<div dir="ltr"><div class="gmail_extra"><div class="gmail_quote">On Wed, Mar 21, 2018 at 4:59 AM, TAY wee-beng <span dir="ltr"><<a href="mailto:zonexo@gmail.com" target="_blank">zonexo@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
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<br>
<div class="m_-619408701181955118moz-cite-prefix">On 19/3/2018 6:32 PM, Matthew Knepley
wrote:<br>
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<div class="gmail_quote">On Mon, Mar 19, 2018 at 5:19 AM, TAY
wee-beng <span dir="ltr"><<a href="mailto:zonexo@gmail.com" target="_blank">zonexo@gmail.com</a>></span>
wrote:<br>
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<div class="m_-619408701181955118m_4970404346621557354moz-cite-prefix">On
17/3/2018 1:15 AM, Matthew Knepley wrote:<br>
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<div class="gmail_quote">On Fri, Mar 16, 2018 at
12:54 PM, TAY wee-beng <span dir="ltr"><<a href="mailto:zonexo@gmail.com" target="_blank">zonexo@gmail.com</a>></span>
wrote:<br>
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<div class="m_-619408701181955118m_4970404346621557354gmail-m_-1748057115269175174moz-cite-prefix">On
15/3/2018 6:21 PM, Matthew Knepley wrote:<br>
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<div class="gmail_quote">On Thu, Mar
15, 2018 at 3:51 PM, TAY wee-beng <span dir="ltr"><<a href="mailto:zonexo@gmail.com" target="_blank">zonexo@gmail.com</a>></span>
wrote:<br>
<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'm running a CFD code which
solves the momentum and Poisson
eqns.<br>
<br>
Due to poor scaling with HYPRE at
higher cpu no., I decided to try
using PETSc with boomeramg and
gamg.<br>
<br>
I tested for some small cases and
it work well. However, for the
large problem which has poor
scaling, it gives an error when I
change my Poisson solver from pure
HYPRE to PETSc with boomeramg and
gamg.<br>
<br>
The error is :<br>
<br>
Caught signal number 11 SEGV:
Segmentation Violation, probably
memory access out of range<br>
<br>
I tried using:<br>
<br>
-poisson_ksp_type richardson
-poisson_pc_type hypre
-poisson_pc_type_hypre boomeramg<br>
<br>
-poisson_ksp_type gmres
-poisson_pc_type hypre
-poisson_pc_type_hypre boomeramg<br>
<br>
-poisson_pc_type gamg
-poisson_pc_gamg_agg_nsmooths 1<br>
<br>
but they all gave similar error.<br>
<br>
So why is this so? How should I
troubleshoot? I am now running a
debug ver of PETSc to check the
error msg.</blockquote>
<div><br>
</div>
<div>1) For anything like this, we
would like to see a stack trace
from the debugger or valgrind
output.</div>
<div><br>
</div>
<div>2) We do have several Poisson
examples. Does it fail for you on
those?</div>
</div>
</div>
</div>
</blockquote>
Hi,<br>
<br>
Can you recommend me some suitable egs? Esp
in Fortran?<br>
</div>
</blockquote>
<div><br>
</div>
<div>Here is 2D Poisson</div>
<div><br>
</div>
<div> <a href="https://bitbucket.org/petsc/petsc/src/4b6141395f14f0c7d1415a2ff0158eec75a27d63/src/snes/examples/tutorials/ex5f.F90?at=master&fileviewer=file-view-default" target="_blank">https://bitbucket.org/petsc/<wbr>petsc/src/4b6141395f14f0c7d141<wbr>5a2ff0158eec75a27d63/src/snes/<wbr>examples/tutorials/ex5f.F90?<wbr>at=master&fileviewer=file-<wbr>view-default</a></div>
<div> </div>
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Hi,<br>
<br>
I tried to use the different options like ML, MG BoomerAMG and while
they worked for the small problem, it failed for the large problem.
I checked and compared the 2D Poisson example with my 3D Poisson
subroutine. I found that my subroutine is very similar to my
momentum subroutine, which is based on KSPSolve:<br>
<br>
0. DMDACreate, DMDACreate3d etc<br>
1. Assemble matrix<br>
2. KSPSetOperators, KSPSetType etc<br>
3. KSPSolve<br>
<br>
However, the 2D Poisson example uses SNESSetDM, SNESSolve etc. So
does it matter if I use SNESSolve or KSPSolve?<br></div></blockquote><div><br></div><div>Not if you are using Algebraic Multigrid. "It failed for the large problem" is not descriptive enough. Please send the output of</div><div><br></div><div> -ksp_view -ksp_monitor_true_residual</div><div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div text="#000000" bgcolor="#FFFFFF">
I also didn't set any nullspace. Is this required for a Poisson eqn
solve?<br></div></blockquote><div><br></div><div>If you only have the constant null space, no. Most AMG packages do that one by default.</div><div><br></div><div> Matt</div><div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div text="#000000" bgcolor="#FFFFFF">
Thanks<br>
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<div> </div>
<div>3) You can also try ML, which
is the same type of MG as GAMG.
