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There was a bug in my fix for parallel which I have fixed. You will need to git fetch git checkout main git branch -D barry/2024-05-27/fix-bug-baij-setvaluesblocked/release git checkout 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> There was a bug in my fix for parallel which I have fixed. You will need to <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><br></div><div> I get the same results with your example with 1,2, and 3 ranks</div><div><br></div><div><br><blockquote type="cite"><div>On May 28, 2024, at 7:45 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,</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!dngbcXmJfofRckcEMElrf4BvXnHLnRh4FePsIwherUCHmsPBqTWSGvW36-62EUO3uDDIffqW8q9rei8toRdYLUY$" moz-do-not-send="true" class="moz-txt-link-freetext">https://gitlab.com/petsc/petsc/-/merge_requests/7578</a>
<div><br>
</div>
</blockquote><p>Thanks very much, that does appear to fix
the bug when I run my test program in
serial.</p><p>If I run it on 2 processes, it is OK with
AIJ matrix type, but with BAIJ I get an
error (see below). Is there another
problem, or I am doing something else
wrong?</p><p>- Adrian<br>
</p><p>[0]PETSC ERROR: ---------------------
Error Message
--------------------------------------------------------------<br>
[0]PETSC ERROR: Petsc has generated
inconsistent data<br>
[0]PETSC ERROR: Incorrect colmap<br>
[0]PETSC ERROR: See <a class="moz-txt-link-freetext" href="https://urldefense.us/v3/__https://petsc.org/release/faq/__;!!G_uCfscf7eWS!dngbcXmJfofRckcEMElrf4BvXnHLnRh4FePsIwherUCHmsPBqTWSGvW36-62EUO3uDDIffqW8q9rei8tCH9MbY4$" 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!dngbcXmJfofRckcEMElrf4BvXnHLnRh4FePsIwherUCHmsPBqTWSGvW36-62EUO3uDDIffqW8q9rei8tCH9MbY4$" 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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-webkit-box-flex-group: revert !important; -webkit-box-lines: revert !important; -webkit-box-ordinal-group: revert !important; -webkit-box-orient: revert !important; -webkit-box-pack: revert !important; -webkit-box-reflect: revert !important; -webkit-column-axis: revert !important; -webkit-column-progression: revert !important; -webkit-cursor-visibility: revert !important; -webkit-font-size-delta: revert !important; -webkit-hyphenate-limit-after: revert !important; -webkit-hyphenate-limit-before: revert !important; -webkit-hyphenate-limit-lines: revert !important; -webkit-initial-letter: revert !important; -webkit-line-align: revert !important; -webkit-line-box-contain: revert !important; -webkit-line-clamp: revert !important; -webkit-line-grid: revert !important; -webkit-line-snap: revert !important; -webkit-marquee-direction: revert !important; -webkit-marquee-increment: revert !important; -webkit-marquee-repetition: revert !important; -webkit-marquee-speed: revert !important; -webkit-marquee-style: revert !important; -webkit-nbsp-mode: revert !important; -webkit-rtl-ordering: revert !important; -webkit-text-decorations-in-effect: revert !important; -webkit-text-fill-color: revert !important; -webkit-text-security: revert !important; -webkit-text-stroke-color: revert !important; -webkit-text-stroke-width: revert !important; -webkit-user-drag: revert !important; -webkit-user-modify: revert !important; -webkit-user-select: revert !important; word-spacing: revert !important; backdrop-filter: revert !important; background-clip: revert !important; background-origin: revert !important; box-shadow: revert !important; mask-composite: revert !important; mask-mode: revert !important; text-combine-upright: revert !important; -webkit-backdrop-filter: revert !important; -webkit-background-clip: revert !important; -webkit-background-origin: revert !important; -webkit-box-shadow: revert !important; -webkit-mask: revert !important; -webkit-mask-composite: revert !important; -webkit-mask-source-type: revert !important; -webkit-text-combine: revert !important; display: block !important; visibility: revert !important; opacity: revert !important; background-color: rgb(208, 216, 220) !important; block-size: revert !important; border-block: revert !important; border-bottom-color: revert !important; border-bottom-style: revert !important; border-bottom-width: revert !important; border-end-end-radius: revert !important; border-end-start-radius: revert !important; border-inline: revert !important; border-left-color: revert !important; border-left-style: revert !important; border-left-width: revert !important; border-right-color: revert !important; border-right-style: revert !important; border-right-width: revert !important; border-start-end-radius: revert !important; border-start-start-radius: revert !important; inset: revert !important; contain-intrinsic-block-size: revert !important; contain-intrinsic-size: revert !important; contain-intrinsic-inline-size: revert !important; height: revert !important; inline-size: revert !important; inset-block: revert !important; inset-inline: revert !important; margin-block: revert !important; margin-inline: revert !important; max-block-size: revert !important; max-height: revert !important; max-inline-size: revert !important; max-width: revert !important; min-block-size: revert !important; min-height: revert !important; min-inline-size: revert !important; overscroll-behavior-block: revert !important; overscroll-behavior-inline: revert !important; overscroll-behavior: revert !important; padding-block: revert !important; padding-inline: revert !important; scroll-margin-block: revert !important; scroll-margin: revert !important; scroll-margin-inline: revert !important; scroll-padding-block: revert !important; scroll-padding: revert !important; scroll-padding-inline: revert !important; width: revert !important; margin: 16px 0px !important; padding: 8px 16px !important; border-radius: 4px !important; min-width: 200px !important; border-top-width: 4px !important; border-top-style: solid !important; border-top-color: rgb(144, 164, 174) !important;">
