[petsc-users] (no subject)

[Jed Brown]

On Sat, Dec 29, 2012 at 1:40 AM, amlan barua <abarua at iit.edu> wrote:

> Hi Barry,
> I wrote the following piece according to your suggestions. Currently it
> does nothing but creates a vector with 1 at 1th position, 2 at 2th and so
> on. But I made it serial, i.e. (n+1)th place is computed using the value of
> nth place. My question, did I do it correctly, i.e. is it safe or results
> may change depending on problem size? This is much faster than
> VecSetValues, I believe the communication is minimum here because I take
> the advantage of ghost points.
> Amlan
>
> PetscInitialize(&argc,&argv,(char *)0,help);
>     ierr = MPI_Comm_size(PETSC_COMM_WORLD, &size); CHKERRQ(ierr);
>     ierr = MPI_Comm_rank(PETSC_COMM_WORLD, &rank); CHKERRQ(ierr);
>     ierr =
> DMDACreate1d(PETSC_COMM_WORLD,DMDA_BOUNDARY_NONE,size*5,1,1,PETSC_NULL,&da);
> CHKERRQ(ierr);
>     ierr = DMCreateGlobalVector(da,&vec); CHKERRQ(ierr);
>     ierr = VecSet(vec,1.00);
>     ierr = DMCreateLocalVector(da,&local);
>     ierr = DMDAGetLocalInfo(da,&info);
>     ierr = DMDAVecGetArray(da,vec,&arr);
>     ierr = DMDAVecGetArray(da,local,&array);
>     temp = 1;
>     for (j=0;j<size;j++) {
>

This is needlessly sequential (or should be).


>        ierr = DMGlobalToLocalBegin(da,vec,INSERT_VALUES,local);
> CHKERRQ(ierr);
>        ierr = DMGlobalToLocalEnd(da,vec,INSERT_VALUES,local);
> CHKERRQ(ierr);
>

You should never use a communication routine while you have access to the
array (*VecGetArray()).


>        if (rank==j) {
>        for (i=info.xs;i<info.xs+info.xm;i++) {
>           if ((!i)==0) {
>             array[i] = array[i] + array[i-1];
>

What sort of recurrence do you actually want to implement. When possible,
it's much better to reorganize so that you can do local work followed by an
MPI_Scan followed by more local work. MPI_Scan is fast (logarithmic).


>             arr[i] = array[i];
>             }
>           }
>        }
>        }
>     ierr = DMDAVecRestoreArray(da,local,&array);
>     ierr = DMDAVecRestoreArray(da,vec,&arr);
>     ierr = VecView(vec,PETSC_VIEWER_STDOUT_WORLD);
>     PetscFinalize();
>     return 0;
>
>
>
> On Thu, Dec 27, 2012 at 10:40 AM, Barry Smith <bsmith at mcs.anl.gov> wrote:
>
>>
>> On Dec 27, 2012, at 10:34 AM, amlan barua <abarua at iit.edu> wrote:
>>
>> > I think I can use VecSetValues, is that right?
>>
>>    Yes you could do that. But since you are using a DMDA you could also
>> use DMGetLocalVector(), DMGlobalToLocalBegin/End() followed by
>> DMDAVecGetArray() to access the ghost values.
>>
>>    Barry
>>
>> > Amlan
>> >
>> >
>> > On Thu, Dec 27, 2012 at 9:04 AM, amlan barua <abarua at iit.edu> wrote:
>> > Hi Barry,
>> > Is this scattering a very costly operation? I have to compute x[i] =
>> f(x[i-1]) where f is known. Since this operation is strictly sequential, I
>> thought of gathering the entire vector on processor 0, do the sequential
>> operation there and scatter the result back. However this is unnecessary
>> because I only need the bordering x[i] values. What can be a better way?
>> > Amlan
>> >
>> >
>> > On Thu, Dec 27, 2012 at 8:18 AM, Barry Smith <bsmith at mcs.anl.gov>
>> wrote:
>> >
>> >   ierr = DMDACreateNaturalVector(da,&natural);CHKERRQ(ierr);
>> >     ierr =
>> DMDAGlobalToNaturalBegin(da,xin,INSERT_VALUES,natural);CHKERRQ(ierr);
>> >     ierr =
>> DMDAGlobalToNaturalEnd(da,xin,INSERT_VALUES,natural);CHKERRQ(ierr);
>> >
>> > Now do VecScatterCreateToZero() from natural and the vector will be in
>> the natural ordering on process zero with the dof interlaced.
>> >
>> >
>> >    Barry
>> >
>> > On Dec 27, 2012, at 12:22 AM, amlan barua <abarua at iit.edu> wrote:
>> >
>> > > Hi,
>> > > Is there an analogue of VecScatterCreateToZero for DA vectors? The
>> DMDA object has more than one degrees of freedom.
>> > > If there isn't any, should I use an IS object to do the scattering?
>> > > Amlan
>> >
>> >
>> >
>>
>>
>
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