File: Test3dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 43969ms, 86.16% of 51031ms total Dropped 821 nodes (cum <= 255.16ms) flat flat% sum% cum cum% 0 0% 0% 50950ms 99.84% __libc_start_call_main 0 0% 0% 50950ms 99.84% __libc_start_main_impl 0 0% 0% 50950ms 99.84% _start 0 0% 0% 50936ms 99.81% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 50936ms 99.81% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 50936ms 99.81% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 50936ms 99.81% main 0 0% 0% 50904ms 99.75% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 50904ms 99.75% CxxTest::TestRunner::runTest (inline) 0 0% 0% 50904ms 99.75% Test3dTissueRepresentativeSimulation::Test3DHoneycombMeshWithGhostNodes 0 0% 0% 50662ms 99.28% AbstractCellBasedSimulation::Solve 0 0% 0% 42237ms 82.77% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 42200ms 82.69% MeshBasedCellPopulation::Update 0 0% 0% 23119ms 45.30% MeshBasedCellPopulation::CreateVoronoiTessellation (inline) 0 0% 0% 23119ms 45.30% MeshBasedCellPopulation::TessellateIfNeeded 226ms 0.44% 0.44% 21023ms 41.20% VertexMesh::VertexMesh 0 0% 0.44% 15531ms 30.43% MutableMesh::ReMesh 0 0% 0.44% 12732ms 24.95% tetgen::tetrahedralize 3ms 0.0059% 0.45% 12596ms 24.68% tetgen::tetgenmesh::delaunizevertices 9ms 0.018% 0.47% 12591ms 24.67% tetgen::tetgenmesh::incrflipdelaunay 524ms 1.03% 1.49% 11203ms 21.95% tetgen::tetgenmesh::lawson 580ms 1.14% 2.63% 10739ms 21.04% TetrahedralMesh::EdgeIterator::operator++ 3047ms 5.97% 8.60% 8614ms 16.88% std::_Rb_tree::_M_lower_bound (inline) 287ms 0.56% 9.16% 8351ms 16.36% VertexElement::AddFace 31ms 0.061% 9.22% 8222ms 16.11% std::set::insert (inline) 244ms 0.48% 9.70% 8106ms 15.88% std::_Rb_tree::find (inline) 197ms 0.39% 10.09% 7727ms 15.14% std::_Rb_tree::_M_insert_unique 0 0% 10.09% 7511ms 14.72% std::set::count (inline) 109ms 0.21% 10.30% 5425ms 10.63% std::less::operator() (inline) 5387ms 10.56% 20.86% 5387ms 10.56% std::operator< (inline) 0 0% 20.86% 4842ms 9.49% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 20.86% 4737ms 9.28% ForwardEulerNumericalMethod::UpdateAllNodePositions 1ms 0.002% 20.86% 4706ms 9.22% AbstractNumericalMethod::ComputeForcesIncludingDamping 251ms 0.49% 21.35% 4696ms 9.20% std::_Rb_tree::_M_insert_ (inline) 4134ms 8.10% 29.45% 4134ms 8.10% std::_Rb_tree_increment 205ms 0.4% 29.85% 3899ms 7.64% operator new 3ms 0.0059% 29.86% 3878ms 7.60% MeshBasedCellPopulation::UpdateNodePairs 2ms 0.0039% 29.86% 3851ms 7.55% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 16ms 0.031% 29.90% 3766ms 7.38% MeshBasedCellPopulation::SpringIterator::operator++ 1032ms 2.02% 31.92% 3593ms 7.04% __GI___libc_malloc 100ms 0.2% 32.11% 3513ms 6.88% tetgen::tetgenmesh::insphere_sos 33ms 0.065% 32.18% 3455ms 6.77% std::__new_allocator::allocate (inline) 0 0% 32.18% 3449ms 6.76% AbstractCellPopulation::WriteResultsToFiles 0 0% 32.18% 3432ms 6.73% std::allocator_traits::allocate (inline) 3110ms 6.09% 38.27% 3399ms 6.66% tetgen::insphere 1135ms 2.22% 40.50% 3145ms 6.16% std::_Rb_tree::_M_get_insert_unique_pos 6ms 0.012% 40.51% 3142ms 6.16% std::_Rb_tree::~_Rb_tree (inline) 992ms 1.94% 42.45% 3134ms 6.14% std::_Rb_tree::_M_erase 0 0% 42.45% 3091ms 6.06% std::set::~set (inline) 768ms 1.50% 43.96% 2946ms 5.77% __GI___libc_free 