File: Test3dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 54902ms, 85.89% of 63924ms total Dropped 855 nodes (cum <= 319.62ms) flat flat% sum% cum cum% 0 0% 0% 63873ms 99.92% __libc_start_call_main 0 0% 0% 63873ms 99.92% __libc_start_main_impl 0 0% 0% 63873ms 99.92% _start 0 0% 0% 63857ms 99.90% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 63857ms 99.90% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 63857ms 99.90% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 63857ms 99.90% main 0 0% 0% 63817ms 99.83% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 63817ms 99.83% CxxTest::TestRunner::runTest (inline) 0 0% 0% 63817ms 99.83% Test3dTissueRepresentativeSimulation::Test3DHoneycombMeshWithGhostNodes 0 0% 0% 63537ms 99.39% AbstractCellBasedSimulation::Solve 0 0% 0% 54320ms 84.98% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 54277ms 84.91% MeshBasedCellPopulation::Update 1ms 0.0016% 0.0016% 29954ms 46.86% MeshBasedCellPopulation::TessellateIfNeeded 0 0% 0.0016% 29952ms 46.86% MeshBasedCellPopulation::CreateVoronoiTessellation (inline) 207ms 0.32% 0.33% 26590ms 41.60% VertexMesh::VertexMesh 0 0% 0.33% 20212ms 31.62% MutableMesh::ReMesh 0 0% 0.33% 15996ms 25.02% tetgen::tetrahedralize 1ms 0.0016% 0.33% 15842ms 24.78% tetgen::tetgenmesh::delaunizevertices 4ms 0.0063% 0.33% 15837ms 24.77% tetgen::tetgenmesh::incrflipdelaunay 537ms 0.84% 1.17% 14140ms 22.12% tetgen::tetgenmesh::lawson 606ms 0.95% 2.12% 12570ms 19.66% TetrahedralMesh::EdgeIterator::operator++ 28ms 0.044% 2.17% 10735ms 16.79% std::set::insert (inline) 243ms 0.38% 2.55% 10290ms 16.10% std::_Rb_tree::_M_insert_unique 394ms 0.62% 3.16% 10127ms 15.84% VertexElement::AddFace 3119ms 4.88% 8.04% 9040ms 14.14% std::_Rb_tree::_M_lower_bound (inline) 303ms 0.47% 8.51% 8614ms 13.48% std::_Rb_tree::find (inline) 0 0% 8.51% 8051ms 12.59% std::set::count (inline) 302ms 0.47% 8.99% 6192ms 9.69% std::_Rb_tree::_M_insert_ (inline) 141ms 0.22% 9.21% 5869ms 9.18% std::less::operator() (inline) 5776ms 9.04% 18.24% 5776ms 9.04% std::operator< (inline) 196ms 0.31% 18.55% 5768ms 9.02% operator new 1ms 0.0016% 18.55% 5511ms 8.62% OffLatticeSimulation::UpdateCellLocationsAndTopology 1312ms 2.05% 20.60% 5479ms 8.57% __GI___libc_malloc 5454ms 8.53% 29.14% 5454ms 8.53% std::_Rb_tree_increment 1ms 0.0016% 29.14% 5380ms 8.42% ForwardEulerNumericalMethod::UpdateAllNodePositions 2ms 0.0031% 29.14% 5347ms 8.36% AbstractNumericalMethod::ComputeForcesIncludingDamping 44ms 0.069% 29.21% 4948ms 7.74% std::__new_allocator::allocate (inline) 0 0% 29.21% 4930ms 7.71% std::allocator_traits::allocate (inline) 2ms 0.0031% 29.21% 4480ms 7.01% MeshBasedCellPopulation::UpdateNodePairs 7ms 0.011% 29.22% 4453ms 6.97% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 4ms 0.0063% 29.23% 4344ms 6.80% std::_Rb_tree::~_Rb_tree (inline) 1496ms 2.34% 31.57% 4337ms 6.78% std::_Rb_tree::_M_erase 11ms 0.017% 31.59% 4332ms 6.78% MeshBasedCellPopulation::SpringIterator::operator++ 273ms 0.43% 32.01% 4301ms 6.73% std::__set_intersection 0 0% 32.01% 4301ms 6.73% std::set_intersection (inline) 0 0% 32.01% 4285ms 6.70% std::set::~set (inline) 1154ms 1.81% 33.82% 4143ms 6.48% __GI___libc_free 1314ms 2.06% 35.88% 4106ms 6.42% std::_Rb_tree::_M_get_insert_unique_pos 0 0% 35.88% 4102ms 6.42% std::_Rb_tree::_M_create_node (inline) 0 0% 35.88% 4070ms 6.37% std::_Rb_tree::_M_get_node (inline) 0 0% 35.88% 4062ms 6.35% std::_Rb_tree::_Alloc_node::operator() (inline) 123ms 0.19% 36.07% 3904ms 6.11% tetgen::tetgenmesh::insphere_sos 3467ms 5.42% 41.49% 3767ms 5.89% tetgen::insphere 58ms 0.091% 41.58% 3761ms 5.88% Node::AddElement 2737ms 4.28% 45.86% 3703ms 5.79% _int_malloc 128ms 0.2% 46.06% 3681ms 5.76% std::__new_allocator::deallocate (inline) 0 0% 46.06% 3664ms 5.73% std::allocator_traits::deallocate (inline) 205ms 0.32% 46.38% 3559ms 5.57% std::_Rb_tree_const_iterator::operator++ (inline) 0 0% 46.38% 3550ms 5.55% AbstractCellPopulation::WriteResultsToFiles 147ms 0.23% 46.61% 3463ms 5.42% tetgen::tetgenmesh::flip23 0 0% 46.61% 3387ms 5.30% VertexMesh::~VertexMesh 6ms 0.0094% 46.62% 3375ms 5.28% TetrahedralMesh::ImportFromMesher 3181ms 4.98% 51.60% 3181ms 4.98% std::_Rb_tree::_S_right (inline) 1428ms 2.23% 53.83% 2988ms 4.67% _int_free 68ms 0.11% 53.94% 2845ms 4.45% MutableElement::AddNode 149ms 0.23% 54.17% 2573ms 4.03% tetgen::tetgenmesh::flip32 210ms 0.33% 54.50% 2429ms 3.80% Node::~Node 174ms 0.27% 54.77% 2398ms 3.75% VertexMesh::GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex 2ms 0.0031% 54.78% 2387ms 3.73% MeshBasedCellPopulationWithGhostNodes::WriteVtkResultsToFile 0 0% 54.78% 2237ms 3.50% std::_Rb_tree_iterator::operator++ (inline) 0 0% 54.78% 2221ms 3.47% std::_Rb_tree::_M_drop_node (inline) 163ms 0.25% 55.03% 2212ms 3.46% VertexMesh::Clear 0 0% 55.03% 2212ms 3.46% std::_Rb_tree::_M_put_node (inline) 216ms 0.34% 55.37% 1917ms 3.00% tetgen::tetgenmesh::enqueueflipface 1891ms 2.96% 58.33% 1891ms 2.96% std::_Rb_tree_insert_and_rebalance 4ms 0.0063% 58.33% 1727ms 2.70% Element::Element 1638ms 2.56% 60.90% 1638ms 2.56% Node::GetIndex 1506ms 2.36% 63.25% 1592ms 2.49% tetgen::orient3d 1019ms 1.59% 64.85% 1507ms 2.36% malloc_consolidate 22ms 0.034% 64.88% 1474ms 2.31% std::_Vector_base::_M_deallocate (inline) 6ms 0.0094% 64.89% 1398ms 2.19% Element::RegisterWithNodes (inline) 0 0% 64.89% 1385ms 2.17% std::vector::~vector (inline) 34ms 0.053% 64.94% 1376ms 2.15% tetgen::tetgenmesh::locate 2ms 0.0031% 64.95% 1303ms 2.04% std::_Vector_base::~_Vector_base (inline) 99ms 0.15% 65.10% 1302ms 2.04% tetgen::tetgenmesh::preciselocate 79ms 0.12% 65.23% 1298ms 2.03% TetrahedralMesh::Clear 6ms 0.0094% 65.24% 1286ms 2.01% _int_free_maybe_consolidate 1140ms 1.78% 67.02% 1140ms 1.78% unlink_chunk 57ms 0.089% 67.11% 1108ms 1.73% std::vector::_M_realloc_insert 90ms 0.14% 67.25% 1107ms 1.73% std::map::operator[] 1087ms 1.70% 68.95% 1087ms 1.70% tetgen::tetgenmesh::triface::triface 886ms 1.39% 70.34% 1063ms 1.66% AbstractElement::GetNodeGlobalIndex 1038ms 1.62% 71.96% 1038ms 1.62% tetgen::tetgenmesh::oppo 0 0% 71.96% 927ms 1.45% std::_Rb_tree::lower_bound (inline) 0 0% 71.96% 927ms 1.45% std::map::lower_bound (inline) 5ms 0.0078% 71.97% 925ms 1.45% VertexMesh::GenerateVerticesFromElementCircumcentres 0 0% 71.97% 916ms 1.43% VoronoiDataWriter::Visit 113ms 0.18% 72.14% 889ms 1.39% std::vector::push_back (inline) 4ms 0.0063% 72.15% 864ms 1.35% std::_Vector_base::_M_allocate (inline) 1ms 0.0016% 72.15% 814ms 1.27% TetrahedralMesh::RefreshJacobianCachedData 301ms 0.47% 72.62% 770ms 1.20% tetgen::tetgenmesh::sym 756ms 1.18% 73.80% 756ms 1.18% [libchaste_mesh.so] 9ms 