File: Test3dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 42599ms, 86.11% of 49468ms total Dropped 806 nodes (cum <= 247.34ms) flat flat% sum% cum cum% 0 0% 0% 49424ms 99.91% __libc_start_call_main 0 0% 0% 49424ms 99.91% __libc_start_main_impl 0 0% 0% 49424ms 99.91% _start 0 0% 0% 49410ms 99.88% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 49410ms 99.88% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 49410ms 99.88% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 49410ms 99.88% main 0 0% 0% 49380ms 99.82% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 49380ms 99.82% CxxTest::TestRunner::runTest (inline) 0 0% 0% 49380ms 99.82% Test3dTissueRepresentativeSimulation::Test3DHoneycombMeshWithGhostNodes 0 0% 0% 49190ms 99.44% AbstractCellBasedSimulation::Solve 0 0% 0% 41001ms 82.88% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 40942ms 82.76% MeshBasedCellPopulation::Update 0 0% 0% 24935ms 50.41% MeshBasedCellPopulation::CreateVoronoiTessellation (inline) 0 0% 0% 24935ms 50.41% MeshBasedCellPopulation::TessellateIfNeeded 225ms 0.45% 0.45% 22850ms 46.19% VertexMesh::VertexMesh 0 0% 0.45% 12454ms 25.18% MutableMesh::ReMesh 437ms 0.88% 1.34% 11054ms 22.35% TetrahedralMesh::EdgeIterator::operator++ 0 0% 1.34% 9593ms 19.39% tetgen::tetrahedralize 0 0% 1.34% 9502ms 19.21% tetgen::tetgenmesh::delaunizevertices 3ms 0.0061% 1.34% 9499ms 19.20% tetgen::tetgenmesh::incrflipdelaunay 34ms 0.069% 1.41% 9296ms 18.79% std::set::insert (inline) 254ms 0.51% 1.93% 8920ms 18.03% VertexElement::AddFace 3570ms 7.22% 9.14% 8793ms 17.78% std::_Rb_tree::_M_lower_bound (inline) 122ms 0.25% 9.39% 8789ms 17.77% std::_Rb_tree::_M_insert_unique 436ms 0.88% 10.27% 8368ms 16.92% tetgen::tetgenmesh::lawson 166ms 0.34% 10.61% 8365ms 16.91% std::_Rb_tree::find (inline) 0 0% 10.61% 7856ms 15.88% std::set::count (inline) 259ms 0.52% 11.13% 5861ms 11.85% std::_Rb_tree::_M_insert_ (inline) 176ms 0.36% 11.49% 5573ms 11.27% operator new 1641ms 3.32% 14.80% 5344ms 10.80% __GI___libc_malloc 65ms 0.13% 14.93% 4856ms 9.82% std::__new_allocator::allocate (inline) 0 0% 14.93% 4838ms 9.78% std::allocator_traits::allocate (inline) 0 0% 14.93% 4818ms 9.74% OffLatticeSimulation::UpdateCellLocationsAndTopology 2ms 0.004% 14.94% 4710ms 9.52% ForwardEulerNumericalMethod::UpdateAllNodePositions 1ms 0.002% 14.94% 4685ms 9.47% AbstractNumericalMethod::ComputeForcesIncludingDamping 4560ms 9.22% 24.16% 4560ms 9.22% std::_Rb_tree_increment 59ms 0.12% 24.28% 4471ms 9.04% std::less::operator() (inline) 4467ms 9.03% 33.31% 4467ms 9.03% std::operator< (inline) 0 0% 33.31% 3966ms 8.02% std::_Rb_tree::_M_create_node (inline) 0 0% 33.31% 3950ms 7.98% std::_Rb_tree::_M_get_node (inline) 0 0% 33.31% 3926ms 7.94% std::_Rb_tree::_Alloc_node::operator() (inline) 2ms 0.004% 33.31% 3863ms 7.81% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 0 0% 33.31% 3836ms 7.75% MeshBasedCellPopulation::UpdateNodePairs 19ms 0.038% 33.35% 3733ms 7.55% MeshBasedCellPopulation::SpringIterator::operator++ 2ms 0.004% 33.35% 3619ms 7.32% std::set_intersection (inline) 216ms 0.44% 33.79% 3617ms 7.31% std::__set_intersection 529ms 