[petsc-users] Modify matrix nonzero structure

Mon May 27 20:37:34 CDT 2024

hi Barry,

On 28/05/24 7:46 am, Barry Smith wrote:
>
>    Thanks for reporting this. It is a bug. I have a fixed branch 
> *barry/2024-05-27/fix-bug-baij-setvaluesblocked/release * and 
> associated merge request 
> https://urldefense.us/v3/__https://gitlab.com/petsc/petsc/-/merge_requests/7578__;!!G_uCfscf7eWS!e6Dvthc2K4dBRQ77JiOwCRZkPap2KZithO5HtDmQtF_1UGlC1EcRKJgoykBF54djkl1-_gepUhj95-78_S9dbu-68mw6cemp$ 
>
Thanks very much, that does appear to fix the bug when I run my test 
program in serial.

If I run it on 2 processes, it is OK with AIJ matrix type, but with BAIJ 
I get an error (see below). Is there another problem, or I am doing 
something else wrong?

- Adrian

[0]PETSC ERROR: --------------------- Error Message 
--------------------------------------------------------------
[0]PETSC ERROR: Petsc has generated inconsistent data
[0]PETSC ERROR: Incorrect colmap
[0]PETSC ERROR: See https://urldefense.us/v3/__https://petsc.org/release/faq/__;!!G_uCfscf7eWS!e6Dvthc2K4dBRQ77JiOwCRZkPap2KZithO5HtDmQtF_1UGlC1EcRKJgoykBF54djkl1-_gepUhj95-78_S9dbu-68p6qYDHU$  for trouble shooting.
[0]PETSC ERROR: Petsc Release Version 3.21.1, unknown
[0]PETSC ERROR: ./matmodify on a main-debug named EN438880 by acro018 
Tue May 28 13:33:46 2024
[0]PETSC ERROR: Configure options --with-x --download-hdf5 
--download-zlib --download-netcdf --download-pnetcdf --download-exodusii 
--download-triangle --download-ptscotch --download-chaco --download-hypre
[0]PETSC ERROR: #1 MatSetValuesBlocked_MPIBAIJ() at 
/home/acro018/software/PETSc/code/src/mat/impls/baij/mpi/mpibaij.c:448
[0]PETSC ERROR: #2 MatSetValuesBlocked() at 
/home/acro018/software/PETSc/code/src/mat/interface/matrix.c:2030
[0]PETSC ERROR: --------------------- Error Message 
--------------------------------------------------------------
[0]PETSC ERROR:   It appears a new error in the code was triggered after 
a previous error, possibly because:
[0]PETSC ERROR:   -  The first error was not properly handled via (for 
example) the use of
[0]PETSC ERROR:      PetscCall(TheFunctionThatErrors()); or
[0]PETSC ERROR:   -  The second error was triggered while handling the 
first error.
[0]PETSC ERROR:   Above is the traceback for the previous unhandled 
error, below the traceback for the next error
[0]PETSC ERROR:   ALL ERRORS in the PETSc libraries are fatal, you 
should add the appropriate error checking to the code
[0]PETSC ERROR: Petsc has generated inconsistent data
[0]PETSC ERROR: Incorrect colmap
[0]PETSC ERROR: See https://urldefense.us/v3/__https://petsc.org/release/faq/__;!!G_uCfscf7eWS!e6Dvthc2K4dBRQ77JiOwCRZkPap2KZithO5HtDmQtF_1UGlC1EcRKJgoykBF54djkl1-_gepUhj95-78_S9dbu-68p6qYDHU$  for trouble shooting.
[0]PETSC ERROR: Petsc Release Version 3.21.1, unknown
[0]PETSC ERROR: ./matmodify on a main-debug named EN438880 by acro018 
Tue May 28 13:33:46 2024
[0]PETSC ERROR: Configure options --with-x --download-hdf5 
--download-zlib --download-netcdf --download-pnetcdf --download-exodusii 
--download-triangle --download-ptscotch --download-chaco --download-hypre
[0]PETSC ERROR: #1 MatSetValuesBlocked_MPIBAIJ() at 
/home/acro018/software/PETSc/code/src/mat/impls/baij/mpi/mpibaij.c:448
[0]PETSC ERROR: #2 MatAssemblyEnd_MPIBAIJ() at 
/home/acro018/software/PETSc/code/src/mat/impls/baij/mpi/mpibaij.c:943
[0]PETSC ERROR: #3 MatAssemblyEnd() at 
/home/acro018/software/PETSc/code/src/mat/interface/matrix.c:5820
[0]PETSC ERROR: #4 matmodify.F90:40

