[petsc-users] Local sizes when creating PETSC MatIS

[José Lorenzo]

I'm using PETSC 3.10 with 64 bits indices.

When I run valgrind I get the following message at the end of the report,
which I don't know how to interpret:

==399672== Invalid read of size 8
==399672==    at 0x5627D05: MatZeroEntries_SeqAIJ (aij.c:1077)
==399672==    by 0x5394A61: MatZeroEntries (matrix.c:5664)
==399672==    by 0x53DEF3F: MatZeroEntries_IS (matis.c:3064)
==399672==    by 0x5394A61: MatZeroEntries (matrix.c:5664)
==399672==    by 0x53B682C: matzeroentries_ (matrixf.c:1024)
==399672==    by 0x415C0B: parallmodule_mp_elementarymatrices_
(parallModule.F90:101)
==399672==    by 0x424C40: MAIN__ (main.F90:414)
==399672==    by 0x40303D: main (in /myproject/)
==399672==  Address 0x4c30 is not stack'd, malloc'd or (recently) free'd

El sáb., 15 jun. 2019 a las 3:58, Stefano Zampini (<
stefano.zampini at gmail.com>) escribió:

> This seems a problem related with your code, I suggest you to run valgrind.
> Which version of PETSc are you using?
>
>
> On Jun 14, 2019, at 3:12 PM, José Lorenzo <joslorgom at gmail.com> wrote:
>
> Following the PETSC examples, I was trying something like:
>
>   call ISLocalToGlobalMappingCreate(PETSC_COMM_WORLD, 1, nidx, idx_global,
> PETSC_COPY_VALUES, ltog, ierr)
>
>   call MatCreateIS(PETSC_COMM_WORLD, 1_ip, proedg(rank), proedg(rank),
> PETSC_DETERMINE, PETSC_DETERMINE, ltog, ltog, An, ierr)
>
>   call MatISSetPreallocation(An, d_nz, PETSC_NULL_INTEGER, o_nz,
> PETSC_NULL_INTEGER, ierr)
>
> with idx_global storing the global indices of both local and ghost edges,
> and proedg(rank) the number of edges at the current processor.
>
> The program crashes in the Preallocation subroutine:
>
> [0]PETSC ERROR: --------------------- Error Message
> --------------------------------------------------------------
> [0]PETSC ERROR: Argument out of range
> [0]PETSC ERROR: nnz cannot be less than 0: local row 4 value
> -7493980938351671286
> [0]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html
> for trouble shooting.
> [0]PETSC ERROR: #1 MatSeqAIJSetPreallocation_SeqAIJ() line 3670 in
> PETSC_DIR/src/mat/impls/aij/seq/aij.c
> [0]PETSC ERROR: #2 MatSeqAIJSetPreallocation() line 3646 in
> PETSC_DIR/src/mat/impls/aij/seq/aij.c
> [0]PETSC ERROR: #3 MatISSetPreallocation_IS() line 1795 in
> PETSC_DIR/src/mat/impls/is/matis.c
>
> And with your suggestion I get the same error during the preallocation
> step.
>
> Thank you.
>
>
> El vie., 14 jun. 2019 a las 14:24, Stefano Zampini (<
> stefano.zampini at gmail.com>) escribió:
>
>> Jose,
>>
>> The local size of the matrix (the one you use in MatSetSizes) tells Petsc
>> what is the size of the local portion of the vectors involved in matrix
>> vector products.
>> It has nothing to do with the size of the local Neumann problem needed by
>> MatIS. These are inferred from the local to global mapping of the degrees
>> of freedom
>> In your case, the  l2g object needs to map all the dofs that corresponds
>> to the local mesh to their global dof numbering (you can take a look here
>> https://epubs.siam.org/doi/abs/10.1137/15M1025785)
>>
>> MatCreate(comm,&A)
>> MatSetSizes(A,PETSC_DECIDE,PETSC_DECIDE,N,N)
>> MatSetType(A,MATIS)
>> MatSetLocalToGlobalMapping(A,l2g,l2g)// this creates the local Neumann
>> matrices
>>
>> For n = 1: number_of_local_elements
>>   Construct element matrix
>>   // you have two alternitives
>>   MatSetValuesLocal(A, // using local ordering of dofs
>>   //or MatSetValues(A, // using global ordering of dofs
>> end
>>
>> On Jun 14, 2019, at 5:09 AM, José Lorenzo via petsc-users <
>> petsc-users at mcs.anl.gov> wrote:
>>
>> I am working with Nedelec Finite Elements and using ghost vectors to
>> store the ghost values of the solution in the edges that do not belong to
>> current processor.
>>
>> Since I have a large contrast in material properties I would like to try
>> the PCBDDC preconditioner in PETSC. Apparently, my matrix needs to be of
>> type MatIS, but I don't get to understand how MatCreateIS would work in my
>> particular case, although I did have a look at mat/ex3.c and ksp/ex59.c
>>
>> I set the local size m to the number of edges in current processor, but I
>> do not know whether I should include the number of ghost edges. And for the
>> local size n should I use the total number of DOFs or proceed as with m?
>>
>>
>> Thanks,
>>
>> Jose
>>
>>
>>
>
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