1.07% 34.86% 3513ms 7.10% __GI___libc_free 2695ms 5.45% 40.31% 3294ms 6.66% _int_malloc 0 0% 40.31% 3231ms 6.53% AbstractCellPopulation::WriteResultsToFiles 62ms 0.13% 40.43% 3219ms 6.51% std::__new_allocator::deallocate (inline) 0 0% 40.43% 3204ms 6.48% std::allocator_traits::deallocate (inline) 1120ms 2.26% 42.70% 3120ms 6.31% std::_Rb_tree::_M_get_insert_unique_pos 1537ms 3.11% 45.81% 2971ms 6.01% _int_free 252ms 0.51% 46.31% 2895ms 5.85% std::_Rb_tree_const_iterator::operator++ (inline) 8ms 0.016% 46.33% 2883ms 5.83% std::_Rb_tree::~_Rb_tree (inline) 62ms 0.13% 46.46% 2875ms 5.81% Node::AddElement 637ms 1.29% 47.74% 2863ms 5.79% std::_Rb_tree::_M_erase 0 0% 47.74% 2857ms 5.78% std::set::~set (inline) 2719ms 5.50% 53.24% 2719ms 5.50% std::_Rb_tree::_S_right (inline) 81ms 0.16% 53.40% 2611ms 5.28% tetgen::tetgenmesh::insphere_sos 2330ms 4.71% 58.11% 2493ms 5.04% tetgen::insphere 237ms 0.48% 58.59% 2411ms 4.87% std::_Rb_tree_iterator::operator++ (inline) 2ms 0.004% 58.60% 2397ms 4.85% VertexMesh::GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex 3ms 0.0061% 58.60% 2323ms 4.70% MeshBasedCellPopulationWithGhostNodes::WriteVtkResultsToFile 2ms 0.004% 58.61% 2165ms 4.38% TetrahedralMesh::ImportFromMesher 0 0% 58.61% 2101ms 4.25% VertexMesh::~VertexMesh 40ms 0.081% 58.69% 2074ms 4.19% MutableElement::AddNode 195ms 0.39% 59.08% 1969ms 3.98% tetgen::tetgenmesh::flip23 0 0% 59.08% 1941ms 3.92% std::_Rb_tree::_M_drop_node (inline) 0 0% 59.08% 1916ms 3.87% std::_Rb_tree::_M_put_node (inline) 1820ms 3.68% 62.76% 1820ms 3.68% [libchaste_mesh.so] 1711ms 3.46% 66.22% 1711ms 3.46% std::_Rb_tree_insert_and_rebalance 7ms 0.014% 66.23% 1487ms 3.01% Element::Element 162ms 0.33% 66.56% 1391ms 2.81% tetgen::tetgenmesh::flip32 822ms 1.66% 68.22% 1336ms 2.70% malloc_consolidate 1256ms 2.54% 70.76% 1325ms 2.68% tetgen::orient3d 6ms 0.012% 70.78% 1294ms 2.62% std::_Vector_base::_M_deallocate (inline) 4ms 0.0081% 70.78% 1216ms 2.46% Element::RegisterWithNodes (inline) 5ms 0.01% 70.79% 1181ms 2.39% _int_free_maybe_consolidate 0 0% 70.79% 1140ms 2.30% std::vector::~vector (inline) 2ms 0.004% 70.80% 1134ms 2.29% std::_Vector_base::~_Vector_base (inline) 1097ms 2.22% 73.01% 1097ms 2.22% Node::GetIndex 84ms 0.17% 73.18% 1063ms 2.15% std::map::operator[] 2ms 0.004% 73.19% 1037ms 2.10% VertexMesh::Clear 27ms 0.055% 73.24% 1021ms 2.06% std::vector::_M_realloc_insert 1ms 0.002% 73.25% 1006ms 2.03% Node::~Node 13ms 0.026% 73.27% 948ms 1.92% tetgen::tetgenmesh::locate 212ms 0.43% 73.70% 946ms 1.91% tetgen::tetgenmesh::enqueueflipface 60ms 0.12% 73.82% 906ms 1.83% tetgen::tetgenmesh::preciselocate 0 0% 73.82% 900ms 1.82% std::_Rb_tree::lower_bound (inline) 0 0% 73.82% 900ms 1.82% std::map::lower_bound (inline) 1ms 0.002% 73.82% 889ms 1.80% std::_Vector_base::_M_allocate (inline) 0 0% 73.82% 855ms 1.73% VertexMesh::GenerateVerticesFromElementCircumcentres 837ms 1.69% 75.52% 837ms 1.69% unlink_chunk 44ms 0.089% 75.60% 786ms 1.59% std::vector::push_back (inline) 0 0% 75.60% 736ms 1.49% VoronoiDataWriter::Visit 2ms 0.004% 75.61% 686ms 1.39% TetrahedralMesh::RefreshJacobianCachedData 1ms 0.002% 75.61% 631ms 