[petsc-users] petsc4py - Convert c example code to Python
Smith, Barry F.
bsmith at mcs.anl.gov
Tue Apr 2 13:29:58 CDT 2019
More explicitly. In the C function you are copying from it uses
ierr = TSSetRHSFunction(ts,r,RHSFunction,&user);CHKERRQ(ierr);
....
ierr = TSSetRHSJacobian(ts,J,J,RHSJacobian,NULL);CHKERRQ(ierr);
But in your code you use
ts.setIFunction(RHS_func, f)
ts.setIJacobian(Jacobian_func, J, J)
This simply will not work, the SetRHS* and SetI* functions are not interchangeable. You functions you provide in the two cases have to be different. See the manual pages for the various routines. And the PETSc users manual.
First get the python working with SetRHS* (confirm identical results to the C program) and then if you want to use the SetI* you must rewrite the RHS_func and Jacobian_func functions that you provide following the explanation in the manual pages and user manual.
Barry
> On Apr 2, 2019, at 9:07 AM, Matthew Knepley via petsc-users <petsc-users at mcs.anl.gov> wrote:
>
> On Tue, Apr 2, 2019 at 4:19 AM Nicola Creati via petsc-users <petsc-users at mcs.anl.gov> wrote:
> Hello, I have run the two codes using: -pc_type lu -ts_monitor
> -snes_monitor -ksp_monitor -ts_max_steps 5. The codes start to diverge
> after the first time step:
>
> In RHS_Function, you never use xdot, but this is an implicit TS. Thus, you are solving the Laplace
> equation, not the heat equation, and you get the exact answer after one step.
>
> Matt
>
> Python run :
>
> 0 TS dt 0.01 time 0.
> 0 SNES Function norm 2.327405179696e+02
> 0 KSP Residual norm 1.939100379240e+00
> 1 KSP Residual norm 1.013760235597e-15
> 1 SNES Function norm 9.538686413612e-14
> 1 TS dt 0.01 time 0.01
> 0 SNES Function norm 8.565210784140e-14
> 0 KSP Residual norm 1.266678408555e-15
> 1 KSP Residual norm 2.663404219322e-31
> 1 SNES Function norm 5.528402779439e-29
> 2 TS dt 0.01 time 0.02
> 0 SNES Function norm 5.829656072531e-29
> 0 KSP Residual norm 3.805606380832e-31
> 1 KSP Residual norm 3.283104975114e-46
> 1 SNES Function norm 1.867771204856e-44
> 3 TS dt 0.01 time 0.03
> 0 SNES Function norm 1.644541571708e-44
> 0 KSP Residual norm 1.969573456719e-46
> 1 KSP Residual norm 1.297976290541e-61
> 1 SNES Function norm 1.780215821230e-59
> 4 TS dt 0.01 time 0.04
> 0 SNES Function norm 1.700894451833e-59
> 5 TS dt 0.01 time 0.05
>
> ex13.c run:
>
> 0 TS dt 0.01 time 0.
> 0 SNES Function norm 2.327405179696e+02
> 0 KSP Residual norm 9.158498731719e-01
> 1 KSP Residual norm 5.129005976821e-16
> 1 SNES Function norm 1.141297389434e-13
> 1 TS dt 0.01 time 0.01
> 0 SNES Function norm 9.158498731719e+01
> 0 KSP Residual norm 4.156347391374e-01
> 1 KSP Residual norm 1.996081836894e-16
> 1 SNES Function norm 3.609761734594e-14
> 2 TS dt 0.01 time 0.02
> 0 SNES Function norm 4.156347391374e+01
> 0 KSP Residual norm 2.203298795311e-01
> 1 KSP Residual norm 9.047356740098e-17
> 1 SNES Function norm 3.292648977280e-14
> 3 TS dt 0.01 time 0.03
> 0 SNES Function norm 2.203298795311e+01
> 0 KSP Residual norm 1.367458644503e-01
> 1 KSP Residual norm 5.055030661919e-17
> 1 SNES Function norm 1.272304808486e-14
> 4 TS dt 0.01 time 0.04
> 0 SNES Function norm 1.367458644503e+01
> 0 KSP Residual norm 9.695393464180e-02
> 1 KSP Residual norm 1.918401734795e-17
> 1 SNES Function norm 1.130247628824e-14
> 5 TS dt 0.01 time 0.05
>
> I rechecked the Python code against the C one but I did not find the
> source of the issue.
