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<div class="moz-cite-prefix">Il 14/10/21 14:37, Matthew Knepley ha
scritto:<br>
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<blockquote type="cite" cite="mid:CAMYG4Gk2RCWOAmtDbKc7Z=BBfYY8NdSe=V899TY29C=jknqL9Q@mail.gmail.com">
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<div dir="ltr">On Wed, Oct 13, 2021 at 6:30 PM Abhishek G.S.
<<a href="mailto:gsabhishek1ags@gmail.com" moz-do-not-send="true">gsabhishek1ags@gmail.com</a>>
wrote:<br>
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<div>Hi,</div>
<div>I need some help with getting the file output working
right.<br>
</div>
<div><br>
</div>
<div>
I am using a DMDACreate3D to initialize my DM. This is
my write function
</div>
<div><br>
</div>
<div>
<div>void write(){</div>
<div>PetscViewer viewer;<br>
PetscViewerHDF5Open(PETSC_COMM_WORLD,filename.c_str(),FILE_MODE_WRITE,&viewer);</div>
<div>
DMDAVecRestoreArray(dm,global_vector,global_array)</div>
<div>VecView(global_vec, viewer);</div>
<div>
DMDAVecGetArray(dm,global_vector,global_array);</div>
<div>PetscViewerDestroy(&viewer);</div>
<div>}</div>
</div>
<div><br>
</div>
<div>1) I have 2 PDE's to solve. Still, I went ahead
creating a single DM with dof=1 and creating two vectors
using the DMCreateGlobalVector(). I want to write the
file out periodically. Should I perform
DMDAVecRestoreArray and DMDAVecGetArray every time is
write out the global_vector? (I know that it is just
indexing the pointers and there is no copying of values.
But I am not sure)</div>
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<div><br>
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<div>I don't think you need the Get/RestoreArray() calls here.</div>
<div> </div>
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<div>2) I am writing out to HDF5 format. I see that the
vecview is supposed to reorder the global_vector based
on the DM. However, when I read the H5 files, I get an
error on ViSIT and my output image becomes a 1D image
rather than a 2D/3D. What might be the reason for this
?.<br>
</div>
<div>Error Msg : "In domain 0, your zonal variable
"avtGhostZones" has 25600 values, but it should have
160. Some values were removed to ensure VisIt runs
smoothly"</div>
<div>I was using a 160x160x1 DM</div>
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<div><br>
</div>
<div>I do not believe we support HDF5 <-->
Visit/Paraview for DMDA. The VecView() is just writing out
the vector as a linear array without mesh details. For</div>
<div>interfacing with the visualization, I think we use .vtu
files. You should be able to get this effect using</div>
<div><br>
</div>
<div> VecViewFromOptions(global_vec, NULL, "-vec_view");</div>
<div><br>
</div>
<div>in your code, and then</div>
<div><br>
</div>
<div> -vec_view vtk:sol.vtu</div>
<div><br>
</div>
<div>on the command line.</div>
</div>
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<p>Hi.</p>
<p>If you want to stick with HDF5, you can also write a XDMF file
with the grid information and open that in Paraview.<br>
</p>
<p>I am attaching some routines that I have written to do that in a
solver that deals with a time dependent PDE system with 2
variables; with them I end up with a single XDMF file that
Paraview can load and which contains references to all timesteps
in my simulations, with each timestep being contained in an HDF5
file on its own. The idea is to call writeDomain at the beginning
of the simulation, writeHDF5 for each timestep that I want to save
and writeSimulationXDMF at the end. (Warning: 3D is in use, while
2D ia almost untested...)<br>
</p>
<p>It's not the optimal solution since (1) all timesteps could be in
the same HDF5 and (2) in each HDF5 i write the vectors separately
and it would be better to dump the entire data in one go and
interpret them as a Nx*Ny*Nz*Nvariables data from the XDMF.
Nevertheless they might be a starting point for you if you wan to
try this approach.<br>
</p>
<p>Matteo<br>
</p>
<blockquote type="cite" cite="mid:CAMYG4Gk2RCWOAmtDbKc7Z=BBfYY8NdSe=V899TY29C=jknqL9Q@mail.gmail.com">
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<div>3) I tried using the "petsc_gen_xdmf.py" to generate
the xdmf files for use in Paraview. Here the key
["viz/geometry"] is missing. The keys present in the
output H5 file are just the two vectors I am writing and
has no info about mesh. Isn't this supposed to come
automatically since the vector is attached to the DM?
How do I sort this out?</div>
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<div><br>
</div>
<div>This support is for unstructured grids, DMPlex and
DMForest.</div>
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<div>4) Can I have multiple vectors attached to the DM by
DMCreateGlobalVector() even though I created the DMDA
using dof=1.</div>
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<div><br>
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<div>Yes.</div>
<div><br>
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<div> Thanks,</div>
<div><br>
</div>
<div> Matt</div>
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<div>thanks,<br>
</div>
<div>Abhishek<br>
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-- <br>
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<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>
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<pre class="moz-signature" cols="72">--
---
Professore Associato in Analisi Numerica
Dipartimento di Scienza e Alta Tecnologia
Università degli Studi dell'Insubria
Via Valleggio, 11 - Como</pre>
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