[petsc-users] DMMG with PBC

[Matthew Knepley]

On Tue, Apr 19, 2011 at 6:26 PM, khalid ashraf <khalid_eee at yahoo.com> wrote:

> >>How much of a difference?
> With the applied XYZPeriodic, if I keep the follwoing lines
>
>  if (i==0 || j==0 || k==0 || i==mx-1 || j==my-1 || k==mz-1){
>           v[0] = 2.0*(HxHydHz + HxHzdHy + HyHzdHx);
>           ierr =
> MatSetValuesStencil(B,1,&row,1,&row,v,INSERT_VALUES);CHKERRQ(ierr);
>         } else
>
>  Then the error between 1proc and 4 procs is only after 5th decimal point.
> However, if I comment out the
> above lines then the results are completely different for 1 and 4 procs.
>

Yes, without this the problem is rank deficient. I suspect that your 5th
decimal place difference
comes from either a) different partitions b) different convergence (stop on
a different iterate) or c)
parallel reordering (but it seems big).

   Matt


> I am attaching the output of some last data points of a 10X10X8 grid.
> 1 proc output:
> -4.40214
> -4.39202
> -4.38693
> -4.38547
> -4.38687
> -4.39047
>
> 4 proc output:
> 0.000188031
> 0.000169784
> 0.000157229
> 0.000178713
> 0.000179637
> 0.000188031
> 0.000169784
> 0.000157229
> 0.000178713
> 0.000179637
>
> I am attaching the faulty code here for your review.
>
> Thanks.
>
> Khalid
>
> static char help[] = "Solves 3D Laplacian using multigrid.\n\n";
>
> #include "petscda.h"
> #include "petscksp.h"
> #include "petscdmmg.h"
> #include "myHeaderfile.h"
>
> extern PetscErrorCode ComputeMatrix(DMMG,Mat,Mat);
> extern PetscErrorCode ComputeRHS(DMMG,Vec);
>
> #undef __FUNCT__
> #define __FUNCT__ "main"
> int main(int argc,char **argv)
> {
>   PetscErrorCode ierr;
>   DMMG           *dmmg;
>   PetscReal      norm;
>   DA             da;
>
>   PetscInitialize(&argc,&argv,(char *)0,help);
>
>   ierr = DMMGCreate(PETSC_COMM_WORLD,1,PETSC_NULL,&dmmg);CHKERRQ(ierr);
>   ierr =
> DACreate3d(PETSC_COMM_WORLD,DA_XYZPERIODIC,DA_STENCIL_STAR,10,10,8,PETSC_DECIDE,PETSC_DECIDE,PETSC_DECIDE,1,1,0,0,0,&da);CHKERRQ(ierr);
>   ierr = DMMGSetDM(dmmg,(DM)da);CHKERRQ(ierr);
>  // ierr = DADestroy(da);CHKERRQ(ierr);
>
>   ierr = DMMGSetKSP(dmmg,ComputeRHS,ComputeMatrix);CHKERRQ(ierr);
>   ierr =DMMGSetNullSpace(dmmg,PETSC_TRUE,0,PETSC_NULL);
>
>  ierr = DMMGSetUp(dmmg);CHKERRQ(ierr);
>   ierr = DMMGSolve(dmmg);CHKERRQ(ierr);
>
>   ierr =
> MatMult(DMMGGetJ(dmmg),DMMGGetx(dmmg),DMMGGetr(dmmg));CHKERRQ(ierr);
>   ierr = VecAXPY(DMMGGetr(dmmg),-1.0,DMMGGetRHS(dmmg));CHKERRQ(ierr);
>   ierr = VecNorm(DMMGGetr(dmmg),NORM_2,&norm);CHKERRQ(ierr);
>   /* ierr = PetscPrintf(PETSC_COMM_WORLD,"Residual norm
> %G\n",norm);CHKERRQ(ierr); */
>   ierr=VecView_VTK(DMMGGetx(dmmg),"X",&appctx);
>
>   ierr = DMMGDestroy(dmmg);CHKERRQ(ierr);
>   ierr = PetscFinalize();CHKERRQ(ierr);
>
>   return 0;
> }
>
> #undef __FUNCT__
> #define __FUNCT__ "ComputeRHS"
> PetscErrorCode ComputeRHS(DMMG dmmg,Vec b)
> {
>   PetscErrorCode ierr;
>   PetscInt       mx,my,mz;
>   PetscScalar    h;
>
>   PetscFunctionBegin;
>   ierr = DAGetInfo((DA)dmmg->dm,0,&mx,&my,&mz,0,0,0,0,0,0,0);CHKERRQ(ierr);
>   h    = 10.0/((mx-1)*(my-1)*(mz-1));
>   ierr = VecSet(b,h);CHKERRQ(ierr);
>   PetscFunctionReturn(0);
> }
>
> #undef __FUNCT__
> #define __FUNCT__ "ComputeMatrix"
> PetscErrorCode ComputeMatrix(DMMG dmmg,Mat jac,Mat B)
> {
>   DA             da = (DA)dmmg->dm;
>   PetscErrorCode ierr;
>   PetscInt       i,j,k,mx,my,mz,xm,ym,zm,xs,ys,zs;
>   PetscScalar    v[7],Hx,Hy,Hz,HxHydHz,HyHzdHx,HxHzdHy;
>   MatStencil     row,col[7];
>
>   ierr = DAGetInfo(da,0,&mx,&my,&mz,0,0,0,0,0,0,0);CHKERRQ(ierr);
>   Hx = 1.0 / (PetscReal)(mx-1); Hy = 1.0 / (PetscReal)(my-1); Hz = 1.0 /
> (PetscReal)(mz-1);
>   HxHydHz = Hx*Hy/Hz; HxHzdHy = Hx*Hz/Hy; HyHzdHx = Hy*Hz/Hx;
>   ierr = DAGetCorners(da,&xs,&ys,&zs,&xm,&ym,&zm);CHKERRQ(ierr);
>
>   for (k=zs; k<zs+zm; k++){
>     for (j=ys; j<ys+ym; j++){
>       for(i=xs; i<xs+xm; i++){
>         row.i = i; row.j = j; row.k = k;
>    /*     if (i==0 || j==0 || k==0 || i==mx-1 || j==my-1 || k==mz-1){
>           v[0] = 2.0*(HxHydHz + HxHzdHy + HyHzdHx);
>           ierr =
> MatSetValuesStencil(B,1,&row,1,&row,v,INSERT_VALUES);CHKERRQ(ierr);
>         } else */
>            {
>           v[0] = -HxHydHz;col[0].i = i; col[0].j = j; col[0].k = k-1;
>           v[1] = -HxHzdHy;col[1].i = i; col[1].j = j-1; col[1].k = k;
>           v[2] = -HyHzdHx;col[2].i = i-1; col[2].j = j; col[2].k = k;
>           v[3] = 2.0*(HxHydHz + HxHzdHy + HyHzdHx);col[3].i = row.i;
> col[3].j = row.j; col[3].k = row.k;
>           v[4] = -HyHzdHx;col[4].i = i+1; col[4].j = j; col[4].k = k;
>           v[5] = -HxHzdHy;col[5].i = i; col[5].j = j+1; col[5].k = k;
>           v[6] = -HxHydHz;col[6].i = i; col[6].j = j; col[6].k = k+1;
>     ierr =
> MatSetValuesStencil(B,1,&row,7,col,v,INSERT_VALUES);CHKERRQ(ierr);
>         }
>       }
>     }
>   }
>   ierr = MatAssemblyBegin(B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
>   ierr = MatAssemblyEnd(B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
>   return 0;
> }
>
>


-- 
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
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