Dear All, sorry for spam because of my poor PETSc knowledge (I am just starting with this nice framework). I think, I figured part of it out. However, I want to point that src/ts/examples/tutorials/ex15.c is misleading. (or maybe it is a bug?) in this example we have TSGetSNES(ts,&snes); MatCreateSNESMF(snes,&Jmf); SNESSetJacobian(snes,Jmf,J,SNESComputeJacobianDefault,NULL); // or this: SNESSetJacobian(snes,Jmf,J,SNESComputeJacobianDefaultColor,0); which implies (I think) that Jacobian would be matrix free. And if one would use PCNONE for preconditioning the matrix would never be allocated. However, it seems in reality it allocates matrix. To avoid it, I used MatCreateSNESMF(snes,&J); SNESSetJacobian(snes,J,J,MatMFFDComputeJacobian,0); which seems to work fine. I am not sure I fully understand the difference and i have zero intuition and I also have no idea what happens with preconditioning in this case. If someone have some useful comets, please share :) (I read the relevant section in PETSc manual, but still not fully understanding what I should use when) Thank you and again sorry for the spam, Oleksandr. On 04/28/2018 07:20 PM, Smith, Barry F. wrote:
~/Src/petsc/src/ts/examples/tutorials $ grep SNESComputeJacobianDefaultColor *.c ex10.c: ierr = SNESSetJacobian(snes,A,B,SNESComputeJacobianDefaultColor,0);CHKERRQ(ierr); ex15.c: ierr = SNESSetJacobian(snes,Jmf,J,SNESComputeJacobianDefaultColor,0);CHKERRQ(ierr); ex17.c: ierr = SNESSetJacobian(snes,J,J,SNESComputeJacobianDefaultColor,0);CHKERRQ(ierr);
I don't think you need to explicitly create the MatFDColoring object.
Please take a look at ex15.c and see if you can get it working like that example. If that doesn't work let us know and we can take a closer look at it.
Barry
On Apr 28, 2018, at 8:05 PM, Oleksandr Koshkarov <[email protected]> wrote:
Hello All,
I hope someone can help :) I think I am doing something wrong, but cannot understand what. I have a huge time dependent system with 3d DMDA data structure and I am evolving it with explicit Runge-Kutta by using TS and basically only using "TSSetRHSFunction". Now I want to repeat it with implicit time stepper (for now Crank-Nicolson) and I am trying to provide finite difference Jacobian and I am failing miserably. I also cannot find appropriate example in PETSc tutorial (if you can point me to working example, it would be great).
Here is my best attempt (what wrong with it?):
DMDACreate3d(PETSC_COMM_WORLD, DM_BOUNDARY_PERIODIC, DM_BOUNDARY_PERIODIC, DM_BOUNDARY_PERIODIC, DMDA_STENCIL_STAR, NX, NY, NZ, PETSC_DECIDE, PETSC_DECIDE, PETSC_DECIDE, 2*3+NC*NS, 1, NULL, NULL, NULL, &da); DMSetUp(da); DMCreateGlobalVector(da,&x); TSCreate(PETSC_COMM_WORLD,&ts); TSSetProblemType(ts,TS_NONLINEAR); TSSetRHSFunction(ts,NULL,compute_RHS,NULL); TSSetMaxTime(ts,T_FINAL); TSSetExactFinalTime(ts,TS_EXACTFINALTIME_STEPOVER); TSSetDM(ts,da); TSSetType(ts,TSCN); //it works with: TSSetType(ts,TSRK); set_IC(da,x); TSSetTimeStep(ts,DT); TSSetSolution(ts,x);
TSGetSNES(ts,&snes); SNESGetKSP(snes,&ksp); KSPGetPC(ksp,&pc); PCSetType(pc,PCNONE);
DMSetMatType(da,MATAIJ); DMCreateMatrix(da,&J); ISColoring iscoloring; MatFDColoring matfdcoloring; DMCreateColoring(da,IS_COLORING_GLOBAL,&iscoloring); MatFDColoringCreate(J,iscoloring,&matfdcoloring);
MatFDColoringSetType(matfdcoloring,MATMFFD_DS);
// I think I do something wrong in the following 3 lines
PetscErrorCode (*temp_f)(SNES,Vec,Vec,void*); SNESGetFunction(snes,NULL,&temp_f,NULL); MatFDColoringSetFunction(matfdcoloring,(PetscErrorCode (*)(void))temp_f,NULL);
MatFDColoringSetUp(J,iscoloring,matfdcoloring);
SNESSetJacobian(snes,J,J,SNESComputeJacobianDefaultColor,matfdcoloring); ISColoringDestroy(&iscoloring);
TSSolve(ts,x);
Thank you,
Oleksandr Koshkarov.