Thanks again Barry, it's working fine for me now too.
- Adrian
On 29/05/24 1:27 pm, Barry Smith wrote:
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> 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> 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!dyTRr3EmobjcjKs0kzURm7EjPlyR-L6yBosZe_dky8HADNvWRJjBCsqt6Quq20DTsiHcW255AIkxd7mdGIssOXoFXVK_OG1L$
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!dyTRr3EmobjcjKs0kzURm7EjPlyR-L6yBosZe_dky8HADNvWRJjBCsqt6Quq20DTsiHcW255AIkxd7mdGIssOXoFXe8LPGgS$ 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!dyTRr3EmobjcjKs0kzURm7EjPlyR-L6yBosZe_dky8HADNvWRJjBCsqt6Quq20DTsiHcW255AIkxd7mdGIssOXoFXe8LPGgS$ 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> 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> 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
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
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
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
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
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
tel: +64 (0)9 923 4611
