File: Test3dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 60403ms, 86.95% of 69465ms total Dropped 879 nodes (cum <= 347.32ms) flat flat% sum% cum cum% 0 0% 0% 69405ms 99.91% __libc_start_call_main 0 0% 0% 69405ms 99.91% __libc_start_main_impl 0 0% 0% 69405ms 99.91% _start 0 0% 0% 69386ms 99.89% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 69386ms 99.89% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 69386ms 99.89% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 69386ms 99.89% main 0 0% 0% 69346ms 99.83% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 69346ms 99.83% CxxTest::TestRunner::runTest (inline) 0 0% 0% 69346ms 99.83% Test3dTissueRepresentativeSimulation::Test3DHoneycombMeshWithGhostNodes 0 0% 0% 69057ms 99.41% AbstractCellBasedSimulation::Solve 0 0% 0% 58435ms 84.12% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 58385ms 84.05% MeshBasedCellPopulation::Update 1ms 0.0014% 0.0014% 33242ms 47.85% MeshBasedCellPopulation::CreateVoronoiTessellation (inline) 0 0% 0.0014% 33242ms 47.85% MeshBasedCellPopulation::TessellateIfNeeded 221ms 0.32% 0.32% 29112ms 41.91% VertexMesh::VertexMesh 0 0% 0.32% 20499ms 29.51% MutableMesh::ReMesh 0 0% 0.32% 15897ms 22.88% tetgen::tetrahedralize 0 0% 0.32% 15748ms 22.67% tetgen::tetgenmesh::delaunizevertices 9ms 0.013% 0.33% 15736ms 22.65% tetgen::tetgenmesh::incrflipdelaunay 596ms 0.86% 1.19% 14210ms 20.46% TetrahedralMesh::EdgeIterator::operator++ 521ms 0.75% 1.94% 14037ms 20.21% tetgen::tetgenmesh::lawson 27ms 0.039% 1.98% 11035ms 15.89% std::set::insert (inline) 3151ms 4.54% 6.52% 10645ms 15.32% std::_Rb_tree::_M_lower_bound (inline) 241ms 0.35% 6.86% 10584ms 15.24% std::_Rb_tree::_M_insert_unique 380ms 0.55% 7.41% 10341ms 14.89% VertexElement::AddFace 300ms 0.43% 7.84% 9951ms 14.33% std::_Rb_tree::find (inline) 0 0% 7.84% 9363ms 13.48% std::set::count (inline) 125ms 0.18% 8.02% 7118ms 10.25% std::less::operator() (inline) 7058ms 10.16% 18.18% 7058ms 10.16% std::operator< (inline) 6751ms 9.72% 27.90% 6751ms 9.72% std::_Rb_tree_increment 333ms 0.48% 28.38% 6228ms 8.97% std::_Rb_tree::_M_insert_ (inline) 0 0% 28.38% 6131ms 8.83% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 28.38% 5961ms 8.58% ForwardEulerNumericalMethod::UpdateAllNodePositions 183ms 0.26% 28.64% 5958ms 8.58% operator new 0 0% 28.64% 5935ms 8.54% AbstractNumericalMethod::ComputeForcesIncludingDamping 1254ms 1.81% 30.45% 5702ms 8.21% __GI___libc_malloc 33ms 0.048% 30.50% 5006ms 7.21% std::__new_allocator::allocate (inline) 0 0% 30.50% 5001ms 7.20% MeshBasedCellPopulation::UpdateNodePairs 0 0% 30.50% 4988ms 7.18% std::allocator_traits::allocate (inline) 9ms 0.013% 30.51% 4978ms 7.17% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 279ms 0.4% 30.91% 4892ms 7.04% std::__set_intersection 0 0% 30.91% 4892ms 7.04% std::set_intersection (inline) 14ms 0.02% 30.93% 4831ms 6.95% MeshBasedCellPopulation::SpringIterator::operator++ 5ms 0.0072% 30.94% 4797ms 6.91% std::_Rb_tree::~_Rb_tree (inline) 1834ms 2.64% 33.58% 4789ms 6.89% std::_Rb_tree::_M_erase 0 0% 33.58% 4734ms 6.81% std::set::~set (inline) 1240ms 1.79% 35.36% 4583ms 6.60% __GI___libc_free 1352ms 1.95% 37.31% 4387ms 6.32% std::_Rb_tree::_M_get_insert_unique_pos 