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<p>The code I am using here is the example 42 of PETSc
(<a class="moz-txt-link-freetext" href="https://www.mcs.anl.gov/petsc/petsc-3.9/src/ksp/ksp/examples/tutorials/ex42.c.html">https://www.mcs.anl.gov/petsc/petsc-3.9/src/ksp/ksp/examples/tutorials/ex42.c.html</a>).
Indeed it solves the Stokes equation. I thought it was a good idea
to use an example you might know (and didn't find any that uses
GAMG functions). I just changed the PCMG setup so that the memory
problem appears. And it appears when adding PCGAMG.</p>
<p>I don't care about the performance or even the result rightness
here, but only about the difference in memory use between 3.6 and
3.10. Do you think finding a more adapted script would help?<br>
</p>
<p>I used the threshold of 0.1 only once, at the beginning, to test
its influence. I used the default threshold (of 0, I guess) for
all the other runs.</p>
<p>Myriam<br>
</p>
<br>
<div class="moz-cite-prefix">Le 03/11/19 à 13:52, Mark Adams a
écrit :<br>
</div>
<blockquote type="cite"
cite="mid:CADOhEh7u95=X8wHuaVhUXTK=Kj62Jm+COJOdPfTyXB_ycvQcZA@mail.gmail.com">
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<div dir="ltr">
<div dir="ltr">In looking at this larger scale run ...
<div><br>
</div>
<div>* Your eigen estimates are much lower than your tiny test
problem. But this is Stokes apparently and it should not
work anyway. Maybe you have a small time step that adds a
lot of mass that brings the eigen estimates down. And your
min eigenvalue (not used) is positive. I would expect
negative for Stokes ...</div>
<div><br>
</div>
<div>* You seem to be setting a threshold value of 0.1 -- that
is very high</div>
<div><br>
</div>
<div>* v3.6 says "using nonzero initial guess" but this is not
in v3.10. Maybe we just stopped printing that.</div>
<div><br>
</div>
<div>* There were some changes to coasening parameters in
going from v3.6 but it does not look like your problem was
effected. (The coarsening algo is non-deterministic by
default and you can see small difference on different runs)</div>
<div><br>
</div>
<div>* We may have also added a "noisy" RHS for eigen
estimates by default from v3.6.</div>
<div><br>
</div>
<div>* And for non-symetric problems you can try
-pc_gamg_agg_nsmooths 0, but again GAMG is not built for
Stokes anyway.</div>
<div><br>
</div>
</div>
</div>
<br>
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">On Tue, Mar 5, 2019 at 11:53
AM Myriam Peyrounette <<a
href="mailto:myriam.peyrounette@idris.fr"
moz-do-not-send="true">myriam.peyrounette@idris.fr</a>>
wrote:<br>
</div>
<blockquote class="gmail_quote" style="margin:0px 0px 0px
0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div bgcolor="#FFFFFF">
<p>I used PCView to display the size of the linear system in
each level of the MG. You'll find the outputs attached to
this mail (zip file) for both the default threshold value
and a value of 0.1, and for both 3.6 and 3.10 PETSc
versions. <br>
</p>
<p>For convenience, I summarized the information in a graph,
also attached (png file).</p>
<p>As you can see, there are slight differences between the
two versions but none is critical, in my opinion. Do you
see anything suspicious in the outputs?</p>
<p>+ I can't find the default threshold value. Do you know
where I can find it?<br>
</p>
<p>Thanks for the follow-up</p>
<p>Myriam<br>
</p>
<br>
<div class="gmail-m_4553173887686987135moz-cite-prefix">Le
03/05/19 à 14:06, Matthew Knepley a écrit :<br>
</div>
<blockquote type="cite">
<div dir="ltr">
<div dir="ltr">On Tue, Mar 5, 2019 at 7:14 AM Myriam
Peyrounette <<a
href="mailto:myriam.peyrounette@idris.fr"
target="_blank" moz-do-not-send="true">myriam.peyrounette@idris.fr</a>>
wrote:<br>
</div>
<div class="gmail_quote">
<blockquote class="gmail_quote" style="margin:0px 0px
0px 0.8ex;border-left:1px solid
rgb(204,204,204);padding-left:1ex">
<div bgcolor="#FFFFFF">
<p>Hi Matt,</p>
<p>I plotted the memory scalings using different
threshold values. The two scalings are slightly
translated (from -22 to -88 mB) but this gain is
neglectable. The 3.6-scaling keeps being robust
while the 3.10-scaling deteriorates.</p>
<p>Do you have any other suggestion?</p>
</div>
</blockquote>
<div>Mark, what is the option she can give to output
all the GAMG data?</div>
<div><br>
</div>
<div>Also, run using -ksp_view. GAMG will report all
the sizes of its grids, so it should be easy to see</div>
<div>if the coarse grid sizes are increasing, and also
what the effect of the threshold value is.</div>
<div><br>
</div>
<div> Thanks,</div>
<div><br>
</div>
<div> Matt <br>
</div>
<blockquote class="gmail_quote" style="margin:0px 0px
0px 0.8ex;border-left:1px solid
rgb(204,204,204);padding-left:1ex">
<div bgcolor="#FFFFFF">
<p>Thanks<br>
</p>
Myriam <br>
<br>
<div
class="gmail-m_4553173887686987135gmail-m_-3242500023102749998moz-cite-prefix">Le
03/02/19 à 02:27, Matthew Knepley a écrit :<br>
</div>
<blockquote type="cite">
<div dir="ltr">
<div dir="ltr">
<div dir="ltr">On Fri, Mar 1, 2019 at 10:53
AM Myriam Peyrounette via petsc-users <<a
href="mailto:petsc-users@mcs.anl.gov"
target="_blank" moz-do-not-send="true">petsc-users@mcs.anl.gov</a>>
wrote:<br>
</div>
<div class="gmail_quote">
<blockquote class="gmail_quote"
style="margin:0px 0px 0px
0.8ex;border-left:1px solid
rgb(204,204,204);padding-left:1ex">Hi,<br>
<br>
I used to run my code with PETSc 3.6.
