AMDiS Usergroup-Meeting

Transcription

1 AMDiS Usergroup-Meeting Simon Praetorius Institut für Wissenschaftliches Rechnen 14. Oktober 2013 Simon Praetorius (TU Dresden IWR) AMDiS-Meeting 14. Oktober / 14

2 Outline 1 Linear solvers PETSc PMTL 2 ArhReader/-Writer 3 Implementation of finite elements 4 Repartitioning 5 Dirichlet boundary conditions 6 Misc other changes Simon Praetorius (TU Dresden IWR) AMDiS-Meeting 14. Oktober / 14

3 Linear solvers / PETSc-Integration connection to PETSc/(P)MTL-Library for sequential and parallel linear algebra backend each problem can have a different backend each backend provides a list of available linear solvers (will be listed/documented somewhere) idea: use the same prameters for different backends and provide a common interface: Parameter-file prob solver: NAME % cg, gmres, direct,... prob solver backend: BACKEND % mtl, p mtl, petsc, p petsc prob solver left/right precon: PRECONDITIONER % diag, ilu,... prob solver tolerance: ATOL prob solver relative tolerance: RTOL prob solver max iteration: NITER prob solver info:... Simon Praetorius (TU Dresden IWR) AMDiS-Meeting 14. Oktober / 14

4 PETSc-Integration for PETSc some additional parameters are allowed/available direct access to PETSc-solver parameters similar to command line arguments manual call of petsc solvers: prob solver: {petsc,petsc-block,petsc-schur,petsc-feti} Parameter-file prob solver: petsc prob solver ksp type: SOLVER-NAME prob solver pc type: PRECON-NAME prob solver petsc prefix: PREFIX (e.g. pfc ) prob solver ksp: COMMANDLINE-ARG (e.g. PREFIX ksp rtol 1.e-3) Problemdependent preconditioner implemented (for example-problems) in amdis/trunk/extensions/preconditioner for mtl, petsc, p mtl, p petsc, for CahnHillard and PFC Simon Praetorius (TU Dresden IWR) AMDiS-Meeting 14. Oktober / 14

5 PMTL-Integration base implementation available, but error leads to data-type overflow small problems up to partition size of DOFs possible source of error not yet found! solvers equal to sequential MTL-version problem-dependent preconditioners similar to seq. MTL implementation (same interface, same solvers, etc.) CMake-Parameters ENABLE PARALLEL DOMAIN: PMTL MTL DIR: pmtl root/share/mtl Parameter-file prob solver backend: p mtl % is set automatically Simon Praetorius (TU Dresden IWR) AMDiS-Meeting 14. Oktober / 14

6 ARH2-fileformat ARH (AMDiS-Refinement-Hierarchy) - fileformat developed by Thomas W and Florian S has some drawbacks: redundancy, support for linear fespace only, no (user)documentation/tests,... Student-group has developed a strategy/algorithm based on ideas from Michael N to extend format to quadratic fespace New format by (Florian, Siqi and me) for arbitrary fespaces with low redundany (no redundany per macro-element) User-Interface Arh2Reader::readFile(SOURCE, TARGET); // SOURCE=filename Arh2Writer::writeFile(SOURCE, TARGET); // TARGET=filename with arguments one of {DOFVector, vector<dofvector>, SystemVector} Parameter file prob output ARH2 format: 1 Simon Praetorius (TU Dresden IWR) AMDiS-Meeting 14. Oktober / 14

7 ARH2-fileformat mesh-description like in ARH1-format one or more value-vectors with different fespace allowed (all living on the same mesh!) collection of tests implemented specification nearly finished then other softwarepackages can implement ARH-Readers/-Writers User-Interface Arh2Reader::readByName(SOURCE, TARGET); // SOURCE=filename read value-vectors with names given by TARGET-names from file. ToDo/Ideas: containerformat for arh-files like PVD-files, PVTU-files for timeseries/partitions/componentfiles Paraview-Plugin to visualize ARH-value-vectors directly Simon Praetorius (TU Dresden IWR) AMDiS-Meeting 14. Oktober / 14

