File: Test3dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 65875ms, 88.81% of 74172ms total Dropped 893 nodes (cum <= 370.86ms) flat flat% sum% cum cum% 0 0% 0% 74114ms 99.92% __libc_start_call_main 0 0% 0% 74114ms 99.92% __libc_start_main_impl 0 0% 0% 74114ms 99.92% _start 0 0% 0% 74098ms 99.90% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 74098ms 99.90% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 74098ms 99.90% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 74098ms 99.90% main 0 0% 0% 74058ms 99.85% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 74058ms 99.85% CxxTest::TestRunner::runTest (inline) 0 0% 0% 74057ms 99.84% Test3dTissueRepresentativeSimulation::Test3DHoneycombMeshWithGhostNodes 0 0% 0% 73767ms 99.45% AbstractCellBasedSimulation::Solve 0 0% 0% 63821ms 86.04% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 63766ms 85.97% MeshBasedCellPopulation::Update 0 0% 0% 40504ms 54.61% MeshBasedCellPopulation::CreateVoronoiTessellation (inline) 0 0% 0% 40504ms 54.61% MeshBasedCellPopulation::TessellateIfNeeded 397ms 0.54% 0.54% 35018ms 47.21% VertexMesh::VertexMesh 0 0% 0.54% 18864ms 25.43% MutableMesh::ReMesh 579ms 0.78% 1.32% 14401ms 19.42% TetrahedralMesh::EdgeIterator::operator++ 1ms 0.0013% 1.32% 13096ms 17.66% tetgen::tetrahedralize 1ms 0.0013% 1.32% 12964ms 17.48% tetgen::tetgenmesh::delaunizevertices 6ms 0.0081% 1.33% 12958ms 17.47% tetgen::tetgenmesh::incrflipdelaunay 27ms 0.036% 1.36% 12900ms 17.39% std::set::insert (inline) 203ms 0.27% 1.64% 12392ms 16.71% std::_Rb_tree::_M_insert_unique 511ms 0.69% 2.33% 11409ms 15.38% VertexElement::AddFace 537ms 0.72% 3.05% 11357ms 15.31% tetgen::tetgenmesh::lawson 3135ms 4.23% 7.28% 10696ms 14.42% std::_Rb_tree::_M_lower_bound (inline) 252ms 0.34% 7.62% 9828ms 13.25% std::_Rb_tree::find (inline) 0 0% 7.62% 9257ms 12.48% std::set::count (inline) 7610ms 10.26% 17.88% 7610ms 10.26% std::_Rb_tree_increment 259ms 0.35% 18.23% 7167ms 9.66% operator new 251ms 0.34% 18.56% 7069ms 9.53% std::_Rb_tree::_M_insert_ (inline) 101ms 0.14% 18.70% 7014ms 9.46% std::less::operator() (inline) 6969ms 9.40% 28.10% 6969ms 9.40% std::operator< (inline) 1033ms 1.39% 29.49% 6840ms 9.22% __GI___libc_malloc 2ms 0.0027% 29.49% 6752ms 9.10% std::set_intersection (inline) 362ms 0.49% 29.98% 6750ms 9.10% std::__set_intersection 0 0% 29.98% 6232ms 8.40% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 29.98% 6050ms 8.16% ForwardEulerNumericalMethod::UpdateAllNodePositions 28ms 0.038% 30.02% 6026ms 8.12% Node::AddElement 1ms 0.0013% 30.02% 6017ms 8.11% AbstractNumericalMethod::ComputeForcesIncludingDamping 197ms 0.27% 30.28% 5847ms 7.88% std::_Rb_tree_const_iterator::operator++ (inline) 52ms 0.07% 30.35% 5721ms 7.71% std::__new_allocator::allocate (inline) 0 0% 30.35% 5704ms 7.69% std::allocator_traits::allocate (inline) 7ms 0.0094% 30.36% 5548ms 7.48% std::_Rb_tree::~_Rb_tree (inline) 2529ms 3.41% 33.77% 5537ms 7.47% std::_Rb_tree::_M_erase 0 0% 33.77% 5524ms 7.45% VertexMesh::~VertexMesh 1333ms 1.80% 35.57% 5467ms 7.37% std::_Rb_tree::_M_get_insert_unique_pos 4003ms 5.40% 40.97% 5462ms 7.36% _int_malloc 0 0% 40.97% 5440ms 