[petsc-users] Insert values into matrix using MatSetValuesStencil
Timothée Nicolas
timothee.nicolas at gmail.com
Wed Sep 23 04:25:06 CDT 2015
Hum, sorry, I don't know. I asked you to provide the definitions of start
and end values of i,j,k, because I was concerned whether you may mess up
the boundaries. Especially because you seem to treat x differently from y
and z. You have the problem also on only 1 process ?
2015-09-23 18:13 GMT+09:00 TAY wee-beng <zonexo at gmail.com>:
> Hi Timothée,
>
> Maybe I can send you part of it 1st. I'm trying to pinpoint why my matrix
> using MatView shows zero for a lot of the values
>
> For i=1,j=1,k=1,
>
> It should be :
>
> Mat Object: 1 MPI processes
> type: seqaij
> row 0: (0, 2) (12, -2)
>
> but now it's:
>
> row 0: (0, 0) (1, 0) (2, 0) (3, 0) (4, 0) (5, 0) (6, 0) (7, 0) (8,
> 0) (12, 0) (13, 0) (14, 0) (24, 0) (25, 0) (26, 0) (96, 0) (97, 0)
> (98, 0) (192, 0) (193, 0) (194, 0)
>
> I used:
>
> *call
> DMDACreate3d(MPI_COMM_WORLD,DM_BOUNDARY_NONE,DM_BOUNDARY_NONE,DM_BOUNDARY_NONE,DMDA_STENCIL_STAR,size_x,size_y,&*
>
>
> *size_z,1,PETSC_DECIDE,PETSC_DECIDE,3,stencil_width,lx,PETSC_NULL_INTEGER,PETSC_NULL_INTEGER,da_uvw_ast,ierr)*
>
> *call DMSetMatType(da_uvw_ast,MATAIJ,ierr)*
>
> * call DMCreateMatrix(da_uvw_ast,A_semi_xyz,ierr)*
>
> * call MatSetFromOptions(A_semi_xyz,ierr)*
>
> *i = 1, j = 1, k = 1*
>
> *row(MatStencil_i,1) = i - 1*
>
> * row(MatStencil_j,1) = j - 1*
>
> * row(MatStencil_k,1) = k - 1*
>
> * row(MatStencil_c,1) = 0*
>
> * col(MatStencil_i,1) = i - 1*
>
> * col(MatStencil_j,1) = j - 1*
>
> * col(MatStencil_k,1) = k - 1*
>
> * col(MatStencil_c,1) = 0*
>
> * value_insert(1) = 2.*
>
> * call
> MatSetValuesStencil(A_mat,ione,row,ione,col(:,1),value_insert(1),INSERT_VALUES,ierr)*
>
> * col(MatStencil_i,2) = i - 1 !north*
>
> * col(MatStencil_j,2) = j + 1 - 1*
>
> * col(MatStencil_k,2) = k - 1*
>
> * col(MatStencil_c,2) = 0*
>
> * value_insert(2) = -2.*
>
> * call
> MatSetValuesStencil(A_mat,ione,row,ione,col(:,2),value_insert(2),INSERT_VALUES,ierr)*
>
> Thank you
>
> Yours sincerely,
>
> TAY wee-beng
>
> On 23/9/2015 4:45 PM, Timothée Nicolas wrote:
>
> Yes, I had understood that, I am doing the same, but with 8 dof. This does
> not change the declaration for row and col.
>
> Can you send (i) the commands you use to create the DMDA, (ii) the
> commands to create the matrix and (iii) those for the definitions of
> ksta2,kend2,jsta2,jend2,size_x ?
>
> Timothée
>
> 2015-09-23 17:37 GMT+09:00 TAY wee-beng <zonexo at gmail.com>:
>
>> Hi Timothée,
>>
>> The matrix is created with 3 dof - u,v,w. So for each i,j,k, there are 3
>> values. Actually I got 3 eqns from the u,v,w momentum eqns. They are not
>> coupled together so I can also solve them individually. But I was told it's
>> faster to group them together. The global indices is something like this:
>>
>> i, j, k, ijk global indices, dof
>> 1 1 1 1 u
>> 1 1 1 2 v
>> 1 1 1 3 w
>> 2 1 1 4 u
>>
>> ...
