File: Test3dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 52856ms, 87.44% of 60446ms total Dropped 862 nodes (cum <= 302.23ms) flat flat% sum% cum cum% 0 0% 0% 60380ms 99.89% __libc_start_call_main 0 0% 0% 60380ms 99.89% __libc_start_main_impl 0 0% 0% 60380ms 99.89% _start 0 0% 0% 60365ms 99.87% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 60365ms 99.87% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 60365ms 99.87% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 60365ms 99.87% main 0 0% 0% 60328ms 99.80% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 60328ms 99.80% CxxTest::TestRunner::runTest (inline) 0 0% 0% 60328ms 99.80% Test3dTissueRepresentativeSimulation::Test3DHoneycombMeshWithGhostNodes 0 0% 0% 60066ms 99.37% AbstractCellBasedSimulation::Solve 0 0% 0% 49365ms 81.67% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 49314ms 81.58% MeshBasedCellPopulation::Update 0 0% 0% 28195ms 46.64% MeshBasedCellPopulation::CreateVoronoiTessellation (inline) 0 0% 0% 28195ms 46.64% MeshBasedCellPopulation::TessellateIfNeeded 217ms 0.36% 0.36% 24857ms 41.12% VertexMesh::VertexMesh 2ms 0.0033% 0.36% 16960ms 28.06% MutableMesh::ReMesh 0 0% 0.36% 12692ms 21.00% tetgen::tetrahedralize 550ms 0.91% 1.27% 12658ms 20.94% TetrahedralMesh::EdgeIterator::operator++ 1ms 0.0017% 1.27% 12558ms 20.78% tetgen::tetgenmesh::delaunizevertices 8ms 0.013% 1.29% 12553ms 20.77% tetgen::tetgenmesh::incrflipdelaunay 541ms 0.9% 2.18% 11157ms 18.46% tetgen::tetgenmesh::lawson 3048ms 5.04% 7.22% 10126ms 16.75% std::_Rb_tree::_M_lower_bound (inline) 28ms 0.046% 7.27% 9799ms 16.21% std::set::insert (inline) 216ms 0.36% 7.63% 9327ms 15.43% std::_Rb_tree::find (inline) 194ms 0.32% 7.95% 9315ms 15.41% std::_Rb_tree::_M_insert_unique 365ms 0.6% 8.55% 9118ms 15.08% VertexElement::AddFace 0 0% 8.55% 8805ms 14.57% std::set::count (inline) 119ms 0.2% 8.75% 6734ms 11.14% std::less::operator() (inline) 6667ms 11.03% 19.78% 6667ms 11.03% std::operator< (inline) 6279ms 10.39% 30.17% 6279ms 10.39% std::_Rb_tree_increment 0 0% 30.17% 5575ms 9.22% OffLatticeSimulation::UpdateCellLocationsAndTopology 276ms 0.46% 30.62% 5501ms 9.10% std::_Rb_tree::_M_insert_ (inline) 0 0% 30.62% 5432ms 8.99% ForwardEulerNumericalMethod::UpdateAllNodePositions 4ms 0.0066% 30.63% 5400ms 8.93% AbstractNumericalMethod::ComputeForcesIncludingDamping 0 0% 30.63% 4989ms 8.25% AbstractCellPopulation::WriteResultsToFiles 195ms 0.32% 30.95% 4967ms 8.22% operator new 1037ms 1.72% 32.67% 4696ms 7.77% __GI___libc_malloc 3ms 0.005% 32.67% 4488ms 7.42% MeshBasedCellPopulation::UpdateNodePairs 11ms 0.018% 32.69% 4468ms 7.39% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 6ms 0.0099% 32.70% 4343ms 7.18% MeshBasedCellPopulation::SpringIterator::operator++ 40ms 0.066% 32.77% 4241ms 7.02% std::__new_allocator::allocate (inline) 8ms 0.013% 32.78% 4236ms 7.01% std::_Rb_tree::~_Rb_tree (inline) 1708ms 2.83% 35.61% 4226ms 6.99% std::_Rb_tree::_M_erase 0 0% 35.61% 4218ms 6.98% std::allocator_traits::allocate (inline) 0 0% 35.61% 4178ms 6.91% std::set::~set (inline) 1201ms 1.99% 37.59% 3938ms 6.51% std::_Rb_tree::_M_get_insert_unique_pos 255ms 0.42% 38.02% 3853ms 6.37% VertexMesh::GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex 1051ms 1.74% 39.75% 3736ms 