1.28% AbstractTwoBodyInteractionForce::AddForceContribution 6ms 0.012% 75.62% 615ms 1.24% AbstractTetrahedralElement::CalculateInverseJacobian 10ms 0.02% 75.64% 608ms 1.23% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 330ms 0.67% 76.31% 597ms 1.21% AbstractElement::GetNodeGlobalIndex 3ms 0.0061% 76.32% 565ms 1.14% boost::numeric::ublas::vector_assign (inline) 335ms 0.68% 76.99% 536ms 1.08% tetgen::tetgenmesh::sym 1ms 0.002% 77.00% 529ms 1.07% boost::numeric::ublas::c_vector::c_vector (inline) 8ms 0.016% 77.01% 528ms 1.07% AbstractTetrahedralElement::CalculateJacobian 0 0% 77.01% 509ms 1.03% std::set::find (inline) 490ms 0.99% 78.00% 490ms 0.99% Node::rGetLocation 0 0% 78.00% 489ms 0.99% std::insert_iterator::operator= (inline) 33ms 0.067% 78.07% 473ms 0.96% __atan2 472ms 0.95% 79.02% 472ms 0.95% tetgen::tetgenmesh::oppo 101ms 0.2% 79.23% 453ms 0.92% std::_Rb_tree_iterator::operator-- (inline) 0 0% 79.23% 444ms 0.9% std::_Rb_tree::_M_insert_unique_ (inline) 393ms 0.79% 80.02% 437ms 0.88% __ieee754_atan2_fma 422ms 0.85% 80.87% 422ms 0.85% std::vector::size (inline) 191ms 0.39% 81.26% 399ms 0.81% AbstractElement::GetNodeLocation 3ms 0.0061% 81.27% 393ms 0.79% TetrahedralMesh::Clear 10ms 0.02% 81.29% 384ms 0.78% Element::CalculateCircumsphere 22ms 0.044% 81.33% 357ms 0.72% AbstractTetrahedralElement::RefreshJacobian 0 0% 81.33% 345ms 0.7% boost::numeric::ublas::inner_prod (inline) 12ms 0.024% 81.36% 345ms 0.7% boost::numeric::ublas::vector_scalar_binary::evaluate 0 0% 81.36% 345ms 0.7% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 84ms 0.17% 81.53% 341ms 0.69% __dynamic_cast 4ms 0.0081% 81.53% 337ms 0.68% Cell::GetCellId 337ms 0.68% 82.21% 337ms 0.68% std::_Rb_tree_decrement 0 0% 82.21% 325ms 0.66% tcache_get (inline) 325ms 0.66% 82.87% 325ms 0.66% tcache_get_n (inline) 14ms 0.028% 82.90% 324ms 0.65% std::vector::insert (inline) 4ms 0.0081% 82.91% 323ms 0.65% CellPropertyCollection::GetPropertiesType (inline) 321ms 0.65% 83.56% 321ms 0.65% boost::numeric::ublas::c_vector::operator() 0 0% 83.56% 310ms 0.63% VertexMeshWriter::WriteVtkUsingMesh 30ms 0.061% 83.62% 309ms 0.62% tetgen::tetgenmesh::enext2fnext 100ms 0.2% 83.82% 306ms 0.62% boost::numeric::ublas::vector_inner_prod::apply (inline) 132ms 0.27% 84.09% 305ms 0.62% Inverse 245ms 0.5% 84.58% 302ms 0.61% tetgen::tetgenmesh::fnextself 193ms 0.39% 84.97% 297ms 0.6% AbstractTetrahedralMesh::GetElement 23ms 0.046% 85.02% 289ms 0.58% tetgen::tetgenmesh::enextfnext 1ms 0.002% 85.02% 287ms 0.58% boost::numeric::ublas::c_vector::operator= (inline) 0 0% 85.02% 265ms 0.54% AbstractCellProperty::IsSubType (inline) 3ms 0.0061% 85.03% 265ms 0.54% AbstractTetrahedralElement::AbstractTetrahedralElement 265ms 0.54% 85.56% 265ms 0.54% tetgen::tetgenmesh::triface::triface 14ms 0.028% 85.59% 264ms 0.53% VertexMesh::CalculateUnitNormalToFaceWithArea 52ms 0.11% 85.70% 263ms 0.53% boost::numeric::ublas::indexing_vector_assign 138ms 0.28% 85.97% 260ms 0.53% tetgen::tetgenmesh::bond 15ms 0.03% 86.01% 258ms 0.52% boost::numeric::ublas::vector_reference::operator() (inline) 54ms 0.11% 86.11% 251ms 0.51% tetgen::tetgenmesh::queue::pop