File: Test3dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 54811ms, 87.29% of 62790ms total Dropped 876 nodes (cum <= 313.95ms) flat flat% sum% cum cum% 0 0% 0% 62732ms 99.91% __libc_start_call_main 0 0% 0% 62732ms 99.91% __libc_start_main_impl 0 0% 0% 62732ms 99.91% _start 0 0% 0% 62716ms 99.88% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 62716ms 99.88% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 62716ms 99.88% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 62716ms 99.88% main 0 0% 0% 62680ms 99.82% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 62680ms 99.82% CxxTest::TestRunner::runTest (inline) 0 0% 0% 62680ms 99.82% Test3dTissueRepresentativeSimulation::Test3DHoneycombMeshWithGhostNodes 0 0% 0% 62410ms 99.39% AbstractCellBasedSimulation::Solve 0 0% 0% 53328ms 84.93% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 53283ms 84.86% MeshBasedCellPopulation::Update 0 0% 0% 31871ms 50.76% MeshBasedCellPopulation::TessellateIfNeeded 0 0% 0% 31868ms 50.75% MeshBasedCellPopulation::CreateVoronoiTessellation (inline) 223ms 0.36% 0.36% 27966ms 44.54% VertexMesh::VertexMesh 0 0% 0.36% 17370ms 27.66% MutableMesh::ReMesh 0 0% 0.36% 12828ms 20.43% tetgen::tetrahedralize 5ms 0.008% 0.36% 12690ms 20.21% tetgen::tetgenmesh::delaunizevertices 7ms 0.011% 0.37% 12679ms 20.19% tetgen::tetgenmesh::incrflipdelaunay 565ms 0.9% 1.27% 12414ms 19.77% TetrahedralMesh::EdgeIterator::operator++ 580ms 0.92% 2.20% 11279ms 17.96% tetgen::tetgenmesh::lawson 34ms 0.054% 2.25% 10801ms 17.20% std::set::insert (inline) 192ms 0.31% 2.56% 10311ms 16.42% std::_Rb_tree::_M_insert_unique 418ms 0.67% 3.22% 9770ms 15.56% VertexElement::AddFace 3115ms 4.96% 8.18% 9153ms 14.58% std::_Rb_tree::_M_lower_bound (inline) 238ms 0.38% 8.56% 8506ms 13.55% std::_Rb_tree::find (inline) 0 0% 8.56% 7939ms 12.64% std::set::count (inline) 268ms 0.43% 8.99% 6051ms 9.64% std::_Rb_tree::_M_insert_ (inline) 5983ms 9.53% 18.52% 5983ms 9.53% std::_Rb_tree_increment 107ms 0.17% 18.69% 5725ms 9.12% std::less::operator() (inline) 5671ms 9.03% 27.72% 5671ms 9.03% std::operator< (inline) 211ms 0.34% 28.06% 5629ms 8.96% operator new 0 0% 28.06% 5431ms 8.65% OffLatticeSimulation::UpdateCellLocationsAndTopology 1054ms 1.68% 29.74% 5351ms 8.52% __GI___libc_malloc 0 0% 29.74% 5282ms 8.41% ForwardEulerNumericalMethod::UpdateAllNodePositions 7ms 0.011% 29.75% 5255ms 8.37% AbstractNumericalMethod::ComputeForcesIncludingDamping 5ms 0.008% 29.75% 4943ms 7.87% std::set_intersection (inline) 305ms 0.49% 30.24% 4938ms 7.86% std::__set_intersection 36ms 0.057% 30.30% 4688ms 7.47% std::__new_allocator::allocate (inline) 0 0% 30.30% 4672ms 7.44% std::allocator_traits::allocate (inline) 8ms 0.013% 30.31% 4524ms 7.20% std::_Rb_tree::~_Rb_tree (inline) 1814ms 2.89% 33.20% 4516ms 7.19% std::_Rb_tree::_M_erase 0 0% 33.20% 4458ms 7.10% std::set::~set (inline) 35ms 0.056% 33.26% 4429ms 7.05% Node::AddElement 1261ms 2.01% 35.26% 4384ms 6.98% std::_Rb_tree::_M_get_insert_unique_pos 1ms 0.0016% 35.27% 4378ms 6.97% MeshBasedCellPopulation::UpdateNodePairs 4ms 0.0064% 35.27% 4368ms 6.96% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 12ms 0.019% 35.29% 4220ms 6.72% MeshBasedCellPopulation::SpringIterator::operator++ 