File: Test3dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 44086ms, 85.99% of 51266ms total Dropped 830 nodes (cum <= 256.33ms) flat flat% sum% cum cum% 0 0% 0% 51206ms 99.88% __libc_start_call_main 0 0% 0% 51206ms 99.88% __libc_start_main_impl 0 0% 0% 51206ms 99.88% _start 0 0% 0% 51190ms 99.85% main 0 0% 0% 51189ms 99.85% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 51189ms 99.85% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 51189ms 99.85% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 51153ms 99.78% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 51153ms 99.78% CxxTest::TestRunner::runTest (inline) 0 0% 0% 51153ms 99.78% Test3dTissueRepresentativeSimulation::Test3DHoneycombMeshWithGhostNodes 0 0% 0% 50907ms 99.30% AbstractCellBasedSimulation::Solve 0 0% 0% 42606ms 83.11% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 42568ms 83.03% MeshBasedCellPopulation::Update 0 0% 0% 23286ms 45.42% MeshBasedCellPopulation::CreateVoronoiTessellation (inline) 0 0% 0% 23286ms 45.42% MeshBasedCellPopulation::TessellateIfNeeded 181ms 0.35% 0.35% 21065ms 41.09% VertexMesh::VertexMesh 0 0% 0.35% 15703ms 30.63% MutableMesh::ReMesh 1ms 0.002% 0.36% 12705ms 24.78% tetgen::tetrahedralize 2ms 0.0039% 0.36% 12562ms 24.50% tetgen::tetgenmesh::delaunizevertices 7ms 0.014% 0.37% 12557ms 24.49% tetgen::tetgenmesh::incrflipdelaunay 543ms 1.06% 1.43% 11223ms 21.89% tetgen::tetgenmesh::lawson 581ms 1.13% 2.57% 10757ms 20.98% TetrahedralMesh::EdgeIterator::operator++ 3089ms 6.03% 8.59% 8599ms 16.77% std::_Rb_tree::_M_lower_bound (inline) 304ms 0.59% 9.18% 8563ms 16.70% VertexElement::AddFace 19ms 0.037% 9.22% 8453ms 16.49% std::set::insert (inline) 243ms 0.47% 9.69% 8113ms 15.83% std::_Rb_tree::find (inline) 170ms 0.33% 10.03% 7947ms 15.50% std::_Rb_tree::_M_insert_unique 0 0% 10.03% 7565ms 14.76% std::set::count (inline) 115ms 0.22% 10.25% 5423ms 10.58% std::less::operator() (inline) 5371ms 10.48% 20.73% 5371ms 10.48% std::operator< (inline) 0 0% 20.73% 4830ms 9.42% OffLatticeSimulation::UpdateCellLocationsAndTopology 269ms 0.52% 21.25% 4811ms 9.38% std::_Rb_tree::_M_insert_ (inline) 0 0% 21.25% 4710ms 9.19% ForwardEulerNumericalMethod::UpdateAllNodePositions 2ms 0.0039% 21.26% 4688ms 9.14% AbstractNumericalMethod::ComputeForcesIncludingDamping 199ms 0.39% 21.64% 4056ms 7.91% operator new 4004ms 7.81% 29.45% 4004ms 7.81% std::_Rb_tree_increment 0 0% 29.45% 3903ms 7.61% MeshBasedCellPopulation::UpdateNodePairs 7ms 0.014% 29.47% 3849ms 7.51% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 1017ms 1.98% 31.45% 3784ms 7.38% __GI___libc_malloc 14ms 0.027% 31.48% 3778ms 7.37% MeshBasedCellPopulation::SpringIterator::operator++ 100ms 0.2% 31.67% 3604ms 7.03% tetgen::tetgenmesh::insphere_sos 34ms 0.066% 31.74% 3567ms 6.96% std::__new_allocator::allocate (inline) 0 0% 31.74% 3553ms 6.93% std::allocator_traits::allocate (inline) 3180ms 6.20% 37.94% 3485ms 6.80% tetgen::insphere 0 0% 37.94% 3337ms 6.51% AbstractCellPopulation::WriteResultsToFiles 11ms 0.021% 37.96% 3320ms 6.48% std::_Rb_tree::~_Rb_tree (inline) 1087ms 2.12% 40.09% 3306ms 6.45% std::_Rb_tree::_M_erase 1197ms 2.33% 42.42% 3293ms 6.42% std::_Rb_tree::_M_get_insert_unique_pos 0 0% 42.42% 3287ms 6.41% std::set::~set (inline) 820ms 1.60% 44.02% 3020ms 