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 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
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<meta http-equiv="content-type" content="text/html; charset=utf-8"></head><body style="overflow-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;"><div><br></div><div>   Adrian,</div><div><br></div>   I could reproduce with 3 MPI ranks.<div><br></div><div>   Another error I had to fix. I also added a test example </div><div><br></div><div>   SInce I rebased the branch you will need to do something like</div><div><br></div><div>   git fetch</div><div>   git checkout main</div><div>   git branch -D barry/2024-05-27/fix-bug-baij-setvaluesblocked/release</div><div>  git checkout barry/2024-05-27/fix-bug-baij-setvaluesblocked/release</div><div><br></div><div>  Thanks for your patience </div><div><br></div><div>   Barry</div><div><br><div><br><blockquote type="cite"><div>On May 27, 2024, at 10:42 PM, Adrian Croucher <a.croucher@auckland.ac.nz> wrote:</div><br class="Apple-interchange-newline"><div>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8">
  
  <div><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!doaVfskPKURsqYgA0bpocyW5cbPLsGwTjv41wqfhw_nlPc6a7scHMULs9UqHfAz74BFdHtbPJ-LBlRkYElrUKjE$" moz-do-not-send="true" class="moz-txt-link-freetext">https://gitlab.com/petsc/petsc/-/merge_requests/7578</a>
                  <div><br>
                  </div>
                </blockquote><p>Thanks very much, that does appear to fix the bug
                  when I run my test program in serial.</p><p>If I run it on 2 processes, it is OK with AIJ matrix
                  type, but with BAIJ I get an error (see below). Is
                  there another problem, or I am doing something else
                  wrong?</p><p>- Adrian<br>
                </p><p>[0]PETSC ERROR: --------------------- Error Message
                  --------------------------------------------------------------<br>
                  [0]PETSC ERROR: Petsc has generated inconsistent data<br>
                  [0]PETSC ERROR: Incorrect colmap<br>
                  [0]PETSC ERROR: See <a class="moz-txt-link-freetext" href="https://urldefense.us/v3/__https://petsc.org/release/faq/__;!!G_uCfscf7eWS!doaVfskPKURsqYgA0bpocyW5cbPLsGwTjv41wqfhw_nlPc6a7scHMULs9UqHfAz74BFdHtbPJ-LBlRkY0Lao4Fs$" 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!doaVfskPKURsqYgA0bpocyW5cbPLsGwTjv41wqfhw_nlPc6a7scHMULs9UqHfAz74BFdHtbPJ-LBlRkY0Lao4Fs$" 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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                                            Message Is From an External
                                            Sender</div>
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overscroll-behavior-block: unset !important; overscroll-behavior-inline: unset !important; overscroll-behavior: unset !important; padding-block: unset !important; padding: unset !important; padding-inline: unset !important; scroll-margin-block: unset !important; scroll-margin: unset !important; scroll-margin-inline: unset !important; scroll-padding-block: unset !important; scroll-padding: unset !important; scroll-padding-inline: unset !important; width: unset !important; margin-top: 2px !important;">This
                                            message came from outside
                                            your organization.</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

</pre>
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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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    <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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