File: Test3dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 51850ms, 85.44% of 60686ms total Dropped 855 nodes (cum <= 303.43ms) flat flat% sum% cum cum% 0 0% 0% 60630ms 99.91% __libc_start_call_main 0 0% 0% 60630ms 99.91% __libc_start_main_impl 0 0% 0% 60630ms 99.91% _start 0 0% 0% 60613ms 99.88% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 60613ms 99.88% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 60613ms 99.88% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 60613ms 99.88% main 0 0% 0% 60576ms 99.82% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 60576ms 99.82% CxxTest::TestRunner::runTest (inline) 0 0% 0% 60576ms 99.82% Test3dTissueRepresentativeSimulation::Test3DHoneycombMeshWithGhostNodes 0 0% 0% 60348ms 99.44% AbstractCellBasedSimulation::Solve 0 0% 0% 50818ms 83.74% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 50758ms 83.64% MeshBasedCellPopulation::Update 0 0% 0% 30869ms 50.87% MeshBasedCellPopulation::TessellateIfNeeded 0 0% 0% 30868ms 50.87% MeshBasedCellPopulation::CreateVoronoiTessellation (inline) 234ms 0.39% 0.39% 27720ms 45.68% VertexMesh::VertexMesh 0 0% 0.39% 15679ms 25.84% MutableMesh::ReMesh 524ms 0.86% 1.25% 12876ms 21.22% TetrahedralMesh::EdgeIterator::operator++ 43ms 0.071% 1.32% 12032ms 19.83% std::set::insert (inline) 151ms 0.25% 1.57% 11436ms 18.84% std::_Rb_tree::_M_insert_unique 0 0% 1.57% 11421ms 18.82% tetgen::tetrahedralize 2ms 0.0033% 1.57% 11308ms 18.63% tetgen::tetgenmesh::delaunizevertices 4ms 0.0066% 1.58% 11302ms 18.62% tetgen::tetgenmesh::incrflipdelaunay 313ms 0.52% 2.09% 10857ms 17.89% VertexElement::AddFace 507ms 0.84% 2.93% 10008ms 16.49% tetgen::tetgenmesh::lawson 4316ms 7.11% 10.04% 9774ms 16.11% std::_Rb_tree::_M_lower_bound (inline) 207ms 0.34% 10.38% 9342ms 15.39% std::_Rb_tree::find (inline) 0 0% 10.38% 8793ms 14.49% std::set::count (inline) 209ms 0.34% 10.73% 7862ms 12.96% operator new 298ms 0.49% 11.22% 7757ms 12.78% std::_Rb_tree::_M_insert_ (inline) 2830ms 4.66% 15.88% 7573ms 12.48% __GI___libc_malloc 55ms 0.091% 15.97% 6735ms 11.10% std::__new_allocator::allocate (inline) 0 0% 15.97% 6710ms 11.06% std::allocator_traits::allocate (inline) 0 0% 15.97% 5715ms 9.42% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 15.97% 5575ms 9.19% ForwardEulerNumericalMethod::UpdateAllNodePositions 0 0% 15.97% 5556ms 9.16% std::_Rb_tree::_M_create_node (inline) 2ms 0.0033% 15.98% 5552ms 9.15% AbstractNumericalMethod::ComputeForcesIncludingDamping 0 0% 15.98% 5531ms 9.11% std::_Rb_tree::_M_get_node (inline) 0 0% 15.98% 5522ms 9.10% std::_Rb_tree::_Alloc_node::operator() (inline) 5038ms 8.30% 24.28% 5038ms 8.30% std::_Rb_tree_increment 86ms 0.14% 24.42% 4743ms 7.82% std::less::operator() (inline) 4732ms 7.80% 32.22% 4732ms 7.80% std::operator< (inline) 898ms 1.48% 33.70% 4717ms 7.77% __GI___libc_free 3ms 0.0049% 33.70% 4537ms 7.48% MeshBasedCellPopulation::UpdateNodePairs 4ms 0.0066% 33.71% 4511ms 7.43% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 25ms 0.041% 33.75% 4398ms 7.25% MeshBasedCellPopulation::SpringIterator::operator++ 23ms 0.038% 33.79% 4381ms 