6.18% __GI___libc_free 4ms 0.0066% 39.76% 3613ms 5.98% std::set_intersection (inline) 1ms 0.0017% 39.76% 3611ms 5.97% std::_Rb_tree_iterator::operator++ (inline) 214ms 0.35% 40.12% 3609ms 5.97% std::__set_intersection 12ms 0.02% 40.14% 3592ms 5.94% Node::AddElement 7ms 0.012% 40.15% 3570ms 5.91% MeshBasedCellPopulationWithGhostNodes::WriteVtkResultsToFile 3510ms 5.81% 45.96% 3510ms 5.81% std::_Rb_tree::_S_right (inline) 99ms 0.16% 46.12% 3492ms 5.78% tetgen::tetgenmesh::insphere_sos 5ms 0.0083% 46.13% 3467ms 5.74% TetrahedralMesh::ImportFromMesher 0 0% 46.13% 3400ms 5.62% std::_Rb_tree::_M_create_node (inline) 3089ms 5.11% 51.24% 3385ms 5.60% tetgen::insphere 0 0% 51.24% 3366ms 5.57% VertexMesh::~VertexMesh 0 0% 51.24% 3364ms 5.57% std::_Rb_tree::_M_get_node (inline) 0 0% 51.24% 3360ms 5.56% std::_Rb_tree::_Alloc_node::operator() (inline) 2396ms 3.96% 55.20% 3296ms 5.45% _int_malloc 139ms 0.23% 55.43% 3275ms 5.42% std::__new_allocator::deallocate (inline) 0 0% 55.43% 3248ms 5.37% std::allocator_traits::deallocate (inline) 182ms 0.3% 55.73% 2950ms 4.88% std::_Rb_tree_const_iterator::operator++ (inline) 204ms 0.34% 56.07% 2706ms 4.48% tetgen::tetgenmesh::flip23 1167ms 1.93% 58.00% 2680ms 4.43% _int_free 68ms 0.11% 58.11% 2584ms 4.27% MutableElement::AddNode 135ms 0.22% 58.34% 2377ms 3.93% Node::~Node 184ms 0.3% 58.64% 2216ms 3.67% VertexMesh::Clear 1930ms 3.19% 61.83% 1930ms 3.19% std::_Rb_tree_insert_and_rebalance 0 0% 61.83% 1861ms 3.08% std::_Rb_tree::_M_drop_node (inline) 0 0% 61.83% 1849ms 3.06% std::_Rb_tree::_M_put_node (inline) 6ms 0.0099% 61.84% 1814ms 3.00% Element::Element 147ms 0.24% 62.09% 1814ms 3.00% tetgen::tetgenmesh::flip32 1658ms 2.74% 64.83% 1658ms 2.74% Node::GetIndex 5ms 0.0083% 64.84% 1460ms 2.42% Element::RegisterWithNodes (inline) 876ms 1.45% 66.29% 1444ms 2.39% malloc_consolidate 13ms 0.022% 66.31% 1412ms 2.34% std::_Vector_base::_M_deallocate (inline) 1309ms 2.17% 68.47% 1399ms 2.31% tetgen::orient3d 1ms 0.0017% 68.48% 1345ms 2.23% std::vector::~vector (inline) 213ms 0.35% 68.83% 1340ms 2.22% TetrahedralMesh::Clear 60ms 0.099% 68.93% 1335ms 2.21% std::map::operator[] 168ms 0.28% 69.21% 1284ms 2.12% tetgen::tetgenmesh::enqueueflipface 6ms 0.0099% 69.22% 1251ms 2.07% _int_free_maybe_consolidate 0 0% 69.22% 1251ms 2.07% std::_Vector_base::~_Vector_base (inline) 0 0% 69.22% 1198ms 1.98% std::_Rb_tree::lower_bound (inline) 0 0% 69.22% 1198ms 1.98% std::map::lower_bound (inline) 34ms 0.056% 69.27% 1173ms 1.94% tetgen::tetgenmesh::locate 3ms 0.005% 69.28% 1168ms 1.93% VoronoiDataWriter::Visit 1110ms 1.84% 71.11% 1110ms 1.84% unlink_chunk 87ms 0.14% 71.26% 1102ms 1.82% tetgen::tetgenmesh::preciselocate 58ms 0.096% 71.35% 1076ms 1.78% std::vector::_M_realloc_insert 5ms 0.0083% 71.36% 984ms 1.63% VertexMesh::GenerateVerticesFromElementCircumcentres 140ms 0.23% 71.59% 916ms 1.52% std::vector::push_back (inline) 872ms 1.44% 73.04% 872ms 1.44% tetgen::tetgenmesh::triface::triface 4ms 0.0066% 73.04% 858ms 1.42% std::_Vector_base::_M_allocate (inline) 458ms 0.76% 73.80% 794ms 1.31% tetgen::tetgenmesh::fnextself 0 0% 73.80% 778ms 1.29% TetrahedralMesh::RefreshJacobianCachedData 748ms 1.24% 75.04% 748ms 1.24% tetgen::tetgenmesh::oppo 3ms 0.005% 75.04% 742ms 1.23% AbstractTwoBodyInteractionForce::AddForceContribution 