0 0% 37.31% 4332ms 6.24% AbstractCellPopulation::WriteResultsToFiles 1ms 0.0014% 37.31% 4162ms 5.99% VertexMesh::~VertexMesh 43ms 0.062% 37.37% 4154ms 5.98% Node::AddElement 201ms 0.29% 37.66% 4127ms 5.94% std::_Rb_tree_const_iterator::operator++ (inline) 2942ms 4.24% 41.90% 4094ms 5.89% _int_malloc 141ms 0.2% 42.10% 4073ms 5.86% std::__new_allocator::deallocate (inline) 0 0% 42.10% 4055ms 5.84% std::allocator_traits::deallocate (inline) 0 0% 42.10% 4000ms 5.76% std::_Rb_tree::_M_create_node (inline) 0 0% 42.10% 3961ms 5.70% std::_Rb_tree::_M_get_node (inline) 0 0% 42.10% 3958ms 5.70% std::_Rb_tree::_Alloc_node::operator() (inline) 115ms 0.17% 42.27% 3889ms 5.60% tetgen::tetgenmesh::insphere_sos 3871ms 5.57% 47.84% 3871ms 5.57% std::_Rb_tree::_S_right (inline) 3464ms 4.99% 52.83% 3760ms 5.41% tetgen::insphere 7ms 0.01% 52.84% 3720ms 5.36% TetrahedralMesh::ImportFromMesher 130ms 0.19% 53.02% 3411ms 4.91% tetgen::tetgenmesh::flip23 1390ms 2.00% 55.02% 3337ms 4.80% _int_free 174ms 0.25% 55.27% 3122ms 4.49% VertexMesh::GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex 77ms 0.11% 55.38% 3091ms 4.45% MutableElement::AddNode 2ms 0.0029% 55.39% 3018ms 4.34% MeshBasedCellPopulationWithGhostNodes::WriteVtkResultsToFile 0 0% 55.39% 2972ms 4.28% std::_Rb_tree_iterator::operator++ (inline) 184ms 0.26% 55.65% 2825ms 4.07% Node::~Node 127ms 0.18% 55.84% 2643ms 3.80% tetgen::tetgenmesh::flip32 187ms 0.27% 56.10% 2572ms 3.70% VertexMesh::Clear 0 0% 56.10% 2232ms 3.21% std::_Rb_tree::_M_drop_node (inline) 0 0% 56.10% 2218ms 3.19% std::_Rb_tree::_M_put_node (inline) 2169ms 3.12% 59.23% 2169ms 3.12% Node::GetIndex 2021ms 2.91% 62.14% 2021ms 2.91% std::_Rb_tree_insert_and_rebalance 1301ms 1.87% 64.01% 1968ms 2.83% malloc_consolidate 3ms 0.0043% 64.01% 1910ms 2.75% Element::Element 32ms 0.046% 64.06% 1867ms 2.69% std::_Vector_base::_M_deallocate (inline) 219ms 0.32% 64.37% 1842ms 2.65% tetgen::tetgenmesh::enqueueflipface 0 0% 64.37% 1809ms 2.60% std::vector::~vector (inline) 1ms 0.0014% 64.38% 1715ms 2.47% std::_Vector_base::~_Vector_base (inline) 4ms 0.0058% 64.38% 1682ms 2.42% _int_free_maybe_consolidate 1547ms 2.23% 66.61% 1635ms 2.35% tetgen::orient3d 9ms 0.013% 66.62% 1573ms 2.26% Element::RegisterWithNodes (inline) 92ms 0.13% 66.75% 1464ms 2.11% TetrahedralMesh::Clear 1430ms 2.06% 68.81% 1430ms 2.06% unlink_chunk 37ms 0.053% 68.87% 1397ms 2.01% tetgen::tetgenmesh::locate 80ms 0.12% 68.98% 1355ms 1.95% std::map::operator[] 79ms 0.11% 69.10% 1312ms 1.89% tetgen::tetgenmesh::preciselocate 0 0% 69.10% 1193ms 1.72% std::_Rb_tree::lower_bound (inline) 0 0% 69.10% 1193ms 1.72% std::map::lower_bound (inline) 71ms 0.1% 69.20% 1192ms 1.72% std::vector::_M_realloc_insert 4ms 0.0058% 69.20% 1181ms 1.70% VertexMesh::GenerateVerticesFromElementCircumcentres 973ms 1.40% 70.60% 1154ms 1.66% AbstractElement::GetNodeGlobalIndex 1054ms 1.52% 72.12% 1054ms 1.52% tetgen::tetgenmesh::oppo 1ms 0.0014% 72.12% 1052ms 1.51% VoronoiDataWriter::Visit 8ms 0.012% 72.13% 1035ms 1.49% std::_Vector_base::_M_allocate (inline) 1014ms 1.46% 73.59% 1014ms 1.46% tetgen::tetgenmesh::triface::triface 142ms 0.2% 73.80% 1001ms 1.44% std::vector::push_back (inline) 0 0% 73.80% 862ms 