7.22% std::_Rb_tree::~_Rb_tree (inline) 1214ms 2.00% 35.79% 4344ms 7.16% std::_Rb_tree::_M_erase 0 0% 35.79% 4338ms 7.15% std::set::~set (inline) 3440ms 5.67% 41.46% 4319ms 7.12% _int_malloc 268ms 0.44% 41.90% 4110ms 6.77% std::__set_intersection 0 0% 41.90% 4110ms 6.77% std::set_intersection (inline) 70ms 0.12% 42.01% 4050ms 6.67% std::__new_allocator::deallocate (inline) 0 0% 42.01% 4043ms 6.66% std::allocator_traits::deallocate (inline) 1426ms 2.35% 44.36% 3888ms 6.41% std::_Rb_tree::_M_get_insert_unique_pos 83ms 0.14% 44.50% 3830ms 6.31% Node::AddElement 2039ms 3.36% 47.86% 3800ms 6.26% _int_free 0 0% 47.86% 3648ms 6.01% AbstractCellPopulation::WriteResultsToFiles 2ms 0.0033% 47.86% 3345ms 5.51% TetrahedralMesh::ImportFromMesher 3305ms 5.45% 53.31% 3305ms 5.45% std::_Rb_tree::_S_right (inline) 286ms 0.47% 53.78% 3294ms 5.43% std::_Rb_tree_const_iterator::operator++ (inline) 0 0% 53.78% 3172ms 5.23% VertexMesh::~VertexMesh 84ms 0.14% 53.92% 3041ms 5.01% tetgen::tetgenmesh::insphere_sos 2719ms 4.48% 58.40% 2931ms 4.83% tetgen::insphere 44ms 0.073% 58.47% 2871ms 4.73% MutableElement::AddNode 0 0% 58.47% 2606ms 4.29% std::_Rb_tree::_M_drop_node (inline) 274ms 0.45% 58.92% 2590ms 4.27% std::_Rb_tree_iterator::operator++ (inline) 3ms 0.0049% 58.93% 2575ms 4.24% VertexMesh::GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex 0 0% 58.93% 2567ms 4.23% std::_Rb_tree::_M_put_node (inline) 1ms 0.0016% 58.93% 2544ms 4.19% MeshBasedCellPopulationWithGhostNodes::WriteVtkResultsToFile 247ms 0.41% 59.34% 2387ms 3.93% tetgen::tetgenmesh::flip23 49ms 0.081% 59.42% 2166ms 3.57% Node::~Node 2083ms 3.43% 62.85% 2083ms 3.43% [libchaste_mesh.so] 3ms 0.0049% 62.85% 2049ms 3.38% VertexMesh::Clear 1990ms 3.28% 66.13% 1990ms 3.28% std::_Rb_tree_insert_and_rebalance 4ms 0.0066% 66.14% 1814ms 2.99% Element::Element 218ms 0.36% 66.50% 1658ms 2.73% tetgen::tetgenmesh::flip32 1538ms 2.53% 69.03% 1604ms 2.64% tetgen::orient3d 4ms 0.0066% 69.04% 1509ms 2.49% Element::RegisterWithNodes (inline) 18ms 0.03% 69.07% 1493ms 2.46% std::_Vector_base::_M_deallocate (inline) 1019ms 1.68% 70.75% 1483ms 2.44% malloc_consolidate 53ms 0.087% 70.84% 1408ms 2.32% std::vector::_M_realloc_insert 0 0% 70.84% 1325ms 2.18% std::vector::~vector (inline) 3ms 0.0049% 70.84% 1273ms 2.10% std::_Vector_base::~_Vector_base (inline) 5ms 0.0082% 70.85% 1271ms 2.09% _int_free_maybe_consolidate 3ms 0.0049% 70.85% 1182ms 1.95% std::_Vector_base::_M_allocate (inline) 88ms 0.15% 71.00% 1141ms 1.88% std::map::operator[] 1105ms 1.82% 72.82% 1105ms 1.82% Node::GetIndex 27ms 0.044% 72.87% 1101ms 1.81% tetgen::tetgenmesh::locate 78ms 0.13% 72.99% 1082ms 1.78% std::vector::push_back (inline) 2ms 0.0033% 73.00% 1074ms 1.77% TetrahedralMesh::Clear 218ms 0.36% 73.36% 1058ms 1.74% tetgen::tetgenmesh::enqueueflipface 4ms 0.0066% 73.36% 1037ms 1.71% VertexMesh::GenerateVerticesFromElementCircumcentres 88ms 0.15% 73.51% 1037ms 1.71% tetgen::tetgenmesh::preciselocate 1014ms 1.67% 75.18% 1014ms 1.67% unlink_chunk 0 0% 75.18% 963ms 1.59% std::_Rb_tree::lower_bound (inline) 0 0% 75.18% 963ms 1.59% std::map::lower_bound (inline) 