File: Test3dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 53392ms, 85.96% of 62112ms total Dropped 889 nodes (cum <= 310.56ms) flat flat% sum% cum cum% 0 0% 0% 62055ms 99.91% __libc_start_call_main 0 0% 0% 62055ms 99.91% __libc_start_main_impl 0 0% 0% 62055ms 99.91% _start 0 0% 0% 62038ms 99.88% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 62038ms 99.88% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 62038ms 99.88% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 62038ms 99.88% main 0 0% 0% 61994ms 99.81% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 61994ms 99.81% CxxTest::TestRunner::runTest (inline) 0 0% 0% 61994ms 99.81% Test3dTissueRepresentativeSimulation::Test3DHoneycombMeshWithGhostNodes 0 0% 0% 61716ms 99.36% AbstractCellBasedSimulation::Solve 0 0% 0% 52632ms 84.74% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 52583ms 84.66% MeshBasedCellPopulation::Update 0 0% 0% 28751ms 46.29% MeshBasedCellPopulation::TessellateIfNeeded 0 0% 0% 28749ms 46.29% MeshBasedCellPopulation::CreateVoronoiTessellation (inline) 186ms 0.3% 0.3% 25608ms 41.23% VertexMesh::VertexMesh 1ms 0.0016% 0.3% 19794ms 31.87% MutableMesh::ReMesh 0 0% 0.3% 15924ms 25.64% tetgen::tetrahedralize 2ms 0.0032% 0.3% 15773ms 25.39% tetgen::tetgenmesh::delaunizevertices 10ms 0.016% 0.32% 15763ms 25.38% tetgen::tetgenmesh::incrflipdelaunay 504ms 0.81% 1.13% 14112ms 22.72% tetgen::tetgenmesh::lawson 639ms 1.03% 2.16% 12298ms 19.80% TetrahedralMesh::EdgeIterator::operator++ 25ms 0.04% 2.20% 10026ms 16.14% std::set::insert (inline) 355ms 0.57% 2.77% 9870ms 15.89% VertexElement::AddFace 279ms 0.45% 3.22% 9622ms 15.49% std::_Rb_tree::_M_insert_unique 3165ms 5.10% 8.32% 8943ms 14.40% std::_Rb_tree::_M_lower_bound (inline) 266ms 0.43% 8.75% 8439ms 13.59% std::_Rb_tree::find (inline) 0 0% 8.75% 7877ms 12.68% std::set::count (inline) 127ms 0.2% 8.95% 5684ms 9.15% std::less::operator() (inline) 337ms 0.54% 9.49% 5662ms 9.12% std::_Rb_tree::_M_insert_ (inline) 5626ms 9.06% 18.55% 5626ms 9.06% std::operator< (inline) 2ms 0.0032% 18.55% 5478ms 8.82% OffLatticeSimulation::UpdateCellLocationsAndTopology 1ms 0.0016% 18.56% 5345ms 8.61% ForwardEulerNumericalMethod::UpdateAllNodePositions 2ms 0.0032% 18.56% 5318ms 8.56% AbstractNumericalMethod::ComputeForcesIncludingDamping 5160ms 8.31% 26.87% 5160ms 8.31% std::_Rb_tree_increment 153ms 0.25% 27.11% 4918ms 7.92% operator new 1172ms 1.89% 29.00% 4717ms 7.59% __GI___libc_malloc 2ms 0.0032% 29.00% 4424ms 7.12% MeshBasedCellPopulation::UpdateNodePairs 6ms 0.0097% 29.01% 4375ms 7.04% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 15ms 0.024% 29.04% 4280ms 6.89% MeshBasedCellPopulation::SpringIterator::operator++ 49ms 0.079% 29.12% 4258ms 6.86% std::__new_allocator::allocate (inline) 0 0% 29.12% 4241ms 6.83% std::allocator_traits::allocate (inline) 9ms 0.014% 29.13% 4215ms 6.79% std::_Rb_tree::~_Rb_tree (inline) 1425ms 2.29% 31.42% 4205ms 6.77% std::_Rb_tree::_M_erase 0 0% 31.42% 4171ms 6.72% std::set::~set (inline) 6ms 0.0097% 31.43% 4053ms 6.53% std::set_intersection (inline) 280ms 0.45% 31.88% 4047ms 6.52% std::__set_intersection 1346ms 2.17% 34.05% 3918ms 6.31% std::_Rb_tree::_M_get_insert_unique_pos 1153ms 1.86% 35.91% 3883ms 6.25% __GI___libc_free 141ms 0.23% 36.13% 3883ms 6.25% tetgen::tetgenmesh::insphere_sos 3439ms 5.54% 41.67% 3735ms 6.01% tetgen::insphere 