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text-align-last: unset !important; text-anchor: unset !important; text-box-edge: unset !important; text-box-trim: unset !important; text-decoration-color: unset !important; text-decoration: unset !important; text-decoration-skip-ink: unset !important; text-decoration-style: unset !important; text-decoration-thickness: unset !important; text-emphasis-color: unset !important; text-emphasis-position: unset !important; text-emphasis-style: unset !important; text-group-align: unset !important; text-indent: unset !important; text-justify: unset !important; text-overflow: unset !important; text-shadow: unset !important; text-transform: unset !important; text-underline-offset: unset !important; text-underline-position: unset !important; text-wrap: unset !important; touch-action: unset !important; transform: unset !important; transform-box: unset !important; transform-origin: unset !important; transform-style: unset !important; transition: unset !important; translate: unset !important; vector-effect: unset !important; 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-webkit-font-size-delta: unset !important; -webkit-hyphenate-limit-after: unset !important; -webkit-hyphenate-limit-before: unset !important; -webkit-hyphenate-limit-lines: unset !important; -webkit-initial-letter: unset !important; -webkit-line-align: unset !important; -webkit-line-box-contain: unset !important; -webkit-line-clamp: unset !important; -webkit-line-grid: unset !important; -webkit-line-snap: unset !important; -webkit-marquee-direction: unset !important; -webkit-marquee-increment: unset !important; -webkit-marquee-repetition: unset !important; -webkit-marquee-speed: unset !important; -webkit-marquee-style: unset !important; -webkit-nbsp-mode: unset !important; -webkit-rtl-ordering: unset !important; -webkit-text-decorations-in-effect: unset !important; -webkit-text-fill-color: unset !important; -webkit-text-security: unset !important; -webkit-text-stroke-color: unset !important; -webkit-text-stroke-width: unset !important; -webkit-user-drag: unset !important; -webkit-user-modify: unset !important; 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max-width: 600px !important;">
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-webkit-box-ordinal-group: unset !important; -webkit-box-orient: unset !important; -webkit-box-pack: unset !important; -webkit-box-reflect: unset !important; -webkit-column-axis: unset !important; -webkit-column-progression: unset !important; -webkit-cursor-visibility: unset !important; -webkit-hyphenate-limit-after: unset !important; -webkit-hyphenate-limit-before: unset !important; -webkit-hyphenate-limit-lines: unset !important; -webkit-initial-letter: unset !important; -webkit-line-align: unset !important; -webkit-line-box-contain: unset !important; -webkit-line-clamp: unset !important; -webkit-line-grid: unset !important; -webkit-line-snap: unset !important; -webkit-nbsp-mode: unset !important; -webkit-rtl-ordering: unset !important; -webkit-text-decorations-in-effect: unset !important; -webkit-text-fill-color: unset !important; -webkit-text-security: unset !important; -webkit-text-stroke-color: unset !important; -webkit-text-stroke-width: unset !important; -webkit-user-drag: unset !important; -webkit-user-modify: unset !important; -webkit-user-select: unset !important; word-spacing: unset !important; background-clip: unset !important; background-origin: unset !important; box-shadow: unset !important; mask-composite: unset !important; mask-mode: unset !important; text-combine-upright: unset !important; -webkit-backdrop-filter: unset !important; -webkit-background-clip: unset !important; -webkit-background-origin: unset !important; -webkit-box-shadow: unset !important; mask-size: unset !important; -webkit-mask: unset !important; -webkit-mask-composite: unset !important; -webkit-mask-source-type: unset !important; -webkit-text-combine: unset !important; display: block !important; visibility: visible !important; opacity: unset !important; background-color: rgb(208, 216, 220) !important; block-size: unset !important; border-block: unset !important; border-radius: unset !important; border-end-end-radius: unset !important; border-end-start-radius: unset !important; border-inline: unset !important; border-start-end-radius: unset !important; border-start-start-radius: unset !important; inset: unset !important; contain-intrinsic-block-size: unset !important; contain-intrinsic-size: unset !important; contain-intrinsic-inline-size: unset !important; height: unset !important; inline-size: unset !important; inset-block: unset !important; inset-inline: unset !important; margin-block: unset !important; margin: unset !important; margin-inline: unset !important; max-block-size: unset !important; max-height: unset !important; max-inline-size: unset !important; max-width: unset !important; min-block-size: unset !important; min-height: unset !important; min-inline-size: unset !important; min-width: unset !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;">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
</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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<br>
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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 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>
</div>
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</blockquote>
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<br>
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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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