Thanks, I will write the stand alone code for it. One more question about the
global and local vector below.
> Subject: Re: [petsc-users] local Vec to global Vec and global 3-D array
> From: bsmith at mcs.anl.gov
> Date: Wed, 15 May 2013 14:09:42 -0500
> To: pengxwang at hotmail.com; petsc-users at mcs.anl.gov
>
>
> On May 15, 2013, at 12:41 PM, Roc Wang <pengxwang at hotmail.com> wrote:
>
> > Thanks, please take a look my further questions.
> >
> > > Subject: Re: [petsc-users] local Vec to global Vec and global 3-D array
> > > From: bsmith at mcs.anl.gov
> > > Date: Wed, 15 May 2013 11:40:03 -0500
> > > CC: petsc-users at mcs.anl.gov
> > > To: pengxwang at hotmail.com
> > >
> > >
> > > On May 15, 2013, at 10:19 AM, Roc Wang <pengxwang at hotmail.com> wrote:
> > >
> > > > Hello,
> > > >
> > > > 1. I am trying to save the solution of a PDE for a 3-D geometry domain.
> > > > I used DM to manage the matrix and vector.
> > > > The solution vector was converted to local 3D arrays on each process
> > > > successfully. But there was errors when the functions
> > > > DMLocalToGlobalBegin() and DMLocalToGlobalEnd() were called.
> > > >
> > > > I built the code by following the example in
> > > > /petsc-3.3-p6/src/dm/examples/tutorials/ex3.c. The codes for this are
> > > > as followings :
> > > >
> > > > /*Get the solution vec */
> > > > ierr = KSPSolve(ksp,PETSC_NULL,PETSC_NULL);CHKERRQ(ierr);
> > > > ierr = KSPGetSolution(ksp,&x);CHKERRQ(ierr);
> > > >
> > > > /* local 3d arrays */
> > > > ierr = DMDAVecGetArray(da, x, &localArray3d ); CHKERRQ(ierr);
> > > >
> > > > /* global 3d array */
> > > > ierr = DMCreateGlobalVector(da,&gsol3d);CHKERRQ(ierr);
> > > > ierr = DMLocalToGlobalBegin(da,x,INSERT_VALUES,gsol3d);CHKERRQ(ierr);
> > > > ierr = DMLocalToGlobalEnd(da,x,INSERT_VALUES,gsol3d);CHKERRQ(ierr);
> > >
> > > The x here must not have been obtained from this da. You need to have
> > > obtained the x somewhere before with DMCreateLocalVector(da,&x) or with a
> > > VecDuplicate from such a vector. Likely the vector put into the KSP is
> > > not from this da.
> >
> > !***************************************
> > The procedure of creating x is like this:
> >
> > call KSPCreate() to build ksp;
> > call DMDACreate3d() to build da;
> > ierr = KSPSetDM(ksp,da); // associate da with ksp;
> >
> > Then after ksp was solved:
> >
> > ierr = KSPSolve(ksp,PETSC_NULL,PETSC_NULL);CHKERRQ(ierr);
> > ierr = KSPGetSolution(ksp,&x);CHKERRQ(ierr);
> > ierr = DMDAVecGetArray(da, x, &localArray3d ); CHKERRQ(ierr);
> >
> > Here, da was associated with the ksp by calling ierr = KSPSetDM(ksp,da).
> > The x here was obtained by calling the KSPGetSolution(ksp,&x), before this
> > I didn't call DMCreateLocalVector(da,&x). It seems Vec x is associated
> > with da since there is no errors when DMDAVecGetArray(da, x, &localArray3d
> > ) was called.
>
> The x from KSPGetSolution() IS a global vector, it is not a global vector.
> You cannot do a local to global from the x global vector.
!*******************************
The x from KSPGetSolution() IS a global vector, it is not a "local" vector? (It
should be a typo :) )
So Can I convert the global x to a 3d array directly? Thank.
>
> > Do you mean I should call DMCreateLocalVector(da,&x) explicitly before ierr
> > = KSPGetSolution(ksp,&x)?
> > !***************************************
> >
> > > >
> > > >
> > > > 2. I am trying to visualize the solution in a 3-D domain by using some
> > > > software such as Tecplot. To my understand, I need to output the
> > > > solution in the format of 3-D array. The vectors of KSP solution in
> > > > PETSc are local vectors on each process. So they have to be assembled
> > > > to a global vector and then converted to a 3-D global array. I am not
> > > > sure if my approach is a good way and if there is some functions in
> > > > PETSc to output the global solutions directly?
> > >
> > > Yes. VecView() on DMDA vectors automatically reorders the entries on the
> > > file to use the natural ordering. There are variety of possible viewers
> > > you can use including binary, ASCII (no good for anything but tiny
> > > problems), VTK, HDF5
> >
> > !***************************************
> > VecView only outputs the vector itself. How to output the indexes of nodes
> > in 3 dimemsions (i,j,k) for each element of the vector, such as:
> >
> > i j k x
> > 0 0 0 1.0
> > 0 0 1 2.0
> > ...
> > m n p 10.0
> > !***************************************
>
> If you want some ASCII format like that, then write a STAND ALONE
> sequential program that reads from the binary file with VecLoad() and then
> outputs the format you want. Never Never ever try to do a parallel output of
> data in this kind of format, it will be slow and hard to write and there is
> no reason to write it.
>
> Barry
>
> > >
> > > Barry
> > >
> > > >
> > > > Part of the error information when DMLocalToGlobalBegin() and
> > > > DMLocalToGlobalEnd() were called
> > > >
> > > > [0]PETSC ERROR: [1]PETSC ERROR: [2]PETSC ERROR: ---------------------
> > > > Error Message ------------------------------------
> > > > [3]PETSC ERROR: --------------------- Error Message
> > > > ------------------------------------
> > > > [2]PETSC ERROR: [3]PETSC ERROR: --------------------- Error Message
> > > > ------------------------------------
> > > > Nonconforming object sizes!
> > > > Nonconforming object sizes!
> > > > [2]PETSC ERROR: [3]PETSC ERROR: Vector wrong size 30 for scatter 60
> > > > (scatter forward and vector from != ctx from size)!
> > > > Vector wrong size 20 for scatter 45 (scatter forward and vector from !=
> > > > ctx from size)!
> > >
>
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