0 0% 41.67% 3491ms 5.62% std::_Rb_tree::_M_create_node (inline) 138ms 0.22% 41.89% 3485ms 5.61% tetgen::tetgenmesh::flip23 150ms 0.24% 42.14% 3462ms 5.57% std::__new_allocator::deallocate (inline) 0 0% 42.14% 3458ms 5.57% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 42.14% 3457ms 5.57% std::_Rb_tree::_M_get_node (inline) 0 0% 42.14% 3447ms 5.55% std::allocator_traits::deallocate (inline) 0 0% 42.14% 3443ms 5.54% AbstractCellPopulation::WriteResultsToFiles 182ms 0.29% 42.43% 3332ms 5.36% std::_Rb_tree_const_iterator::operator++ (inline) 44ms 0.071% 42.50% 3292ms 5.30% Node::AddElement 0 0% 42.50% 3162ms 5.09% VertexMesh::~VertexMesh 2333ms 3.76% 46.26% 3160ms 5.09% _int_malloc 9ms 0.014% 46.27% 3095ms 4.98% TetrahedralMesh::ImportFromMesher 2994ms 4.82% 51.09% 2994ms 4.82% std::_Rb_tree::_S_right (inline) 1363ms 2.19% 53.28% 2728ms 4.39% _int_free 72ms 0.12% 53.40% 2627ms 4.23% MutableElement::AddNode 138ms 0.22% 53.62% 2462ms 3.96% tetgen::tetgenmesh::flip32 4ms 0.0064% 53.63% 2333ms 3.76% MeshBasedCellPopulationWithGhostNodes::WriteVtkResultsToFile 170ms 0.27% 53.90% 2314ms 3.73% Node::~Node 166ms 0.27% 54.17% 2313ms 3.72% VertexMesh::GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex 0 0% 54.17% 2163ms 3.48% std::_Rb_tree::_M_drop_node (inline) 0 0% 54.17% 2155ms 3.47% std::_Rb_tree_iterator::operator++ (inline) 0 0% 54.17% 2154ms 3.47% std::_Rb_tree::_M_put_node (inline) 159ms 0.26% 54.43% 2137ms 3.44% VertexMesh::Clear 1912ms 3.08% 57.50% 1912ms 3.08% std::_Rb_tree_insert_and_rebalance 233ms 0.38% 57.88% 1773ms 2.85% tetgen::tetgenmesh::enqueueflipface 1501ms 2.42% 60.30% 1575ms 2.54% tetgen::orient3d 1529ms 2.46% 62.76% 1529ms 2.46% Node::GetIndex 8ms 0.013% 62.77% 1474ms 2.37% Element::Element 45ms 0.072% 62.84% 1356ms 2.18% tetgen::tetgenmesh::locate 79ms 0.13% 62.97% 1323ms 2.13% TetrahedralMesh::Clear 23ms 0.037% 63.01% 1316ms 2.12% std::_Vector_base::_M_deallocate (inline) 875ms 1.41% 64.42% 1306ms 2.10% malloc_consolidate 97ms 0.16% 64.57% 1269ms 2.04% tetgen::tetgenmesh::preciselocate 1ms 0.0016% 64.57% 1255ms 2.02% std::vector::~vector (inline) 0 0% 64.57% 1143ms 1.84% std::_Vector_base::~_Vector_base (inline) 10ms 0.016% 64.59% 1132ms 1.82% _int_free_maybe_consolidate 880ms 1.42% 66.01% 1126ms 1.81% AbstractElement::GetNodeGlobalIndex 6ms 0.0097% 66.02% 1124ms 1.81% Element::RegisterWithNodes (inline) 81ms 0.13% 66.15% 1100ms 1.77% std::map::operator[] 1083ms 1.74% 67.89% 1083ms 1.74% tetgen::tetgenmesh::triface::triface 1039ms 1.67% 69.56% 1039ms 1.67% unlink_chunk 56ms 0.09% 69.65% 1021ms 1.64% std::vector::_M_realloc_insert 978ms 1.57% 71.23% 978ms 1.57% tetgen::tetgenmesh::oppo 0 0% 71.23% 947ms 1.52% std::_Rb_tree::lower_bound (inline) 0 0% 71.23% 947ms 1.52% std::map::lower_bound (inline) 0 0% 71.23% 874ms 1.41% VoronoiDataWriter::Visit 6ms 0.0097% 71.24% 860ms 1.38% VertexMesh::GenerateVerticesFromElementCircumcentres 104ms 0.17% 71.40% 816ms 1.31% std::vector::push_back (inline) 811ms 1.31% 72.71% 811ms 1.31% [libchaste_mesh.so] 4ms 0.0064% 72.72% 788ms 1.27% std::_Vector_base::_M_allocate (inline) 0 0% 72.72% 772ms 1.24% AbstractTwoBodyInteractionForce::AddForceContribution 1ms 0.0016% 72.72% 753ms 1.21% TetrahedralMesh::RefreshJacobianCachedData 746ms 1.20% 73.92% 746ms 1.20% tetgen::tetgenmesh::triface::operator= 20ms 0.032% 73.95% 738ms 