>>
>> Hope it's clearer now.
>>
>> Ok, I changed the stencil, it's now working.
>>
>> Thank you
>>
>> Yours sincerely,
>>
>> TAY wee-beng
>>
>> On 23/9/2015 4:22 PM, Timothée Nicolas wrote:
>>
>> Can you also tell how you created the matrix ? Just in case you created
>> it with the 1 dof DMDA, it would not work if you try to input values at
>> places where it is not allocated (which could explain the error message)
>>
>> 2015-09-23 17:18 GMT+09:00 Timothée Nicolas <
>> <timothee.nicolas at gmail.com>timothee.nicolas at gmail.com>:
>>
>>> The first thing that strikes me is your definition of the stencils
>>>
>>> *MatStencil :: row(6,1),col(6,7)*
>>>
>>> Why is it not defined with
>>>
>>> *MatStencil :: row(4,1),col(4,7)*
>>>
>>> instead ?
>>>
>>> Where does the 6 come from ?
>>>
>>> Timothée
>>>
>>>
>>> 2015-09-23 17:14 GMT+09:00 TAY wee-beng < <zonexo at gmail.com>
>>> zonexo at gmail.com>:
>>>
>>>> Hi,
>>>>
>>>> I have successfully used MatSetValuesStencil to insert values into a
>>>> Poisson eqn matrix which has 1 DOF (pressure). Now I'm trying to insert
>>>> values in a momentum eqn matrix which has 3 DOF (u,v,w)
>>>>
>>>> However, I got the error:
>>>>
>>>> *[0]PETSC ERROR: --------------------- Error Message
>>>> ----------------------------*
>>>> *----------------------------------*
>>>> *[0]PETSC ERROR: Argument out of range*
>>>> *[0]PETSC ERROR: Inserting a new nonzero at (111,5) in the matrix*
>>>> *[0]PETSC ERROR: See
>>>> http://www.mcs.anl.gov/petsc/documentation/faq.html
>>>> <http://www.mcs.anl.gov/petsc/documentation/faq.html> for trou*
>>>> *ble shooting.*
>>>>
>>>> I wonder what's wrong. For the momentum eqn, for each DOF, at at node
>>>> (dof,i,j,k), I have coupling i +/- 1, j +/- 1 and k +/- 1.
>>>>
>>>> The error happens at 111,5, which corresponds to i = 2, j = 2, k = 2,
>>>> which is an internal node.
>>>>
>>>> Here's part of my code below. Hope someone can help. Thanks!
>>>>
>>>> *PetscScalar :: value_insert(7)*
>>>>
>>>> *MatStencil :: row(6,1),col(6,7)*
>>>>
>>>> *ione = 1; iseven = 7*
>>>>
>>>> *if (cell_type == 'u') then*
>>>>
>>>> * offset = 1*
>>>>
>>>> *else if (cell_type == 'v') then*
>>>>
>>>> * offset = 2*
>>>>
>>>> *else if (cell_type == 'w') then*
>>>>
>>>> * offset = 3*
>>>>
>>>> *end if*
>>>>
>>>> *do k=ksta2,kend2*
>>>>
>>>> * do j = jsta2,jend2*
>>>>
>>>> * do i=2,size_x-1*
>>>>
>>>> * row(MatStencil_i,1) = i - 1*
>>>>
>>>> * row(MatStencil_j,1) = j - 1*
>>>>
>>>> * row(MatStencil_k,1) = k - 1*
>>>>
>>>> * row(MatStencil_c,1) = offset - 1*
