File: Test3dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 50931ms, 86.48% of 58896ms total Dropped 875 nodes (cum <= 294.48ms) flat flat% sum% cum cum% 0 0% 0% 58837ms 99.90% __libc_start_call_main 0 0% 0% 58837ms 99.90% __libc_start_main_impl 0 0% 0% 58837ms 99.90% _start 0 0% 0% 58823ms 99.88% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 58823ms 99.88% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 58823ms 99.88% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 58823ms 99.88% main 0 0% 0% 58788ms 99.82% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 58788ms 99.82% CxxTest::TestRunner::runTest (inline) 0 0% 0% 58788ms 99.82% Test3dTissueRepresentativeSimulation::Test3DHoneycombMeshWithGhostNodes 0 0% 0% 58503ms 99.33% AbstractCellBasedSimulation::Solve 0 0% 0% 49605ms 84.22% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 49562ms 84.15% MeshBasedCellPopulation::Update 0 0% 0% 28822ms 48.94% MeshBasedCellPopulation::TessellateIfNeeded 0 0% 0% 28821ms 48.94% MeshBasedCellPopulation::CreateVoronoiTessellation (inline) 180ms 0.31% 0.31% 25328ms 43.00% VertexMesh::VertexMesh 0 0% 0.31% 16896ms 28.69% MutableMesh::ReMesh 0 0% 0.31% 12681ms 21.53% tetgen::tetrahedralize 2ms 0.0034% 0.31% 12544ms 21.30% tetgen::tetgenmesh::delaunizevertices 13ms 0.022% 0.33% 12538ms 21.29% tetgen::tetgenmesh::incrflipdelaunay 566ms 0.96% 1.29% 11724ms 19.91% TetrahedralMesh::EdgeIterator::operator++ 528ms 0.9% 2.19% 11130ms 18.90% tetgen::tetgenmesh::lawson 29ms 0.049% 2.24% 10242ms 17.39% std::set::insert (inline) 240ms 0.41% 2.65% 9724ms 16.51% std::_Rb_tree::_M_insert_unique 349ms 0.59% 3.24% 9243ms 15.69% VertexElement::AddFace 3104ms 5.27% 8.51% 8919ms 15.14% std::_Rb_tree::_M_lower_bound (inline) 225ms 0.38% 8.89% 8294ms 14.08% std::_Rb_tree::find (inline) 0 0% 8.89% 7706ms 13.08% std::set::count (inline) 297ms 0.5% 9.39% 5809ms 9.86% std::_Rb_tree::_M_insert_ (inline) 111ms 0.19% 9.58% 5575ms 9.47% std::less::operator() (inline) 5527ms 9.38% 18.97% 5527ms 9.38% std::operator< (inline) 0 0% 18.97% 5220ms 8.86% OffLatticeSimulation::UpdateCellLocationsAndTopology 219ms 0.37% 19.34% 5122ms 8.70% operator new 0 0% 19.34% 5085ms 8.63% ForwardEulerNumericalMethod::UpdateAllNodePositions 5057ms 8.59% 27.93% 5057ms 8.59% std::_Rb_tree_increment 4ms 0.0068% 27.93% 5055ms 8.58% AbstractNumericalMethod::ComputeForcesIncludingDamping 1106ms 1.88% 29.81% 4831ms 8.20% __GI___libc_malloc 55ms 0.093% 29.90% 4337ms 7.36% std::__new_allocator::allocate (inline) 0 0% 29.90% 4314ms 7.32% std::allocator_traits::allocate (inline) 6ms 0.01% 29.91% 4290ms 7.28% std::_Rb_tree::~_Rb_tree (inline) 1717ms 2.92% 32.83% 4283ms 7.27% std::_Rb_tree::_M_erase 0 0% 32.83% 4233ms 7.19% std::set::~set (inline) 3ms 0.0051% 32.83% 4199ms 7.13% MeshBasedCellPopulation::UpdateNodePairs 2ms 0.0034% 32.84% 4180ms 7.10% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 14ms 0.024% 32.86% 4034ms 6.85% MeshBasedCellPopulation::SpringIterator::operator++ 265ms 0.45% 33.31% 3997ms 6.79% std::__set_intersection 0 0% 33.31% 3997ms 6.79% std::set_intersection (inline) 1220ms 2.07% 35.38% 3994ms 6.78% std::_Rb_tree::_M_get_insert_unique_pos 1140ms 1.94% 37.32% 3864ms 6.56% __GI___libc_free 28ms 0.048% 37.37% 3829ms 6.50% Node::AddElement 