>   Barry
>
>
>> On May 26, 2024, at 10:45 PM, Adrian Croucher 
>> <a.croucher at auckland.ac.nz> wrote:
>>
>> hi,
>>
>> I've been trying creating a matrix with DMCreateMatrix() and then 
>> adding extra blocks of nonzeros into it using MatSetValuesBlocked(), 
>> but getting some unexpected results if I set the matrix type to BAIJ. 
>> It seems to behave as expected if I use matrix type AIJ.
>>
>> I've attached a minimal example program. It reads in the DMPlex from 
>> file, sets up a section on it, creates a matrix (blocksize 2) and 
>> then inserts a single 2x2 block at global block indices (0,7). It 
>> views the matrix before and after the insertion.
>>
>> If I run with "-dm_mat_type aij" it gives the expected results, but 
>> with "-dm_mat_type baij" it doesn't - e.g. if run in serial, it adds 
>> the new nonzeros in the right place but also adds a whole lot of 
>> other duplicated entries in block row 0.
>>
>> Is there something I'm not understanding about BAIJ, or about 
>> MatSetValuesBlocked()? or possibly some other mistake?
>>
>> - Adrian
>>
>> On 20/05/24 12:24 pm, Barry Smith wrote:
>>>
>>>    You can call MatSetOption(mat,MAT_NEW_NONZERO_LOCATION_ERR) then 
>>> insert the new values. If it is just a handful of new insertions the 
>>> extra time should be small.
>>>
>>>     Making a copy of the matrix won't give you a new matrix that is 
>>> any faster to insert into so best to just use the same matrix.
>>>
>>>   Barry
>>>
>>>
>>>> On May 19, 2024, at 7:44 PM, Adrian Croucher 
>>>> <a.croucher at auckland.ac.nz> wrote:
>>>>
>>>> This Message Is From an External Sender
>>>> This message came from outside your organization.
>>>> hi,
>>>>
>>>> I have a Jacobian matrix created using DMCreateMatrix(). What would be
>>>> the best way to add extra nonzero entries into it?
>>>>
>>>> I'm guessing that DMCreateMatrix() allocates the storage so the nonzero
>>>> structure can't really be easily modified. Would it be a case of
>>>> creating a new matrix, copying the nonzero entries from the original one
>>>> and then adding the extra ones, before calling MatSetUp() or similar? If
>>>> so, how exactly would you copy the nonzero structure from the original
>>>> matrix?
>>>>
>>>> Background: the flow problem I'm solving (on a DMPlex with finite volume
>>>> method) has complex source terms that depend on the solution (e.g.
>>>> pressure), and can also depend on other source terms. A simple example
>>>> is when fluid is extracted from one location, with a pressure-dependent
>>>> flow rate, and some of it is then reinjected in another location. This
>>>> can result in poor nonlinear solver convergence. I think the reason is
>>>> that there are effectively missing Jacobian entries in the row for the
>>>> reinjection cell, which should have an additional dependence on the
>>>> solution in the cell where fluid is extracted.
>>>>
>>>> - Adrian
>>>>
>>>> -- 
>>>> Dr Adrian Croucher
>>>> Senior Research Fellow
>>>> Department of Engineering Science
>>>> Waipapa Taumata Rau / University of Auckland, New Zealand
>>>> email:a.croucher at auckland.ac.nz
>>>> tel: +64 (0)9 923 4611
>>>>
>>>>
>>>
>> -- 
>> Dr Adrian Croucher
>> Senior Research Fellow
>> Department of Engineering Science
>> Waipapa Taumata Rau / University of Auckland, New Zealand
>> email:a.croucher at auckland.ac.nz
>> tel: +64 (0)9 923 4611
>> <3x3grid.exo><matmodify.F90>
>
-- 
Dr Adrian Croucher
Senior Research Fellow
Department of Engineering Science
Waipapa Taumata Rau / University of Auckland, New Zealand
email:a.croucher at auckland.ac.nz
tel: +64 (0)9 923 4611
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