Since I upgraded the PETSc version<br>
to 3.10, this code has a bad memory
scaling.<br>
<br>
To report this issue, I took the PETSc
script ex42.c and slightly<br>
modified it so that the KSP and PC
configurations are the same as in my<br>
code. In particular, I use a
"personnalised" multi-grid method. The<br>
modifications are indicated by the
keyword "TopBridge" in the attached<br>
scripts.<br>
<br>
To plot the memory (weak) scaling, I ran
four calculations for each<br>
script with increasing problem sizes and
computations cores:<br>
<br>
1. 100,000 elts on 4 cores<br>
2. 1 million elts on 40 cores<br>
3. 10 millions elts on 400 cores<br>
4. 100 millions elts on 4,000 cores<br>
<br>
The resulting graph is also attached.
The scaling using PETSc 3.10<br>
clearly deteriorates for large cases,
while the one using PETSc 3.6 is<br>
robust.<br>
<br>
After a few tests, I found that the
scaling is mostly sensitive to the<br>
use of the AMG method for the coarse
grid (line 1780 in<br>
main_ex42_petsc36.cc). In particular,
the performance strongly<br>
deteriorates when commenting lines 1777
to 1790 (in main_ex42_petsc36.cc).<br>
<br>
Do you have any idea of what changed
between version 3.6 and version<br>
3.10 that may imply such degradation?<br>
</blockquote>
<div><br>
</div>
<div>I believe the default values for
PCGAMG changed between versions. It
sounds like the coarsening rate</div>
<div>is not great enough, so that these
grids are too large. This can be set
using:</div>
<div><br>
</div>
<div> <a
href="https://www.mcs.anl.gov/petsc/petsc-current/docs/manualpages/PC/PCGAMGSetThreshold.html"
target="_blank" moz-do-not-send="true">https://www.mcs.anl.gov/petsc/petsc-current/docs/manualpages/PC/PCGAMGSetThreshold.html</a></div>
<div><br>
</div>
<div>There is some explanation of this
effect on that page. Let us know if
setting this does not correct the
situation.</div>
<div><br>
</div>
<div> Thanks,</div>
<div><br>
</div>
<div> Matt</div>
<div> </div>
<blockquote class="gmail_quote"
style="margin:0px 0px 0px
0.8ex;border-left:1px solid
rgb(204,204,204);padding-left:1ex"> Let
me know if you need further information.<br>
<br>
Best,<br>
<br>
Myriam Peyrounette<br>
<br>
<br>
-- <br>
Myriam Peyrounette<br>
CNRS/IDRIS - HLST<br>
--<br>
<br>
</blockquote>
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<div><br>
</div>
-- <br>
<div dir="ltr"
class="gmail-m_4553173887686987135gmail-m_-3242500023102749998gmail_signature">
<div dir="ltr">
<div>
<div dir="ltr">
<div>
<div dir="ltr">
<div>What most experimenters
take for granted before they
begin their experiments is
infinitely more interesting
than any results to which
their experiments lead.<br>
-- Norbert Wiener</div>
<div><br>
</div>
<div><a
href="http://www.cse.buffalo.edu/%7Eknepley/"
target="_blank"
moz-do-not-send="true">https://www.cse.buffalo.edu/~knepley/</a><br>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</blockquote>
<br>
<pre class="gmail-m_4553173887686987135gmail-m_-3242500023102749998moz-signature" cols="72">--
Myriam Peyrounette
CNRS/IDRIS - HLST
--
</pre>
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</blockquote>
</div>
<br clear="all">
<div><br>
</div>
-- <br>
<div dir="ltr"
class="gmail-m_4553173887686987135gmail_signature">
<div dir="ltr">
<div>
<div dir="ltr">
<div>
<div dir="ltr">
<div>What most experimenters take for
granted before they begin their
experiments is infinitely more interesting
than any results to which their
experiments lead.<br>
-- Norbert Wiener</div>
<div><br>
</div>
<div><a
href="http://www.cse.buffalo.edu/%7Eknepley/"
target="_blank" moz-do-not-send="true">https://www.cse.buffalo.edu/~knepley/</a><br>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</blockquote>
<br>
<pre class="gmail-m_4553173887686987135moz-signature" cols="72">--
Myriam Peyrounette
CNRS/IDRIS - HLST
--
</pre>
</div>
</blockquote>
</div>
</blockquote>
<br>
<pre class="moz-signature" cols="72">--
Myriam Peyrounette
CNRS/IDRIS - HLST
--
</pre>
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