File: Test3dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 43904ms, 85.71% of 51225ms total Dropped 833 nodes (cum <= 256.12ms) flat flat% sum% cum cum% 0 0% 0% 51188ms 99.93% __libc_start_call_main 0 0% 0% 51188ms 99.93% __libc_start_main_impl 0 0% 0% 51188ms 99.93% _start 0 0% 0% 51172ms 99.90% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 51172ms 99.90% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 51172ms 99.90% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 51172ms 99.90% main 0 0% 0% 51140ms 99.83% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 51140ms 99.83% CxxTest::TestRunner::runTest (inline) 0 0% 0% 51140ms 99.83% Test3dTissueRepresentativeSimulation::Test3DHoneycombMeshWithGhostNodes 0 0% 0% 50947ms 99.46% AbstractCellBasedSimulation::Solve 0 0% 0% 42585ms 83.13% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 42517ms 83.00% MeshBasedCellPopulation::Update 0 0% 0% 25908ms 50.58% MeshBasedCellPopulation::CreateVoronoiTessellation (inline) 0 0% 0% 25908ms 50.58% MeshBasedCellPopulation::TessellateIfNeeded 225ms 0.44% 0.44% 23277ms 45.44% VertexMesh::VertexMesh 0 0% 0.44% 13003ms 25.38% MutableMesh::ReMesh 461ms 0.9% 1.34% 11236ms 21.93% TetrahedralMesh::EdgeIterator::operator++ 30ms 0.059% 1.40% 9677ms 18.89% std::set::insert (inline) 0 0% 1.40% 9613ms 18.77% tetgen::tetrahedralize 3ms 0.0059% 1.40% 9512ms 18.57% tetgen::tetgenmesh::delaunizevertices 5ms 0.0098% 1.41% 9507ms 18.56% tetgen::tetgenmesh::incrflipdelaunay 134ms 0.26% 1.67% 9228ms 18.01% std::_Rb_tree::_M_insert_unique 247ms 0.48% 2.16% 9017ms 17.60% VertexElement::AddFace 3603ms 7.03% 9.19% 8740ms 17.06% std::_Rb_tree::_M_lower_bound (inline) 169ms 0.33% 9.52% 8366ms 16.33% std::_Rb_tree::find (inline) 396ms 0.77% 10.29% 8343ms 16.29% tetgen::tetgenmesh::lawson 0 0% 10.29% 7925ms 15.47% std::set::count (inline) 250ms 0.49% 10.78% 6103ms 11.91% std::_Rb_tree::_M_insert_ (inline) 185ms 0.36% 11.14% 6069ms 11.85% operator new 2014ms 3.93% 15.07% 5826ms 11.37% __GI___libc_malloc 66ms 0.13% 15.20% 5221ms 10.19% std::__new_allocator::allocate (inline) 0 0% 15.20% 5200ms 10.15% std::allocator_traits::allocate (inline) 0 0% 15.20% 4901ms 9.57% OffLatticeSimulation::UpdateCellLocationsAndTopology 1ms 0.002% 15.21% 4784ms 9.34% ForwardEulerNumericalMethod::UpdateAllNodePositions 3ms 0.0059% 15.21% 4762ms 9.30% AbstractNumericalMethod::ComputeForcesIncludingDamping 4601ms 8.98% 24.19% 4601ms 8.98% std::_Rb_tree_increment 4540ms 8.86% 33.06% 4540ms 8.86% std::operator< (inline) 48ms 0.094% 33.15% 4524ms 8.83% std::less::operator() (inline) 0 0% 33.15% 4260ms 8.32% std::_Rb_tree::_M_create_node (inline) 0 0% 33.15% 4243ms 8.28% std::_Rb_tree::_M_get_node (inline) 0 0% 33.15% 4227ms 8.25% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 33.15% 3897ms 7.61% MeshBasedCellPopulation::UpdateNodePairs 657ms 1.28% 34.43% 3892ms 7.60% __GI___libc_free 2ms 0.0039% 34.44% 3888ms 7.59% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 15ms 0.029% 34.47% 3776ms 7.37% MeshBasedCellPopulation::SpringIterator::operator++ 1ms 0.002% 34.47% 3668ms 7.16% std::set_intersection (inline) 254ms 0.5% 34.96% 3667ms 7.16% std::__set_intersection 2826ms 5.52% 40.48% 3445ms 6.73% _int_malloc 15ms 0.029% 40.51% 3406ms 6.65% std::_Rb_tree::~_Rb_tree (inline) 41ms 0.08% 40.59% 3389ms 6.62% std::__new_allocator::deallocate (inline) 935ms 1.83% 42.41% 3380ms 6.60% std::_Rb_tree::_M_erase 0 0% 42.41% 3376ms 6.59% std::set::~set (inline) 0 0% 42.41% 3373ms 6.58% std::allocator_traits::deallocate (inline) 0 0% 42.41% 3314ms 6.47% AbstractCellPopulation::WriteResultsToFiles 1140ms 2.23% 44.64% 3269ms 6.38% std::_Rb_tree::_M_get_insert_unique_pos 1652ms 3.22% 47.87% 3215ms 6.28% _int_free 68ms 0.13% 48.00% 3022ms 5.90% Node::AddElement 224ms 0.44% 48.44% 2918ms 5.70% std::_Rb_tree_const_iterator::operator++ (inline) 2830ms 5.52% 53.96% 2830ms 5.52% std::_Rb_tree::_S_right (inline) 0 0% 53.96% 2649ms 5.17% VertexMesh::~VertexMesh 4ms 0.0078% 53.97% 2591ms 5.06% TetrahedralMesh::ImportFromMesher 83ms 0.16% 54.13% 2531ms 4.94% tetgen::tetgenmesh::insphere_sos 250ms 0.49% 54.62% 2427ms 4.74% std::_Rb_tree_iterator::operator++ (inline) 2240ms 4.37% 58.99% 2426ms 4.74% tetgen::insphere 1ms 0.002% 58.99% 2416ms 4.72% VertexMesh::GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex 3ms 0.0059% 59.00% 2357ms 4.60% MeshBasedCellPopulationWithGhostNodes::WriteVtkResultsToFile 47ms 0.092% 59.09% 2190ms 4.28% MutableElement::AddNode 0 0% 59.09% 2058ms 4.02% std::_Rb_tree::_M_drop_node (inline) 0 0% 59.09% 2029ms 3.96% std::_Rb_tree::_M_put_node (inline) 218ms 0.43% 59.52% 2026ms 3.96% tetgen::tetgenmesh::flip23 1790ms 3.49% 63.01% 1790ms 3.49% [libchaste_mesh.so] 1669ms 3.26% 66.27% 1669ms 3.26% std::_Rb_tree_insert_and_rebalance 21ms 0.041% 66.31% 1595ms 3.11% Node::~Node 3ms 0.0059% 66.32% 1580ms 3.08% VertexMesh::Clear 4ms 0.0078% 66.32% 1527ms 2.98% Element::Element 180ms 0.35% 66.67% 1383ms 2.70% tetgen::tetgenmesh::flip32 846ms 1.65% 68.33% 1365ms 2.66% malloc_consolidate 17ms 0.033% 68.36% 1361ms 2.66% std::_Vector_base::_M_deallocate (inline) 1307ms 2.55% 70.91% 1359ms 2.65% tetgen::orient3d 0 0% 70.91% 1268ms 2.48% std::vector::~vector (inline) 4ms 0.0078% 70.92% 1264ms 2.47% Element::RegisterWithNodes (inline) 0 0% 70.92% 1207ms 2.36% std::_Vector_base::~_Vector_base (inline) 5ms 0.0098% 70.93% 1198ms 2.34% _int_free_maybe_consolidate 47ms 0.092% 71.02% 1092ms 2.13% std::vector::_M_realloc_insert 1022ms 2.00% 73.02% 1022ms 2.00% Node::GetIndex 67ms 0.13% 73.15% 1010ms 1.97% std::map::operator[] 2ms 0.0039% 73.15% 959ms 1.87% std::_Vector_base::_M_allocate (inline) 27ms 0.053% 73.20% 956ms 1.87% tetgen::tetgenmesh::locate 188ms 0.37% 73.57% 939ms 1.83% tetgen::tetgenmesh::enqueueflipface 3ms 0.0059% 73.58% 899ms 1.76% VertexMesh::GenerateVerticesFromElementCircumcentres 79ms 0.15% 73.73% 898ms 1.75% tetgen::tetgenmesh::preciselocate 0 0% 73.73% 870ms 1.70% std::_Rb_tree::lower_bound (inline) 0 0% 73.73% 870ms 1.70% std::map::lower_bound (inline) 870ms 1.70% 75.43% 870ms 1.70% unlink_chunk 42ms 0.082% 75.51% 843ms 1.65% std::vector::push_back (inline) 1ms 0.002% 75.51% 786ms 1.53% TetrahedralMesh::RefreshJacobianCachedData 0 0% 75.51% 775ms 1.51% VoronoiDataWriter::Visit 