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There may be good reasons to want to read / write in a given ordering: post-processing an existing computation, applying non trivial boundary conditions that need to be computed separately, or restarting a computation on a different number of processors.
<div class="">Also, Exodus has restriction on cell ordering (cells in an element block must be numbered sequentially) so the distributed cell ordering may not be acceptable.</div>
<div class="">Exodus 6 introduced element sets which are free of this limitation, but as far as I know, no mesh generator or post processing deals with elements sets.<br class="">
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<div class="">I ended up inverting the migration SF, broadcast the distributed section back to the original mesh, then generate SFnatural using DMPlexCreateGlobalToNaturalSF. It is ugly but done only once.</div>
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<div class="">Still about exodus, I now have parallel (MPIIO through parallel netcdf) I/O working for nodal (linear and quadratic Lagrange elements) and zonal fields (in exodus jargon) in natural and standard ordering. I can have pull request and documented
examples and tests ready in a few days.</div>
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<div class="">Blaise</div>
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<div><br class="">
<blockquote type="cite" class="">
<div class="">On Nov 27, 2017, at 10:21 PM, Jed Brown <<a href="mailto:jed@jedbrown.org" class="">jed@jedbrown.org</a>> wrote:</div>
<br class="Apple-interchange-newline">
<div class=""><span style="font-family: SourceCodePro-Regular; font-size: 11px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; float: none; display: inline !important;" class="">Matthew
Knepley <</span><a href="mailto:knepley@gmail.com" style="font-family: SourceCodePro-Regular; font-size: 11px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px;" class="">knepley@gmail.com</a><span style="font-family: SourceCodePro-Regular; font-size: 11px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; float: none; display: inline !important;" class="">>
writes:</span><br style="font-family: SourceCodePro-Regular; font-size: 11px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">
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<blockquote type="cite" style="font-family: SourceCodePro-Regular; font-size: 11px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px;" class="">
On Mon, Nov 27, 2017 at 9:24 PM, Jed Brown <<a href="mailto:jed@jedbrown.org" class="">jed@jedbrown.org</a>> wrote:<br class="">
<br class="">
<blockquote type="cite" class="">Matthew Knepley <<a href="mailto:knepley@gmail.com" class="">knepley@gmail.com</a>> writes:<br class="">
<br class="">
<blockquote type="cite" class="">On Mon, Nov 27, 2017 at 8:08 PM, Jed Brown <<a href="mailto:jed@jedbrown.org" class="">jed@jedbrown.org</a>> wrote:<br class="">
<br class="">
<blockquote type="cite" class="">I don't know the answer to your question (Matt?), but do you really need<br class="">
to reorder the entire mesh or would it be sufficient to label your<br class="">
points with their original numbering?<br class="">
</blockquote>
<br class="">
<br class="">
Maybe I am wrong, but I think it amounts to the same thing. If we are<br class="">
</blockquote>
going<br class="">
<blockquote type="cite" class="">to output things in parallel,<br class="">
we would need to communicate to he writing process, which this<br class="">
</blockquote>
essentially<br class="">
<blockquote type="cite" class="">does.<br class="">
</blockquote>
<br class="">
Writing a label doesn't require redistribution of the mesh. It's possible<br class="">
to do parallel IO.<br class="">
<br class="">
</blockquote>
<br class="">
My understanding is that 3rd party programs want the mesh in the<br class="">
original order, so we want it ordered in the HDF5 file in the original<br class="">
order. You could I guess write it in the order, but it seems messy to<br class="">
write stuff all over the place in the file. Is that what you mean?<br class="">
</blockquote>
<br style="font-family: SourceCodePro-Regular; font-size: 11px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">
<span style="font-family: SourceCodePro-Regular; font-size: 11px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; float: none; display: inline !important;" class="">What
is the third-party program doing? It might be easier for it to</span><br style="font-family: SourceCodePro-Regular; font-size: 11px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">
<span style="font-family: SourceCodePro-Regular; font-size: 11px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; float: none; display: inline !important;" class="">apply
the permutation than for PETSc to redistribute in order to write</span><br style="font-family: SourceCodePro-Regular; font-size: 11px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">
<span style="font-family: SourceCodePro-Regular; font-size: 11px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; float: none; display: inline !important;" class="">the
file in a possibly poor ordering.</span></div>
</blockquote>
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Department of Mathematics and Center for Computation & Technology</div>
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Louisiana State University, Baton Rouge, LA 70803, USA</div>
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Tel. +1 (225) 578 1612, Fax +1 (225) 578 4276 <a href="http://www.math.lsu.edu/~bourdin" class="">
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