5.89% __GI___libc_free 0 0% 44.02% 2912ms 5.68% std::_Rb_tree::_M_create_node (inline) 0 0% 44.02% 2888ms 5.63% std::_Rb_tree::_Alloc_node::operator() (inline) 0 0% 44.02% 2881ms 5.62% std::_Rb_tree::_M_get_node (inline) 125ms 0.24% 44.26% 2822ms 5.50% std::__new_allocator::deallocate (inline) 203ms 0.4% 44.66% 2795ms 5.45% std::__set_intersection 0 0% 44.66% 2795ms 5.45% std::set_intersection (inline) 0 0% 44.66% 2793ms 5.45% std::allocator_traits::deallocate (inline) 214ms 0.42% 45.08% 2644ms 5.16% tetgen::tetgenmesh::flip23 24ms 0.047% 45.12% 2499ms 4.87% Node::AddElement 1883ms 3.67% 48.80% 2415ms 4.71% _int_malloc 2340ms 4.56% 53.36% 2340ms 4.56% std::_Rb_tree::_S_right (inline) 194ms 0.38% 53.74% 2335ms 4.55% VertexMesh::GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex 6ms 0.012% 53.75% 2315ms 4.52% TetrahedralMesh::ImportFromMesher 2ms 0.0039% 53.75% 2296ms 4.48% MeshBasedCellPopulationWithGhostNodes::WriteVtkResultsToFile 0 0% 53.75% 2235ms 4.36% VertexMesh::~VertexMesh 1169ms 2.28% 56.04% 2198ms 4.29% _int_free 1ms 0.002% 56.04% 2151ms 4.20% std::_Rb_tree_iterator::operator++ (inline) 196ms 0.38% 56.42% 2149ms 4.19% std::_Rb_tree_const_iterator::operator++ (inline) 73ms 0.14% 56.56% 1889ms 3.68% MutableElement::AddNode 167ms 0.33% 56.89% 1855ms 3.62% tetgen::tetgenmesh::flip32 0 0% 56.89% 1792ms 3.50% std::_Rb_tree::_M_drop_node (inline) 0 0% 56.89% 1774ms 3.46% std::_Rb_tree::_M_put_node (inline) 1718ms 3.35% 60.24% 1718ms 3.35% std::_Rb_tree_insert_and_rebalance 104ms 0.2% 60.44% 1465ms 2.86% VertexMesh::Clear 71ms 0.14% 60.58% 1460ms 2.85% Node::~Node 2ms 0.0039% 60.58% 1321ms 2.58% Element::Element 1227ms 2.39% 62.98% 1311ms 2.56% tetgen::orient3d 175ms 0.34% 63.32% 1311ms 2.56% tetgen::tetgenmesh::enqueueflipface 1163ms 2.27% 65.59% 1163ms 2.27% Node::GetIndex 32ms 0.062% 65.65% 1116ms 2.18% tetgen::tetgenmesh::locate 11ms 0.021% 65.67% 1030ms 2.01% std::_Vector_base::_M_deallocate (inline) 78ms 0.15% 65.82% 1027ms 2.00% tetgen::tetgenmesh::preciselocate 56ms 0.11% 65.93% 1021ms 1.99% std::map::operator[] 7ms 0.014% 65.95% 1018ms 1.99% Element::RegisterWithNodes (inline) 614ms 1.20% 67.14% 974ms 1.90% malloc_consolidate 1ms 0.002% 67.15% 960ms 1.87% std::vector::~vector (inline) 936ms 1.83% 68.97% 936ms 1.83% tetgen::tetgenmesh::triface::triface 62ms 0.12% 69.09% 904ms 1.76% std::vector::_M_realloc_insert 0 0% 69.09% 900ms 1.76% std::_Rb_tree::lower_bound (inline) 0 0% 69.09% 900ms 1.76% std::map::lower_bound (inline) 9ms 0.018% 69.11% 851ms 1.66% _int_free_maybe_consolidate 0 0% 69.11% 851ms 1.66% std::_Vector_base::~_Vector_base (inline) 0 0% 69.11% 841ms 1.64% VoronoiDataWriter::Visit 111ms 0.22% 69.33% 755ms 1.47% std::vector::push_back (inline) 2ms 0.0039% 69.33% 748ms 1.46% VertexMesh::GenerateVerticesFromElementCircumcentres 74ms 0.14% 69.47% 732ms 1.43% TetrahedralMesh::Clear 373ms 0.73% 70.20% 718ms 1.40% tetgen::tetgenmesh::fnextself 0 0% 70.20% 694ms 1.35% AbstractTwoBodyInteractionForce::AddForceContribution 3ms 0.0059% 70.21% 675ms 1.32% std::_Vector_base::_M_allocate (inline) 0 0% 70.21% 673ms 1.31% TetrahedralMesh::RefreshJacobianCachedData 672ms 1.31% 71.52% 672ms 1.31% [libchaste_mesh.so] 15ms 0.029% 71.55% 664ms 1.30% boost::numeric::ublas::vector_assign (inline) 10ms 0.02% 71.57% 651ms 