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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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max-width: 600px !important;">
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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" href="mailto:a.croucher@auckland.ac.nz">a.croucher@auckland.ac.nz</a>
tel: +64 (0)9 923 4611</pre>
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