petsc-master 2016-01-13
Report Typos and Errors
petsc-master 2016-01-13
Report Typos and Errors
petsc-master 2016-01-13
Report Typos and Errors
petsc-master 2016-01-13
Report Typos and Errors
petsc-master 2016-01-13
Report Typos and Errors

## PETSc Hands On

PETSc comes with a large number of example codes to illustrate usage. The three main sets are in:

- ODEs - src/ts/examples/tutorials
- Nonlinear problems - src/snes/examples/tutorials
- Linear problems - src/ksp/ksp/examples/tutorials

## Example 1: Linear Poisson equation on a 2D grid

WHAT THIS EXAMPLE DEMONSTRATES:

- Using command line options
- Using Linear Solvers
- Handling a simple structured grid

FURTHER DETAILS:

- Mathematical description of the problem
- the source code

DO THE FOLLOWING:

- Compile src/ksp/ksp/examples/tutorials/ex50.c

            cd petsc/src/ksp/ksp/examples/tutorials
            make ex50

- Run a 1 processor example with a 3x3 mesh and view the matrix assembled

           mpiexec -n 1 ./ex50  -da_grid_x 4 -da_grid_y 4 -mat_view     [Expected output]

- Run with a 120x120 mesh on 16 processors using superlu_dist and view the solver options used

           mpiexec -n 16 ./ex50  -da_grid_x 120 -da_grid_y 120 -pc_type lu -pc_factor_mat_solver_package superlu_dist -ksp_monitor -ksp_view     [Expected output]

- Run with a 2049x2049 grid using multigrid solver on 16 processors with 10 multigrid levels

           mpiexec -n 16 ./ex50 -da_grid_x 2049 -da_grid_y 2049 -pc_type mg -pc_mg_levels 10 -ksp_monitor     [Expected output]

## Example 2: Nonlinear ODE arising from a time-dependent one dimensional PDE

WHAT THIS EXAMPLE DEMONSTRATES:

- Using command line options
- Handling a simple structured grid
- Using the ODE integrator
- Using call-back functions

FURTHER DETAILS:

- Mathematical description of the problem
- the source code

DO THE FOLLOWING:

- Compile src/ts/examples/tutorials/ex2.c

            cd petsc/src/ts/examples/tutorials
            make ex2

- Run a 1 processor example on the default grid with all the default solver options

           mpiexec -n 1 ./ex2 -ts_max_steps 10 -ts_monitor     [Expected output]

- Run with the same options on 4 processors plus monitor convergence of the nonlinear and linear solvers

           mpiexec -n 4 ./ex2 -ts_max_steps 10 -ts_monitor -snes_monitor -ksp_monitor     [Expected output]

- Run with the same options on 16 processors with 128 grid points

           mpiexec -n 16 ./ex2 -ts_max_steps 10 -ts_monitor -M 128     [Expected output]

## Example 3: Nonlinear PDE on a structured grid

WHAT THIS EXAMPLE DEMONSTRATES:

- Handling a 2d structured grid
- Using the nonlinear solvers
- Changing the default linear solver

FURTHER DETAILS:

- Mathematical description of the problem
- main program source code
- physics source code

DO THE FOLLOWING:

- Compile src/snes/examples/tutorials/ex19.c

            cd petsc/src/snes/examples/tutorials/
            make ex19

- Run a 16 processor example with six levels of grid refinement, monitor the convergence of the nonlinear and linear solver and examine the exact solver used

           mpiexec -n 16 ./ex19 -da_refine 6 -snes_monitor -ksp_monitor -snes_view     [Expected output]

- Run with the same options but use geometric multigrid as the linear solver

           mpiexec -n 16 ./ex19 -da_refine 6 -snes_monitor -ksp_monitor -snes_view -pc_type mg     [Expected output]

  Note this requires many fewer iterations than the default solver
- Run with the same options but use algebraic multigrid (hypre's BoomerAMG) as the linear solver

           mpiexec -n 16 ./ex19 -da_refine 6 -snes_monitor -ksp_monitor -snes_view -pc_type hypre     [Expected output]

