<div dir="ltr">I'm not aware of the difference between a distance-2 coloring and a 1-coloring. What is the difference? Yes, I mean that my Jacibain stencil has 33 entires; it is a 3x3x3 cube with 6 extra cells on the middle of each of the 6 faces. For that stencil you can find an analytic coloring that requires 35 evaluations. The issue I have arises from the application of boundary conditions; The normal residual evaluation extrapolates values to halo cells and then these halo values are communicated. I am assembling the matrix using forward mode AD and in a fashion that doesn't require communication; the idea is to peturb "halo" cells in addition to the "real" cells and this eliminates the communication for the halo exchange. However, I didn't have a way of relating the extrapolated values from a different processor with the real cell on the other processor. It's a little confusing and fairly specific to the CFD solver I'm using. <div>
<br></div><div>If I could get a global coloring that was somewhat close to what I can get analytically, I'd use that since it is simpler and requires less modification. </div><div><br></div><div>Gaetan</div></div><div class="gmail_extra">
<br><br><div class="gmail_quote">On Tue, Nov 5, 2013 at 4:08 PM, Peter Brune <span dir="ltr"><<a href="mailto:prbrune@gmail.com" target="_blank">prbrune@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><br><div class="gmail_quote"><div class="im">On Tue, Nov 5, 2013 at 11:07 AM, Gaetan Kenway <span dir="ltr"><<a href="mailto:gaetank@gmail.com" target="_blank">gaetank@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">Hi Peter<div><br></div><div>Thanks for the info. I actually already have a coloring that is done through the discretrization that is near optimal. The issue is that I have a funny interprocessor dependence that is tricky to do my own sequential coloring. So I was looking at doing it in a global, parallel sense. For interest, I tried using the matGetColor() on my assembled matrix just to see how many colors it would take. My discretrization coloring has 35 colors (for a stencil with 33 cells) and the matGetColor() resulted in approximately 78 colors or about twice as many. </div>
</div></blockquote><div><br></div></div><div>Jacobian coloring requires a column, or distance-2 coloring of the matrix. The distance-2 colorings we get from the serial algorithms aren't that bad, so I suspect that you might be doing a 1-coloring from your mesh; I assume that you mean that your residual/Jacobian stencil has 33 entries rather than some distance-2 thing? How did the problems with your coloring manifest themselves?</div>
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<div><br></div><div>- Peter</div></font></span><div class="im"><div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">
<div><br></div><div>Thanks,</div><div><br></div><div>Gaetan</div></div><div><div><div class="gmail_extra"><br><br><div class="gmail_quote">On Tue, Nov 5, 2013 at 11:39 AM, Peter Brune <span dir="ltr"><<a href="mailto:brune@mcs.anl.gov" target="_blank">brune@mcs.anl.gov</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><br><div class="gmail_quote"><div>On Tue, Nov 5, 2013 at 10:29 AM, Gaetan Kenway <span dir="ltr"><<a href="mailto:gaetank@gmail.com" target="_blank">gaetank@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">Hi <div><br></div><div>I have a quick question regarding the MatGetColoring() function. According to the documentation, </div>
<div><br></div><div> "For parallel matrices currently converts to sequential matrix and uses the sequential coloring on that."</div>
<div><br></div></div></blockquote><div><br></div></div><div>The meaning of this is that it transfers the parallel matrix to a single processor and does the coloring there, not that it only considers on-processor entries. What comes out is therefore a valid column coloring of the whole matrix. Parallel matrix coloring is in development but is not quite ready for public consumption. Anecdotal evidence suggests that the serial coloring does not become a bottleneck on small parallel runs.</div>
<div><br></div><div>A good option is to provide the coloring through your discretization. This will often be more efficient than the matrix colorings, as you know the structure of your problem.</div><span><font color="#888888"><div>
<br></div><div>- Peter</div></font></span><div>
<div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div></div><div>I am wondering does this give actually give a valid parallel coloring? My application is a cell centered multi-block finite volume code, (with block-based decomposition) and the communications are done using a two level exchange of halo cells. I would like to use FD (actually forward mode AD to compute the jacbian matrix). So, what I'm wondering is, if a cell with color 0 is perturbed on processor 0, is it guaranteed that a residual on processor 1, that is influenced by the 0-colored cell on proc zero is *only* influenced by the color 0 from proc 0 and not a 0-colored cell on proc 1?</div>
<div><br></div><div>I hope that is clear</div><div><br></div><div>Thank you,</div><div><br></div><div>Gaetan Kenway</div><div><br></div><div><br></div><div><br></div><div><br></div><div><br></div></div>
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