0 0% 37.37% 3539ms 6.01% VertexMesh::~VertexMesh 0 0% 37.37% 3532ms 6.00% std::_Rb_tree::_M_create_node (inline) 0 0% 37.37% 3514ms 5.97% AbstractCellPopulation::WriteResultsToFiles 0 0% 37.37% 3501ms 5.94% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 37.37% 3481ms 5.91% std::_Rb_tree::_M_get_node (inline) 116ms 0.2% 37.56% 3464ms 5.88% tetgen::tetgenmesh::insphere_sos 2530ms 4.30% 41.86% 3403ms 5.78% _int_malloc 7ms 0.012% 41.87% 3397ms 5.77% TetrahedralMesh::ImportFromMesher 126ms 0.21% 42.08% 3385ms 5.75% std::__new_allocator::deallocate (inline) 0 0% 42.08% 3367ms 5.72% std::allocator_traits::deallocate (inline) 3361ms 5.71% 47.79% 3361ms 5.71% std::_Rb_tree::_S_right (inline) 3029ms 5.14% 52.93% 3332ms 5.66% tetgen::insphere 167ms 0.28% 53.22% 3219ms 5.47% std::_Rb_tree_const_iterator::operator++ (inline) 84ms 0.14% 53.36% 3052ms 5.18% MutableElement::AddNode 1210ms 2.05% 55.41% 2720ms 4.62% _int_free 200ms 0.34% 55.75% 2662ms 4.52% tetgen::tetgenmesh::flip23 195ms 0.33% 56.09% 2547ms 4.32% Node::~Node 219ms 0.37% 56.46% 2353ms 4.00% VertexMesh::Clear 2ms 0.0034% 56.46% 2323ms 3.94% MeshBasedCellPopulationWithGhostNodes::WriteVtkResultsToFile 214ms 0.36% 56.82% 2319ms 3.94% VertexMesh::GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex 0 0% 56.82% 2118ms 3.60% std::_Rb_tree_iterator::operator++ (inline) 2094ms 3.56% 60.38% 2094ms 3.56% std::_Rb_tree_insert_and_rebalance 0 0% 60.38% 1920ms 3.26% std::_Rb_tree::_M_drop_node (inline) 0 0% 60.38% 1906ms 3.24% std::_Rb_tree::_M_put_node (inline) 160ms 0.27% 60.65% 1906ms 3.24% tetgen::tetgenmesh::flip32 6ms 0.01% 60.66% 1606ms 2.73% Element::Element 995ms 1.69% 62.35% 1476ms 2.51% malloc_consolidate 15ms 0.025% 62.38% 1476ms 2.51% std::_Vector_base::_M_deallocate (inline) 230ms 0.39% 62.77% 1458ms 2.48% TetrahedralMesh::Clear 1427ms 2.42% 65.19% 1427ms 2.42% Node::GetIndex 1302ms 2.21% 67.40% 1390ms 2.36% tetgen::orient3d 0 0% 67.40% 1360ms 2.31% std::vector::~vector (inline) 0 0% 67.40% 1291ms 2.19% std::_Vector_base::~_Vector_base (inline) 189ms 0.32% 67.72% 1282ms 2.18% tetgen::tetgenmesh::enqueueflipface 7ms 0.012% 67.73% 1275ms 2.16% _int_free_maybe_consolidate 6ms 0.01% 67.74% 1269ms 2.15% Element::RegisterWithNodes (inline) 41ms 0.07% 67.81% 1189ms 2.02% tetgen::tetgenmesh::locate 68ms 0.12% 67.93% 1166ms 1.98% std::map::operator[] 97ms 0.16% 68.09% 1110ms 1.88% tetgen::tetgenmesh::preciselocate 1082ms 1.84% 69.93% 1082ms 1.84% unlink_chunk 59ms 0.1% 70.03% 1081ms 1.84% std::vector::_M_realloc_insert 0 0% 70.03% 1027ms 1.74% std::_Rb_tree::lower_bound (inline) 0 0% 70.03% 1027ms 1.74% std::map::lower_bound (inline) 1ms 0.0017% 70.03% 966ms 1.64% VertexMesh::GenerateVerticesFromElementCircumcentres 0 0% 70.03% 945ms 1.60% VoronoiDataWriter::Visit 792ms 1.34% 71.38% 929ms 1.58% AbstractElement::GetNodeGlobalIndex 129ms 0.22% 71.60% 885ms 1.50% std::vector::push_back (inline) 885ms 1.50% 73.10% 885ms 1.50% tetgen::tetgenmesh::triface::triface 3ms 0.0051% 73.10% 836ms 1.42% std::_Vector_base::_M_allocate (inline) 470ms 0.8% 73.90% 797ms 1.35% tetgen::tetgenmesh::fnextself 0 0% 73.90% 795ms 1.35% TetrahedralMesh::RefreshJacobianCachedData 10ms 0.017% 73.92% 718ms 1.22% AbstractTetrahedralElement::CalculateInverseJacobian 0 0% 73.92% 715ms 