File: Test3dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 56042ms, 87.16% of 64296ms total Dropped 889 nodes (cum <= 321.48ms) flat flat% sum% cum cum% 0 0% 0% 64229ms 99.90% __libc_start_call_main 0 0% 0% 64229ms 99.90% __libc_start_main_impl 0 0% 0% 64229ms 99.90% _start 0 0% 0% 64212ms 99.87% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 64212ms 99.87% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 64212ms 99.87% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 64212ms 99.87% main 0 0% 0% 64177ms 99.81% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 64177ms 99.81% CxxTest::TestRunner::runTest (inline) 0 0% 0% 64177ms 99.81% Test3dTissueRepresentativeSimulation::Test3DHoneycombMeshWithGhostNodes 0 0% 0% 63913ms 99.40% AbstractCellBasedSimulation::Solve 0 0% 0% 52848ms 82.19% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 52787ms 82.10% MeshBasedCellPopulation::Update 0 0% 0% 30973ms 48.17% MeshBasedCellPopulation::CreateVoronoiTessellation (inline) 0 0% 0% 30973ms 48.17% MeshBasedCellPopulation::TessellateIfNeeded 205ms 0.32% 0.32% 27210ms 42.32% VertexMesh::VertexMesh 1ms 0.0016% 0.32% 17489ms 27.20% MutableMesh::ReMesh 581ms 0.9% 1.22% 13222ms 20.56% TetrahedralMesh::EdgeIterator::operator++ 2ms 0.0031% 1.23% 12781ms 19.88% tetgen::tetrahedralize 1ms 0.0016% 1.23% 12642ms 19.66% tetgen::tetgenmesh::delaunizevertices 12ms 0.019% 1.25% 12638ms 19.66% tetgen::tetgenmesh::incrflipdelaunay 572ms 0.89% 2.14% 11270ms 17.53% tetgen::tetgenmesh::lawson 35ms 0.054% 2.19% 10616ms 16.51% std::set::insert (inline) 3051ms 4.75% 6.94% 10223ms 15.90% std::_Rb_tree::_M_lower_bound (inline) 204ms 0.32% 7.25% 10101ms 15.71% std::_Rb_tree::_M_insert_unique 381ms 0.59% 7.85% 9632ms 14.98% VertexElement::AddFace 254ms 0.4% 8.24% 9487ms 14.76% std::_Rb_tree::find (inline) 0 0% 8.24% 8888ms 13.82% std::set::count (inline) 6951ms 10.81% 19.05% 6951ms 10.81% std::_Rb_tree_increment 120ms 0.19% 19.24% 6742ms 10.49% std::less::operator() (inline) 6675ms 10.38% 29.62% 6675ms 10.38% std::operator< (inline) 253ms 0.39% 30.01% 5939ms 9.24% std::_Rb_tree::_M_insert_ (inline) 0 0% 30.01% 5811ms 9.04% OffLatticeSimulation::UpdateCellLocationsAndTopology 1ms 0.0016% 30.02% 5653ms 8.79% ForwardEulerNumericalMethod::UpdateAllNodePositions 4ms 0.0062% 30.02% 5624ms 8.75% AbstractNumericalMethod::ComputeForcesIncludingDamping 206ms 0.32% 30.34% 5576ms 8.67% operator new 1090ms 1.70% 32.04% 5309ms 8.26% __GI___libc_malloc 0 0% 32.04% 5105ms 7.94% AbstractCellPopulation::WriteResultsToFiles 64ms 0.1% 32.14% 4706ms 7.32% std::__new_allocator::allocate (inline) 2ms 0.0031% 32.14% 4691ms 7.30% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 0 0% 32.14% 4687ms 7.29% std::allocator_traits::allocate (inline) 2ms 0.0031% 32.14% 4664ms 7.25% MeshBasedCellPopulation::UpdateNodePairs 12ms 0.019% 32.16% 4537ms 7.06% std::_Rb_tree::~_Rb_tree (inline) 1808ms 2.81% 34.97% 4524ms 7.04% std::_Rb_tree::_M_erase 12ms 0.019% 34.99% 4517ms 7.03% MeshBasedCellPopulation::SpringIterator::operator++ 0 0% 34.99% 4478ms 6.96% std::set::~set (inline) 1ms 0.0016% 34.99% 4380ms 6.81% std::set_intersection (inline) 281ms 0.44% 35.43% 4379ms 6.81% std::__set_intersection 1267ms 1.97% 37.40% 4272ms 