7.33% std::set::~set (inline) 5404ms 7.29% 48.25% 5404ms 7.29% std::_Rb_tree::_S_right (inline) 1381ms 1.86% 50.11% 5217ms 7.03% __GI___libc_free 4ms 0.0054% 50.12% 5009ms 6.75% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 1ms 0.0013% 50.12% 4789ms 6.46% MeshBasedCellPopulation::UpdateNodePairs 7ms 0.0094% 50.13% 4705ms 6.34% TetrahedralMesh::ImportFromMesher 12ms 0.016% 50.15% 4585ms 6.18% MeshBasedCellPopulation::SpringIterator::operator++ 0 0% 50.15% 4545ms 6.13% std::_Rb_tree::_M_create_node (inline) 0 0% 50.15% 4512ms 6.08% std::_Rb_tree::_Alloc_node::operator() (inline) 117ms 0.16% 50.30% 4508ms 6.08% std::__new_allocator::deallocate (inline) 0 0% 50.30% 4485ms 6.05% std::allocator_traits::deallocate (inline) 0 0% 50.30% 4474ms 6.03% std::_Rb_tree::_M_get_node (inline) 62ms 0.084% 50.39% 4349ms 5.86% MutableElement::AddNode 1181ms 1.59% 51.98% 3832ms 5.17% _int_free 241ms 0.32% 52.31% 3549ms 4.78% Node::~Node 0 0% 52.31% 3526ms 4.75% AbstractCellPopulation::WriteResultsToFiles 109ms 0.15% 52.45% 3516ms 4.74% tetgen::tetgenmesh::insphere_sos 3104ms 4.18% 56.64% 3393ms 4.57% tetgen::insphere 3313ms 4.47% 61.10% 3313ms 4.47% Node::GetIndex 260ms 0.35% 61.45% 3310ms 4.46% VertexMesh::Clear 254ms 0.34% 61.80% 2825ms 3.81% tetgen::tetgenmesh::flip23 1864ms 2.51% 64.31% 2745ms 3.70% malloc_consolidate 0 0% 64.31% 2572ms 3.47% Element::Element 15ms 0.02% 64.33% 2519ms 3.40% std::_Vector_base::_M_deallocate (inline) 2443ms 3.29% 67.62% 2443ms 3.29% std::_Rb_tree_insert_and_rebalance 6ms 0.0081% 67.63% 2374ms 3.20% _int_free_maybe_consolidate 0 0% 67.63% 2354ms 3.17% std::vector::~vector (inline) 0 0% 67.63% 2322ms 3.13% std::_Vector_base::~_Vector_base (inline) 5ms 0.0067% 67.64% 2293ms 3.09% MeshBasedCellPopulationWithGhostNodes::WriteVtkResultsToFile 197ms 0.27% 67.90% 2238ms 3.02% VertexMesh::GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex 7ms 0.0094% 67.91% 2189ms 2.95% Element::RegisterWithNodes (inline) 2ms 0.0027% 67.92% 2065ms 2.78% std::_Rb_tree_iterator::operator++ (inline) 0 0% 67.92% 1995ms 2.69% std::_Rb_tree::_M_drop_node (inline) 0 0% 67.92% 1980ms 2.67% std::_Rb_tree::_M_put_node (inline) 1935ms 2.61% 70.53% 1935ms 2.61% unlink_chunk 149ms 0.2% 70.73% 1894ms 2.55% tetgen::tetgenmesh::flip32 8ms 0.011% 70.74% 1744ms 2.35% VertexMesh::GenerateVerticesFromElementCircumcentres 240ms 0.32% 71.06% 1672ms 2.25% TetrahedralMesh::Clear 63ms 0.085% 71.15% 1454ms 1.96% std::map::operator[] 47ms 0.063% 71.21% 1422ms 1.92% std::vector::_M_realloc_insert 1280ms 1.73% 72.93% 1366ms 1.84% tetgen::orient3d 49ms 0.066% 73.00% 1344ms 1.81% tetgen::tetgenmesh::locate 191ms 0.26% 73.26% 1318ms 1.78% tetgen::tetgenmesh::enqueueflipface 0 0% 73.26% 1301ms 1.75% std::_Rb_tree::lower_bound (inline) 0 0% 73.26% 1301ms 1.75% std::map::lower_bound (inline) 1124ms 1.52% 74.77% 1268ms 1.71% AbstractElement::GetNodeGlobalIndex 10ms 0.013% 74.79% 1240ms 1.67% std::_Vector_base::_M_allocate (inline) 98ms 0.13% 74.92% 1231ms 1.66% tetgen::tetgenmesh::preciselocate 100ms 0.13% 75.05% 1184ms 1.60% std::vector::push_back (inline) 504ms 0.68% 75.73% 1100ms 1.48% AbstractElement::GetNodeLocation 