  Note this requires many fewer iterations than the default solver but requires more iterations than geometric multigrid
- Run on 4 processors with the default linear solver and profile the run

           mpiexec -n 4 ./ex19 -da_refine 6 -log_summary     [Expected output]

  Search for the line beginning with SNESSolve, the fourth column gives the time for the nonlinear solve.
- Run on 4 processors with the geometric multigrid linear solver and profile the run

           mpiexec -n 4 ./ex19 -da_refine 6 -log_summary -pc_type mg     [Expected output]

  Compare the runtime for SNESSolve to the case with the default solver
- Run on 16 processors with the default linear solver and profile the run

           mpiexec -n 16 ./ex19 -da_refine 6 -log_summary     [Expected output]

  Compare the runtime for SNESSolve to the 4 processor case with the default solver, what is the speedup?
- Run on 16 processors with the geometric multigrid linear solver and profile the run

           mpiexec -n 16 ./ex19 -da_refine 6 -log_summary -pc_type mg     [Expected output]

  Compare the runtime for the SNESSolve to the 4 processor case with multigrid, what is the speedup? Why is the speedup for multigrid lower than the speedup for the default solver?

## Example 4: Linear Stokes-type PDE on a structured grid

WHAT THIS EXAMPLE DEMONSTRATES:

- Handling a 3d structured grid
- Controlling linear solver options
- Selecting composible preconditioners
- Solving a Stokes problem
- Adding your own problem specific visualization

FURTHER DETAILS:

- Mathematical description of the problem
- main program source code
- physics source code

DO THE FOLLOWING:

- Compile src/ksp/ksp/examples/tutorials/ex42.c

            cd petsc/src/ksp/ksp/examples/tutorials
            make ex42

- Solve with the default solver

           mpiexec -n 4 ./ex42  -stokes_ksp_monitor   [Expected output]

  Note the poor convergence for even a very small problem
- Solve with a solver appropriate for Stoke's problems -stokes_pc_type fieldsplit -stokes_pc_fieldsplit_type schur

           mpiexec -n 4 ./ex42  -stokes_ksp_monitor -stokes_pc_type fieldsplit -stokes_pc_fieldsplit_type schur  [Expected output]

- Solve with a finer mesh

           mpiexec -n 16 ./ex42  -mx 40 -stokes_ksp_monitor  -stokes_pc_type fieldsplit -stokes_pc_fieldsplit_type schur  [Expected output]

## Example 5: Nonlinear time dependent PDE on Unstructured Grid

WHAT THIS EXAMPLE DEMONSTRATES:

- Changing the default ODE integrator
- Handling unstructured grids
- Registering your own interchangeable physics and algorithm modules

FURTHER DETAILS:

- Mathematical description of the problem
- main program source code
- source code of physics modules

DO THE FOLLOWING:

- Compile src/ts/examples/tutorials/ex11.c

            cd petsc/src/ts/examples/tutorials
            make ex11

- Run simple advection through a tiny hybrid mesh

           mpiexec -n 1 ./ex11 -f ${PETSC_DIR}/share/petsc/datafiles/meshes/sevenside.exo      [Expected output]

- Run simple advection through a small mesh with a Rosenbrock-W solver

           mpiexec -n 1 ./ex11 -f ${PETSC_DIR}/share/petsc/datafiles/meshes/sevenside.exo -ts_type rosw      [Expected output]

- Run simple advection through a larger quadrilateral mesh of an annulus with least squares reconstruction and no limiting, monitoring the error

           mpiexec -n 16 ./ex11 -f ${PETSC_DIR}/share/petsc/datafiles/meshes/annulus-20.exo -monitor Error -advect_sol_type bump -petscfv_type leastsquares -petsclimiter_type sin [Expected output]

  Compare turning to the error after turning off reconstruction.
- Run shallow water on the larger mesh with least squares reconstruction and minmod limiting, monitoring water Height (integral is conserved) and Energy (not conserved)

           mpiexec -n 4 ./ex11 -f ${PETSC_DIR}/share/petsc/datafiles/meshes/annulus-20.exo -physics sw -monitor Height,Energy -petscfv_type leastsquares -petsclimiter_type minmod [Expected output]