6.64% std::_Rb_tree::_M_get_insert_unique_pos 25ms 0.039% 37.44% 4228ms 6.58% Node::AddElement 1205ms 1.87% 39.32% 4074ms 6.34% __GI___libc_free 3949ms 6.14% 45.46% 3949ms 6.14% std::_Rb_tree::_S_right (inline) 2837ms 4.41% 49.87% 3874ms 6.03% _int_malloc 231ms 0.36% 50.23% 3862ms 6.01% VertexMesh::GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex 7ms 0.011% 50.24% 3828ms 5.95% TetrahedralMesh::ImportFromMesher 0 0% 50.24% 3790ms 5.89% VertexMesh::~VertexMesh 0 0% 50.24% 3761ms 5.85% std::_Rb_tree::_M_create_node (inline) 0 0% 50.24% 3717ms 5.78% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 50.24% 3711ms 5.77% std::_Rb_tree::_M_get_node (inline) 1ms 0.0016% 50.24% 3652ms 5.68% std::_Rb_tree_iterator::operator++ (inline) 6ms 0.0093% 50.25% 3604ms 5.61% MeshBasedCellPopulationWithGhostNodes::WriteVtkResultsToFile 136ms 0.21% 50.46% 3583ms 5.57% std::__new_allocator::deallocate (inline) 177ms 0.28% 50.74% 3578ms 5.56% std::_Rb_tree_const_iterator::operator++ (inline) 0 0% 50.74% 3565ms 5.54% std::allocator_traits::deallocate (inline) 112ms 0.17% 50.91% 3558ms 5.53% tetgen::tetgenmesh::insphere_sos 3142ms 4.89% 55.80% 3435ms 5.34% tetgen::insphere 84ms 0.13% 55.93% 3133ms 4.87% MutableElement::AddNode 1174ms 1.83% 57.75% 2867ms 4.46% _int_free 203ms 0.32% 58.07% 2672ms 4.16% Node::~Node 188ms 0.29% 58.36% 2621ms 4.08% tetgen::tetgenmesh::flip23 228ms 0.35% 58.72% 2435ms 3.79% VertexMesh::Clear 2080ms 3.24% 61.95% 2080ms 3.24% std::_Rb_tree_insert_and_rebalance 0 0% 61.95% 1922ms 2.99% std::_Rb_tree::_M_drop_node (inline) 4ms 0.0062% 61.96% 1919ms 2.98% Element::Element 0 0% 61.96% 1911ms 2.97% std::_Rb_tree::_M_put_node (inline) 1859ms 2.89% 64.85% 1859ms 2.89% Node::GetIndex 153ms 0.24% 65.09% 1814ms 2.82% tetgen::tetgenmesh::flip32 1071ms 1.67% 66.75% 1712ms 2.66% malloc_consolidate 21ms 0.033% 66.79% 1674ms 2.60% std::_Vector_base::_M_deallocate (inline) 6ms 0.0093% 66.80% 1591ms 2.47% Element::RegisterWithNodes (inline) 0 0% 66.80% 1537ms 2.39% std::vector::~vector (inline) 230ms 0.36% 67.15% 1528ms 2.38% TetrahedralMesh::Clear 0 0% 67.15% 1489ms 2.32% std::_Vector_base::~_Vector_base (inline) 9ms 0.014% 67.17% 1466ms 2.28% _int_free_maybe_consolidate 1311ms 2.04% 69.21% 1401ms 2.18% tetgen::orient3d 1312ms 2.04% 71.25% 1312ms 2.04% unlink_chunk 54ms 0.084% 71.33% 1306ms 2.03% std::map::operator[] 157ms 0.24% 71.58% 1244ms 1.93% tetgen::tetgenmesh::enqueueflipface 2ms 0.0031% 71.58% 1236ms 1.92% VoronoiDataWriter::Visit 62ms 0.096% 71.67% 1173ms 1.82% std::vector::_M_realloc_insert 0 0% 71.67% 1164ms 1.81% std::_Rb_tree::lower_bound (inline) 0 0% 71.67% 1164ms 1.81% std::map::lower_bound (inline) 40ms 0.062% 71.74% 1159ms 1.80% tetgen::tetgenmesh::locate 4ms 0.0062% 71.74% 1118ms 1.74% VertexMesh::GenerateVerticesFromElementCircumcentres 87ms 0.14% 71.88% 1068ms 1.66% tetgen::tetgenmesh::preciselocate 876ms 1.36% 73.24% 1026ms 1.60% AbstractElement::GetNodeGlobalIndex 3ms 0.0047% 73.25% 979ms 1.52% std::_Vector_base::_M_allocate (inline) 119ms 0.19% 73.43% 973ms 1.51% std::vector::push_back (inline) 855ms 1.33% 74.76% 855ms 1.33% tetgen::tetgenmesh::triface::triface 0 0% 74.76% 850ms 1.32% TetrahedralMesh::RefreshJacobianCachedData 10ms 0.016% 74.78% 765ms 1.19% AbstractTetrahedralElement::CalculateInverseJacobian 