<div dir="ltr"><div class="gmail_extra"><div class="gmail_quote">On Thu, Sep 14, 2017 at 11:43 AM, Adriano Côrtes <span dir="ltr"><<a href="mailto:adrimacortes@gmail.com" target="_blank">adrimacortes@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">Dear Matthew,<div><br></div><div>Thank you for your return. It worked, but this prompts another question. So why PetscViewer does not write both files (.h5 and .xmf) directly, instead of having to post-proc the .h5 file (in serial)?</div></div></blockquote><div><br></div><div>1) Maintenance: Changing the Python is much easier than changing the C you would add to generate it</div><div><br></div><div>2) Performance: On big parallel system, writing files is expensive so I wanted to minimize what I had to do.</div><div><br></div><div>3) Robustness: Moving 1 file around is much easier than remembering 2. I just always regenerate the xdmf when needed.</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>And what about big 3D simulations? PETSc always serialize the output of the distributed dmplex? Is there a way to output one .h5 per mesh partition? </div></div></blockquote><div><br></div><div>Given the way I/O is structured on big machines, we believe the multiple file route is a huge mistake. Also, all our measurements</div><div>say that sending some data on the network is not noticeable given the disk access costs.</div><div><br></div><div> Thanks,</div><div><br></div><div> Matt</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>Best regards,</div><div>Adriano.</div><div><br></div></div><div class="gmail_extra"><br><div class="gmail_quote">2017-09-14 12:00 GMT-03:00 Matthew Knepley <span dir="ltr"><<a href="mailto:knepley@gmail.com" target="_blank">knepley@gmail.com</a>></span>:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div class="gmail_extra"><div class="gmail_quote"><span>On Thu, Sep 14, 2017 at 10:30 AM, Adriano Côrtes <span dir="ltr"><<a href="mailto:adrimacortes@gmail.com" target="_blank">adrimacortes@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">Dear all,<div><br></div><div>I am running the SNES ex12 and I'm passing the options -dm_view hdf5:sol.h5 -vec_view hdf5:sol.h5::append to generate an output file. The .h5 file is generated, but I'm not being able to load it in Paraview (5.4.0-64bits). Paraview recognizes the file and offers severel options to read it, here is the complete list</div><div><br></div><div><div>Chombo Files</div><div>GTC Files</div><div>M3DC1 Files</div><div>Multilevel 3D Plasma Files</div><div>PFLOTRAN Files</div><div>Pixie Files</div><div>Tetrad Files</div><div>UNIC Files</div><div>VizSchema Files</div></div><div><br></div><div>The problem is none of the options above work :(</div><div>I'm using the configure option '-download-hdf5' and it installs hdf5 version 1.8.18</div><div>Any hint of how to fix it and have the visualization working?</div></div></blockquote><div><br></div></span><div>Yes, Paraview does not directly read HDF5. It needs you to tell it what the data in the HDF5 file means. You do</div><div>this by creating a *.xdmf file, which is XML. We provide a tool</div><div><br></div><div> $PETSC_DIR/bin/petsc_gen_xdmf.<wbr>py <HDF5 file></div><div><br></div><div>which should automatically produce this file for you. Let us know if it does not work.</div><div><br></div><div> Thanks,</div><div><br></div><div> Matt</div><span><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>Best regards,</div><div>Adriano.</div><span class="m_9207681235008088159m_4870260283422625554HOEnZb"><font color="#888888">
<div><div><br></div>-- <br><div class="m_9207681235008088159m_4870260283422625554m_-3323842891076612192gmail_signature"><div dir="ltr"><div><div dir="ltr"><div>Adriano Côrtes<br>==============================<wbr>===================<br><i>Campus Duque de Caxias and</i></div><div><i>High-performance Computing Center (NACAD/COPPE)</i></div><div>Federal University of Rio de Janeiro (UFRJ)</div></div></div></div></div>
</div></font></span></div>
</blockquote></span></div><span class="m_9207681235008088159HOEnZb"><font color="#888888"><br><br clear="all"><span class="HOEnZb"><font color="#888888"><div><br></div>-- <br><div class="m_9207681235008088159m_4870260283422625554gmail_signature" data-smartmail="gmail_signature"><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.caam.rice.edu/~mk51/" target="_blank">http://www.caam.rice.edu/~mk51<wbr>/</a><br></div></div></div>
</font></span></font></span></div></div><span class="HOEnZb"><font color="#888888">
</font></span></blockquote></div><span class="HOEnZb"><font color="#888888"><br><br clear="all"><div><br></div>-- <br><div class="m_9207681235008088159gmail_signature" data-smartmail="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div>Adriano Côrtes<br>==============================<wbr>===================<br><i>Campus Duque de Caxias and</i></div><div><i>High-performance Computing Center (NACAD/COPPE)</i></div><div>Federal University of Rio de Janeiro (UFRJ)</div></div></div></div></div>
</font></span></div>
</blockquote></div><br><br clear="all"><div><br></div>-- <br><div class="gmail_signature" data-smartmail="gmail_signature"><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.caam.rice.edu/~mk51/" target="_blank">http://www.caam.rice.edu/~mk51/</a><br></div></div></div>
</div></div>