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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
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<p>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.</p>
<p>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.<br>
</p>
<p>- Adrian<br>
</p>
<div class="moz-cite-prefix">On 28/05/24 2:13 pm, Barry Smith wrote:<br>
</div>
<blockquote type="cite" cite="mid:E0FD4003-FD1F-4153-B255-E31CD7E09204@petsc.dev">
<div> 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.</div>
<div><br>
</div>
<div><br id="lineBreakAtBeginningOfMessage">
<div><br>
<blockquote type="cite">
<div>On May 27, 2024, at 9:37 PM, Adrian Croucher
<a class="moz-txt-link-rfc2396E" href="mailto:a.croucher@auckland.ac.nz"><a.croucher@auckland.ac.nz></a> wrote:</div>
<br class="Apple-interchange-newline">
<div>
<div>
<p>hi Barry,<br>
</p>
<div class="moz-cite-prefix">On 28/05/24 7:46 am, Barry
Smith wrote:<br>
</div>
<blockquote type="cite" cite="mid:7C12E83C-CE60-4DEF-8999-ADD22D09A69D@petsc.dev">
<div><br>
</div>
Thanks for reporting this. It is a bug. I have a
fixed branch <b style="color: rgb(200, 20, 201); font-family: Menlo; font-size: 14px;">barry/2024-05-27/fix-bug-baij-setvaluesblocked/release </b> and
associated merge request <a href="https://urldefense.us/v3/__https://gitlab.com/petsc/petsc/-/merge_requests/7578__;!!G_uCfscf7eWS!dtDmIxQzHvnehLcuzdtJxWThxViUdu26r8fjum7PCvvKQp2PyZxpEZ0D1gvG1OsEvRs-sAisLmK-51Z7g4GONJEssSbd8xUJ$" moz-do-not-send="true" class="moz-txt-link-freetext">https://gitlab.com/petsc/petsc/-/merge_requests/7578</a>
<div><br>
</div>
</blockquote>
<p>Thanks very much, that does appear to fix the bug
when I run my test program in serial.</p>
<p>If I run it on 2 processes, it is OK with AIJ matrix
type, but with BAIJ I get an error (see below). Is
there another problem, or I am doing something else
wrong?</p>
<p>- Adrian<br>
</p>
<p>[0]PETSC ERROR: --------------------- Error Message
--------------------------------------------------------------<br>
[0]PETSC ERROR: Petsc has generated inconsistent data<br>
[0]PETSC ERROR: Incorrect colmap<br>
[0]PETSC ERROR: See <a class="moz-txt-link-freetext" href="https://urldefense.us/v3/__https://petsc.org/release/faq/__;!!G_uCfscf7eWS!dtDmIxQzHvnehLcuzdtJxWThxViUdu26r8fjum7PCvvKQp2PyZxpEZ0D1gvG1OsEvRs-sAisLmK-51Z7g4GONJEssfaywInx$" moz-do-not-send="true">https://petsc.org/release/faq/</a>
for trouble shooting.<br>
[0]PETSC ERROR: Petsc Release Version 3.21.1, unknown
<br>
[0]PETSC ERROR: ./matmodify on a main-debug named
EN438880 by acro018 Tue May 28 13:33:46 2024<br>
[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<br>
[0]PETSC ERROR: #1 MatSetValuesBlocked_MPIBAIJ() at
/home/acro018/software/PETSc/code/src/mat/impls/baij/mpi/mpibaij.c:448<br>
[0]PETSC ERROR: #2 MatSetValuesBlocked() at
/home/acro018/software/PETSc/code/src/mat/interface/matrix.c:2030<br>
[0]PETSC ERROR: --------------------- Error Message
--------------------------------------------------------------<br>
[0]PETSC ERROR: It appears a new error in the code
was triggered after a previous error, possibly
because:<br>
[0]PETSC ERROR: - The first error was not properly
handled via (for example) the use of<br>
[0]PETSC ERROR:
PetscCall(TheFunctionThatErrors()); or<br>
[0]PETSC ERROR: - The second error was triggered
while handling the first error.<br>
[0]PETSC ERROR: Above is the traceback for the
previous unhandled error, below the traceback for the
next error<br>
[0]PETSC ERROR: ALL ERRORS in the PETSc libraries
are fatal, you should add the appropriate error
checking to the code<br>
[0]PETSC ERROR: Petsc has generated inconsistent data<br>
[0]PETSC ERROR: Incorrect colmap<br>
[0]PETSC ERROR: See <a class="moz-txt-link-freetext" href="https://urldefense.us/v3/__https://petsc.org/release/faq/__;!!G_uCfscf7eWS!dtDmIxQzHvnehLcuzdtJxWThxViUdu26r8fjum7PCvvKQp2PyZxpEZ0D1gvG1OsEvRs-sAisLmK-51Z7g4GONJEssfaywInx$" moz-do-not-send="true">https://petsc.org/release/faq/</a>
for trouble shooting.<br>
[0]PETSC ERROR: Petsc Release Version 3.21.1, unknown
<br>
[0]PETSC ERROR: ./matmodify on a main-debug named