308ms 0.48% 75.26% 749ms 1.16% AbstractElement::GetNodeLocation 399ms 0.62% 75.88% 738ms 1.15% tetgen::tetgenmesh::fnextself 15ms 0.023% 75.90% 736ms 1.14% AbstractTetrahedralElement::CalculateJacobian 1ms 0.0016% 75.90% 733ms 1.14% AbstractTwoBodyInteractionForce::AddForceContribution 706ms 1.10% 77.00% 706ms 1.10% Node::rGetLocation 18ms 0.028% 77.03% 688ms 1.07% boost::numeric::ublas::vector_assign (inline) 14ms 0.022% 77.05% 683ms 1.06% AbstractVariableSizeTwoBodyInteractionForce::CalculateForceBetweenNodes 11ms 0.017% 77.07% 662ms 1.03% boost::numeric::ublas::c_vector::c_vector (inline) 57ms 0.089% 77.15% 660ms 1.03% __atan2 657ms 1.02% 78.18% 657ms 1.02% tetgen::tetgenmesh::oppo 628ms 0.98% 79.15% 628ms 0.98% [libchaste_mesh.so] 621ms 0.97% 80.12% 621ms 0.97% tetgen::tetgenmesh::triface::operator= 620ms 0.96% 81.08% 620ms 0.96% AbstractElement::IsDeleted 486ms 0.76% 81.84% 603ms 0.94% __ieee754_atan2_fma 0 0% 81.84% 595ms 0.93% std::set::find (inline) 20ms 0.031% 81.87% 574ms 0.89% Element::CalculateCircumsphere 28ms 0.044% 81.91% 536ms 0.83% AbstractTetrahedralElement::RefreshJacobian 533ms 0.83% 82.74% 533ms 0.83% std::vector::size (inline) 0 0% 82.74% 514ms 0.8% boost::numeric::ublas::inner_prod (inline) 4ms 0.0062% 82.75% 513ms 0.8% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 25ms 0.039% 82.79% 509ms 0.79% boost::numeric::ublas::vector_scalar_binary::evaluate 0 0% 82.79% 505ms 0.79% std::insert_iterator::operator= (inline) 51ms 0.079% 82.87% 479ms 0.74% tetgen::tetgenmesh::enext2fnext 36ms 0.056% 82.92% 479ms 0.74% tetgen::tetgenmesh::enextfnext 0 0% 82.92% 459ms 0.71% std::_Rb_tree::_M_insert_unique_ (inline) 102ms 0.16% 83.08% 439ms 0.68% boost::numeric::ublas::indexing_vector_assign 25ms 0.039% 83.12% 432ms 0.67% VertexMesh::CalculateUnitNormalToFaceWithArea 5ms 0.0078% 83.13% 423ms 0.66% CellPropertyCollection::GetPropertiesType (inline) 182ms 0.28% 83.41% 419ms 0.65% boost::numeric::ublas::vector_inner_prod::apply (inline) 417ms 0.65% 84.06% 417ms 0.65% tetgen::tetgenmesh::org 7ms 0.011% 84.07% 409ms 0.64% Cell::GetCellId 267ms 0.42% 84.49% 408ms 0.63% tetgen::tetgenmesh::sym 404ms 0.63% 85.11% 404ms 0.63% boost::numeric::ublas::c_vector::operator() 224ms 0.35% 85.46% 400ms 0.62% AbstractTetrahedralMesh::GetElement 83ms 0.13% 85.59% 397ms 0.62% __dynamic_cast 15ms 0.023% 85.61% 397ms 0.62% tetgen::tetgenmesh::queue::push 0 0% 85.61% 395ms 0.61% VertexMeshWriter::WriteVtkUsingMesh 28ms 0.044% 85.66% 392ms 0.61% std::_Rb_tree_iterator::operator-- (inline) 10ms 0.016% 85.67% 389ms 0.61% boost::numeric::ublas::c_vector::operator= (inline) 261ms 0.41% 86.08% 378ms 0.59% tetgen::tetgenmesh::link::add 0 0% 86.08% 373ms 0.58% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 263ms 0.41% 86.49% 367ms 0.57% tetgen::tetgenmesh::bond 351ms 0.55% 87.03% 351ms 0.55% std::_Rb_tree_decrement 4ms 0.0062% 87.04% 341ms 0.53% AbstractCellProperty::IsSubType (inline) 7ms 0.011% 87.05% 338ms 0.53% std::vector::insert (inline) 4ms 0.0062% 87.06% 324ms 0.5% AbstractTetrahedralElement::AbstractTetrahedralElement 9ms 0.014% 87.07% 323ms 0.5% VertexElement::~VertexElement 58ms 0.09% 87.16% 323ms 0.5% boost::numeric::ublas::vector_reference::operator() (inline)