1.24% TetrahedralMesh::RefreshJacobianCachedData 808ms 1.16% 74.96% 808ms 1.16% [libchaste_mesh.so] 355ms 0.51% 75.47% 791ms 1.14% AbstractElement::GetNodeLocation 784ms 1.13% 76.60% 784ms 1.13% Node::rGetLocation 15ms 0.022% 76.62% 756ms 1.09% AbstractTetrahedralElement::CalculateInverseJacobian 1ms 0.0014% 76.62% 740ms 1.07% AbstractTwoBodyInteractionForce::AddForceContribution 299ms 0.43% 77.05% 730ms 1.05% tetgen::tetgenmesh::sym 716ms 1.03% 78.09% 716ms 1.03% AbstractElement::IsDeleted 10ms 0.014% 78.10% 684ms 0.98% AbstractVariableSizeTwoBodyInteractionForce::CalculateForceBetweenNodes 13ms 0.019% 78.12% 683ms 0.98% AbstractTetrahedralElement::CalculateJacobian 46ms 0.066% 78.18% 683ms 0.98% __atan2 667ms 0.96% 79.14% 667ms 0.96% tetgen::tetgenmesh::triface::operator= 384ms 0.55% 79.70% 647ms 0.93% tetgen::tetgenmesh::fnextself 514ms 0.74% 80.44% 632ms 0.91% __ieee754_atan2_fma 15ms 0.022% 80.46% 624ms 0.9% boost::numeric::ublas::vector_assign (inline) 41ms 0.059% 80.52% 617ms 0.89% tetgen::tetgenmesh::queue::push 219ms 0.32% 80.83% 611ms 0.88% tetgen::tetgenmesh::bond 8ms 0.012% 80.85% 600ms 0.86% boost::numeric::ublas::c_vector::c_vector (inline) 597ms 0.86% 81.70% 597ms 0.86% std::vector::size (inline) 57ms 0.082% 81.79% 595ms 0.86% tetgen::tetgenmesh::enext2fnext 0 0% 81.79% 582ms 0.84% std::set::find (inline) 355ms 0.51% 82.30% 576ms 0.83% tetgen::tetgenmesh::link::add 13ms 0.019% 82.32% 573ms 0.82% Element::CalculateCircumsphere 52ms 0.075% 82.39% 564ms 0.81% tetgen::tetgenmesh::enextfnext 38ms 0.055% 82.45% 525ms 0.76% AbstractTetrahedralElement::RefreshJacobian 521ms 0.75% 83.20% 521ms 0.75% tetgen::tetgenmesh::org 0 0% 83.20% 518ms 0.75% boost::numeric::ublas::inner_prod (inline) 3ms 0.0043% 83.20% 513ms 0.74% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 40ms 0.058% 83.26% 510ms 0.73% boost::numeric::ublas::vector_scalar_binary::evaluate 0 0% 83.26% 480ms 0.69% std::insert_iterator::operator= (inline) 445ms 0.64% 83.90% 445ms 0.64% tetgen::tetgenmesh::decode 0 0% 83.90% 423ms 0.61% std::_Rb_tree::_M_insert_unique_ (inline) 18ms 0.026% 83.92% 417ms 0.6% VertexMesh::CalculateUnitNormalToFaceWithArea 190ms 0.27% 84.20% 413ms 0.59% boost::numeric::ublas::vector_inner_prod::apply (inline) 2ms 0.0029% 84.20% 410ms 0.59% CellPropertyCollection::GetPropertiesType (inline) 26ms 0.037% 84.24% 406ms 0.58% std::_Rb_tree_iterator::operator-- (inline) 196ms 0.28% 84.52% 402ms 0.58% AbstractTetrahedralMesh::GetElement 0 0% 84.52% 400ms 0.58% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 0 0% 84.52% 399ms 0.57% VertexMeshWriter::WriteVtkUsingMesh 6ms 0.0086% 84.53% 394ms 0.57% VertexElement::~VertexElement 384ms 0.55% 85.08% 384ms 0.55% tetgen::tetgenmesh::encode 4ms 0.0058% 85.09% 379ms 0.55% Cell::GetCellId 378ms 0.54% 85.63% 378ms 0.54% boost::numeric::ublas::c_vector::operator() 2ms 0.0029% 85.63% 375ms 0.54% boost::numeric::ublas::c_vector::operator= (inline) 95ms 0.14% 85.77% 374ms 0.54% boost::numeric::ublas::indexing_vector_assign 97ms 0.14% 85.91% 368ms 0.53% __dynamic_cast 362ms 0.52% 86.43% 362ms 0.52% std::_Rb_tree_decrement 15ms 0.022% 86.45% 358ms 0.52% std::vector::insert (inline) 348ms 0.5% 86.95% 348ms 0.5% tetgen::tetgenmesh::pointmark