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 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@ auckland. ac. nz>
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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>  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.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>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!a-WLgSheyFC0FTQZJMgBXbqQiUtMfEJ-WXOnM0Xk_uUt-YMpC-sVyd0_nw778-iWSIz2bcFj6voBN0jevQdqDnE$" moz-do-not-send="true" class="moz-txt-link-freetext">https://gitlab.com/petsc/petsc/-/merge_requests/7578</a>
      <div><br>
      </div>
    </blockquote><p>Thanks very much, that does appear to fix the bug when I run my
      test program in serial.</p><p>If I run it on 2 processes, it is OK with AIJ matrix type, but
      with BAIJ I get an error (see below). Is there another problem, or
      I am doing something else wrong?</p><p>- Adrian<br>
    </p><p>[0]PETSC ERROR: --------------------- Error Message
      --------------------------------------------------------------<br>
      [0]PETSC ERROR: Petsc has generated inconsistent data<br>
      [0]PETSC ERROR: Incorrect colmap<br>
      [0]PETSC ERROR: See <a class="moz-txt-link-freetext" href="https://urldefense.us/v3/__https://petsc.org/release/faq/__;!!G_uCfscf7eWS!a-WLgSheyFC0FTQZJMgBXbqQiUtMfEJ-WXOnM0Xk_uUt-YMpC-sVyd0_nw778-iWSIz2bcFj6voBN0jeEw_ISG0$">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!a-WLgSheyFC0FTQZJMgBXbqQiUtMfEJ-WXOnM0Xk_uUt-YMpC-sVyd0_nw778-iWSIz2bcFj6voBN0jeEw_ISG0$">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"><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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ehavior-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
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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" href="mailto:a.croucher@auckland.ac.nz">a.croucher@auckland.ac.nz</a>
tel: +64 (0)9 923 4611</pre>
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