<html>
<head>
<meta http-equiv="Content-Type" content="text/html; charset=Windows-1252">
</head>
<body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;">
<div>Resending to the list:</div>
<div><br>
<blockquote type="cite">
<div dir="ltr">
<div class="gmail_extra">
<div class="gmail_quote">
<blockquote class="gmail_quote" style="margin: 0px 0px 0px 0.8ex; border-left-width: 1px; border-left-color: rgb(204, 204, 204); border-left-style: solid; padding-left: 1ex; position: static; z-index: auto;">
<div style="word-wrap: break-word;">
<div>
<div class="">
<div><br>
</div>
</div>
<div>I saw that. Does it mean that all heavy data is duplicated in the hdf5 file, i.e. that /fields contains values that petsc understands and /viz is for visualization?</div>
</div>
</div>
</blockquote>
<div><br>
</div>
<div>Yes, this is controlled by the viewer format. I saw no way to get xmf to look at scattered data, so duplication was inevitable.</div>
</div>
</div>
</div>
</blockquote>
<div><br>
</div>
<div>There are two issues:</div>
<div>projection into linear / bilinear elements that xdmf understands and scattered data.</div>
<div>I think that one way to deal with the later is to create one grid per cell set. the hierarchy should be </div>
<div>
<div> <Grid Name="TimeSeries" GridType="Collection" CollectionType="Temporal"></div>
<div> <Time TimeType="HyperSlab”></div>
<div><span class="Apple-tab-span" style="white-space: pre;"></span>:</div>
<div><span class="Apple-tab-span" style="white-space: pre;"></span>:</div>
<div> </Time></div>
<div> <Grid Name="Mesh" GridType="Collection" CollectionType="Spatial"></div>
</div>
</div>
<blockquote style="margin: 0px 0px 0px 40px; border: none; padding: 0px;">
<div><Grid Name="cellset000001" GridType="Uniform"><span class="Apple-tab-span" style="white-space: pre;">
</span></div>
<div>:</div>
<div>:</div>
<div></Grid></div>
</blockquote>
<div>
<div>
<blockquote style="margin: 0px 0px 0px 40px; border: none; padding: 0px;">
<div><Grid Name="cellset000002" GridType="Uniform"><span class="Apple-tab-span" style="white-space: pre;">
</span></div>
<div>:</div>
<div>:</div>
<div></Grid></div>
</blockquote>
<div>
<div></div>
</div>
<div> </Grid></div>
<div>i.e. one connectivity table per cell set instead of a global one. This also addresses the issue of different element types</div>
<div>Lastly, when no interpolation is needed, we do not need to duplicate results in the hdf5 file this way.</div>
<div><br>
</div>
<div>How hard would it be to split the connectivity table in the hdf5 file? Once this is done, I can try to write a xmd file by hand for reference.</div>
<div><br>
</div>
</div>
<blockquote type="cite">
<div dir="ltr">
<div class="gmail_extra">
<div class="gmail_quote">
<blockquote class="gmail_quote" style="margin: 0px 0px 0px 0.8ex; border-left-width: 1px; border-left-color: rgb(204, 204, 204); border-left-style: solid; padding-left: 1ex;">
<div style="word-wrap: break-word;">The xmf generation script fails on it, most likely because I don’t have a /time section in the file. My workaround is to replace l. 209 with time = [0,1]. </div>
</blockquote>
<div><br>
</div>
<div>The xmf script works on it now.</div>
</div>
</div>
</div>
</blockquote>
<div><br>
</div>
<div>Did you push your changes? I have switched to next but still get an error:</div>
<div>
<div style="margin: 0px; font-family: 'Source Code Pro';">bourdin@galerkin:DMComplex $ $PETSC_DIR/bin/pythonscripts/petsc_gen_xdmf.py TwoSquares.h5 </div>
<div style="margin: 0px; font-family: 'Source Code Pro';">Traceback (most recent call last):</div>
<div style="margin: 0px; font-family: 'Source Code Pro';"> File "/opt/HPC/petsc-dev/bin/pythonscripts/petsc_gen_xdmf.py", line 220, in <module></div>
<div style="margin: 0px; font-family: 'Source Code Pro';"> generateXdmf(sys.argv[1])</div>
<div style="margin: 0px; font-family: 'Source Code Pro';"> File "/opt/HPC/petsc-dev/bin/pythonscripts/petsc_gen_xdmf.py", line 215, in generateXdmf</div>
<div style="margin: 0px; font-family: 'Source Code Pro';"> Xdmf(xdmfFilename).write(hdfFilename, topoPath, numCells, numCorners, cellDim, geomPath, numVertices, spaceDim, time, vfields, cfields)</div>
<div style="margin: 0px; font-family: 'Source Code Pro';"> File "/opt/HPC/petsc-dev/bin/pythonscripts/petsc_gen_xdmf.py", line 176, in write</div>
<div style="margin: 0px; font-family: 'Source Code Pro';"> self.writeSpaceGridHeader(fp, numCells, numCorners, cellDim, spaceDim)</div>
<div style="margin: 0px; font-family: 'Source Code Pro';"> File "/opt/HPC/petsc-dev/bin/pythonscripts/petsc_gen_xdmf.py", line 75, in writeSpaceGridHeader</div>
<div style="margin: 0px; font-family: 'Source Code Pro';"> ''' % (self.cellMap[cellDim][numCorners], numCells, "XYZ" if spaceDim > 2 else "XY"))</div>
<div style="margin: 0px; font-family: 'Source Code Pro';">KeyError: 1</div>
<div><br>
</div>
</div>
<blockquote type="cite">
<div dir="ltr">
<div class="gmail_extra">I need to understand how xmf treats these mixes meshes. This is where help would be useful.</div>
<div class="gmail_extra">The checkpointing works with them however.</div>
</div>
</blockquote>
<div><br>
</div>
</div>
I struggled with the same problem until Jinghua Ge, our viz expert and xmf / hdf5 guru, suggested to use a spatial collection of spatial grids.
<div><br>
</div>
<div>Blaise<br>
<div apple-content-edited="true"><span class="Apple-style-span" style="border-collapse: separate; border-spacing: 0px;"><span class="Apple-style-span" style="border-collapse: separate; orphans: 2; widows: 2; border-spacing: 0px;">
<div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;">
<span class="Apple-style-span" style="border-collapse: separate; border-spacing: 0px;">
<div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;">
<span class="Apple-style-span" style="border-collapse: separate; border-spacing: 0px;">
<div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;">
<div style="margin: 0px;">-- </div>
<div style="margin: 0px;">Department of Mathematics and Center for Computation & Technology</div>
<div style="margin: 0px;">Louisiana State University, Baton Rouge, LA 70803, USA</div>
<div style="margin: 0px;">Tel. +1 (225) 578 1612, Fax +1 (225) 578 4276 <a href="http://www.math.lsu.edu/~bourdin">http://www.math.lsu.edu/~bourdin</a></div>
</div>
</span></div>
</span></div>
</span></span></div>
</div>
</body>
</html>