1.19% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 9ms 0.014% 73.97% 699ms 1.13% AbstractTetrahedralElement::CalculateInverseJacobian 274ms 0.44% 74.41% 696ms 1.12% tetgen::tetgenmesh::sym 66ms 0.11% 74.51% 641ms 1.03% tetgen::tetgenmesh::enext2fnext 380ms 0.61% 75.13% 637ms 1.03% tetgen::tetgenmesh::fnextself 623ms 1.00% 76.13% 623ms 1.00% std::vector::size (inline) 17ms 0.027% 76.16% 620ms 1% boost::numeric::ublas::vector_assign (inline) 47ms 0.076% 76.23% 617ms 0.99% __atan2 11ms 0.018% 76.25% 613ms 0.99% boost::numeric::ublas::c_vector::c_vector (inline) 12ms 0.019% 76.27% 612ms 0.99% AbstractTetrahedralElement::CalculateJacobian 57ms 0.092% 76.36% 579ms 0.93% tetgen::tetgenmesh::enextfnext 439ms 0.71% 77.07% 566ms 0.91% __ieee754_atan2_fma 0 0% 77.07% 560ms 0.9% std::set::find (inline) 26ms 0.042% 77.11% 560ms 0.9% tetgen::tetgenmesh::queue::push 0 0% 77.11% 547ms 0.88% boost::numeric::ublas::inner_prod (inline) 545ms 0.88% 77.99% 545ms 0.88% Node::rGetLocation 42ms 0.068% 78.05% 545ms 0.88% boost::numeric::ublas::vector_scalar_binary::evaluate 0 0% 78.05% 545ms 0.88% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 236ms 0.38% 78.43% 541ms 0.87% AbstractElement::GetNodeLocation 345ms 0.56% 78.99% 534ms 0.86% tetgen::tetgenmesh::link::add 223ms 0.36% 79.35% 528ms 0.85% tetgen::tetgenmesh::bond 504ms 0.81% 80.16% 504ms 0.81% tetgen::tetgenmesh::org 492ms 0.79% 80.95% 492ms 0.79% AbstractElement::IsDeleted 4ms 0.0064% 80.96% 483ms 0.78% CellPropertyCollection::GetPropertiesType (inline) 258ms 0.42% 81.37% 478ms 0.77% AbstractTetrahedralMesh::GetElement 105ms 0.17% 81.54% 464ms 0.75% __dynamic_cast 20ms 0.032% 81.58% 459ms 0.74% Element::CalculateCircumsphere 1ms 0.0016% 81.58% 450ms 0.72% Cell::GetCellId 449ms 0.72% 82.30% 449ms 0.72% tetgen::tetgenmesh::decode 79ms 0.13% 82.43% 449ms 0.72% tetgen::tetgenmesh::queue::pop 188ms 0.3% 82.73% 439ms 0.71% boost::numeric::ublas::vector_inner_prod::apply (inline) 0 0% 82.73% 439ms 0.71% std::insert_iterator::operator= (inline) 42ms 0.068% 82.80% 428ms 0.69% AbstractTetrahedralElement::RefreshJacobian 25ms 0.04% 82.84% 418ms 0.67% std::_Rb_tree_iterator::operator-- (inline) 404ms 0.65% 83.49% 404ms 0.65% boost::numeric::ublas::c_vector::operator() 3ms 0.0048% 83.49% 397ms 0.64% AbstractCellProperty::IsSubType (inline) 17ms 0.027% 83.52% 388ms 0.62% VertexMesh::CalculateUnitNormalToFaceWithArea 0 0% 83.52% 388ms 0.62% VertexMeshWriter::WriteVtkUsingMesh 101ms 0.16% 83.68% 382ms 0.62% boost::numeric::ublas::indexing_vector_assign 1ms 0.0016% 83.68% 376ms 0.61% std::_Rb_tree::_M_insert_unique_ (inline) 372ms 0.6% 84.28% 372ms 0.6% std::_Rb_tree_decrement 5ms 0.008% 84.29% 368ms 0.59% boost::numeric::ublas::c_vector::operator= (inline) 187ms 0.3% 84.59% 363ms 0.58% tetgen::tetgenmesh::link::deletenode 8ms 0.013% 84.61% 359ms 0.58% VertexElement::~VertexElement 139ms 0.22% 84.83% 357ms 0.57% Inverse 6ms 0.0097% 84.84% 342ms 0.55% AbstractTetrahedralElement::AbstractTetrahedralElement 10ms 0.016% 84.85% 331ms 0.53% std::vector::insert (inline) 0 0% 84.85% 329ms 0.53% tcache_get (inline) 329ms 0.53% 85.38% 329ms 0.53% tcache_get_n (inline) 40ms 0.064% 85.45% 320ms 0.52% boost::numeric::ublas::vector_reference::operator() (inline) 0 0% 85.45% 318ms 0.51% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 318ms 0.51% 85.96% 318ms 0.51% tetgen::tetgenmesh::pointmark