File: Test3dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 50647ms, 87.44% of 57924ms total Dropped 837 nodes (cum <= 289.62ms) flat flat% sum% cum cum% 0 0% 0% 57862ms 99.89% __libc_start_call_main 0 0% 0% 57862ms 99.89% __libc_start_main_impl 0 0% 0% 57862ms 99.89% _start 0 0% 0% 57847ms 99.87% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 57847ms 99.87% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 57847ms 99.87% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 57847ms 99.87% main 0 0% 0% 57812ms 99.81% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 57812ms 99.81% CxxTest::TestRunner::runTest (inline) 0 0% 0% 57812ms 99.81% Test3dTissueRepresentativeSimulation::Test3DHoneycombMeshWithGhostNodes 0 0% 0% 57562ms 99.38% AbstractCellBasedSimulation::Solve 0 0% 0% 47397ms 81.83% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 47349ms 81.74% MeshBasedCellPopulation::Update 0 0% 0% 26391ms 45.56% MeshBasedCellPopulation::TessellateIfNeeded 0 0% 0% 26389ms 45.56% MeshBasedCellPopulation::CreateVoronoiTessellation (inline) 183ms 0.32% 0.32% 23637ms 40.81% VertexMesh::VertexMesh 0 0% 0.32% 16973ms 29.30% MutableMesh::ReMesh 0 0% 0.32% 13218ms 22.82% tetgen::tetrahedralize 2ms 0.0035% 0.32% 13072ms 22.57% tetgen::tetgenmesh::delaunizevertices 6ms 0.01% 0.33% 13068ms 22.56% tetgen::tetgenmesh::incrflipdelaunay 540ms 0.93% 1.26% 12128ms 20.94% TetrahedralMesh::EdgeIterator::operator++ 536ms 0.93% 2.19% 11601ms 20.03% tetgen::tetgenmesh::lawson 2883ms 4.98% 7.16% 9781ms 16.89% std::_Rb_tree::_M_lower_bound (inline) 24ms 0.041% 7.21% 9440ms 16.30% std::set::insert (inline) 241ms 0.42% 7.62% 9015ms 15.56% std::_Rb_tree::find (inline) 346ms 0.6% 8.22% 8993ms 15.53% VertexElement::AddFace 195ms 0.34% 8.56% 8966ms 15.48% std::_Rb_tree::_M_insert_unique 0 0% 8.56% 8490ms 14.66% std::set::count (inline) 108ms 0.19% 8.74% 6538ms 11.29% std::less::operator() (inline) 6488ms 11.20% 19.94% 6488ms 11.20% std::operator< (inline) 5623ms 9.71% 29.65% 5623ms 9.71% std::_Rb_tree_increment 1ms 0.0017% 29.65% 5361ms 9.26% OffLatticeSimulation::UpdateCellLocationsAndTopology 273ms 0.47% 30.12% 5318ms 9.18% std::_Rb_tree::_M_insert_ (inline) 0 0% 30.12% 5223ms 9.02% ForwardEulerNumericalMethod::UpdateAllNodePositions 1ms 0.0017% 30.13% 5196ms 8.97% AbstractNumericalMethod::ComputeForcesIncludingDamping 0 0% 30.13% 4671ms 8.06% AbstractCellPopulation::WriteResultsToFiles 236ms 0.41% 30.53% 4567ms 7.88% operator new 0 0% 30.53% 4315ms 7.45% MeshBasedCellPopulation::UpdateNodePairs 8ms 0.014% 30.55% 4278ms 7.39% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 1048ms 1.81% 32.36% 4253ms 7.34% __GI___libc_malloc 9ms 0.016% 32.37% 4177ms 7.21% MeshBasedCellPopulation::SpringIterator::operator++ 34ms 0.059% 32.43% 3972ms 6.86% std::__new_allocator::allocate (inline) 0 0% 32.43% 3952ms 6.82% std::allocator_traits::allocate (inline) 10ms 0.017% 32.45% 3795ms 6.55% std::_Rb_tree::~_Rb_tree (inline) 1457ms 2.52% 34.96% 3782ms 6.53% std::_Rb_tree::_M_erase 0 0% 34.96% 3749ms 6.47% std::set::~set (inline) 1181ms 2.04% 37.00% 3733ms 6.44% std::_Rb_tree::_M_get_insert_unique_pos 79ms 0.14% 37.14% 3528ms 6.09% tetgen::tetgenmesh::insphere_sos 212ms 0.37% 37.50% 3503ms 6.05% VertexMesh::GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex 3155ms 5.45% 