1072ms 1.45% 77.18% 1072ms 1.45% Node::rGetLocation 0 0% 77.18% 1034ms 1.39% TetrahedralMesh::RefreshJacobianCachedData 3ms 0.004% 77.18% 973ms 1.31% VoronoiDataWriter::Visit 971ms 1.31% 78.49% 971ms 1.31% AbstractElement::IsDeleted 19ms 0.026% 78.52% 876ms 1.18% AbstractTetrahedralElement::CalculateJacobian 860ms 1.16% 79.68% 860ms 1.16% tetgen::tetgenmesh::triface::triface 497ms 0.67% 80.35% 857ms 1.16% tetgen::tetgenmesh::fnextself 9ms 0.012% 80.36% 853ms 1.15% AbstractTetrahedralElement::CalculateInverseJacobian 2ms 0.0027% 80.36% 763ms 1.03% AbstractTwoBodyInteractionForce::AddForceContribution 757ms 1.02% 81.38% 757ms 1.02% tetgen::tetgenmesh::oppo 23ms 0.031% 81.41% 751ms 1.01% Element::CalculateCircumsphere 51ms 0.069% 81.48% 705ms 0.95% AbstractTetrahedralElement::RefreshJacobian 13ms 0.018% 81.50% 697ms 0.94% boost::numeric::ublas::c_vector::c_vector (inline) 21ms 0.028% 81.53% 697ms 0.94% boost::numeric::ublas::vector_assign (inline) 14ms 0.019% 81.55% 681ms 0.92% AbstractVariableSizeTwoBodyInteractionForce::CalculateForceBetweenNodes 662ms 0.89% 82.44% 662ms 0.89% [libchaste_mesh.so] 647ms 0.87% 83.31% 647ms 0.87% std::vector::size (inline) 50ms 0.067% 83.38% 632ms 0.85% __atan2 596ms 0.8% 84.18% 596ms 0.8% tetgen::tetgenmesh::triface::operator= 463ms 0.62% 84.81% 582ms 0.78% __ieee754_atan2_fma 0 0% 84.81% 565ms 0.76% std::set::find (inline) 34ms 0.046% 84.85% 565ms 0.76% tetgen::tetgenmesh::enextfnext 0 0% 84.85% 526ms 0.71% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 347ms 0.47% 85.32% 517ms 0.7% tetgen::tetgenmesh::sym 52ms 0.07% 85.39% 516ms 0.7% tetgen::tetgenmesh::enext2fnext 0 0% 85.39% 513ms 0.69% std::insert_iterator::operator= (inline) 17ms 0.023% 85.41% 481ms 0.65% VertexMesh::CalculateUnitNormalToFaceWithArea 0 0% 85.41% 473ms 0.64% boost::numeric::ublas::inner_prod (inline) 1ms 0.0013% 85.41% 470ms 0.63% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 35ms 0.047% 85.46% 469ms 0.63% boost::numeric::ublas::vector_scalar_binary::evaluate 0 0% 85.46% 461ms 0.62% std::_Rb_tree::_M_insert_unique_ (inline) 26ms 0.035% 85.50% 459ms 0.62% tetgen::tetgenmesh::queue::push 247ms 0.33% 85.83% 437ms 0.59% AbstractTetrahedralMesh::GetElement 114ms 0.15% 85.98% 434ms 0.59% boost::numeric::ublas::indexing_vector_assign 434ms 0.59% 86.57% 434ms 0.59% tetgen::tetgenmesh::org 312ms 0.42% 86.99% 433ms 0.58% tetgen::tetgenmesh::link::add 420ms 0.57% 87.56% 420ms 0.57% boost::numeric::ublas::c_vector::operator() 3ms 0.004% 87.56% 417ms 0.56% boost::numeric::ublas::c_vector::operator= (inline) 17ms 0.023% 87.58% 416ms 0.56% std::_Rb_tree_iterator::operator-- (inline) 0 0% 87.58% 414ms 0.56% VertexMeshWriter::WriteVtkUsingMesh 4ms 0.0054% 87.59% 396ms 0.53% CellPropertyCollection::GetPropertiesType (inline) 272ms 0.37% 87.96% 388ms 0.52% tetgen::tetgenmesh::bond 99ms 0.13% 88.09% 386ms 0.52% __dynamic_cast 4ms 0.0054% 88.09% 383ms 0.52% AbstractTetrahedralElement::AbstractTetrahedralElement 2ms 0.0027% 88.10% 378ms 0.51% Cell::GetCellId 377ms 0.51% 88.60% 377ms 0.51% std::_Rb_tree_decrement 155ms 0.21% 88.81% 371ms 0.5% boost::numeric::ublas::vector_inner_prod::apply (inline)