1.27% AbstractVariableSizeTwoBodyInteractionForce::CalculateForceBetweenNodes 647ms 1.26% 72.83% 647ms 1.26% unlink_chunk 645ms 1.26% 74.09% 645ms 1.26% tetgen::tetgenmesh::oppo 15ms 0.029% 74.12% 638ms 1.24% boost::numeric::ublas::c_vector::c_vector (inline) 7ms 0.014% 74.13% 637ms 1.24% AbstractTetrahedralElement::CalculateInverseJacobian 586ms 1.14% 75.27% 586ms 1.14% tetgen::tetgenmesh::triface::operator= 44ms 0.086% 75.36% 575ms 1.12% __atan2 20ms 0.039% 75.40% 566ms 1.10% AbstractTetrahedralElement::CalculateJacobian 0 0% 75.40% 543ms 1.06% std::set::find (inline) 424ms 0.83% 76.23% 535ms 1.04% AbstractElement::GetNodeGlobalIndex 412ms 0.8% 77.03% 531ms 1.04% __ieee754_atan2_fma 0 0% 77.03% 512ms 1% std::insert_iterator::operator= (inline) 321ms 0.63% 77.66% 472ms 0.92% tetgen::tetgenmesh::sym 44ms 0.086% 77.74% 470ms 0.92% tetgen::tetgenmesh::enextfnext 189ms 0.37% 78.11% 463ms 0.9% AbstractElement::GetNodeLocation 49ms 0.096% 78.21% 463ms 0.9% tetgen::tetgenmesh::enext2fnext 0 0% 78.21% 459ms 0.9% std::_Rb_tree::_M_insert_unique_ (inline) 0 0% 78.21% 448ms 0.87% boost::numeric::ublas::inner_prod (inline) 5ms 0.0098% 78.22% 445ms 0.87% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 28ms 0.055% 78.27% 440ms 0.86% boost::numeric::ublas::vector_scalar_binary::evaluate 11ms 0.021% 78.29% 422ms 0.82% Element::CalculateCircumsphere 112ms 0.22% 78.51% 408ms 0.8% boost::numeric::ublas::indexing_vector_assign 407ms 0.79% 79.30% 407ms 0.79% std::vector::size (inline) 31ms 0.06% 79.36% 406ms 0.79% tetgen::tetgenmesh::queue::push 209ms 0.41% 79.77% 403ms 0.79% AbstractTetrahedralMesh::GetElement 31ms 0.06% 79.83% 390ms 0.76% AbstractTetrahedralElement::RefreshJacobian 6ms 0.012% 79.84% 385ms 0.75% Cell::GetCellId 380ms 0.74% 80.59% 380ms 0.74% Node::rGetLocation 27ms 0.053% 80.64% 378ms 0.74% std::_Rb_tree_iterator::operator-- (inline) 377ms 0.74% 81.37% 377ms 0.74% boost::numeric::ublas::c_vector::operator() 1ms 0.002% 81.38% 374ms 0.73% CellPropertyCollection::GetPropertiesType (inline) 95ms 0.19% 81.56% 372ms 0.73% __dynamic_cast 272ms 0.53% 82.09% 370ms 0.72% tetgen::tetgenmesh::link::add 0 0% 82.09% 368ms 0.72% VertexMeshWriter::WriteVtkUsingMesh 8ms 0.016% 82.11% 363ms 0.71% boost::numeric::ublas::c_vector::operator= (inline) 150ms 0.29% 82.40% 353ms 0.69% boost::numeric::ublas::vector_inner_prod::apply (inline) 251ms 0.49% 82.89% 348ms 0.68% tetgen::tetgenmesh::bond 347ms 0.68% 83.57% 347ms 0.68% tetgen::tetgenmesh::org 329ms 0.64% 84.21% 329ms 0.64% std::_Rb_tree_decrement 15ms 0.029% 84.24% 326ms 0.64% VertexMesh::CalculateUnitNormalToFaceWithArea 150ms 0.29% 84.53% 319ms 0.62% Inverse 2ms 0.0039% 84.53% 315ms 0.61% tcache_get (inline) 313ms 0.61% 85.14% 313ms 0.61% tcache_get_n (inline) 1ms 0.002% 85.15% 311ms 0.61% AbstractCellProperty::IsSubType (inline) 52ms 0.1% 85.25% 307ms 0.6% boost::numeric::ublas::vector_reference::operator() (inline) 42ms 0.082% 85.33% 305ms 0.59% tetgen::insphereadapt 3ms 0.0059% 85.34% 302ms 0.59% AbstractTetrahedralElement::AbstractTetrahedralElement 60ms 0.12% 85.45% 283ms 0.55% tetgen::tetgenmesh::queue::pop 6ms 0.012% 85.46% 280ms 0.55% VertexElement::~VertexElement 10ms 0.02% 85.48% 275ms 0.54% std::vector::insert (inline) 262ms 0.51% 85.99% 262ms 0.51% tetgen::tetgenmesh::pointmark