(--download-ml).</div>
<div><br>
</div>
</div>
</div>
</div>
</blockquote>
</div>
</blockquote>
</div>
</div>
</div>
</blockquote>
I have recompiled PETSc with ML. Is there an example
command line options which I can use for ML?<br>
</div>
</blockquote>
<div><br>
</div>
<div>-pc_type ml</div>
<div> </div>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div text="#000000" bgcolor="#FFFFFF"> Another question is
generally speaking, is geometric multigrid (GMG) faster
than algebraic?<br>
</div>
</blockquote>
<div><br>
</div>
<div>No, only for the setup time.</div>
<div> </div>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div text="#000000" bgcolor="#FFFFFF"> I tested on a small
problem and the time taken varies from 1.15min (HYPRE,
geometric) to 3.25 (GAMG). BoomerAMG is 1.45min.<br>
</div>
</blockquote>
<div><br>
</div>
<div>I am not sure what you are running when you say Hypre
geometric.</div>
<div> </div>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div text="#000000" bgcolor="#FFFFFF"> Besides HYPRE, is
there any other GMG I can use? <br>
</div>
</blockquote>
<div><br>
</div>
<div>As I said above, it does not converge any faster and
the solve is not faster, its all setup time, so small
problems will look faster.</div>
<div>You should be doing 10-20 iterates. If you are doing
more, MG is not working.<br>
</div>
<div><br>
</div>
<div>If you truly have a structured grid, then use DMDA in
PETSc and you can use GMG with</div>
<div><br>
</div>
<div> -pc_type mg -pc_mg_nlevels <n></div>
<div><br>
</div>
<div> Matt</div>
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My cluster can't connect to the internet.
Where can I 1st download it?<br>
<br>
Similarly, how can I find out the location
of the ext software by myself?<br>
</div>
</blockquote>
<div><br>
</div>
<div>The locations are all in the configure
Python modules:</div>
<div><br>
</div>
<div> <a href="https://bitbucket.org/petsc/petsc/src/4b6141395f14f0c7d1415a2ff0158eec75a27d63/config/BuildSystem/config/packages/ml.py?at=master&fileviewer=file-view-default" target="_blank">https://bitbucket.org/petsc/<wbr>petsc/src/4b6141395f14f0c7d141<wbr>5a2ff0158eec75a27d63/config/<wbr>BuildSystem/config/packages/<wbr>ml.py?at=master&fileviewer=<wbr>file-view-default</a></div>
<div><br>
</div>
<div> Thanks,</div>
<div><br>
</div>
<div> Matt</div>
<div> </div>
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<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"><span class="m_-619408701181955118m_4970404346621557354gmail-m_-1748057115269175174HOEnZb"><font color="#888888"><br>
-- <br>
Thank you very much.<br>
<br>
Yours sincerely,<br>
<br>
==============================<wbr>==================<br>
TAY Wee-Beng (Zheng Weiming)
郑伟明<br>
Personal research webpage: <a href="http://tayweebeng.wixsite.com/website" rel="noreferrer" target="_blank">http://tayweebeng.wixsite.com/<wbr>website</a><br>
Youtube research showcase: <a href="https://www.youtube.com/channel/UC72ZHtvQNMpNs2uRTSToiLA" rel="noreferrer" target="_blank">https://www.youtube.com/channe<wbr>l/UC72ZHtvQNMpNs2uRTSToiLA</a><br>
linkedin: <a href="http://www.linkedin.com/in/tay-weebeng" rel="noreferrer" target="_blank">www.linkedin.com/in/tay-weeben<wbr>g</a><br>
==============================<wbr>==================<br>
<br>
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<span class="m_-619408701181955118HOEnZb"><font color="#888888"> <span class="m_-619408701181955118m_4970404346621557354gmail-HOEnZb"><font color="#888888">
<div><br>
</div>
-- <br>
<div class="m_-619408701181955118m_4970404346621557354gmail-m_-1748057115269175174gmail_signature">
<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.caam.rice.edu/%7Emk51/" target="_blank">https://www.cse.buffalo.edu/~k<wbr>nepley/</a><br>
</div>
</div>
</div>
</div>
</div>
</font></span></font></span></div>
<span class="m_-619408701181955118HOEnZb"><font color="#888888"> </font></span></div>
<span class="m_-619408701181955118HOEnZb"><font color="#888888">
</font></span></blockquote>
<span class="m_-619408701181955118HOEnZb"><font color="#888888">
<br>
</font></span></div>
<span class="m_-619408701181955118HOEnZb"><font color="#888888"> </font></span></blockquote>
<span class="m_-619408701181955118HOEnZb"><font color="#888888"> </font></span></div>
<span class="m_-619408701181955118HOEnZb"><font color="#888888"> <br>
<br clear="all"><span class="HOEnZb"><font color="#888888">
<div><br>
</div>
-- <br>
<div class="m_-619408701181955118m_4970404346621557354gmail_signature">
<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.caam.rice.edu/%7Emk51/" target="_blank">https://www.cse.buffalo.edu/~k<wbr>nepley/</a><br>
</div>
</div>
</div>
</div>
</div>
</font></span></font></span></div><span class="HOEnZb"><font color="#888888">
</font></span></div><span class="HOEnZb"><font color="#888888">
</font></span></blockquote><span class="HOEnZb"><font color="#888888">
<br>
</font></span></div><span class="HOEnZb"><font color="#888888">
</font></span></blockquote><span class="HOEnZb"><font color="#888888">
</font></span></div><span class="HOEnZb"><font color="#888888">
<br>
<br clear="all">
<div><br>
</div>
-- <br>
<div class="m_-619408701181955118gmail_signature" data-smartmail="gmail_signature">
<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.caam.rice.edu/%7Emk51/" target="_blank">https://www.cse.buffalo.edu/~<wbr>knepley/</a><br>
</div>
</div>
</div>
</div>
</div>
</font></span></div>
</div>
</blockquote>
<br>
</div>
</blockquote></div><br><br clear="all"><div><br></div>-- <br><div class="gmail_signature" data-smartmail="gmail_signature"><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.caam.rice.edu/~mk51/" target="_blank">https://www.cse.buffalo.edu/~knepley/</a><br></div></div></div></div></div>
</div></div>