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I'm not sure what you mean with this question?<br>
The external CFD code, if that was what you referred to, can be run
in parallel.<br>
<br>
<div class="moz-cite-prefix">Am 17.10.2017 um 11:11 schrieb Matthew
Knepley:<br>
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cite="mid:CAMYG4Gn6-kOCpfDhg2MzRSA8WSfJK1AS1WKU5_xPqO=rapqW5w@mail.gmail.com">
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<div class="gmail_quote">On Tue, Oct 17, 2017 at 4:21 AM,
Michael Werner <span dir="ltr"><<a
href="mailto:michael.werner@dlr.de" target="_blank"
moz-do-not-send="true">michael.werner@dlr.de</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
<div text="#000000" bgcolor="#FFFFFF"> That's something
I'm still struggling with. In the serial case, I can
simply extract the values from the original grid, and
since the ordering of the Jacobian is the same there is
no problem. In the parallel case this is still a more or
less open question. That's why I thought about
reordering the Jacobian. As long as the position of the
individual IDs is the same for both, I don't have to
care about their absolute position.<br>
<br>
I also wanted to thank you for your previous answer, it
seems that the application ordering might be what I'm
looking for. However, in the meantime I stumbled about
another problem, that I have to solve first. My new
problem is, that I call the external code within the
shell matrix' multiply call. But in a parallel case,
this call obviously gets called once per process. So
right now I'm trying to circumvent this, so it might
take a while before I'm able to come back to the
original problem...<br>
</div>
</blockquote>
<div><br>
</div>
<div>I am not understanding. Is your original code parallel?</div>
<div><br>
</div>
<div> Thanks,</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"> Kind regards,<br>
Michael<br>
<br>
<div class="m_-5791166958946276202moz-cite-prefix">Am
16.10.2017 um 17:25 schrieb Praveen C:<br>
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<blockquote type="cite">
<div dir="ltr">I am interested to learn more about how
this works. How are the vectors created if the ids
are not contiguous in a partition ?
<div><br>
</div>
<div>Thanks</div>
<div>praveen</div>
</div>
<div class="gmail_extra"><br>
<div class="gmail_quote">On Mon, Oct 16, 2017 at
2:02 PM, Stefano Zampini <span dir="ltr"><<a
href="mailto:stefano.zampini@gmail.com"
target="_blank" moz-do-not-send="true">stefano.zampini@gmail.com</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0
0 .8ex;border-left:1px #ccc
solid;padding-left:1ex">
<div dir="ltr"><br>
<div class="gmail_extra"><br>
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<div class="m_-5791166958946276202h5">2017-10-16
10:26 GMT+03:00 Michael Werner <span
dir="ltr"><<a
href="mailto:michael.werner@dlr.de"
target="_blank"
moz-do-not-send="true">michael.werner@dlr.de</a>></span>:<br>
<blockquote class="gmail_quote"
style="margin:0px 0px 0px
0.8ex;border-left:1px solid
rgb(204,204,204);padding-left:1ex">Hello,<br>
<br>
I'm having trouble with
parallelizing a matrix-free code
with PETSc. In this code, I use an
external CFD code to provide the
matrix-vector product for an
iterative solver in PETSc. To
increase convergence rate, I'm using
an explicitly stored Jacobian matrix
to precondition the solver. This
works fine for serial runs. However,
when I try to use multiple
processes, I face the problem that
PETSc decomposes the preconditioner
matrix, and probably also the shell
matrix, in a different way than the
external CFD code decomposes the
grid.<br>
<br>
The Jacobian matrix is built in a
way, that its rows and columns
correspond to the global IDs of the
individual points in my CFD mesh<br>
<br>
The CFD code decomposes the domain
based on the proximity of points to
each other, so that the resulting
subgrids are coherent. However,
since its an unstructured grid,
those subgrids are not necessarily
made up of points with successive
global IDs. This is a problem, since
PETSc seems to partition the matrix
in coherent slices.<br>
<br>
I'm not sure what the best approach
to this problem might be. Is it
maybe possible to exactly tell
PETSc, which rows/columns it should
assign to the individual processes?<br>
<br>
</blockquote>
<div><br>
</div>
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</div>
<div>If you are explicitly setting the
values in your Jacobians via
MatSetValues(), you can create a
ISLocalToGlobalMapping </div>
<div><br>
</div>
<div><a
href="http://www.mcs.anl.gov/petsc/petsc-current/docs/manualpages/IS/ISLocalToGlobalMappingCreate.html"
target="_blank" moz-do-not-send="true">http://www.mcs.anl.gov/petsc/p<wbr>etsc-current/docs/manualpages/<wbr>IS/ISLocalToGlobalMappingCreat<wbr>e.html</a></div>
<div><br>
</div>
<div>that maps the numbering you use for
the Jacobians to their counterpart in
the CFD ordering, then call
MatSetLocalToGlobalMapping and then use
MatSetValuesLocal with the same
arguments you are calling MatSetValues
now.</div>
<div><br>
</div>
<div>Otherwise, you can play with the
application ordering <a
href="http://www.mcs.anl.gov/petsc/petsc-current/docs/manualpages/AO/index.html"
target="_blank" moz-do-not-send="true">http://www.mcs.anl.gov/petsc/p<wbr>etsc-current/docs/manualpages/<wbr>AO/index.html</a></div>
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color="#888888">
<div> </div>
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-- <br>
<div
class="m_-5791166958946276202m_-5153143099617110787gmail_signature">Stefano</div>
</font></span></font></span></div>
<span class="HOEnZb"><font color="#888888"> </font></span></div>
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<span class="HOEnZb"><font color="#888888"> </font></span></div>
<span class="HOEnZb"><font color="#888888"> <br>
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<span class="HOEnZb"><font color="#888888"> <br>
<pre class="m_-5791166958946276202moz-signature" cols="72">--
______________________________<wbr>______________________
Deutsches Zentrum für Luft- und Raumfahrt e.V. (DLR)
Institut für Aerodynamik und Strömungstechnik | <a href="https://maps.google.com/?q=Bunsenstr.+10+%7C+37073+G%C3%B6ttingen&entry=gmail&source=g" moz-do-not-send="true">Bunsenstr. 10 | 37073 Göttingen</a>
Michael Werner
Telefon 0551 709-2627 | Telefax 0551 709-2811 | <a class="m_-5791166958946276202moz-txt-link-abbreviated" href="mailto:Michael.Werner@dlr.de" target="_blank" moz-do-not-send="true">Michael.Werner@dlr.de</a>
DLR.de
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<div><br>
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-- <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/%7Emk51/"
target="_blank" moz-do-not-send="true">https://www.cse.buffalo.edu/~knepley/</a><br>
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<pre class="moz-signature" cols="72">--
____________________________________________________
Deutsches Zentrum für Luft- und Raumfahrt e.V. (DLR)
Institut für Aerodynamik und Strömungstechnik | Bunsenstr. 10 | 37073 Göttingen
Michael Werner
Telefon 0551 709-2627 | Telefax 0551 709-2811 | <a class="moz-txt-link-abbreviated" href="mailto:Michael.Werner@dlr.de">Michael.Werner@dlr.de</a>
DLR.de
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