>>>>
>>>> * value_insert = 0.d0*
>>>>
>>>> * col(MatStencil_i,3) = i + 1 - 1 !east*
>>>>
>>>> * col(MatStencil_j,3) = j - 1*
>>>>
>>>> * col(MatStencil_k,3) = k - 1*
>>>>
>>>> * col(MatStencil_c,3) = offset - 1*
>>>>
>>>> * value_insert(3) = -(
>>>> 1./(cell_x(i)%pd_E+cell_x(i+1)%pd_W))*(c_yz(j,k)%fc_E)*inv_Re*
>>>>
>>>> * col(MatStencil_i,5) = i - 1 - 1 !west*
>>>>
>>>> * col(MatStencil_j,5) = j - 1*
>>>>
>>>> * col(MatStencil_k,5) = k - 1*
>>>>
>>>> * col(MatStencil_c,5) = offset - 1*
>>>>
>>>> * value_insert(5) = -(
>>>> 1./(cell_x(i)%pd_W+cell_x(i-1)%pd_E))*(c_yz(j,k)%fc_E)*inv_Re*
>>>>
>>>> * col(MatStencil_i,2) = i - 1 !north*
>>>>
>>>> * col(MatStencil_j,2) = j + 1 - 1*
>>>>
>>>> * col(MatStencil_k,2) = k - 1*
>>>>
>>>> * col(MatStencil_c,2) = offset - 1*
>>>>
>>>> * value_insert(2) = -(
>>>> 1./(cell_y(j)%pd_N+cell_y(j+1)%pd_S))*(c_zx(i,k)%fc_N)*inv_Re*
>>>>
>>>> * col(MatStencil_i,4) = i - 1 !south*
>>>>
>>>> * col(MatStencil_j,4) = j - 1 - 1*
>>>>
>>>> * col(MatStencil_k,4) = k - 1*
>>>>
>>>> * col(MatStencil_c,4) = offset - 1*
>>>>
>>>> * value_insert(4) = -(
>>>> 1./(cell_y(j)%pd_S+cell_y(j-1)%pd_N))*(c_zx(i,k)%fc_N)*inv_Re*
>>>>
>>>> * col(MatStencil_i,6) = i - 1 !front*
>>>>
>>>> * col(MatStencil_j,6) = j - 1*
>>>>
>>>> * col(MatStencil_k,6) = k + 1 - 1*
>>>>
>>>> * col(MatStencil_c,6) = offset - 1*
>>>>
>>>> * value_insert(6) = -(
>>>> 1./(cell_z(k)%pd_F+cell_z(k+1)%pd_B))*(c_xy(i,j)%fc_F)*inv_Re*
>>>>
>>>> * col(MatStencil_i,7) = i - 1 !back*
>>>>
>>>> * col(MatStencil_j,7) = j - 1*
>>>>
>>>> * col(MatStencil_k,7) = k - 1 - 1*
>>>>
>>>> * col(MatStencil_c,7) = offset - 1*
>>>>
>>>> * value_insert(7) = -(
>>>> 1./(cell_z(k)%pd_B+cell_z(k-1)%pd_F))*(c_xy(i,j)%fc_F)*inv_Re*
>>>>
>>>> * col(MatStencil_i,1) = i - 1*
>>>>
>>>> * col(MatStencil_j,1) = j - 1*
>>>>
>>>> * col(MatStencil_k,1) = k - 1*
>>>>
>>>> * col(MatStencil_c,1) = offset - 1*
>>>>
>>>> * value_insert(1) = 2.*c(i,j,k)%vol/del_t -
>>>> (value_insert(2)+value_insert(3)+value_insert(4)+value_insert(5)+value_insert(6)+value_insert(7))*
>>>>
>>>> * call
>>>> MatSetValuesStencil(A_semi_xyz,ione,row,iseven,col,value_insert,INSERT_VALUES,ierr)*
>>>>
>>>> * end do*
>>>>
>>>> * end do*
>>>>
>>>> *end do *
>>>>
>>>> Thank you
>>>>
>>>> Yours sincerely,
>>>>
>>>> TAY wee-beng
>>>>
>>>>
>>>>
>>>
>>
>>
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.mcs.anl.gov/pipermail/petsc-users/attachments/20150923/f1b00ce5/attachment-0001.html>
More information about the petsc-users
mailing list