595ms 0.98% 76.03% 724ms 1.20% AbstractElement::GetNodeGlobalIndex 6ms 0.0099% 76.04% 713ms 1.18% AbstractTetrahedralElement::CalculateInverseJacobian 12ms 0.02% 76.06% 695ms 1.15% AbstractTetrahedralElement::CalculateJacobian 18ms 0.03% 76.09% 689ms 1.14% boost::numeric::ublas::c_vector::c_vector (inline) 17ms 0.028% 76.11% 688ms 1.14% boost::numeric::ublas::vector_assign (inline) 63ms 0.1% 76.22% 680ms 1.12% __atan2 8ms 0.013% 76.23% 679ms 1.12% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 278ms 0.46% 76.69% 676ms 1.12% AbstractElement::GetNodeLocation 667ms 1.10% 77.80% 667ms 1.10% [libchaste_mesh.so] 494ms 0.82% 78.61% 617ms 1.02% __ieee754_atan2_fma 584ms 0.97% 79.58% 584ms 0.97% Node::rGetLocation 552ms 0.91% 80.49% 552ms 0.91% tetgen::tetgenmesh::triface::operator= 43ms 0.071% 80.56% 534ms 0.88% tetgen::tetgenmesh::enext2fnext 0 0% 80.56% 517ms 0.86% std::set::find (inline) 39ms 0.065% 80.63% 515ms 0.85% AbstractTetrahedralElement::RefreshJacobian 11ms 0.018% 80.65% 511ms 0.85% Element::CalculateCircumsphere 0 0% 80.65% 478ms 0.79% std::insert_iterator::operator= (inline) 0 0% 80.65% 469ms 0.78% boost::numeric::ublas::inner_prod (inline) 42ms 0.069% 80.72% 469ms 0.78% tetgen::tetgenmesh::enextfnext 4ms 0.0066% 80.72% 459ms 0.76% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 27ms 0.045% 80.77% 455ms 0.75% boost::numeric::ublas::vector_scalar_binary::evaluate 451ms 0.75% 81.51% 451ms 0.75% std::vector::size (inline) 119ms 0.2% 81.71% 429ms 0.71% boost::numeric::ublas::indexing_vector_assign 425ms 0.7% 82.41% 425ms 0.7% AbstractElement::IsDeleted 239ms 0.4% 82.81% 424ms 0.7% AbstractTetrahedralMesh::GetElement 0 0% 82.81% 421ms 0.7% std::_Rb_tree::_M_insert_unique_ (inline) 5ms 0.0083% 82.82% 419ms 0.69% CellPropertyCollection::GetPropertiesType (inline) 4ms 0.0066% 82.82% 417ms 0.69% boost::numeric::ublas::c_vector::operator= (inline) 5ms 0.0083% 82.83% 411ms 0.68% Cell::GetCellId 89ms 0.15% 82.98% 402ms 0.67% __dynamic_cast 258ms 0.43% 83.41% 402ms 0.67% tetgen::tetgenmesh::sym 401ms 0.66% 84.07% 401ms 0.66% boost::numeric::ublas::c_vector::operator() 397ms 0.66% 84.73% 397ms 0.66% tetgen::tetgenmesh::org 21ms 0.035% 84.76% 396ms 0.66% tetgen::tetgenmesh::queue::push 0 0% 84.76% 394ms 0.65% VertexMeshWriter::WriteVtkUsingMesh 160ms 0.26% 85.02% 383ms 0.63% boost::numeric::ublas::vector_inner_prod::apply (inline) 262ms 0.43% 85.46% 373ms 0.62% tetgen::tetgenmesh::link::add 277ms 0.46% 85.92% 368ms 0.61% tetgen::tetgenmesh::bond 24ms 0.04% 85.96% 363ms 0.6% std::_Rb_tree_iterator::operator-- (inline) 17ms 0.028% 85.98% 357ms 0.59% VertexMesh::CalculateUnitNormalToFaceWithArea 3ms 0.005% 85.99% 350ms 0.58% AbstractTetrahedralElement::AbstractTetrahedralElement 0 0% 85.99% 339ms 0.56% tcache_get (inline) 339ms 0.56% 86.55% 339ms 0.56% tcache_get_n (inline) 3ms 0.005% 86.55% 336ms 0.56% AbstractCellProperty::IsSubType (inline) 16ms 0.026% 86.58% 323ms 0.53% std::vector::insert (inline) 7ms 0.012% 86.59% 322ms 0.53% VertexElement::~VertexElement 322ms 0.53% 87.13% 322ms 0.53% std::_Rb_tree_decrement 138ms 0.23% 87.35% 320ms 0.53% Inverse 0 0% 87.35% 319ms 0.53% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 54ms 0.089% 87.44% 318ms 0.53% boost::numeric::ublas::vector_reference::operator() (inline)