File: Test3dOffLatticeRepresentativeSimulation Type: cpu Showing nodes accounting for 56295ms, 86.74% of 64898ms total Dropped 915 nodes (cum <= 324.49ms) flat flat% sum% cum cum% 0 0% 0% 64830ms 99.90% __libc_start_call_main 0 0% 0% 64830ms 99.90% __libc_start_main_impl 0 0% 0% 64830ms 99.90% _start 0 0% 0% 64813ms 99.87% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 64813ms 99.87% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 64813ms 99.87% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 64813ms 99.87% main 0 0% 0% 64771ms 99.80% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 64771ms 99.80% CxxTest::TestRunner::runTest (inline) 0 0% 0% 64771ms 99.80% Test3dTissueRepresentativeSimulation::Test3DHoneycombMeshWithGhostNodes 0 0% 0% 64488ms 99.37% AbstractCellBasedSimulation::Solve 0 0% 0% 55101ms 84.90% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0% 55054ms 84.83% MeshBasedCellPopulation::Update 0 0% 0% 30718ms 47.33% MeshBasedCellPopulation::TessellateIfNeeded 1ms 0.0015% 0.0015% 30716ms 47.33% MeshBasedCellPopulation::CreateVoronoiTessellation (inline) 207ms 0.32% 0.32% 27012ms 41.62% VertexMesh::VertexMesh 0 0% 0.32% 20209ms 31.14% MutableMesh::ReMesh 0 0% 0.32% 16044ms 24.72% tetgen::tetrahedralize 3ms 0.0046% 0.33% 15893ms 24.49% tetgen::tetgenmesh::delaunizevertices 9ms 0.014% 0.34% 15882ms 24.47% tetgen::tetgenmesh::incrflipdelaunay 505ms 0.78% 1.12% 14294ms 22.03% tetgen::tetgenmesh::lawson 620ms 0.96% 2.07% 12858ms 19.81% TetrahedralMesh::EdgeIterator::operator++ 29ms 0.045% 2.12% 10541ms 16.24% std::set::insert (inline) 411ms 0.63% 2.75% 10128ms 15.61% VertexElement::AddFace 275ms 0.42% 3.17% 10120ms 15.59% std::_Rb_tree::_M_insert_unique 3225ms 4.97% 8.14% 9214ms 14.20% std::_Rb_tree::_M_lower_bound (inline) 292ms 0.45% 8.59% 8727ms 13.45% std::_Rb_tree::find (inline) 0 0% 8.59% 8117ms 12.51% std::set::count (inline) 319ms 0.49% 9.09% 5950ms 9.17% std::_Rb_tree::_M_insert_ (inline) 109ms 0.17% 9.25% 5844ms 9.00% std::less::operator() (inline) 5788ms 8.92% 18.17% 5788ms 8.92% std::operator< (inline) 0 0% 18.17% 5616ms 8.65% OffLatticeSimulation::UpdateCellLocationsAndTopology 0 0% 18.17% 5476ms 8.44% ForwardEulerNumericalMethod::UpdateAllNodePositions 5465ms 8.42% 26.59% 5465ms 8.42% std::_Rb_tree_increment 5ms 0.0077% 26.60% 5447ms 8.39% AbstractNumericalMethod::ComputeForcesIncludingDamping 184ms 0.28% 26.88% 5408ms 8.33% operator new 1252ms 1.93% 28.81% 5152ms 7.94% __GI___libc_malloc 42ms 0.065% 28.88% 4615ms 7.11% std::__new_allocator::allocate (inline) 0 0% 28.88% 4598ms 7.08% std::allocator_traits::allocate (inline) 4ms 0.0062% 28.88% 4518ms 6.96% std::_Rb_tree::~_Rb_tree (inline) 8ms 0.012% 28.90% 4517ms 6.96% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 1614ms 2.49% 31.38% 4511ms 6.95% std::_Rb_tree::_M_erase 0 0% 31.38% 4503ms 6.94% MeshBasedCellPopulation::UpdateNodePairs 0 0% 31.38% 4470ms 6.89% std::set::~set (inline) 14ms 0.022% 31.40% 4352ms 6.71% MeshBasedCellPopulation::SpringIterator::operator++ 1241ms 1.91% 33.32% 4340ms 6.69% __GI___libc_free 2ms 0.0031% 33.32% 4268ms 6.58% std::set_intersection (inline) 276ms 0.43% 33.75% 4266ms 6.57% std::__set_intersection 1457ms 2.25% 35.99% 4146ms 6.39% std::_Rb_tree::_M_get_insert_unique_pos 144ms 0.22% 36.21% 3817ms 5.88% std::__new_allocator::deallocate (inline) 0 0% 36.21% 3804ms 5.86% std::allocator_traits::deallocate (inline) 107ms 0.16% 36.38% 3764ms 5.80% tetgen::tetgenmesh::insphere_sos 0 0% 36.38% 3731ms 5.75% std::_Rb_tree::_M_create_node (inline) 0 0% 36.38% 3730ms 5.75% VertexMesh::~VertexMesh 0 0% 36.38% 3698ms 5.70% std::_Rb_tree::_Alloc_node::operator() (inline) 126ms 0.19% 36.57% 3698ms 5.70% tetgen::tetgenmesh::flip23 0 0% 36.57% 3695ms 5.69% std::_Rb_tree::_M_get_node (inline) 3337ms 5.14% 41.71% 3646ms 5.62% tetgen::insphere 55ms 0.085% 41.80% 3617ms 5.57% Node::AddElement 0 0% 41.80% 3610ms 5.56% AbstractCellPopulation::WriteResultsToFiles 2626ms 4.05% 45.84% 3565ms 5.49% _int_malloc 188ms 0.29% 46.13% 3555ms 5.48% std::_Rb_tree_const_iterator::operator++ (inline) 7ms 0.011% 46.14% 3343ms 5.15% TetrahedralMesh::ImportFromMesher 3212ms 4.95% 51.09% 3212ms 4.95% std::_Rb_tree::_S_right (inline) 1424ms 2.19% 53.29% 3095ms 4.77% _int_free 74ms 0.11% 53.40% 2906ms 4.48% MutableElement::AddNode 195ms 0.3% 53.70% 2648ms 4.08% Node::~Node 135ms 0.21% 53.91% 2522ms 3.89% tetgen::tetgenmesh::flip32 159ms 0.24% 54.16% 2441ms 3.76% VertexMesh::Clear 204ms 0.31% 54.47% 2435ms 3.75% VertexMesh::GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex 5ms 0.0077% 54.48% 2429ms 3.74% MeshBasedCellPopulationWithGhostNodes::WriteVtkResultsToFile 1ms 0.0015% 54.48% 2244ms 3.46% std::_Rb_tree_iterator::operator++ (inline) 0 0% 54.48% 2232ms 3.44% std::_Rb_tree::_M_drop_node (inline) 0 0% 54.48% 2217ms 3.42% std::_Rb_tree::_M_put_node (inline) 2006ms 3.09% 57.57% 2006ms 3.09% std::_Rb_tree_insert_and_rebalance 222ms 0.34% 57.91% 1969ms 3.03% tetgen::tetgenmesh::enqueueflipface 1774ms 2.73% 60.65% 1774ms 2.73% Node::GetIndex 1568ms 2.42% 63.06% 1639ms 2.53% tetgen::orient3d 26ms 0.04% 63.10% 1613ms 2.49% std::_Vector_base::_M_deallocate (inline) 1121ms 1.73% 64.83% 1592ms 2.45% malloc_consolidate 7ms 0.011% 64.84% 1568ms 2.42% Element::Element 0 0% 64.84% 1537ms 2.37% std::vector::~vector (inline) 1ms 0.0015% 64.84% 1444ms 2.23% std::_Vector_base::~_Vector_base (inline) 108ms 0.17% 65.01% 1418ms 2.18% TetrahedralMesh::Clear 5ms 0.0077% 65.02% 1382ms 2.13% _int_free_maybe_consolidate 30ms 0.046% 65.06% 1292ms 1.99% tetgen::tetgenmesh::locate 6ms 0.0092% 65.07% 1210ms 1.86% Element::RegisterWithNodes (inline) 76ms 0.12% 65.19% 1207ms 1.86% tetgen::tetgenmesh::preciselocate 924ms 1.42% 66.61% 1141ms 1.76% AbstractElement::GetNodeGlobalIndex 58ms 0.089% 66.70% 1140ms 1.76% std::vector::_M_realloc_insert 64ms 0.099% 66.80% 1128ms 1.74% std::map::operator[] 1124ms 1.73% 68.53% 1124ms 1.73% unlink_chunk 1088ms 1.68% 70.21% 1088ms 1.68% tetgen::tetgenmesh::oppo 6ms 0.0092% 70.22% 1028ms 1.58% VertexMesh::GenerateVerticesFromElementCircumcentres 1015ms 1.56% 71.78% 1015ms 1.56% tetgen::tetgenmesh::triface::triface 0 0% 71.78% 978ms 1.51% std::_Rb_tree::lower_bound (inline) 0 0% 71.78% 978ms 1.51% std::map::lower_bound (inline) 119ms 0.18% 71.97% 938ms 1.45% std::vector::push_back (inline) 0 0% 71.97% 930ms 1.43% VoronoiDataWriter::Visit 2ms 0.0031% 71.97% 905ms 1.39% std::_Vector_base::_M_allocate (inline) 842ms 1.30% 73.27% 842ms 1.30% [libchaste_mesh.so] 298ms 0.46% 73.72% 841ms 1.30% tetgen::tetgenmesh::sym 0 0% 73.72% 804ms 1.24% TetrahedralMesh::RefreshJacobianCachedData 0 0% 73.72% 735ms 1.13% AbstractTwoBodyInteractionForce::AddForceContribution 