0.014% 73.82% 726ms 1.14% AbstractTetrahedralElement::CalculateInverseJacobian 724ms 1.13% 74.95% 724ms 1.13% tetgen::tetgenmesh::triface::operator= 1ms 0.0016% 74.95% 714ms 1.12% AbstractTwoBodyInteractionForce::AddForceContribution 16ms 0.025% 74.98% 679ms 1.06% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 52ms 0.081% 75.06% 660ms 1.03% tetgen::tetgenmesh::queue::push 60ms 0.094% 75.15% 652ms 1.02% __atan2 12ms 0.019% 75.17% 650ms 1.02% boost::numeric::ublas::c_vector::c_vector (inline) 23ms 0.036% 75.21% 650ms 1.02% boost::numeric::ublas::vector_assign (inline) 15ms 0.023% 75.23% 646ms 1.01% AbstractTetrahedralElement::CalculateJacobian 371ms 0.58% 75.81% 646ms 1.01% tetgen::tetgenmesh::fnextself 302ms 0.47% 76.28% 634ms 0.99% AbstractElement::GetNodeLocation 625ms 0.98% 77.26% 625ms 0.98% AbstractElement::IsDeleted 351ms 0.55% 77.81% 607ms 0.95% tetgen::tetgenmesh::link::add 43ms 0.067% 77.88% 599ms 0.94% tetgen::tetgenmesh::enext2fnext 448ms 0.7% 78.58% 586ms 0.92% __ieee754_atan2_fma 61ms 0.095% 78.67% 582ms 0.91% tetgen::tetgenmesh::enextfnext 0 0% 78.67% 561ms 0.88% std::set::find (inline) 558ms 0.87% 79.55% 558ms 0.87% std::vector::size (inline) 557ms 0.87% 80.42% 557ms 0.87% Node::rGetLocation 556ms 0.87% 81.29% 556ms 0.87% tetgen::tetgenmesh::org 0 0% 81.29% 541ms 0.85% boost::numeric::ublas::inner_prod (inline) 222ms 0.35% 81.64% 540ms 0.84% tetgen::tetgenmesh::bond 36ms 0.056% 81.69% 539ms 0.84% boost::numeric::ublas::vector_scalar_binary::evaluate 0 0% 81.69% 539ms 0.84% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 484ms 0.76% 82.45% 484ms 0.76% tetgen::tetgenmesh::decode 0 0% 82.45% 477ms 0.75% std::insert_iterator::operator= (inline) 32ms 0.05% 82.50% 469ms 0.73% AbstractTetrahedralElement::RefreshJacobian 16ms 0.025% 82.52% 459ms 0.72% Element::CalculateCircumsphere 196ms 0.31% 82.83% 438ms 0.69% boost::numeric::ublas::vector_inner_prod::apply (inline) 0 0% 82.83% 428ms 0.67% tcache_get (inline) 428ms 0.67% 83.50% 428ms 0.67% tcache_get_n (inline) 30ms 0.047% 83.55% 424ms 0.66% std::_Rb_tree_iterator::operator-- (inline) 0 0% 83.55% 411ms 0.64% std::_Rb_tree::_M_insert_unique_ (inline) 17ms 0.027% 83.57% 405ms 0.63% VertexMesh::CalculateUnitNormalToFaceWithArea 404ms 0.63% 84.21% 404ms 0.63% boost::numeric::ublas::c_vector::operator() 6ms 0.0094% 84.22% 404ms 0.63% boost::numeric::ublas::c_vector::operator= (inline) 206ms 0.32% 84.54% 400ms 0.63% AbstractTetrahedralMesh::GetElement 6ms 0.0094% 84.55% 395ms 0.62% CellPropertyCollection::GetPropertiesType (inline) 116ms 0.18% 84.73% 391ms 0.61% __dynamic_cast 0 0% 84.73% 388ms 0.61% VertexMeshWriter::WriteVtkUsingMesh 91ms 0.14% 84.87% 382ms 0.6% boost::numeric::ublas::indexing_vector_assign 1ms 0.0016% 84.87% 380ms 0.59% Cell::GetCellId 364ms 0.57% 85.44% 364ms 0.57% std::_Rb_tree_decrement 15ms 0.023% 85.47% 355ms 0.56% std::vector::insert (inline) 5ms 0.0078% 85.47% 354ms 0.55% VertexElement::~VertexElement 135ms 0.21% 85.68% 340ms 0.53% Inverse 0 0% 85.68% 340ms 0.53% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 48ms 0.075% 85.76% 328ms 0.51% boost::numeric::ublas::vector_reference::operator() (inline) 6ms 0.0094% 85.77% 327ms 0.51% AbstractTetrahedralElement::AbstractTetrahedralElement 75ms 0.12% 85.89% 326ms 0.51% tetgen::tetgenmesh::queue::pop