1273ms 2.03% 37.32% 4211ms 6.71% __GI___libc_free 205ms 0.33% 37.64% 4149ms 6.61% std::_Rb_tree_const_iterator::operator++ (inline) 2930ms 4.67% 42.31% 3977ms 6.33% _int_malloc 1ms 0.0016% 42.31% 3937ms 6.27% VertexMesh::~VertexMesh 3924ms 6.25% 48.56% 3924ms 6.25% std::_Rb_tree::_S_right (inline) 0 0% 48.56% 3790ms 6.04% std::_Rb_tree::_M_create_node (inline) 0 0% 48.56% 3762ms 5.99% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 48.56% 3734ms 5.95% std::_Rb_tree::_M_get_node (inline) 122ms 0.19% 48.76% 3698ms 5.89% std::__new_allocator::deallocate (inline) 0 0% 48.76% 3680ms 5.86% std::allocator_traits::deallocate (inline) 9ms 0.014% 48.77% 3632ms 5.78% TetrahedralMesh::ImportFromMesher 125ms 0.2% 48.97% 3554ms 5.66% tetgen::tetgenmesh::insphere_sos 84ms 0.13% 49.10% 3510ms 5.59% MutableElement::AddNode 0 0% 49.10% 3509ms 5.59% AbstractCellPopulation::WriteResultsToFiles 3132ms 4.99% 54.09% 3414ms 5.44% tetgen::insphere 1178ms 1.88% 55.97% 2937ms 4.68% _int_free 213ms 0.34% 56.31% 2768ms 4.41% tetgen::tetgenmesh::flip23 180ms 0.29% 56.59% 2706ms 4.31% Node::~Node 198ms 0.32% 56.91% 2500ms 3.98% VertexMesh::Clear 217ms 0.35% 57.25% 2345ms 3.73% VertexMesh::GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex 5ms 0.008% 57.26% 2331ms 3.71% MeshBasedCellPopulationWithGhostNodes::WriteVtkResultsToFile 2ms 0.0032% 57.27% 2152ms 3.43% std::_Rb_tree_iterator::operator++ (inline) 2125ms 3.38% 60.65% 2125ms 3.38% std::_Rb_tree_insert_and_rebalance 1996ms 3.18% 63.83% 1996ms 3.18% Node::GetIndex 0 0% 63.83% 1941ms 3.09% std::_Rb_tree::_M_drop_node (inline) 0 0% 63.83% 1933ms 3.08% std::_Rb_tree::_M_put_node (inline) 6ms 0.0096% 63.84% 1811ms 2.88% Element::Element 163ms 0.26% 64.10% 1797ms 2.86% tetgen::tetgenmesh::flip32 1242ms 1.98% 66.08% 1778ms 2.83% malloc_consolidate 15ms 0.024% 66.10% 1762ms 2.81% std::_Vector_base::_M_deallocate (inline) 0 0% 66.10% 1619ms 2.58% std::vector::~vector (inline) 2ms 0.0032% 66.10% 1570ms 2.50% std::_Vector_base::~_Vector_base (inline) 8ms 0.013% 66.12% 1518ms 2.42% _int_free_maybe_consolidate 4ms 0.0064% 66.12% 1473ms 2.35% Element::RegisterWithNodes (inline) 216ms 0.34% 66.47% 1450ms 2.31% TetrahedralMesh::Clear 1243ms 1.98% 68.45% 1327ms 2.11% tetgen::orient3d 1237ms 1.97% 70.42% 1237ms 1.97% unlink_chunk 88ms 0.14% 70.56% 1203ms 1.92% std::vector::_M_realloc_insert 55ms 0.088% 70.64% 1194ms 1.90% std::map::operator[] 41ms 0.065% 70.71% 1167ms 1.86% tetgen::tetgenmesh::locate 184ms 0.29% 71.00% 1164ms 1.85% tetgen::tetgenmesh::enqueueflipface 3ms 0.0048% 71.01% 1136ms 1.81% VertexMesh::GenerateVerticesFromElementCircumcentres 970ms 1.54% 72.55% 1122ms 1.79% AbstractElement::GetNodeGlobalIndex 103ms 0.16% 72.72% 1076ms 1.71% tetgen::tetgenmesh::preciselocate 0 0% 72.72% 1061ms 1.69% std::_Rb_tree::lower_bound (inline) 0 0% 72.72% 1061ms 1.69% std::map::lower_bound (inline) 4ms 0.0064% 72.72% 942ms 1.50% std::_Vector_base::_M_allocate (inline) 100ms 0.16% 72.88% 939ms 1.50% std::vector::push_back (inline) 1ms 0.0016% 72.88% 938ms 1.49% VoronoiDataWriter::Visit 1ms 0.0016% 72.88% 893ms 1.42% TetrahedralMesh::RefreshJacobianCachedData 865ms 1.38% 74.26% 865ms 1.38% tetgen::tetgenmesh::triface::triface 475ms 0.76% 75.02% 862ms 