8 A new finite element AMDiS provides an interface to implement arbitrary finite elements Up to now only Lagrange FE up to order 4 included Student-group has developed 2D Mini-Element (linear Lagrange FE (P1) + bubble function) Some properties of Mini-element: non-nodal basis functions (i.e. (i, j) : ψ i (x j ) δ ij ) non-nested basis functions (i.e. i : (a j ) j : ψ c i j a jψ f j ) Mini-Element for velocity comp. + P1 for pressure gives stable stokes element Parameter-file prob finite element space[i]: FE-NAME prob fespace[i]: FE-NAME % abbreviation prob polynomial degree[i]: DEG % for backward compatibility with FE-NAME one of {P1-P4, P1+bubble} Simon Praetorius (TU Dresden IWR) AMDiS-Meeting 14. Oktober / 14

9 Status of bubble-functions ToDo: implementation is usable lots of tests already implemented (some can be used to test Lagrange functions as well) example will be included in AMDiS demo-folder Some AMDiS functions must be modified to allow non-nodal basis functions (e.g. transformdof, interpol) non-nested property requires the extension of the AMDiS interface (e.g. refinementconserved()) extension to 1D, 3D required eventually testing the implementation of Lagrange-functions (difference to expected properties) Simon Praetorius (TU Dresden IWR) AMDiS-Meeting 14. Oktober / 14

10 Repartitioning Usage start parallel computing on initial domain decomposition, when solution developes repartition domain recently 1 Bug removed (coupled problems, non-equal fespaces) repartitioning after 1 timestep? After solveinitialproblem()? User-interface must be modified! some users yet have problems when using repartitioning! after problem-initialization: meshdistributor addinterchangevector(vector); with meshdistributor globally available, VECTOR: e.g. DOFVector Parameter-file parallel repartitioning: 1 parallel repartition ith change: 20 parallel repartition only once: 1 %?? Simon Praetorius (TU Dresden IWR) AMDiS-Meeting 14. Oktober / 14

11 Repartitioning - Who uses which functionality? automatic repartitioning (imbalancing) Repartitioning when imbalancing greater than bound parallel repartitioning imbalance: 0.2 using Meta-ARH files, or element-weights file (provides relation MacroElement weightening - e.g. number of leaf elements) Parameter-file parallel partitioner read meta arh: FILENAME MESHNAME macro weights: FILENAME Usage structure/content of Meta-ARH files? No documentation, but converter in amdis/trunk/tools/arhtools./createmetaarh nprocs input arh output meta arh Simon Praetorius (TU Dresden IWR) AMDiS-Meeting 14. Oktober / 14

12 ExtendedProblemStat - DirichletBC Usage DirichletBC in AMDiS not prefered over e.g. NeumannBC/RobinBC, some situations can not be handled by boundary strategy boundary with higher boundary number prefered (importent in corners/common edges) only edges (2D), faces (3D) can be specified! No point-dirichletbc. ExtendedProblemStat provides interface for these situations: DirichletBC alway added after all other BC assembled! many different descriptions of boundary-region and values available user-interface now equal to AMDiS-interface prob adddirichletbc(region, ROW, COL, VALUE); with REGION one of {Boundary-Number, DOF-Index, WorldVector, SignedDist(Fct/DOFVector), MeshIndicator}, VALUE one of {double, DOFVector, AbstractFunction} [pointers stored internally] Simon Praetorius (TU Dresden IWR) AMDiS-Meeting 14. Oktober / 14

13 Other changes Coupling structures (CouplingProblemStat, CouplingIterationInterface, CouplingTimeInterface) CouplingBaseProblem[2, 2 cxx11] for use with BaseProblem classes (generalized to accept mixed baseproblem-types) Navier-Stokes, CahnHillard, PFC demos added to amdis/trunk/extensions/demo/other directory documentation of some functionality of extensions started in amdis/trunk/extensions/doc Some more ideas: Plugin-module for AMDiS (e.g. provide new external solvers as plugin for user-program) extension of quadrature-class to allow user-defined quadrature-rules (e.g. Newton-Cotes instead of Gauss-quadrature) Masslumping higher order operator-terms (we need jump terms over inner edges) interface for time-integrators/non-linear solvers must be reworked! Simon Praetorius (TU Dresden IWR) AMDiS-Meeting 14. Oktober / 14

14 Thanks for your attention. Questions / Discussion Simon Praetorius (TU Dresden IWR) AMDiS-Meeting 14. Oktober / 14