152ms 0.3% 44.26% 2788ms 5.46% std::__new_allocator::deallocate (inline) 0 0% 44.26% 2773ms 5.43% std::_Rb_tree::_M_create_node (inline) 2ms 0.0039% 44.26% 2766ms 5.42% std::set_intersection (inline) 192ms 0.38% 44.64% 2764ms 5.42% std::__set_intersection 0 0% 44.64% 2758ms 5.40% std::allocator_traits::deallocate (inline) 0 0% 44.64% 2743ms 5.38% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 44.64% 2743ms 5.38% std::_Rb_tree::_M_get_node (inline) 188ms 0.37% 45.00% 2672ms 5.24% tetgen::tetgenmesh::flip23 188ms 0.37% 45.37% 2449ms 4.80% VertexMesh::GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex 3ms 0.0059% 45.38% 2413ms 4.73% MeshBasedCellPopulationWithGhostNodes::WriteVtkResultsToFile 32ms 0.063% 45.44% 2367ms 4.64% Node::AddElement 2320ms 4.55% 49.99% 2320ms 4.55% std::_Rb_tree::_S_right (inline) 1ms 0.002% 49.99% 2276ms 4.46% std::_Rb_tree_iterator::operator++ (inline) 1710ms 3.35% 53.34% 2240ms 4.39% _int_malloc 1197ms 2.35% 55.69% 2174ms 4.26% _int_free 176ms 0.34% 56.03% 2157ms 4.23% std::_Rb_tree_const_iterator::operator++ (inline) 0 0% 56.03% 2107ms 4.13% VertexMesh::~VertexMesh 11ms 0.022% 56.05% 2106ms 4.13% TetrahedralMesh::ImportFromMesher 60ms 0.12% 56.17% 1859ms 3.64% MutableElement::AddNode 142ms 0.28% 56.45% 1847ms 3.62% tetgen::tetgenmesh::flip32 1760ms 3.45% 59.90% 1760ms 3.45% std::_Rb_tree_insert_and_rebalance 0 0% 59.90% 1758ms 3.44% std::_Rb_tree::_M_drop_node (inline) 0 0% 59.90% 1753ms 3.44% std::_Rb_tree::_M_put_node (inline) 1298ms 2.54% 62.44% 1396ms 2.74% tetgen::orient3d 87ms 0.17% 62.61% 1359ms 2.66% VertexMesh::Clear 68ms 0.13% 62.74% 1315ms 2.58% Node::~Node 4ms 0.0078% 62.75% 1276ms 2.50% Element::Element 172ms 0.34% 63.09% 1259ms 2.47% tetgen::tetgenmesh::enqueueflipface 1200ms 2.35% 65.44% 1200ms 2.35% Node::GetIndex 29ms 0.057% 65.50% 1151ms 2.26% tetgen::tetgenmesh::locate 101ms 0.2% 65.70% 1072ms 2.10% tetgen::tetgenmesh::preciselocate 72ms 0.14% 65.84% 1066ms 2.09% std::map::operator[] 13ms 0.025% 65.86% 1018ms 1.99% std::_Vector_base::_M_deallocate (inline) 2ms 0.0039% 65.87% 949ms 1.86% Element::RegisterWithNodes (inline) 572ms 1.12% 66.99% 945ms 1.85% malloc_consolidate 56ms 0.11% 67.10% 935ms 1.83% std::vector::_M_realloc_insert 0 0% 67.10% 926ms 1.81% std::_Rb_tree::lower_bound (inline) 0 0% 67.10% 926ms 1.81% std::map::lower_bound (inline) 0 0% 67.10% 904ms 1.77% std::vector::~vector (inline) 900ms 1.76% 68.86% 900ms 1.76% tetgen::tetgenmesh::triface::triface 3ms 0.0059% 68.87% 834ms 1.63% VoronoiDataWriter::Visit 0 0% 68.87% 826ms 1.62% std::_Vector_base::~_Vector_base (inline) 8ms 0.016% 68.88% 819ms 1.60% _int_free_maybe_consolidate 433ms 0.85% 69.73% 783ms 1.53% tetgen::tetgenmesh::fnextself 79ms 0.15% 69.88% 731ms 1.43% std::vector::push_back (inline) 3ms 0.0059% 69.89% 729ms 1.43% VertexMesh::GenerateVerticesFromElementCircumcentres 2ms 0.0039% 69.89% 711ms 1.39% AbstractTwoBodyInteractionForce::AddForceContribution 710ms 1.39% 71.29% 710ms 1.39% tetgen::tetgenmesh::oppo 1ms 0.002% 71.29% 690ms 1.35% std::_Vector_base::_M_allocate (inline) 18ms 0.035% 71.32% 682ms 1.34% boost::numeric::ublas::vector_assign (inline) 1ms 0.002% 71.33% 677ms 1.33% TetrahedralMesh::RefreshJacobianCachedData 15ms 0.029% 71.35% 669ms 1.31% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 