>
> # Example 13 petsc TS
> import sys, petsc4py
> petsc4py.init(sys.argv)
>
> from petsc4py import PETSc
> from mpi4py import MPI
> import numpy as np
> import math
>
> def RHS_func(ts, t, X, xdot, F):
> da = ts.getDM()
> localU = da.getLocalVec()
>
> da.globalToLocal(X, localU)
>
> mx, my = da.getSizes()
>
> hx, hy = [1.0/(m-1) for m in [mx, my]]
> sx = 1.0/(hx*hx)
> sy = 1.0/(hy*hy)
>
> uarray = localU.getArray(readonly=1).reshape(8, 8, order='C')
> f = F.getArray(readonly=0).reshape(8, 8, order='C')
>
> (xs, xm), (ys, ym) = da.getRanges()
> for j in range(ys, ym):
> for i in range(xs, xm):
> if i == 0 or j == 0 or i == (mx-1) or j == (my-1):
> f[i,j] = uarray[i,j]
> continue
> u = uarray[i,j]
> uxx = (-2.0 * u + uarray[i, j-1] + uarray[i, j+1]) * sx
> uyy = (-2.0 * u + uarray[i-1, j] + uarray[i+1, j])* sy
> f[i, j] = uxx + uyy
> F.assemble()
> #PETSc.Log.logFlops(11.0*xm*ym)
>
>
> def Jacobian_func(ts, t, x, xdot, a, A, B):
> mx, my = da.getSizes()
> hx = 1.0/(mx-1)
> hy = 1.0/(my-1)
> sx = 1.0/(hx*hx)
> sy = 1.0/(hy*hy)
>
> B.setOption(PETSc.Mat.Option.NEW_NONZERO_ALLOCATION_ERR, False)
> B.zeroEntries()
>
> (i0, i1), (j0, j1) = da.getRanges()
> row = PETSc.Mat.Stencil()
> col = PETSc.Mat.Stencil()
>
> for i in range(j0, j1):
> for j in range(i0, i1):
> row.index = (i,j)
> row.field = 0
> if i == 0 or j== 0 or i==(my-1) or j==(mx-1):
> B.setValueStencil(row, row, 1.0)
> else:
> for index, value in [
> ((i-1, j), sx),
> ((i+1, j), sx),
> ((i, j-1), sy),
> ((i, j+1), sy),
> ((i, j), -2*sx - 2*sy)]:
> col.index = index
> col.field = 0
> B.setValueStencil(row, col, value)
>
> B.assemble()
> #B.view()
> if A != B: B.assemble()
>
> return PETSc.Mat.Structure.SAME_NONZERO_PATTERN
>
> def make_initial_solution(da, U, c):
> mx, my = da.getSizes()
> hx = 1.0/(mx-1)
> hy = 1.0/(my-1)
> (xs, xm), (ys, ym) = da.getRanges()
>
> u = U.getArray(readonly=0).reshape(8, 8, order='C')
>
> for j in range(ys, ym):
> y = j*hy
> for i in range(xs, xm):
> x = i*hx
> r = math.sqrt((x-0.5)**2+(y-0.5)**2)
> if r < (0.125):
> u[i, j] = math.exp(c*r*r*r)
> else:
> u[i, j] = 0.0
> U.assemble()
> #U.view()
>
>
> def monitor(ts, i, t, x):
> xx = x[:].tolist()
> history.append((i, t, xx))
>
>
> history = []
> nx = 8
> ny = 8
> da = PETSc.DMDA().create([nx, ny], stencil_type=
> PETSc.DA.StencilType.STAR, stencil_width=1, dof=1)
>
> da.setFromOptions()
> da.setUp()
>
> u = da.createGlobalVec()
> f = u.duplicate()
>
> c = -30.0
>
> ts = PETSc.TS().create()
> ts.setDM(da)
> ts.setType(ts.Type.BEULER)
>
> ts.setIFunction(RHS_func, f)
>
> da.setMatType('aij')
> J = da.createMat()
> ts.setIJacobian(Jacobian_func, J, J)
>
> ftime = 1.0
> ts.setMaxTime(ftime)
> ts.setExactFinalTime(PETSc.TS.ExactFinalTime.STEPOVER)
>
> make_initial_solution(da, u, c)
> dt = 0.01
>
> ts.setMonitor(monitor)
> ts.setTimeStep(dt)
> ts.setFromOptions()
> ts.solve(u)
>
> ftime = ts.getSolveTime()
> steps = ts.getStepNumber()
>
> Thanks.
>
> Nicola
>
>
> --
>
> Nicola Creati
> Istituto Nazionale di Oceanografia e di Geofisica Sperimentale - OGS www.inogs.it
> Dipartimento di Geofisica della Litosfera Geophysics of Lithosphere Department
> CARS (Cartography and Remote Sensing) Research Group http://www.inogs.it/Cars/
> Borgo Grotta Gigante 42/c 34010 Sgonico - Trieste - ITALY ncreati at ogs.trieste.it
> off. +39 040 2140 213
> fax. +39 040 327307
>
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>
>
>
> --
> What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead.
> -- Norbert Wiener
>
> https://www.cse.buffalo.edu/~knepley/
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