8ms 0.012% 73.74% 721ms 1.11% AbstractTetrahedralElement::CalculateInverseJacobian 18ms 0.028% 73.76% 704ms 1.08% GeneralisedLinearSpringForce::CalculateForceBetweenNodes 693ms 1.07% 74.83% 693ms 1.07% AbstractElement::IsDeleted 280ms 0.43% 75.26% 668ms 1.03% AbstractElement::GetNodeLocation 12ms 0.018% 75.28% 654ms 1.01% AbstractTetrahedralElement::CalculateJacobian 51ms 0.079% 75.36% 647ms 1% __atan2 10ms 0.015% 75.38% 647ms 1% boost::numeric::ublas::vector_assign (inline) 642ms 0.99% 76.37% 642ms 0.99% tetgen::tetgenmesh::triface::operator= 392ms 0.6% 76.97% 640ms 0.99% tetgen::tetgenmesh::fnextself 42ms 0.065% 77.03% 639ms 0.98% tetgen::tetgenmesh::queue::push 12ms 0.018% 77.05% 636ms 0.98% boost::numeric::ublas::c_vector::c_vector (inline) 626ms 0.96% 78.02% 626ms 0.96% std::vector::size (inline) 259ms 0.4% 78.42% 612ms 0.94% tetgen::tetgenmesh::bond 610ms 0.94% 79.36% 610ms 0.94% Node::rGetLocation 0 0% 79.36% 607ms 0.94% std::set::find (inline) 340ms 0.52% 79.88% 597ms 0.92% tetgen::tetgenmesh::link::add 473ms 0.73% 80.61% 590ms 0.91% __ieee754_atan2_fma 60ms 0.092% 80.70% 588ms 0.91% tetgen::tetgenmesh::enext2fnext 568ms 0.88% 81.58% 568ms 0.88% tetgen::tetgenmesh::decode 59ms 0.091% 81.67% 565ms 0.87% tetgen::tetgenmesh::enextfnext 14ms 0.022% 81.69% 528ms 0.81% Element::CalculateCircumsphere 0 0% 81.69% 512ms 0.79% boost::numeric::ublas::inner_prod (inline) 1ms 0.0015% 81.69% 507ms 0.78% boost::numeric::ublas::vector_scalar_binary::operator double (inline) 37ms 0.057% 81.75% 506ms 0.78% boost::numeric::ublas::vector_scalar_binary::evaluate 49ms 0.076% 81.82% 472ms 0.73% AbstractTetrahedralElement::RefreshJacobian 0 0% 81.82% 440ms 0.68% std::insert_iterator::operator= (inline) 438ms 0.67% 82.50% 438ms 0.67% tetgen::tetgenmesh::org 22ms 0.034% 82.53% 422ms 0.65% std::_Rb_tree_iterator::operator-- (inline) 4ms 0.0062% 82.54% 420ms 0.65% CellPropertyCollection::GetPropertiesType (inline) 210ms 0.32% 82.86% 419ms 0.65% AbstractTetrahedralMesh::GetElement 15ms 0.023% 82.89% 419ms 0.65% VertexMesh::CalculateUnitNormalToFaceWithArea 100ms 0.15% 83.04% 415ms 0.64% boost::numeric::ublas::indexing_vector_assign 7ms 0.011% 83.05% 412ms 0.63% VertexElement::~VertexElement 191ms 0.29% 83.34% 411ms 0.63% boost::numeric::ublas::vector_inner_prod::apply (inline) 99ms 0.15% 83.50% 404ms 0.62% __dynamic_cast 404ms 0.62% 84.12% 404ms 0.62% tetgen::tetgenmesh::pointmark 397ms 0.61% 84.73% 397ms 0.61% boost::numeric::ublas::c_vector::operator() 6ms 0.0092% 84.74% 396ms 0.61% boost::numeric::ublas::c_vector::operator= (inline) 0 0% 84.74% 394ms 0.61% VertexMeshWriter::WriteVtkUsingMesh 4ms 0.0062% 84.75% 391ms 0.6% Cell::GetCellId 0 0% 84.75% 390ms 0.6% std::_Rb_tree::_M_insert_unique_ (inline) 368ms 0.57% 85.31% 368ms 0.57% std::_Rb_tree_decrement 12ms 0.018% 85.33% 352ms 0.54% AbstractTetrahedralElement::AbstractTetrahedralElement 351ms 0.54% 85.87% 351ms 0.54% tetgen::tetgenmesh::face::face 17ms 0.026% 85.90% 349ms 0.54% std::vector::insert (inline) 110ms 0.17% 86.07% 346ms 0.53% Inverse 0 0% 86.07% 344ms 0.53% TetrahedralMesh::EdgeIterator::~EdgeIterator (inline) 339ms 0.52% 86.59% 339ms 0.52% tetgen::tetgenmesh::encode 5ms 0.0077% 86.60% 338ms 0.52% AbstractCellProperty::IsSubType (inline) 94ms 0.14% 86.74% 327ms 0.5% tetgen::tetgenmesh::queue::pop