[petsc-users] Modify matrix nonzero structure

Adrian Croucher a.croucher at auckland.ac.nz
Mon May 27 21:42:23 CDT 2024 

Hmm, that's a bit weird. I haven't modified the test code - I checked 
the file date to make sure. I also tried deleting my PETSc build dir and 
rebuilding it, then rebuilding the test code. I still get the error if I 
run on 2 ranks with -dm_mat_type (or -mat_type) baij or mpibaij, but 
it's fine on aij or mpiaij.

My actual (non-test) code is however working ok now, in serial or 
parallel. So I don't think this should hold up merging your bugfix.

- Adrian

On 28/05/24 2:13 pm, Barry Smith wrote:
>   When I run the exact code you sent with two ranks and—mat_type 
> mpibaij, it runs as expected. If you modified the code in any way to 
> demonstrate the bug, please send the modified code.
>
>
>
>> On May 27, 2024, at 9:37 PM, Adrian Croucher 
>> <a.croucher at auckland.ac.nz> wrote:
>>
>> 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!dtDmIxQzHvnehLcuzdtJxWThxViUdu26r8fjum7PCvvKQp2PyZxpEZ0D1gvG1OsEvRs-sAisLmK-51Z7g4GONJEssSbd8xUJ$ 
>>>
>> 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!dtDmIxQzHvnehLcuzdtJxWThxViUdu26r8fjum7PCvvKQp2PyZxpEZ0D1gvG1OsEvRs-sAisLmK-51Z7g4GONJEssfaywInx$  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!dtDmIxQzHvnehLcuzdtJxWThxViUdu26r8fjum7PCvvKQp2PyZxpEZ0D1gvG1OsEvRs-sAisLmK-51Z7g4GONJEssfaywInx$  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
>
-- 
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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