1.37% tetgen::tetgenmesh::fnextself 12ms 0.019% 75.04% 780ms 1.24% AbstractTetrahedralElement::CalculateInverseJacobian 359ms 0.57% 75.61% 765ms 1.22% AbstractElement::GetNodeLocation 747ms 1.19% 76.80% 747ms 1.19% AbstractElement::IsDeleted 17ms 0.027% 76.83% 735ms 1.17% AbstractTetrahedralElement::CalculateJacobian 722ms 1.15% 77.98% 722ms 1.15% Node::rGetLocation 0 0% 77.98% 708ms 1.13% AbstractTwoBodyInteractionForce::AddForceContribution 14ms 0.022% 78.00% 668ms 1.06% AbstractVariableSizeTwoBodyInteractionForce::CalculateForceBetweenNodes 15ms 0.024% 78.02% 663ms 1.06% boost::numeric::ublas::vector_assign (inline) 635ms 1.01% 79.03% 635ms 1.01% [libchaste_mesh.so] 4ms 0.0064% 79.04% 621ms 0.99% boost::numeric::ublas::c_vector::c_vector (inline) 614ms 0.98% 80.02% 614ms 0.98% tetgen::tetgenmesh::oppo 599ms 0.95% 80.97% 599ms 0.95% tetgen::tetgenmesh::triface::operator= 46ms 0.073% 81.04% 582ms 0.93% __atan2 14ms 0.022% 81.07% 565ms 0.9% Element::CalculateCircumsphere 0 0% 81.07% 562ms 0.9% std::set::find (inline) 49ms 0.078% 81.15% 561ms 0.89% AbstractTetrahedralElement::RefreshJacobian 35ms 0.056% 81.20% 547ms 0.87% tetgen::tetgenmesh::enext2fnext 33ms 0.053% 81.25% 537ms 0.86% tetgen::tetgenmesh::enextfnext 432ms 0.69% 81.94% 536ms 0.85% __ieee754_atan2_fma 534ms 0.85% 82.79% 534ms 0.85% std::vector::size (inline) 0 0% 82.79% 483ms 0.77% std::insert_iterator::operator= (inline) 0 0% 82.79% 479ms 0.76% boost::numeric::ublas::inner_prod (inline) 2ms 0.0032% 82.80% 476ms 0.76% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 29ms 0.046% 82.84% 474ms 0.75% boost::numeric::ublas::vector_scalar_binary::evaluate 288ms 0.46% 83.30% 441ms 0.7% tetgen::tetgenmesh::sym 117ms 0.19% 83.49% 432ms 0.69% boost::numeric::ublas::indexing_vector_assign 0 0% 83.49% 431ms 0.69% std::_Rb_tree::_M_insert_unique_ (inline) 233ms 0.37% 83.86% 414ms 0.66% AbstractTetrahedralMesh::GetElement 406ms 0.65% 84.50% 406ms 0.65% boost::numeric::ublas::c_vector::operator() 29ms 0.046% 84.55% 405ms 0.65% std::_Rb_tree_iterator::operator-- (inline) 4ms 0.0064% 84.56% 402ms 0.64% CellPropertyCollection::GetPropertiesType (inline) 0 0% 84.56% 395ms 0.63% VertexMeshWriter::WriteVtkUsingMesh 285ms 0.45% 85.01% 393ms 0.63% tetgen::tetgenmesh::bond 16ms 0.025% 85.04% 391ms 0.62% VertexMesh::CalculateUnitNormalToFaceWithArea 2ms 0.0032% 85.04% 390ms 0.62% Cell::GetCellId 174ms 0.28% 85.32% 389ms 0.62% boost::numeric::ublas::vector_inner_prod::apply (inline) 12ms 0.019% 85.34% 389ms 0.62% std::vector::insert (inline) 22ms 0.035% 85.37% 384ms 0.61% tetgen::tetgenmesh::queue::push 85ms 0.14% 85.51% 383ms 0.61% __dynamic_cast 0 0% 85.51% 380ms 0.61% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 3ms 0.0048% 85.51% 376ms 0.6% boost::numeric::ublas::c_vector::operator= (inline) 362ms 0.58% 86.09% 362ms 0.58% tetgen::tetgenmesh::org 239ms 0.38% 86.47% 358ms 0.57% tetgen::tetgenmesh::link::add 356ms 0.57% 87.03% 356ms 0.57% std::_Rb_tree_decrement 4ms 0.0064% 87.04% 338ms 0.54% VertexElement::~VertexElement 3ms 0.0048% 87.05% 330ms 0.53% AbstractTetrahedralElement::AbstractTetrahedralElement 3ms 0.0048% 87.05% 327ms 0.52% AbstractCellProperty::IsSubType (inline) 152ms 0.24% 87.29% 320ms 0.51% Inverse