1.21% AbstractTwoBodyInteractionForce::AddForceContribution 15ms 0.025% 73.94% 674ms 1.14% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 15ms 0.025% 73.97% 671ms 1.14% AbstractTetrahedralElement::CalculateJacobian 49ms 0.083% 74.05% 658ms 1.12% __atan2 14ms 0.024% 74.08% 650ms 1.10% boost::numeric::ublas::vector_assign (inline) 638ms 1.08% 75.16% 638ms 1.08% tetgen::tetgenmesh::oppo 636ms 1.08% 76.24% 636ms 1.08% [libchaste_mesh.so] 278ms 0.47% 76.71% 630ms 1.07% AbstractElement::GetNodeLocation 7ms 0.012% 76.72% 624ms 1.06% boost::numeric::ublas::c_vector::c_vector (inline) 483ms 0.82% 77.54% 608ms 1.03% __ieee754_atan2_fma 0 0% 77.54% 586ms 0.99% std::set::find (inline) 582ms 0.99% 78.53% 582ms 0.99% Node::rGetLocation 564ms 0.96% 79.49% 564ms 0.96% AbstractElement::IsDeleted 554ms 0.94% 80.43% 554ms 0.94% tetgen::tetgenmesh::triface::operator= 53ms 0.09% 80.52% 520ms 0.88% tetgen::tetgenmesh::enextfnext 48ms 0.081% 80.60% 519ms 0.88% tetgen::tetgenmesh::enext2fnext 0 0% 80.60% 504ms 0.86% std::insert_iterator::operator= (inline) 500ms 0.85% 81.45% 500ms 0.85% std::vector::size (inline) 23ms 0.039% 81.49% 494ms 0.84% Element::CalculateCircumsphere 45ms 0.076% 81.57% 483ms 0.82% AbstractTetrahedralElement::RefreshJacobian 0 0% 81.57% 474ms 0.8% boost::numeric::ublas::inner_prod (inline) 5ms 0.0085% 81.57% 471ms 0.8% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 29ms 0.049% 81.62% 466ms 0.79% boost::numeric::ublas::vector_scalar_binary::evaluate 0 0% 81.62% 458ms 0.78% std::_Rb_tree::_M_insert_unique_ (inline) 280ms 0.48% 82.10% 438ms 0.74% tetgen::tetgenmesh::sym 107ms 0.18% 82.28% 422ms 0.72% boost::numeric::ublas::indexing_vector_assign 13ms 0.022% 82.30% 417ms 0.71% VertexMesh::CalculateUnitNormalToFaceWithArea 247ms 0.42% 82.72% 412ms 0.7% AbstractTetrahedralMesh::GetElement 21ms 0.036% 82.76% 407ms 0.69% std::_Rb_tree_iterator::operator-- (inline) 406ms 0.69% 83.45% 406ms 0.69% boost::numeric::ublas::c_vector::operator() 6ms 0.01% 83.46% 404ms 0.69% CellPropertyCollection::GetPropertiesType (inline) 75ms 0.13% 83.58% 399ms 0.68% __dynamic_cast 2ms 0.0034% 83.59% 395ms 0.67% boost::numeric::ublas::c_vector::operator= (inline) 0 0% 83.59% 394ms 0.67% VertexMeshWriter::WriteVtkUsingMesh 5ms 0.0085% 83.60% 388ms 0.66% Cell::GetCellId 20ms 0.034% 83.63% 386ms 0.66% tetgen::tetgenmesh::queue::push 168ms 0.29% 83.92% 383ms 0.65% boost::numeric::ublas::vector_inner_prod::apply (inline) 375ms 0.64% 84.55% 375ms 0.64% tetgen::tetgenmesh::org 365ms 0.62% 85.17% 365ms 0.62% std::_Rb_tree_decrement 259ms 0.44% 85.61% 363ms 0.62% tetgen::tetgenmesh::link::add 251ms 0.43% 86.04% 334ms 0.57% tetgen::tetgenmesh::bond 6ms 0.01% 86.05% 332ms 0.56% std::vector::insert (inline) 4ms 0.0068% 86.06% 330ms 0.56% AbstractTetrahedralElement::AbstractTetrahedralElement 147ms 0.25% 86.30% 326ms 0.55% Inverse 2ms 0.0034% 86.31% 324ms 0.55% AbstractCellProperty::IsSubType (inline) 0 0% 86.31% 324ms 0.55% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 6ms 0.01% 86.32% 310ms 0.53% VertexElement::~VertexElement 58ms 0.098% 86.42% 306ms 0.52% boost::numeric::ublas::vector_reference::operator() (inline) 31ms 0.053% 86.47% 303ms 0.51% tetgen::insphereadapt 4ms 0.0068% 86.48% 299ms 0.51% VertexMesh::GetVolumeOfElement