4ms 0.0078% 75.52% 716ms 1.40% TetrahedralMesh::Clear 1ms 0.002% 75.52% 685ms 1.34% AbstractTetrahedralElement::CalculateInverseJacobian 391ms 0.76% 76.29% 675ms 1.32% AbstractElement::GetNodeGlobalIndex 1ms 0.002% 76.29% 644ms 1.26% AbstractTwoBodyInteractionForce::AddForceContribution 7ms 0.014% 76.30% 619ms 1.21% AbstractVariableSizeTwoBodyInteractionForce::CalculateForceBetweenNodes 8ms 0.016% 76.32% 612ms 1.19% boost::numeric::ublas::vector_assign (inline) 4ms 0.0078% 76.32% 595ms 1.16% boost::numeric::ublas::c_vector::c_vector (inline) 9ms 0.018% 76.34% 548ms 1.07% AbstractTetrahedralElement::CalculateJacobian 312ms 0.61% 76.95% 524ms 1.02% tetgen::tetgenmesh::sym 22ms 0.043% 76.99% 487ms 0.95% __atan2 280ms 0.55% 77.54% 485ms 0.95% AbstractElement::GetNodeLocation 472ms 0.92% 78.46% 472ms 0.92% std::vector::size (inline) 471ms 0.92% 79.38% 471ms 0.92% Node::rGetLocation 102ms 0.2% 79.58% 465ms 0.91% std::_Rb_tree_iterator::operator-- (inline) 462ms 0.9% 80.48% 462ms 0.9% tetgen::tetgenmesh::oppo 415ms 0.81% 81.29% 461ms 0.9% __ieee754_atan2_fma 0 0% 81.29% 453ms 0.88% std::insert_iterator::operator= (inline) 0 0% 81.29% 438ms 0.86% std::set::find (inline) 19ms 0.037% 81.33% 421ms 0.82% Element::CalculateCircumsphere 32ms 0.062% 81.39% 418ms 0.82% AbstractTetrahedralElement::RefreshJacobian 0 0% 81.39% 402ms 0.78% std::_Rb_tree::_M_insert_unique_ (inline) 123ms 0.24% 81.63% 357ms 0.7% Inverse 1ms 0.002% 81.63% 354ms 0.69% Cell::GetCellId 6ms 0.012% 81.65% 343ms 0.67% CellPropertyCollection::GetPropertiesType (inline) 338ms 0.66% 82.31% 338ms 0.66% std::_Rb_tree_decrement 15ms 0.029% 82.33% 338ms 0.66% std::vector::insert (inline) 0 0% 82.33% 328ms 0.64% VertexMeshWriter::WriteVtkUsingMesh 306ms 0.6% 82.93% 306ms 0.6% boost::numeric::ublas::c_vector::operator() 74ms 0.14% 83.08% 306ms 0.6% boost::numeric::ublas::indexing_vector_assign 0 0% 83.08% 305ms 0.6% tcache_get (inline) 305ms 0.6% 83.67% 305ms 0.6% tcache_get_n (inline) 17ms 0.033% 83.71% 300ms 0.59% VertexMesh::CalculateUnitNormalToFaceWithArea 0 0% 83.71% 296ms 0.58% boost::numeric::ublas::inner_prod (inline) 14ms 0.027% 83.73% 294ms 0.57% boost::numeric::ublas::vector_scalar_binary::evaluate 0 0% 83.73% 294ms 0.57% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 197ms 0.38% 84.12% 290ms 0.57% AbstractTetrahedralMesh::GetElement 2ms 0.0039% 84.12% 289ms 0.56% boost::numeric::ublas::c_vector::operator= (inline) 29ms 0.057% 84.18% 285ms 0.56% tetgen::tetgenmesh::enextfnext 279ms 0.54% 84.72% 279ms 0.54% tetgen::tetgenmesh::triface::triface 44ms 0.086% 84.81% 275ms 0.54% tetgen::tetgenmesh::queue::push 75ms 0.15% 84.95% 272ms 0.53% __dynamic_cast 21ms 0.041% 85.00% 269ms 0.53% tetgen::tetgenmesh::enext2fnext 10ms 0.02% 85.02% 268ms 0.52% boost::numeric::ublas::vector_reference::operator() (inline) 62ms 0.12% 85.14% 263ms 0.51% tetgen::tetgenmesh::queue::pop 214ms 0.42% 85.55% 262ms 0.51% tetgen::tetgenmesh::fnextself 76ms 0.15% 85.70% 260ms 0.51% boost::numeric::ublas::vector_inner_prod::apply (inline) 3ms 0.0059% 85.71% 258ms 0.5% AbstractTetrahedralElement::AbstractTetrahedralElement