[petsc-users] Modify matrix nonzero structure

Mon May 27 21:13:18 CDT 2024

  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!a-WLgSheyFC0FTQZJMgBXbqQiUtMfEJ-WXOnM0Xk_uUt-YMpC-sVyd0_nw778-iWSIz2bcFj6voBN0jevQdqDnE$ 
>> 
> 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!a-WLgSheyFC0FTQZJMgBXbqQiUtMfEJ-WXOnM0Xk_uUt-YMpC-sVyd0_nw778-iWSIz2bcFj6voBN0jeEw_ISG0$  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!a-WLgSheyFC0FTQZJMgBXbqQiUtMfEJ-WXOnM0Xk_uUt-YMpC-sVyd0_nw778-iWSIz2bcFj6voBN0jeEw_ISG0$  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> <mailto: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> <mailto: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 <mailto: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 <mailto: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 <mailto:a.croucher at auckland.ac.nz>
> tel: +64 (0)9 923 4611

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