[petsc-users] Union of sequential vecs

Mon Dec 12 09:00:43 CST 2022

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?

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

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<mailto:petsc-users at mcs.anl.gov>> wrote:
Thank you Mark and Barry.

@Mark Adams<mailto: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<mailto:mfadams at lbl.gov>>
Date: Friday, 9 December 2022 at 21:08
To: Chockalingam, Karthikeyan (STFC,DL,HC) <karthikeyan.chockalingam at stfc.ac.uk<mailto:karthikeyan.chockalingam at stfc.ac.uk>>
Cc: Barry Smith <bsmith at petsc.dev<mailto:bsmith at petsc.dev>>, petsc-users at mcs.anl.gov<mailto:petsc-users at mcs.anl.gov> <petsc-users at mcs.anl.gov<mailto: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<mailto: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<mailto:bsmith at petsc.dev>>
Date: Friday, 9 December 2022 at 20:04
To: Chockalingam, Karthikeyan (STFC,DL,HC) <karthikeyan.chockalingam at stfc.ac.uk<mailto:karthikeyan.chockalingam at stfc.ac.uk>>
Cc: petsc-users at mcs.anl.gov<mailto:petsc-users at mcs.anl.gov> <petsc-users at mcs.anl.gov<mailto: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<mailto: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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