[petsc-users] Modify matrix nonzero structure
Adrian Croucher
a.croucher at auckland.ac.nz
Tue May 28 18:45:47 CDT 2024
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.croucher at 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.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!bEqLWafwqHADoOBGkMAUu-5jnxuJg95froHeBJtxmkLCGFqP1MFGgnLKOgYILALF3hYWj_cgiKOh5rEeun-2sybwJhqMoBbg$
>>>>>
>>>> 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!bEqLWafwqHADoOBGkMAUu-5jnxuJg95froHeBJtxmkLCGFqP1MFGgnLKOgYILALF3hYWj_cgiKOh5rEeun-2sybwJvu9iBaG$ 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!bEqLWafwqHADoOBGkMAUu-5jnxuJg95froHeBJtxmkLCGFqP1MFGgnLKOgYILALF3hYWj_cgiKOh5rEeun-2sybwJvu9iBaG$ 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
>
--
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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