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 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
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  <body>
    <p>hi Barry,</p>
    <p>Thanks, that change has fixed the error on 2 ranks for me.</p>
    <p>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?</p>
    <p>- Adrian<br>
    </p>
    <div class="moz-cite-prefix">On 29/05/24 4:33 am, Barry Smith wrote:<br>
    </div>
    <blockquote type="cite" cite="mid:D11806DB-6C7E-4C9E-81B2-DBD125CB4A33@petsc.dev">
      
      <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 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>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" moz-do-not-send="true"><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!bEqLWafwqHADoOBGkMAUu-5jnxuJg95froHeBJtxmkLCGFqP1MFGgnLKOgYILALF3hYWj_cgiKOh5rEeun-2sybwJhqMoBbg$" moz-do-not-send="true" class="moz-txt-link-freetext">https://gitlab.com/petsc/petsc/-/merge_requests/7578</a>
                              <div><br>
                              </div>
                            </blockquote>
                            <p>Thanks very much, that does appear to fix
                              the bug when I run my test program in
                              serial.</p>
                            <p>If I run it on 2 processes, it is OK with
                              AIJ matrix type, but with BAIJ I get an
                              error (see below). Is there another
                              problem, or I am doing something else
                              wrong?</p>
                            <p>- Adrian<br>
                            </p>
                            <p>[0]PETSC ERROR: ---------------------
                              Error Message
                              --------------------------------------------------------------<br>
                              [0]PETSC ERROR: Petsc has generated
                              inconsistent data<br>
                              [0]PETSC ERROR: Incorrect colmap<br>
                              [0]PETSC ERROR: See <a class="moz-txt-link-freetext" href="https://urldefense.us/v3/__https://petsc.org/release/faq/__;!!G_uCfscf7eWS!bEqLWafwqHADoOBGkMAUu-5jnxuJg95froHeBJtxmkLCGFqP1MFGgnLKOgYILALF3hYWj_cgiKOh5rEeun-2sybwJvu9iBaG$" 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!bEqLWafwqHADoOBGkMAUu-5jnxuJg95froHeBJtxmkLCGFqP1MFGgnLKOgYILALF3hYWj_cgiKOh5rEeun-2sybwJvu9iBaG$" 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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!important; 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 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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