipface 1903ms 2.90% 61.71% 1903ms 2.90% std::_Rb_tree_insert_and_rebalance 7ms 0.011% 61.72% 1674ms 2.55% Element::Element 1482ms 2.26% 63.98% 1560ms 2.38% tetgen::orient3d 899ms 1.37% 65.35% 1441ms 2.20% malloc_consolidate 29ms 0.044% 65.39% 1415ms 2.16% std::_Vector_base::_M_deallocate (inline) 33ms 0.05% 65.44% 1363ms 2.08% tetgen::tetgenmesh::locate 69ms 0.11% 65.55% 1349ms 2.05% std::map::operator[] 0 0% 65.55% 1345ms 2.05% std::vector::~vector (inline) 88ms 0.13% 65.68% 1331ms 2.03% TetrahedralMesh::Clear 6ms 0.0091% 65.69% 1297ms 1.98% Element::RegisterWithNodes (inline) 105ms 0.16% 65.85% 1282ms 1.95% tetgen::tetgenmesh::preciselocate 1ms 0.0015% 65.85% 1259ms 1.92% std::_Vector_base::~_Vector_base (inline) 6ms 0.0091% 65.86% 1218ms 1.86% _int_free_maybe_consolidate 1197ms 1.82% 67.68% 1197ms 1.82% unlink_chunk 0 0% 67.68% 1187ms 1.81% std::_Rb_tree::lower_bound (inline) 0 0% 67.68% 1187ms 1.81% std::map::lower_bound (inline) 52ms 0.079% 67.76% 1102ms 1.68% std::vector::_M_realloc_insert 857ms 1.31% 69.07% 1069ms 1.63% AbstractElement::GetNodeGlobalIndex 1069ms 1.63% 70.70% 1069ms 1.63% tetgen::tetgenmesh::triface::triface 2ms 0.003% 70.70% 1032ms 1.57% VoronoiDataWriter::Visit 963ms 1.47% 72.17% 963ms 1.47% tetgen::tetgenmesh::oppo 2ms 0.003% 72.17% 947ms 1.44% VertexMesh::GenerateVerticesFromElementCircumcentres 2ms 0.003% 72.17% 919ms 1.40% std::_Vector_base::_M_allocate (inline) 127ms 0.19% 72.37% 918ms 1.40% std::vector::push_back (inline) 350ms 0.53% 72.90% 821ms 1.25% tetgen::tetgenmesh::sym 794ms 1.21% 74.11% 794ms 1.21% [libchaste_mesh.so] 0 0% 74.11% 791ms 1.20% TetrahedralMesh::RefreshJacobianCachedData 781ms 1.19% 75.30% 781ms 1.19% tetgen::tetgenmesh::triface::operator= 1ms 0.0015% 75.30% 755ms 1.15% AbstractTwoBodyInteractionForce::AddForceContribution 36ms 0.055% 75.36% 719ms 1.10% tetgen::tetgenmesh::queue::push 14ms 0.021% 75.38% 713ms 1.09% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 12ms 0.018% 75.40% 706ms 1.08% AbstractTetrahedralElement::CalculateInverseJacobian 386ms 0.59% 75.98% 683ms 1.04% tetgen::tetgenmesh::fnextself 410ms 0.62% 76.61% 682ms 1.04% tetgen::tetgenmesh::link::add 17ms 0.026% 76.63% 669ms 1.02% AbstractTetrahedralElement::CalculateJacobian 279ms 0.43% 77.06% 651ms 0.99% AbstractElement::GetNodeLocation 648ms 0.99% 78.05% 648ms 0.99% Node::rGetLocation 8ms 0.012% 78.06% 609ms 0.93% boost::numeric::ublas::vector_assign (inline) 45ms 0.069% 78.13% 599ms 0.91% tetgen::tetgenmesh::enextfnext 0 0% 78.13% 596ms 0.91% std::set::find (inline) 52ms 0.079% 78.21% 595ms 0.91% __atan2 49ms 0.075% 78.28% 584ms 0.89% tetgen::tetgenmesh::enext2fnext 583ms 0.89% 79.17% 583ms 0.89% std::vector::size (inline) 213ms 0.32% 79.49% 581ms 0.89% tetgen::tetgenmesh::bond 577ms 0.88% 80.37% 577ms 0.88% AbstractElement::IsDeleted 7ms 0.011% 80.38% 574ms 0.87% boost::numeric::ublas::c_vector::c_vector (inline) 552ms 0.84% 81.22% 552ms 0.84% tetgen::tetgenmesh::org 389ms 0.59% 81.82% 540ms 0.82% __ieee754_atan2_fma 0 0% 81.82% 514ms 0.78% boost::numeric::ublas::inner_prod (inline) 37ms 0.056% 81.87% 510ms 0.78% boost::numeric::ublas::vector_scalar_binary::evaluate 0 0% 81.87% 510ms 0.78% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 491ms 0.75% 82.62% 491ms 0.75% tetgen::tetgenmesh::decode 51ms 0.078% 82.70% 483ms 0.74% AbstractTetrahedralElement::RefreshJacobian 18ms 0.027% 82.73% 482ms 0.73% Element::CalculateCircumsphere 38ms 0.058% 82.78% 452ms 0.69% std::_Rb_tree_iterator::operator-- (inline) 0 0% 82.78% 450ms 0.69% std::insert_iterator::operator= (inline) 437ms 0.67% 83.45% 437ms 0.67% tetgen::tetgenmesh::pointmark 112ms 0.17% 83.62% 414ms 0.63% __dynamic_cast 1ms 0.0015% 83.62% 409ms 0.62% CellPropertyCollection::GetPropertiesType (inline) 17ms 0.026% 83.65% 408ms 0.62% VertexMesh::CalculateUnitNormalToFaceWithArea 194ms 0.3% 83.94% 404ms 0.62% AbstractTetrahedralMesh::GetElement 191ms 0.29% 84.23% 404ms 0.62% boost::numeric::ublas::vector_inner_prod::apply (inline) 0 0% 84.23% 403ms 0.61% std::_Rb_tree::_M_insert_unique_ (inline) 399ms 0.61% 84.84% 399ms 0.61% boost::numeric::ublas::c_vector::operator() 0 0% 84.84% 398ms 0.61% VertexMeshWriter::WriteVtkUsingMesh 4ms 0.0061% 84.85% 390ms 0.59% Cell::GetCellId 390ms 0.59% 85.44% 390ms 0.59% std::_Rb_tree_decrement 4ms 0.0061% 85.45% 383ms 0.58% boost::numeric::ublas::c_vector::operator= (inline) 84ms 0.13% 85.58% 375ms 0.57% boost::numeric::ublas::indexing_vector_assign 4ms 0.0061% 85.58% 371ms 0.57% AbstractTetrahedralElement::AbstractTetrahedralElement 0 0% 85.58% 352ms 0.54% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 7ms 0.011% 85.59% 350ms 0.53% VertexElement::~VertexElement 350ms 0.53% 86.13% 350ms 0.53% tetgen::tetgenmesh::encode 122ms 0.19% 86.31% 338ms 0.51% Inverse 15ms 0.023% 86.33% 335ms 0.51% std::vector::insert (inline) 1ms 0.0015% 86.34% 332ms 0.51% AbstractCellProperty::IsSubType (inline)