EN438880 by acro018 Tue May 28 13:33:46 2024<br>
[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<br>
[0]PETSC ERROR: #1 MatSetValuesBlocked_MPIBAIJ() at
/home/acro018/software/PETSc/code/src/mat/impls/baij/mpi/mpibaij.c:448<br>
[0]PETSC ERROR: #2 MatAssemblyEnd_MPIBAIJ() at
/home/acro018/software/PETSc/code/src/mat/impls/baij/mpi/mpibaij.c:943<br>
[0]PETSC ERROR: #3 MatAssemblyEnd() at
/home/acro018/software/PETSc/code/src/mat/interface/matrix.c:5820<br>
[0]PETSC ERROR: #4 matmodify.F90:40<br>
</p>
<p><br>
</p>
<blockquote type="cite" cite="mid:7C12E83C-CE60-4DEF-8999-ADD22D09A69D@petsc.dev">
<div> Barry</div>
<div><br>
<div><br>
<blockquote type="cite">
<div>On May 26, 2024, at 10:45 PM, Adrian
Croucher <a class="moz-txt-link-rfc2396E" href="mailto:a.croucher@auckland.ac.nz" moz-do-not-send="true"><a.croucher@auckland.ac.nz></a>
wrote:</div>
<br class="Apple-interchange-newline">
<div>
<div>
<p>hi,</p>
<p>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.</p>
<p>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.<br>
</p>
<p>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.<br>
</p>
<p>Is there something I'm not understanding
about BAIJ, or about
MatSetValuesBlocked()? or possibly some
other mistake?<br>
</p>
<p>- Adrian<br>
</p>
<div class="moz-cite-prefix">On 20/05/24
12:24 pm, Barry Smith wrote:<br>
</div>
<blockquote type="cite" cite="mid:4368DA96-759E-4831-8BCF-710F265A4728@petsc.dev">
<div><br>
</div>
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.
<div><br>
</div>
<div> 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.</div>
<div><br>
</div>
<div> Barry</div>
<div><br id="lineBreakAtBeginningOfMessage">
<div><br>
<blockquote type="cite">
<div>On May 19, 2024, at 7:44 PM,
Adrian Croucher <a class="moz-txt-link-rfc2396E" href="mailto:a.croucher@auckland.ac.nz" moz-do-not-send="true"><a.croucher@auckland.ac.nz></a>
wrote:</div>
<br class="Apple-interchange-newline">
<div>
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scroll-margin-inline: unset !important; scroll-padding-block: unset !important; scroll-padding: unset !important; scroll-padding-inline: unset !important; width: unset !important;">This
Message Is From an External
Sender</div>
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<pre style="caret-color: rgb(0, 0, 0); font-size: 18px; font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; font-family: sans-serif; white-space: pre-wrap; overflow-wrap: break-word;">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 href="mailto:a.croucher@auckland.ac.nz" moz-do-not-send="true" class="moz-txt-link-freetext">a.croucher@auckland.ac.nz</a>
tel: +64 (0)9 923 4611
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<pre class="moz-signature" cols="72">--
Dr Adrian Croucher
Senior Research Fellow
Department of Engineering Science
Waipapa Taumata Rau / University of Auckland, New Zealand
email: <a class="moz-txt-link-abbreviated moz-txt-link-freetext" href="mailto:a.croucher@auckland.ac.nz" moz-do-not-send="true">a.croucher@auckland.ac.nz</a>
tel: +64 (0)9 923 4611</pre>
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<span id="cid:5C5BDD81-E016-4C86-A345-FBE276CEAD22"><3x3grid.exo></span><span id="cid:E2D65CD8-6EFF-4063-A2F0-2CC0FD711C52"><matmodify.F90></span></div>
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<pre class="moz-signature" cols="72">--
Dr Adrian Croucher
Senior Research Fellow
Department of Engineering Science
Waipapa Taumata Rau / University of Auckland, New Zealand
email: <a class="moz-txt-link-abbreviated moz-txt-link-freetext" href="mailto:a.croucher@auckland.ac.nz" moz-do-not-send="true">a.croucher@auckland.ac.nz</a>
tel: +64 (0)9 923 4611</pre>
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</blockquote>
<pre class="moz-signature" cols="72">--
Dr Adrian Croucher
Senior Research Fellow
Department of Engineering Science
Waipapa Taumata Rau / University of Auckland, New Zealand
email: <a class="moz-txt-link-abbreviated" href="mailto:a.croucher@auckland.ac.nz">a.croucher@auckland.ac.nz</a>
tel: +64 (0)9 923 4611</pre>
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