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<div class="moz-cite-prefix">On 5/10/2012 5:17 PM, Jed Brown wrote:<br>
</div>
<blockquote
cite="mid:CAM9tzSkSnmBYVfnPbpgeUj=N3_8RnGdxd0CTbMJU2_SCxd5LAw@mail.gmail.com"
type="cite">Now most of the time is spent in PCApply, though an
inordinate amount is still in VecScatterEnd, indicating that
either your partition is very bad or the machine has contention
(either with other jobs, zombie processes, incorrect affinity,
over-subscribed).
<div>
<br>
</div>
<div>In any case, you can try changing the smoother. For example,
try skipping the Chebyshev iterations and just use one iteration
of SOR...<br>
</div>
</blockquote>
<br>
May I know where can I find all the options for GAMG? I can't find
it in the manual.<br>
<br>
I also used -info for the GAMG and what does these mean:<br>
<br>
1. [9] MatAssemblyBegin_MPIAIJ(): Stash has 14396 entries, uses 1
mallocs<br>
<br>
How serious is this? Does it mean there's a lot of mallocs going on?
Do I correct this by using higher d_nz and o_nz?<br>
<br>
2. [4] MatAssemblyEnd_SeqAIJ(): Matrix size: 112785 X 112785;
storage space: 0 unneeded,3628127 used<br>
[4] MatAssemblyEnd_SeqAIJ(): Number of mallocs during MatSetValues()
is 0<br>
[4] MatAssemblyEnd_SeqAIJ(): Maximum nonzeros in any row is 59<br>
<br>
When I use MatCreateAIJ, my d_nz and o_nz are both 7. If the row is
59, does it mean that my d_nz and o_nz are too small. Must I set it
to the maximum nonzeros given by -info?<br>
<br>
3. [0] MatSetOption_SeqAIJ(): Option STRUCTURALLY_SYMMETRIC ignored<br>
<br>
My Poisson matrix is symmetrical, so why is it ignored?<br>
<blockquote
cite="mid:CAM9tzSkSnmBYVfnPbpgeUj=N3_8RnGdxd0CTbMJU2_SCxd5LAw@mail.gmail.com"
type="cite">
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<div class="gmail_quote">On Fri, Oct 5, 2012 at 10:08 AM, TAY
wee-beng <span dir="ltr"><<a moz-do-not-send="true"
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">
<div class="HOEnZb">
<div class="h5">On 4/10/2012 11:44 PM, Satish Balay wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
On Thu, 4 Oct 2012, Matthew Knepley wrote:<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
the Mom-Z solve is bad because the assembly of the
operator is<br>
screwed up. You are communicating too many values.
So, jsut go into<br>
your code and count how many off process entries you
set.<br>
</blockquote>
running with '-info' should give debug info regarding
this<br>
communication [stack size used for messages, and the
number of mallocs<br>
needed etc..]<br>
<br>
Satish<br>
</blockquote>
<br>
</div>
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Ok, I found my problem. I was using:<br>
<br>
PetscLogStage stage<br>
<br>
and the time for the poisson eqn got combined into that of
the momentum_z solve. Hence the confusion in results.<br>
<br>
I have attached the new results. The time is taken up mainly
by GAMG. I am using:<br>
<br>
-poisson_pc_gamg_agg_nsmooths 1<br>
-poisson_pc_type gamg<br>
<br>
What are the possible ways to improve the efficiency or
reduce the time?<br>
<br>
If I use HYPRE's geometric multigrid, performance is
somewhat better, such that momentum_x/y/z accounts for a
total of 15% computing time.<br>
<br>
From the log_summary, for the momentum eqns, it seems that
MatAssembly is the main problem, is that so?<br>
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