<div dir="ltr"><div dir="ltr">On Tue, May 31, 2022 at 7:39 AM Lidia <<a href="mailto:lidia.varsh@mail.ioffe.ru">lidia.varsh@mail.ioffe.ru</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>
<p>Matt, Mark, thank you much for your answers!</p>
<p><br>
</p>
<p>Now we have run example # 5 on our computer cluster and on the
local server and also have not seen any performance increase, but
by unclear reason running times on the local server are much
better than on the cluster.</p></div></blockquote><div>I suspect that you are trying to get speedup without increasing the memory bandwidth:</div><div><br></div><div> <a href="https://petsc.org/main/faq/#what-kind-of-parallel-computers-or-clusters-are-needed-to-use-petsc-or-why-do-i-get-little-speedup">https://petsc.org/main/faq/#what-kind-of-parallel-computers-or-clusters-are-needed-to-use-petsc-or-why-do-i-get-little-speedup</a></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>
<p>Now we will try to run petsc #5 example inside a docker container
on our server and see if the problem is in our environment. I'll
write you the results of this test as soon as we get it.</p>
<p>The ksp_monitor outs for the 5th test at the current local server
configuration (for 2 and 4 mpi processes) and for the cluster (for
1 and 3 mpi processes) are attached .</p>
<p><br>
</p>
<p>And one more question. Potentially we can use 10 nodes and 96
threads at each node on our cluster. What do you think, which
combination of numbers of mpi processes and openmp threads may be
the best for the 5th example?<br>
</p>
<p>Thank you!<br>
</p>
<p><br>
</p>
Best,<br>
Lidiia<br>
<div><br>
</div>
<div>On 31.05.2022 05:42, Mark Adams wrote:<br>
</div>
<blockquote type="cite">
<div dir="ltr">And if you see "NO" change in performance I suspect
the solver/matrix is all on one processor.
<div>(PETSc does not use threads by default so threads should
not change anything).</div>
<div><br>
</div>
<div>As Matt said, it is best to start with a PETSc example that
does something like what you want (parallel linear solve, see
src/ksp/ksp/tutorials for examples), and then add your code to
it.</div>
<div>That way you get the basic infrastructure in place for you,
which is pretty obscure to the uninitiated.</div>
<div><br>
</div>
<div>Mark</div>
</div>
<br>
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">On Mon, May 30, 2022 at 10:18
PM Matthew Knepley <<a href="mailto:knepley@gmail.com" target="_blank">knepley@gmail.com</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 dir="ltr">
<div dir="ltr">On Mon, May 30, 2022 at 10:12 PM Lidia <<a href="mailto:lidia.varsh@mail.ioffe.ru" target="_blank">lidia.varsh@mail.ioffe.ru</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">Dear colleagues,<br>
<br>
Is here anyone who have solved big sparse linear
matrices using PETSC?<br>
</blockquote>
<div><br>
</div>
<div>There are lots of publications with this kind of
data. Here is one recent one: <a href="https://arxiv.org/abs/2204.01722" target="_blank">https://arxiv.org/abs/2204.01722</a></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"> We have found NO
performance improvement while using more and more mpi <br>
processes (1-2-3) and open-mp threads (from 1 to 72
threads). Did anyone <br>
faced to this problem? Does anyone know any possible
reasons of such <br>
behaviour?<br>
</blockquote>
<div><br>
</div>
<div>Solver behavior is dependent on the input matrix. The
only general-purpose solvers</div>
<div>are direct, but they do not scale linearly and have
high memory requirements.</div>
<div><br>
</div>
<div>Thus, in order to make progress you will have to be
specific about your matrices.</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"> We use AMG
preconditioner and GMRES solver from KSP package, as our
<br>
matrix is large (from 100 000 to 1e+6 rows and columns),
sparse, <br>
non-symmetric and includes both positive and negative
values. But <br>
performance problems also exist while using CG solvers
with symmetric <br>
matrices.<br>
</blockquote>
<div><br>
</div>
<div>There are many PETSc examples, such as example 5 for
the Laplacian, that exhibit</div>
<div>good scaling with both AMG and GMG.</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"> Could anyone help us
to set appropriate options of the preconditioner <br>
and solver? Now we use default parameters, maybe they
are not the best, <br>
but we do not know a good combination. Or maybe you
could suggest any <br>
other pairs of preconditioner+solver for such tasks?<br>
<br>
I can provide more information: the matrices that we
solve, c++ script <br>
to run solving using petsc and any statistics obtained
by our runs.<br>
</blockquote>
<div><br>
</div>
<div>First, please provide a description of the linear
system, and the output of</div>
<div><br>
</div>
<div> -ksp_view -ksp_monitor_true_residual
-ksp_converged_reason -log_view</div>
<div><br>
</div>
<div>for each test case.</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"> Thank you in
advance!<br>
<br>
Best regards,<br>
Lidiia Varshavchik,<br>
Ioffe Institute, St. Petersburg, Russia<br>
</blockquote>
</div>
<br clear="all">
<div><br>
</div>
-- <br>
<div dir="ltr">
<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/~knepley/" target="_blank">https://www.cse.buffalo.edu/~knepley/</a><br>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</blockquote>
</div>
</blockquote>
</div>
</blockquote></div><br clear="all"><div><br></div>-- <br><div dir="ltr" class="gmail_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/~knepley/" target="_blank">https://www.cse.buffalo.edu/~knepley/</a><br></div></div></div></div></div></div></div></div>