12ms 0.024% 71.38% 660ms 1.29% boost::numeric::ublas::c_vector::c_vector (inline) 8ms 0.016% 71.39% 648ms 1.27% AbstractTetrahedralElement::CalculateInverseJacobian 641ms 1.26% 72.65% 641ms 1.26% [libchaste_mesh.so] 629ms 1.23% 73.88% 629ms 1.23% unlink_chunk 53ms 0.1% 73.99% 626ms 1.23% __atan2 0 0% 73.99% 591ms 1.16% std::set::find (inline) 591ms 1.16% 75.14% 591ms 1.16% tetgen::tetgenmesh::triface::operator= 14ms 0.027% 75.17% 588ms 1.15% AbstractTetrahedralElement::CalculateJacobian 449ms 0.88% 76.05% 571ms 1.12% __ieee754_atan2_fma 46ms 0.09% 76.14% 563ms 1.10% TetrahedralMesh::Clear 47ms 0.092% 76.23% 502ms 0.98% tetgen::tetgenmesh::enextfnext 397ms 0.78% 77.01% 501ms 0.98% AbstractElement::GetNodeGlobalIndex 0 0% 77.01% 491ms 0.96% std::insert_iterator::operator= (inline) 36ms 0.071% 77.08% 489ms 0.96% tetgen::tetgenmesh::enext2fnext 190ms 0.37% 77.45% 472ms 0.92% AbstractElement::GetNodeLocation 0 0% 77.45% 467ms 0.92% boost::numeric::ublas::inner_prod (inline) 3ms 0.0059% 77.46% 467ms 0.92% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 33ms 0.065% 77.53% 464ms 0.91% boost::numeric::ublas::vector_scalar_binary::evaluate 445ms 0.87% 78.40% 445ms 0.87% boost::numeric::ublas::c_vector::operator() 233ms 0.46% 78.85% 443ms 0.87% AbstractTetrahedralMesh::GetElement 0 0% 78.85% 439ms 0.86% std::_Rb_tree::_M_insert_unique_ (inline) 109ms 0.21% 79.07% 432ms 0.85% boost::numeric::ublas::indexing_vector_assign 18ms 0.035% 79.10% 423ms 0.83% Element::CalculateCircumsphere 47ms 0.092% 79.19% 414ms 0.81% AbstractTetrahedralElement::RefreshJacobian 6ms 0.012% 79.21% 400ms 0.78% boost::numeric::ublas::c_vector::operator= (inline) 400ms 0.78% 79.99% 400ms 0.78% std::vector::size (inline) 2ms 0.0039% 79.99% 398ms 0.78% CellPropertyCollection::GetPropertiesType (inline) 254ms 0.5% 80.49% 391ms 0.77% tetgen::tetgenmesh::sym 6ms 0.012% 80.50% 388ms 0.76% Cell::GetCellId 388ms 0.76% 81.26% 388ms 0.76% Node::rGetLocation 171ms 0.34% 81.60% 386ms 0.76% boost::numeric::ublas::vector_inner_prod::apply (inline) 23ms 0.045% 81.64% 376ms 0.74% tetgen::tetgenmesh::queue::push 245ms 0.48% 82.12% 371ms 0.73% tetgen::tetgenmesh::bond 89ms 0.17% 82.30% 367ms 0.72% __dynamic_cast 0 0% 82.30% 366ms 0.72% VertexMeshWriter::WriteVtkUsingMesh 232ms 0.45% 82.75% 348ms 0.68% tetgen::tetgenmesh::link::add 14ms 0.027% 82.78% 337ms 0.66% std::_Rb_tree_iterator::operator-- (inline) 142ms 0.28% 83.06% 335ms 0.66% Inverse 11ms 0.022% 83.08% 328ms 0.64% VertexMesh::CalculateUnitNormalToFaceWithArea 4ms 0.0078% 83.09% 324ms 0.63% AbstractTetrahedralElement::AbstractTetrahedralElement 50ms 0.098% 83.19% 323ms 0.63% boost::numeric::ublas::vector_reference::operator() (inline) 314ms 0.62% 83.80% 314ms 0.62% tetgen::tetgenmesh::org 2ms 0.0039% 83.81% 313ms 0.61% AbstractCellProperty::IsSubType (inline) 16ms 0.031% 83.84% 311ms 0.61% std::vector::insert (inline) 58ms 0.11% 83.95% 307ms 0.6% tetgen::tetgenmesh::queue::pop 306ms 0.6% 84.55% 306ms 0.6% std::_Rb_tree_decrement 0 0% 84.55% 299ms 0.59% tcache_get (inline) 299ms 0.59% 85.14% 299ms 0.59% tcache_get_n (inline) 34ms 0.067% 85.20% 289ms 0.57% tetgen::insphereadapt 280ms 0.55% 85.75% 280ms 0.55% tetgen::tetgenmesh::pointmark 209ms 0.41% 86.16% 266ms 0.52% boost::numeric::ublas::c_matrix::operator()