532ms 0.88% 76.06% 920ms 1.52% AbstractElement::GetNodeGlobalIndex 0 0% 76.06% 886ms 1.46% VoronoiDataWriter::Visit 0 0% 76.06% 885ms 1.46% TetrahedralMesh::RefreshJacobianCachedData 4ms 0.0066% 76.06% 807ms 1.33% AbstractTwoBodyInteractionForce::AddForceContribution 6ms 0.0099% 76.07% 803ms 1.32% AbstractTetrahedralElement::CalculateInverseJacobian 17ms 0.028% 76.10% 782ms 1.29% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 8ms 0.013% 76.11% 705ms 1.16% boost::numeric::ublas::vector_assign (inline) 13ms 0.021% 76.13% 688ms 1.13% boost::numeric::ublas::c_vector::c_vector (inline) 664ms 1.09% 77.23% 664ms 1.09% Node::rGetLocation 386ms 0.64% 77.86% 631ms 1.04% tetgen::tetgenmesh::sym 11ms 0.018% 77.88% 629ms 1.04% AbstractTetrahedralElement::CalculateJacobian 604ms 1% 78.88% 604ms 1% std::vector::size (inline) 282ms 0.46% 79.34% 572ms 0.94% AbstractElement::GetNodeLocation 0 0% 79.34% 568ms 0.94% std::insert_iterator::operator= (inline) 30ms 0.049% 79.39% 548ms 0.9% __atan2 0 0% 79.39% 545ms 0.9% std::set::find (inline) 13ms 0.021% 79.41% 541ms 0.89% Element::CalculateCircumsphere 0 0% 79.41% 518ms 0.85% std::_Rb_tree::_M_insert_unique_ (inline) 456ms 0.75% 80.17% 512ms 0.84% __ieee754_atan2_fma 510ms 0.84% 81.01% 510ms 0.84% tetgen::tetgenmesh::oppo 88ms 0.15% 81.15% 503ms 0.83% std::_Rb_tree_iterator::operator-- (inline) 38ms 0.063% 81.21% 484ms 0.8% AbstractTetrahedralElement::RefreshJacobian 7ms 0.012% 81.22% 475ms 0.78% CellPropertyCollection::GetPropertiesType (inline) 16ms 0.026% 81.25% 453ms 0.75% std::vector::insert (inline) 1ms 0.0016% 81.25% 451ms 0.74% Cell::GetCellId 177ms 0.29% 81.54% 421ms 0.69% Inverse 0 0% 81.54% 404ms 0.67% boost::numeric::ublas::inner_prod (inline) 25ms 0.041% 81.59% 404ms 0.67% boost::numeric::ublas::vector_scalar_binary::evaluate 0 0% 81.59% 404ms 0.67% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 390ms 0.64% 82.23% 390ms 0.64% std::_Rb_tree_decrement 101ms 0.17% 82.39% 382ms 0.63% __dynamic_cast 381ms 0.63% 83.02% 381ms 0.63% boost::numeric::ublas::c_vector::operator() 0 0% 83.02% 378ms 0.62% VertexMeshWriter::WriteVtkUsingMesh 13ms 0.021% 83.04% 350ms 0.58% VertexMesh::CalculateUnitNormalToFaceWithArea 1ms 0.0016% 83.05% 350ms 0.58% boost::numeric::ublas::c_vector::operator= (inline) 111ms 0.18% 83.23% 348ms 0.57% boost::numeric::ublas::vector_inner_prod::apply (inline) 40ms 0.066% 83.29% 334ms 0.55% tetgen::tetgenmesh::enext2fnext 24ms 0.04% 83.33% 333ms 0.55% boost::numeric::ublas::vector_reference::operator() (inline) 8ms 0.013% 83.35% 332ms 0.55% AbstractCellProperty::IsSubType (inline) 0 0% 83.35% 329ms 0.54% tcache_get (inline) 329ms 0.54% 83.89% 329ms 0.54% tcache_get_n (inline) 167ms 0.28% 84.16% 327ms 0.54% tetgen::tetgenmesh::bond 29ms 0.048% 84.21% 320ms 0.53% tetgen::tetgenmesh::enextfnext 259ms 0.43% 84.64% 320ms 0.53% tetgen::tetgenmesh::fnextself 112ms 0.18% 84.82% 319ms 0.53% _int_free_merge_chunk 227ms 0.37% 85.20% 314ms 0.52% AbstractTetrahedralMesh::GetElement 61ms 0.1% 85.30% 314ms 0.52% tetgen::tetgenmesh::queue::push 86ms 0.14% 85.44% 312ms 0.51% tetgen::tetgenmesh::queue::pop