There was a bug in my fix for parallel which I have fixed. You will need to
git fetch
git checkout main
git branch -D barry/2024-05-27/fix-bug-baij-setvaluesblocked/release
git checkout barry/2024-05-27/fix-bug-baij-setvaluesblocked/release
I get the same results with your example with 1,2, and 3 ranks
> On May 28, 2024, at 7:45 PM, Adrian Croucher <a.crouc...@auckland.ac.nz>
> wrote:
>
> hi Barry,
>
> Thanks, that change has fixed the error on 2 ranks for me.
>
> When I run on 3 ranks, there is no error, but it doesn't actually add the
> extra values in to the matrix. Do you see that behaviour too?
>
> - Adrian
>
> On 29/05/24 4:33 am, Barry Smith wrote:
>>
>> Adrian,
>>
>> I could reproduce with 3 MPI ranks.
>>
>> Another error I had to fix. I also added a test example
>>
>> SInce I rebased the branch you will need to do something like
>>
>> git fetch
>> git checkout main
>> git branch -D barry/2024-05-27/fix-bug-baij-setvaluesblocked/release
>> git checkout barry/2024-05-27/fix-bug-baij-setvaluesblocked/release
>>
>> Thanks for your patience
>>
>> Barry
>>
>>
>>> On May 27, 2024, at 10:42 PM, Adrian Croucher <a.crouc...@auckland.ac.nz>
>>> <mailto:a.crouc...@auckland.ac.nz> wrote:
>>>
>>> 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.crouc...@auckland.ac.nz>
>>>>> <mailto:a.crouc...@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!dngbcXmJfofRckcEMElrf4BvXnHLnRh4FePsIwherUCHmsPBqTWSGvW36-62EUO3uDDIffqW8q9rei8toRdYLUY$
>>>>>>
>>>>>>
>>>>> 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!dngbcXmJfofRckcEMElrf4BvXnHLnRh4FePsIwherUCHmsPBqTWSGvW36-62EUO3uDDIffqW8q9rei8tCH9MbY4$
>>>>> 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!dngbcXmJfofRckcEMElrf4BvXnHLnRh4FePsIwherUCHmsPBqTWSGvW36-62EUO3uDDIffqW8q9rei8tCH9MbY4$
>>>>> 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.crouc...@auckland.ac.nz> <mailto:a.crouc...@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.crouc...@auckland.ac.nz> <mailto:a.crouc...@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.crouc...@auckland.ac.nz <mailto:a.crouc...@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.crouc...@auckland.ac.nz <mailto:a.crouc...@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.crouc...@auckland.ac.nz <mailto:a.crouc...@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.crouc...@auckland.ac.nz <mailto:a.crouc...@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.crouc...@auckland.ac.nz <mailto:a.crouc...@auckland.ac.nz>
> tel: +64 (0)9 923 4611