42.95% 3436ms 5.93% tetgen::insphere 962ms 1.66% 44.61% 3346ms 5.78% __GI___libc_free 13ms 0.022% 44.63% 3334ms 5.76% std::set_intersection (inline) 238ms 0.41% 45.05% 3321ms 5.73% std::__set_intersection 3ms 0.0052% 45.05% 3311ms 5.72% MeshBasedCellPopulationWithGhostNodes::WriteVtkResultsToFile 0 0% 45.05% 3300ms 5.70% std::_Rb_tree_iterator::operator++ (inline) 0 0% 45.05% 3221ms 5.56% std::_Rb_tree::_M_create_node (inline) 24ms 0.041% 45.09% 3203ms 5.53% Node::AddElement 0 0% 45.09% 3191ms 5.51% std::_Rb_tree::_M_get_node (inline) 0 0% 45.09% 3184ms 5.50% std::_Rb_tree::_Alloc_node::operator() (inline) 3149ms 5.44% 50.53% 3149ms 5.44% std::_Rb_tree::_S_right (inline) 6ms 0.01% 50.54% 2993ms 5.17% TetrahedralMesh::ImportFromMesher 119ms 0.21% 50.74% 2971ms 5.13% std::__new_allocator::deallocate (inline) 0 0% 50.74% 2958ms 5.11% std::allocator_traits::deallocate (inline) 2103ms 3.63% 54.37% 2823ms 4.87% _int_malloc 0 0% 54.37% 2770ms 4.78% VertexMesh::~VertexMesh 193ms 0.33% 54.71% 2679ms 4.63% tetgen::tetgenmesh::flip23 217ms 0.37% 55.08% 2642ms 4.56% std::_Rb_tree_const_iterator::operator++ (inline) 1145ms 1.98% 57.06% 2383ms 4.11% _int_free 70ms 0.12% 57.18% 2357ms 4.07% MutableElement::AddNode 164ms 0.28% 57.46% 2047ms 3.53% tetgen::tetgenmesh::flip32 108ms 0.19% 57.65% 1965ms 3.39% Node::~Node 1915ms 3.31% 60.96% 1915ms 3.31% std::_Rb_tree_insert_and_rebalance 141ms 0.24% 61.20% 1849ms 3.19% VertexMesh::Clear 0 0% 61.20% 1780ms 3.07% std::_Rb_tree::_M_drop_node (inline) 0 0% 61.20% 1769ms 3.05% std::_Rb_tree::_M_put_node (inline) 1ms 0.0017% 61.20% 1638ms 2.83% Element::Element 160ms 0.28% 61.48% 1557ms 2.69% tetgen::tetgenmesh::enqueueflipface 1496ms 2.58% 64.06% 1496ms 2.58% Node::GetIndex 1344ms 2.32% 66.38% 1423ms 2.46% tetgen::orient3d 2ms 0.0035% 66.38% 1287ms 2.22% Element::RegisterWithNodes (inline) 77ms 0.13% 66.52% 1272ms 2.20% std::map::operator[] 32ms 0.055% 66.57% 1227ms 2.12% tetgen::tetgenmesh::locate 682ms 1.18% 67.75% 1207ms 2.08% malloc_consolidate 18ms 0.031% 67.78% 1207ms 2.08% std::_Vector_base::_M_deallocate (inline) 0 0% 67.78% 1144ms 1.98% std::vector::~vector (inline) 98ms 0.17% 67.95% 1141ms 1.97% tetgen::tetgenmesh::preciselocate 0 0% 67.95% 1130ms 1.95% std::_Rb_tree::lower_bound (inline) 0 0% 67.95% 1130ms 1.95% std::map::lower_bound (inline) 0 0% 67.95% 1117ms 1.93% VoronoiDataWriter::Visit 122ms 0.21% 68.16% 1083ms 1.87% TetrahedralMesh::Clear 9ms 0.016% 68.18% 1040ms 1.80% _int_free_maybe_consolidate 62ms 0.11% 68.28% 1038ms 1.79% std::vector::_M_realloc_insert 2ms 0.0035% 68.29% 1034ms 1.79% std::_Vector_base::~_Vector_base (inline) 958ms 1.65% 69.94% 958ms 1.65% unlink_chunk 945ms 1.63% 71.57% 945ms 1.63% tetgen::tetgenmesh::triface::triface 3ms 0.0052% 71.58% 875ms 1.51% VertexMesh::GenerateVerticesFromElementCircumcentres 102ms 0.18% 71.75% 838ms 1.45% std::vector::push_back (inline) 775ms 1.34% 73.09% 775ms 1.34% tetgen::tetgenmesh::oppo 5ms 0.0086% 73.10% 766ms 1.32% std::_Vector_base::_M_allocate (inline) 0 0% 73.10% 746ms 1.29% TetrahedralMesh::RefreshJacobianCachedData 0 0% 73.10% 722ms 1.25% AbstractTwoBodyInteractionForce::AddForceContribution 712ms 1.23% 74.33% 712ms 1.23% tetgen::tetgenmesh::triface::operator= 9ms 0.016% 74.34% 692ms 1.19% AbstractTetrahedralElement::CalculateInverseJacobian 13ms 