[petsc-users] Union of sequential vecs

[Matthew Knepley]

On Mon, Dec 12, 2022 at 10:00 AM Karthikeyan Chockalingam - STFC UKRI <
karthikeyan.chockalingam at stfc.ac.uk> wrote:

> Thank you Matt and Blaise.
>
>
>
> I will try out IS (though I have not it before)
>
> (i)                  Can IS be of different size, on different
> processors, and still call ISALLGather?
>
Yes.

> (ii)                Can IS be passed as row indices to MatZeroRowsColumns?
>

https://petsc.org/main/docs/manualpages/Mat/MatZeroRowsColumnsIS/

  Thanks,

     Matt


> I will look into DMlabels and start a different thread if needed.
>
>
>
> Best,
>
> Karthik.
>
>
>
>
>
>
>
> *From: *Matthew Knepley <knepley at gmail.com>
> *Date: *Saturday, 10 December 2022 at 02:20
> *To: *Chockalingam, Karthikeyan (STFC,DL,HC) <
> karthikeyan.chockalingam at stfc.ac.uk>
> *Cc: *Mark Adams <mfadams at lbl.gov>, petsc-users at mcs.anl.gov <
> petsc-users at mcs.anl.gov>
> *Subject: *Re: [petsc-users] Union of sequential vecs
>
> On Fri, Dec 9, 2022 at 6:50 PM Karthikeyan Chockalingam - STFC UKRI via
> petsc-users <petsc-users at mcs.anl.gov> wrote:
>
> Thank you Mark and Barry.
>
>
>
> @Mark Adams <mfadams at lbl.gov> I follow you for the most part. Shouldn’t R
> be an MPI Vector?
>
>
>
> Here it goes:
>
>
>
> Q[Vec[i]] for all "i" in my local (sequential) "Vec".
>
> Compute number of local nonzeros in Q, call it n.
>
>
>
> //Create a MPI Vector R, with local size n
>
>
>
> VecCreate(PETSC_COMM_WORLD, &R);
>
> VecSetType(R, VECMPI);
>
> VecSetSizes(R, *n*, PETSC_DECIDE);
>
>
>
> //Populate MPI Vector R with local (sequential) "Vec".
>
>
>
> VecGetOwnershipRange(R, &istart, &iend);
>
> local_size = iend - istart; //The local_size should be ‘*n*’ right?
>
> VecGetArray(R, &values);
>
>   *for* (i = 0; i < local_size; i++) {
>
>     values[i] = Vec[i];
>
>   }
>
> VecRestoreArray(R, &values);
>
>
>
> //Scatter R to all processors
>
>
>
> Vec            V_SEQ;
>
> VecScatter     ctx;
>
>
>
> VecScatterCreateToAll(R,&ctx,&V_SEQ);
>
>
>
> //Remove duplicates in V_SEQ
>
> How can I use PetscSortRemoveDupsInt to remove duplicates in V_SEQ?
>
>
>
>
>
> Physics behind:
>
> I am reading a parallel mesh, and want to mark all the boundary nodes. I
> use a local (sequential) Vec to store the boundary nodes for each parallel
> partition. Hence, local Vecs can end up with duplicate node index among
> them, which I would like to get rid of when I combine all of them together.
>
>
>
> 1) Blaise is right you should use an IS, not a Vec, to hold node indices.
> His solution is only a few lines, so I would use it.
>
>
>
> 2) I would not recommend doing things this way in the first place. PETSc
> can manage parallel meshes scalably, marking boundaries using DMLabel
> objects.
>
>
>
>   Thanks,
>
>
>
>      Matt
>
>
>
> Best,
>
> Karthik.
>
>
>
>
>
>
>
>
>
> *From: *Mark Adams <mfadams at lbl.gov>
> *Date: *Friday, 9 December 2022 at 21:08
> *To: *Chockalingam, Karthikeyan (STFC,DL,HC) <
> karthikeyan.chockalingam at stfc.ac.uk>
> *Cc: *Barry Smith <bsmith at petsc.dev>, petsc-users at mcs.anl.gov <
> petsc-users at mcs.anl.gov>
> *Subject: *Re: [petsc-users] Union of sequential vecs
>
> If your space is pretty compact, eg, (0,12), you could create an MPI
> vector Q of size 13, say, and each processor can add 1.0 to Q[Vec[i]], for
> all "i" in my local "Vec".
>
> Then each processor can count the number of local nonzeros in Q, call it
> n, create a new vector, R, with local size n, then set R[i] = global index
> of the nonzero for each nonzero in Q, i=0:n.
>
> Do some sort of vec-scatter-to-all with R to get what you want.
>
>
>
> Does that work?
>
>
>
> Mark
>
>
>
>
>
> On Fri, Dec 9, 2022 at 3:25 PM Karthikeyan Chockalingam - STFC UKRI via
> petsc-users <petsc-users at mcs.anl.gov> wrote:
>
> That is where I am stuck, *I don’t know* who to combine them to get Vec =
> {2,5,7,8,10,11,12}.
>
> I just want them in an MPI vector.
>
>
>
> I finally plan to call VecScatterCreateToAll so that all processor gets a
> copy.
>
>
>
> Thank you.
>
>
>
> Kind regards,
>
> Karthik.
>
>
>
> *From: *Barry Smith <bsmith at petsc.dev>
> *Date: *Friday, 9 December 2022 at 20:04
> *To: *Chockalingam, Karthikeyan (STFC,DL,HC) <
> karthikeyan.chockalingam at stfc.ac.uk>
> *Cc: *petsc-users at mcs.anl.gov <petsc-users at mcs.anl.gov>
> *Subject: *Re: [petsc-users] Union of sequential vecs
>
>
>
>   How are you combining them to get Vec = {2,5,7,8,10,11,12}?
>
>
>
>   Do you want the values to remain on the same MPI rank as before, just in
> an MPI vector?
>
>
>
>
>
>
>
> On Dec 9, 2022, at 2:28 PM, Karthikeyan Chockalingam - STFC UKRI via
> petsc-users <petsc-users at mcs.anl.gov> wrote:
>
>
>
> Hi,
>
>
>
> I want to take the union of a set of sequential vectors, each living in a
> different processor.
>
>
>
> Say,
>
> Vec_Seq1 = {2,5,7}
>
> Vec_Seq2 = {5,8,10,11}
>
> Vec_Seq3 = {5,2,12}.
>
>
>
> Finally, get the union of all them Vec = {2,5,7,8,10,11,12}.
>
>
>
> I initially wanted to create a parallel vector and insert the (sequential
> vector) values but I do not know, to which index to insert the values to.
> But I do know the total size of Vec (which in this case is 7).
>
>
>
> Any help is much appreciated.
>
>
>
> Kind regards,
>
> Karthik.
>
>
>
>
>
>
>
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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/
> <http://www.cse.buffalo.edu/~knepley/>
>


-- 
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/ <http://www.cse.buffalo.edu/~knepley/>
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