[petsc-users] Local and global size of IS
Eda Oktay
eda.oktay at metu.edu.tr
Tue Apr 2 05:54:38 CDT 2019
Hi Barry,
I did what you said but now I get the error in ISSetPermutation that index
set is not a permutation. ı think it is because since I selected indices on
each process as you said. I did the following, did I understand you wrong:
PetscMPIInt rank,size;
MPI_Comm_rank(PETSC_COMM_WORLD, &rank);
MPI_Comm_size(PETSC_COMM_WORLD, &size);
PetscInt *idxx,ss;
ss = siz/size;
PetscMalloc1(ss,&idxx);
if (rank != size-1) {
j =0;
for (i=rank*ss; i<(rank+1)*ss; i++) {
idxx[j] = idx[i];
j++;
}
} else {
j =0;
for (i=rank*ss; i<siz; i++) {
idxx[j] = idx[i];
j++;
}
}
Smith, Barry F. <bsmith at mcs.anl.gov>, 31 Mar 2019 Paz, 01:47 tarihinde şunu
yazdı:
>
>
> > On Mar 27, 2019, at 7:33 AM, Eda Oktay via petsc-users <
> petsc-users at mcs.anl.gov> wrote:
> >
> > Hello,
> >
> > I am trying to permute a matrix A(of size 2n*2n) according to a sorted
> eigenvector vr (of size 2n) in parallel using 2 processors (processor
> number can change).
>
> I don't understand your rational for wanting to permute the matrix
> rows/columns based on a sorted eigenvector?
>
> > However, I get an error in MatPermute line stating that arguments are
> out of range and a new nonzero caused a malloc even if I used MatSetOption.
> >
> > I discovered that this may be because of the unequality of local sizes
> of is (and newIS) and local size of A.
> >
> > Since I allocate index set idx according to size of the vector vr,
> global size of is becomes 2n and the local size is also 2n (I think it
> should be n since both A and vr has local sizes n because of the number of
> processors). If I change the size of idx, then because of VecGetArrayRead,
> I think is is created wrongly.
> >
> > So, how can I make both global and local sizes of is,newIS and A?
> >
> > Below, you can see the part of my program.
> >
> > Thanks,
> >
> > Eda
> >
> > ierr = VecGetSize(vr,&siz);CHKERRQ(ierr);
> > ierr = PetscMalloc1(siz,&idx);CHKERRQ(ierr);
> > for (i=0; i<siz;i++) idx[i] = i;
>
> VecGetArray only gives you access to the local portion of the vector,
> not the entire vector so you cannot do the next two lines of code
> > ierr = VecGetArrayRead(vr,&avr);CHKERRQ(ierr);
>
> The sort routine is sequential; it knows nothing about parallelism so
> each process is just sorting its part. Hence this code won't work as
> expected
>
> > ierr = PetscSortRealWithPermutation(siz,avr,idx);CHKERRQ(ierr);
>
> If you need to sort the parallel vector and get the entire permutation
> then you need to do the following
>
> 1) communicate the entire vector to each process, you can use
> VecScatterCreateToAll() for this
> 2) call VecGetArray on the new vector (that contains all entries on each
> process)
> 3) Call PetscSortRealWithPermutation() on the entire vector on each
> process
> 4) select out a piece of the resulting indices idx on each process; for
> example with two processes I think rank = 0 would get the first half of the
> idx and rank = 1 would get the second half.
> >
> > ierr =
> ISCreateGeneral(PETSC_COMM_SELF,siz,idx,PETSC_COPY_VALUES,&is);CHKERRQ(ierr);
>
> > ierr = ISSetPermutation(is);CHKERRQ(ierr);
>
> You don't need to duplicate the is, just pass it in twice.
>
> > ierr = ISDuplicate(is,&newIS);CHKERRQ(ierr);
>
> You should definitely not need the next line. The A matrix is untouched
> by the subroutine call so you don't need to change its allocation options
>
> >
> MatSetOption(A,MAT_NEW_NONZERO_ALLOCATION_ERR,PETSC_FALSE);CHKERRQ(ierr);
> > ierr = MatPermute(A,is,newIS,&PL);CHKERRQ(ierr);
>
>
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