0.022% 74.37% 675ms 1.17% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 525ms 0.91% 75.27% 668ms 1.15% AbstractElement::GetNodeGlobalIndex 18ms 0.031% 75.30% 665ms 1.15% boost::numeric::ublas::vector_assign (inline) 18ms 0.031% 75.33% 664ms 1.15% AbstractTetrahedralElement::CalculateJacobian 650ms 1.12% 76.46% 650ms 1.12% [libchaste_mesh.so] 302ms 0.52% 76.98% 631ms 1.09% tetgen::tetgenmesh::fnextself 243ms 0.42% 77.40% 626ms 1.08% AbstractElement::GetNodeLocation 10ms 0.017% 77.42% 613ms 1.06% boost::numeric::ublas::c_vector::c_vector (inline) 52ms 0.09% 77.51% 603ms 1.04% __atan2 24ms 0.041% 77.55% 555ms 0.96% tetgen::tetgenmesh::queue::push 434ms 0.75% 78.30% 551ms 0.95% __ieee754_atan2_fma 536ms 0.93% 79.22% 536ms 0.93% Node::rGetLocation 437ms 0.75% 79.98% 522ms 0.9% tetgen::tetgenmesh::link::add 0 0% 79.98% 520ms 0.9% std::set::find (inline) 35ms 0.06% 80.04% 488ms 0.84% AbstractTetrahedralElement::RefreshJacobian 0 0% 80.04% 487ms 0.84% boost::numeric::ublas::inner_prod (inline) 5ms 0.0086% 80.04% 484ms 0.84% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 14ms 0.024% 80.07% 483ms 0.83% Element::CalculateCircumsphere 480ms 0.83% 80.90% 480ms 0.83% std::vector::size (inline) 32ms 0.055% 80.95% 479ms 0.83% boost::numeric::ublas::vector_scalar_binary::evaluate 0 0% 80.95% 474ms 0.82% std::insert_iterator::operator= (inline) 253ms 0.44% 81.39% 447ms 0.77% AbstractTetrahedralMesh::GetElement 135ms 0.23% 81.62% 438ms 0.76% boost::numeric::ublas::indexing_vector_assign 0 0% 81.62% 418ms 0.72% std::_Rb_tree::_M_insert_unique_ (inline) 32ms 0.055% 81.68% 416ms 0.72% tetgen::tetgenmesh::enext2fnext 21ms 0.036% 81.71% 409ms 0.71% VertexMesh::CalculateUnitNormalToFaceWithArea 263ms 0.45% 82.17% 405ms 0.7% tetgen::tetgenmesh::sym 192ms 0.33% 82.50% 396ms 0.68% boost::numeric::ublas::vector_inner_prod::apply (inline) 0 0% 82.50% 394ms 0.68% VertexMeshWriter::WriteVtkUsingMesh 103ms 0.18% 82.68% 390ms 0.67% __dynamic_cast 42ms 0.073% 82.75% 390ms 0.67% tetgen::tetgenmesh::enextfnext 1ms 0.0017% 82.75% 387ms 0.67% CellPropertyCollection::GetPropertiesType (inline) 385ms 0.66% 83.42% 385ms 0.66% boost::numeric::ublas::c_vector::operator() 8ms 0.014% 83.43% 385ms 0.66% boost::numeric::ublas::c_vector::operator= (inline) 383ms 0.66% 84.09% 383ms 0.66% tetgen::tetgenmesh::org 15ms 0.026% 84.12% 375ms 0.65% std::_Rb_tree_iterator::operator-- (inline) 4ms 0.0069% 84.12% 374ms 0.65% Cell::GetCellId 5ms 0.0086% 84.13% 352ms 0.61% AbstractTetrahedralElement::AbstractTetrahedralElement 270ms 0.47% 84.60% 346ms 0.6% tetgen::tetgenmesh::bond 345ms 0.6% 85.19% 345ms 0.6% tetgen::tetgenmesh::pointmark 343ms 0.59% 85.79% 343ms 0.59% std::_Rb_tree_decrement 341ms 0.59% 86.38% 341ms 0.59% AbstractElement::IsDeleted 0 0% 86.38% 341ms 0.59% tcache_get (inline) 341ms 0.59% 86.96% 341ms 0.59% tcache_get_n (inline) 2ms 0.0035% 86.97% 322ms 0.56% AbstractCellProperty::IsSubType (inline) 7ms 0.012% 86.98% 322ms 0.56% VertexElement::~VertexElement 139ms 0.24% 87.22% 320ms 0.55% Inverse 6ms 0.01% 87.23% 317ms 0.55% std::vector::insert (inline) 63ms 0.11% 87.34% 307ms 0.53% tetgen::tetgenmesh::queue::pop 0 0% 87.34% 303ms 0.52% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 57ms 0.098% 87.44% 302ms 0.52% boost::numeric::ublas::vector_reference::operator() (inline)